Mitochondrial Eve and the young-earth timeline: the literature

Merge note, October 2026: This catalogue was merged with the source register of the second draft (EVE2) and the revision note of the third draft (ASTRA). It still carries some earlier working assessments in its entries. For the current interpretation of the egg study, the germline bottleneck and its corrections, homoplasmy, ancient sampling times and POLG, use the merged article and the revision record, which supersede any older assessment written below. The earlier 30/170 branch allocation and the unconditional 1.36 times annual-rate ceiling are withdrawn. Each entry now ends with a line giving its library key, the earlier keys it went by, whether any draft cited it, and, for a source nobody cited, the reason it was considered and not used. The full second-draft register is kept unedited as research/source-register.md, and the merge's own checks and library defects are listed at the end of this page.

This page exists so that nobody has to take the rest of the article on trust. Every source it rests on is listed here with what it actually measured, who wrote it, and which way it cuts.

A catalogue of the literature on the human mitochondrial clock — the founding papers, the pedigree mutation-rate measurements, the phylogenetic calibrations, the ancient-DNA rate estimates, the explanations offered for the gap between them, the young-earth clock proposals, and their critics.

It is deliberately not a reading list of things that agree with this site. Sources are tagged by the direction they cut, and a reader who wants only the strongest material against the young-earth reading can filter for undercuts and read those first. Several of the entries that hurt the young-earth case worst are creationist publications, and at least one mainstream paper is tagged supports.

How to read an entry

Units. The field unique to this subject, and the reason most public argument about it is worthless. Mitochondrial mutation rates get quoted in at least five incompatible ways: per site per year, per site per generation, per site per million years, per whole genome per generation, and "one new mutation every N births". A rate of 2.5 × 10^-6 per site per year and a rate of 1.7 × 10^-8 per site per year differ by a factor of 147, and both numbers are real published measurements of things that sound like the same quantity. Every entry here states the unit the source used and the same figure converted to two common units: mutations per site per year, and mutations across the whole 16,569 bp genome per 25-year generation. Where a conversion needed an assumption, the assumption is stated.

Region. A rate for the control region is not a rate for the coding region, and the two differ by more than an order of magnitude. The control region (the D-loop) is about 1,100 bp of the 16,569 bp molecule, and within it the two hypervariable segments HVR1 (359 bp) and HVR2 (315 bp) are faster again, with individual hotspot sites faster still. A rate measured on 610 bp of hypervariable sequence cannot be multiplied up to the whole genome, and doing so is one of the commonest errors on both sides. Every entry states the region sequenced.

Mutation or substitution. The most important distinction here after units. A mutation is a new variant appearing in one mitochondrial genome in one cell. A substitution is a variant that has replaced its predecessor throughout a lineage. Because a human cell carries hundreds to thousands of mitochondrial genomes, a new mutation normally appears as a heteroplasmy — a minority variant — and most heteroplasmies are lost within a generation or two at the germline bottleneck. Pedigree studies mostly count heteroplasmies. Phylogenetic studies count substitutions. Whether those two rates should be equal is a real technical question with a real answer, and this catalogue keeps the two quantities in separate columns rather than letting them blur.

Measurement or model. A count of the sequence differences between a mother and her child is a measurement. A rate obtained by dividing human–chimpanzee sequence difference by an assumed 5-million-year divergence is a model, and its output cannot then be offered as evidence for the divergence date. Both kinds appear in this literature, often in the same paragraph. Every entry is tagged.

Calibration. For every rate that came out of a phylogeny, this catalogue records what the clock was set by: an ape divergence date, an archaeological colonisation event, a radiocarbon-dated ancient genome, or nothing external at all. A reader who suspects the whole enterprise of circularity can go straight down this column and see exactly which estimates are independent of deep-time assumptions and which are not. Some are. Some are not.

Direction. Whether the source supports, undercuts, or complicates a young mitochondrial MRCA. Assigned by what the source shows, not by what its author believes.

Camp. Disclosure, not a verdict. A creationist who publishes original sequence analysis in Nucleic Acids Research is worth more, not less, for having done it there, and the tag exists so a reader can weigh a source rather than being told what to think.

Field definitions

Field	Values
`topic`	founding-papers, pedigree-rate, phylogenetic-rate, ancient-dna, rate-gap, selection, heteroplasmy, bottleneck, saturation, tree-topology, diversity, archaics, genealogy, yec-clock, critique, forensics, other-species, method, history
`camp`	mainstream, creationist, old-earth-christian, counter-apologetics, unaffiliated
`type`	measurement, model, compilation, review, book, popular, news, preprint, database, blog, forum
`access`	OA, paywalled, preprint, book, database, web
`region`	whole-genome, coding, control-region, HVR1, HVR2, HVR1+2, restriction-map, n/a (for theory, simulation, news and commentary, which sequence nothing)
`calibration`	ape-divergence, archaeological, radiocarbon-tip, internal, none, n/a
`direction`	supports, undercuts, mixed, background
`library`	added at the end of each entry in the October 2026 merge: the source's key in `sources/`, any earlier keys, and whether a draft cited it

The founding papers, and the concept

Four things should come out of this group. First, "mitochondrial Eve" is a single-locus most recent common ancestor, and her existence was a published prediction of ordinary neutral demography — Avise, Neigel & Arnold worked it out in 1984, three years before Cann, Stoneking & Wilson made it famous, so the claim that an Eve was unexpected and required an ad-hoc bottleneck is datably false. Second, the 1987 African-root inference did not survive its critics: Maddison, Templeton and Hedges et al. showed between 1991 and 1993 that the "minimum-length" tree was not minimum-length and that equally parsimonious trees had non-African roots, which took the paper's 22:4 sign test down with them. Third, what survived — a single recent root, and higher African diversity — was re-established later on different evidence (complete-genome sequencing from Ingman et al. 2000 onward), not by rescuing the 1987 parsimony argument. Fourth, the dates in this group are almost all model outputs, calibrated either on assumed archaeological colonisation dates (Cann 1987) or on an assumed human–chimpanzee divergence (Vigilant 1991, Ingman 2000), and none of them can be offered as independent evidence for the assumption they were built on. The words "Eve" and "Adam" appear zero times in the 1987 paper; the name came from the news pages.

Brown 1980, human mtDNA polymorphism

Brown, W. M. "Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis." Proceedings of the National Academy of Sciences 77(6):3605-3609 (1980). PNAS 1980 — full bibliographic record not independently verified in the research sweep; the notes cite it only as "Brown 1980 (PNAS)".

topic founding-papers · camp mainstream · type measurement · access paywalled · region restriction-map · calibration none · direction background

What it measured. Restriction-endonuclease digestion patterns of human mtDNA from a panel of individuals, the first survey to quantify how little sequence variation human mitochondria carry. Numbers not verified in this sweep.

Why it matters here. It is the actual first-publication claim of a recent human mtDNA common ancestor, seven years before Cann et al. — and it is the paper Robert Carter's 2025 CMI article should have cited where it cited Anderson et al. 1981 instead. Read only at second hand; do not quote figures from it until someone reads the paper.

Anderson et al. 1981, the Cambridge Reference Sequence

Anderson, S. et al. "Sequence and organization of the human mitochondrial genome." Nature 290(5806):457-465 (1981). Bibliographic details taken from Carter 2025's reference list, not independently verified.

topic founding-papers · camp mainstream · type measurement · access paywalled · region whole-genome · calibration n/a · direction background

What it measured. The complete 16,569 bp sequence of one human mitochondrial genome, plus its gene organisation. This sequence became the Cambridge Reference Sequence (rCRS), the coordinate frame in which every position number in this literature is quoted.

Why it matters here. It supplies the 16,569 bp denominator used in every unit conversion on this page. It also anchors a documented citation error: Carter 2025 writes that "Mitochondrial Eve was 'discovered' in 1981" and cites this paper, which sequenced one genome and did not propose, discover or date any common maternal ancestor.

Library. No library record. used: no. Considered and not used: background or method source, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft. Its bibliographic details were taken second-hand from Carter 2025's reference list.

Avise, Neigel & Arnold 1984, lineage survivorship

Avise, J. C., Neigel, J. E. & Arnold, J. "Demographic influences on mitochondrial DNA lineage survivorship in animal populations." Journal of Molecular Evolution 20(2):99-105 (1984). doi:10.1007/BF02257369 PMID 6433037 (abstract verified via NCBI eutils; full text not obtained)

topic founding-papers · camp mainstream · type model · access paywalled · region n/a · calibration n/a · direction undercuts

What it measured. Branching-process models and simulations of matrilineal survivorship under a range of demographic scenarios. Result: in a stable population founded by n females and held at carrying capacity k = n, it is highly probable that within about 4n generations every descendant traces to a single founder female.

Why it matters here. This is the dated refutation of the standard creationist line that an "Eve" was unexpected and that a bottleneck was bolted onto evolutionary theory afterwards to explain her. It was published in 1984 — three years before Cann et al. 1987 — and it produces a single founding matriline without any bottleneck. It directly contradicts Wieland 1998 ("it was not something that was expected by evolutionists") and Carter 2025 ("they had no way of predicting Eve's existence before they discovered her"). Read in abstract only.

Library. key: avise-1984, was: avise-1984b, was: avise-1984c. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

Cann, Stoneking & Wilson 1987, the paper itself

Cann, R. L., Stoneking, M. & Wilson, A. C. "Mitochondrial DNA and human evolution." Nature 325(6099):31-36 (1987). doi:10.1038/325031a0 PMID 3025745 Publisher page https://www.nature.com/articles/325031a0 [paywalled — redirects to idp.nature.com]. Full-text transcription (OCR, visible errors): https://www.mun.ca/biology/scarr/Cann,%20et_%20al_%20Mitochondrial%20DNA%20and%20Human%20Evolution.htm [verified]

topic founding-papers · camp mainstream · type measurement · access paywalled · region restriction-map · calibration archaeological · direction mixed

What it measured. Restriction maps of mtDNA from 147 people (145 placentas plus the HeLa and GM 3043 cell lines), cut with 12 enzymes, identifying 467 independent restriction sites of which 195 were polymorphic and only 93 were phylogenetically informative — about 370 sites per individual, roughly 9% of the 16,569 bp genome. Nothing was sequenced. Mean pairwise sequence divergence was 0.32% (range 0–1.3%); the ancestral type linked mtDNAs differing by an average of 0.57%. The African sample was 20 people, of whom 18 were Black Americans and only 2 were born in sub-Saharan Africa — the paper says so on p. 32, and reports that 12 of the 18 carried African-diagnostic markers.

Rate as published / normalised. Published as a between-lineage divergence of 2–4% per million years, calibrated on assumed colonisation dates of 30 ka for New Guinea, 40 ka for Australia and 12 ka for the New World. Halving for the per-lineage rate: 1.0–2.0 × 10^-8 per site per year; at 16,569 bp and 25 years per generation, 4.14 × 10^-3 to 8.28 × 10^-3 mutations per genome per generation (4.97–9.94 × 10^-3 at 30 years). Note this is a substitution rate inferred from a calibration, not a measured mutation rate.

Why it matters here. It is the source of the "200,000 years" figure — 0.57% ÷ 2–4% per Myr = 142,500–285,000 years, published as "140,000–290,000". Two things the article should say plainly: the date is a model output resting on archaeological colonisation dates, not a measurement; and the African root rested on a single sign test (22:4 informative sites favouring the published tree over a five-race candelabra) that did not survive 1991-92. Two honest caveats in the authors' own text also cut against creationist framing: they treated a bottleneck as an open question for future testing, and they noted the continual extinction of lineages whose carriers left no mtDNA. Flag: the transcription gives "140,000-280,000 years" on p. 35 and "140,000-290,000" on p. 33; the arithmetic favours 290,000 and the 280,000 figure should not be quoted until the printed page is checked.

Library. key: cann-1987. File: web/cann-1987_mitochondrial-dna-and-human-evolution-transcription.html. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Wainscoat 1987, the News & Views that named her

Wainscoat, J. "Human evolution. Out of the garden of Eden." Nature 325:13 (1987). doi:10.1038/325013a0 PMID 3796736 (record verified via NCBI eutils; item itself [paywalled], not read)

topic founding-papers · camp mainstream · type news · access paywalled · region n/a · calibration n/a · direction background

What it measured. Nothing; it is the commentary piece accompanying Cann et al. in the same issue of Nature.

Why it matters here. The Embryo Project Encyclopedia credits a News & Views item in that issue with coining the term "mitochondrial Eve," and this is the only candidate item. Not read — the attribution is currently second-hand, and the article should not state that Wainscoat coined the phrase until someone reads the page.

Library. No library record. used: no. Considered and not used: it was read only at second hand or not at all, so nothing in it can be quoted. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

Tierney 1988, the Newsweek cover story

Tierney, J. "The Search for Adam and Eve." Newsweek 111 (11 January 1988):46-52. PDF reprint (University of Virginia course page): https://i.b5z.net/i/u/736324/i/IN_SEARCH_FOR_ADAM___EVE.pdf [verified]. Original UVa host http://www.virginia.edu/woodson/courses/aas102%20(spring%2001)/articles/tierney.html [dead]

topic history · camp unaffiliated · type popular · access web · region n/a · calibration n/a · direction mixed

What it measured. Nothing; it is the magazine cover story that put "Eve" into public circulation, including interviews with Allan Wilson and John Avise.

Why it matters here. It corrects a claim both sides make loosely. The text got it right — its opening paragraph says she "was not the only woman on earth," and Wilson is quoted saying "I worry about the term 'Eve' a little bit because of the implication that in her generation there were only two people. We are not saying that … maybe a few thousand." The cover art got it wrong (a garden, a serpent, one couple). It also contains the Pitcairn Island analogy that Carl Wieland's 1998 creationist article later reuses, which suggests where the creationist framing came from. The 1988 piece explicitly notes the conflict with "the Bible's Eve … calculated to have lived 5,992 years ago."

Library. key: tierney-1988. File: papers/tierney-1988_search-for-adam-and-eve.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Vigilant et al. 1991, the sequencing follow-up

Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. & Wilson, A. C. "African populations and the evolution of human mitochondrial DNA." Science 253:1503-1507 (27 September 1991). doi:10.1126/science.1840702 PMID 1840702 (abstract verified via NCBI eutils; full text [paywalled])

topic founding-papers · camp mainstream · type measurement · access paywalled · region HVR1+2 · calibration ape-divergence · direction background

What it measured. Sequenced two hypervariable control-region segments in 189 people, including 121 native Africans, plus a chimpanzee sequence for rooting. Reported a tree with many deep branches leading exclusively to African mtDNAs and a TMRCA of 166,000–249,000 years.

Why it matters here. It fixed the sampling weakness of 1987 (native Africans, not African-Americans) and introduced a new one: the clock is now set by the human–chimpanzee divergence, so the TMRCA is a model output that assumes the split date and cannot be evidence for it. Its hypervariable-region data is also what the 1991-92 critics tore apart, because saturation at fast control-region sites makes parsimony trees non-unique.

Maddison 1991, the African root re-examined

Maddison, D. R. "African origin of human mitochondrial DNA reexamined." Systematic Zoology 40(3):355-363 (1991). doi:10.1093/sysbio/40.3.355 https://academic.oup.com/sysbio/article-abstract/40/3/355/1655455 [paywalled — metadata only]; JSTOR https://www.jstor.org/stable/2992325 [403 unauthenticated; reachable with the site JSTOR account, online read only]

topic critique · camp mainstream · type model · access paywalled · region restriction-map · calibration none · direction mixed

What it measured. A parsimony reanalysis of Cann et al.'s restriction-site data, finding trees shorter than their published "minimum-length" tree, including trees with non-African roots.

Why it matters here. This is the paper that broke the 1987 African-root argument, and it shows that a headline result from a flagship Nature paper can be wrong on its own data. It does not support a young MRCA — it says nothing about the date — which is why it is tagged mixed rather than supports. Not read. The specific figures floating around ("10,000 more parsimonious trees", "trees five steps shorter", "10²⁶⁷ topologies") reach us only through Bednarik 2013, a polemical secondary source, and must not be printed until someone reads Maddison directly.

Barinaga 1992, "'African Eve' backers beat a retreat"

Barinaga, M. "'African Eve' backers beat a retreat." Science 255(5045):686-687 (7 February 1992). doi:10.1126/science.1738842 PMID 1738842 [paywalled], not read

topic history · camp mainstream · type news · access paywalled · region n/a · calibration n/a · direction mixed

What it measured. Nothing; contemporaneous news reporting of the authors' concession in the same issue that carried the Templeton and Hedges technical comments.

Why it matters here. It is the cleanest contemporary evidence that the retreat was public and acknowledged at the time, not a later creationist gloss. Not read.

Library. key: barinaga-1992, was: barinaga-1992b, was: barinaga-1992c. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

Templeton 1992, technical comment

Templeton, A. R. "Human origins and analysis of mitochondrial DNA sequences." Science 255(5045):737 (7 February 1992). doi:10.1126/science.1590849 PMID 1590849 https://www.science.org/doi/10.1126/science.1590849 [dead for us — HTTP 403]; no OA copy per Unpaywall

topic critique · camp mainstream · type model · access paywalled · region HVR1+2 · calibration none · direction mixed

What it measured. A reanalysis showing the parsimony support for an African root in Vigilant et al. 1991 was not statistically significant.

Why it matters here. Half of the pair of technical comments that ended the first phase of the Eve debate. Like Maddison, it undercuts a mainstream inference without touching the date, so it is not evidence for a young MRCA. Not read.

Hedges et al. 1992, technical comment

Hedges, S. B., Kumar, S., Tamura, K. & Stoneking, M. "Human origins and analysis of mitochondrial DNA sequences." Science 255(5045):737-739 (7 February 1992). doi:10.1126/science.1738849 PMID 1738849 [paywalled], not read

topic critique · camp mainstream · type model · access paywalled · region HVR1+2 · calibration none · direction mixed

What it measured. The same reanalysis result, from a group that included Mark Stoneking, an author of the original 1987 paper.

Why it matters here. The strongest possible form of the critique: one of the original authors co-published the demonstration that the tree-based African-root claim did not hold. That is what makes the 1991-92 episode a genuine self-correction rather than a partisan dispute. Not read.

Maddison, Ruvolo & Swofford 1992, control-region topologies

Maddison, D. R., Ruvolo, M. & Swofford, D. L. "Geographic origins of human mitochondrial DNA: phylogenetic evidence from control region sequences." Systematic Biology 41(1):111-124 (1992). [paywalled], not read

topic critique · camp mainstream · type model · access paywalled · region control-region · calibration none · direction mixed

What it measured. A phylogenetic reanalysis of human mtDNA control-region sequences and the geographic placement of the root.

Why it matters here. The extension of the Maddison 1991 result from restriction-site data to the sequence data of Vigilant et al. 1991, and one of the three papers Richards & Macaulay 2001 cite when they write that "there were millions of plausible alternative trees, many of which did not show the same pattern of an African root." Not read.

Wills 1992, comment in Nature

Wills, C. "Human origins." Nature 356(6368):389-390 (2 April 1992). doi:10.1038/356389b0 PMID 1557117 [paywalled], not read

topic critique · camp mainstream · type news · access paywalled · region n/a · calibration n/a · direction background

What it measured. Nothing; a comment on Cann et al. 1987 published five years afterwards.

Why it matters here. Part of the 1992 wave of published second thoughts. Not read; listed for completeness.

Gibbons 1992, "wounded, but not dead yet"

Gibbons, A. "Mitochondrial Eve: wounded, but not dead yet." Science 257(5072):873-875 (14 August 1992). doi:10.1126/science.1502551 PMID 1502551 [paywalled], not read

topic history · camp mainstream · type news · access paywalled · region n/a · calibration n/a · direction mixed

What it measured. Nothing; follow-up news reporting six months after the retreat.

Why it matters here. Its title is the accurate summary of the outcome and should be used as such: the African-root argument was wounded, the existence of a recent single-locus MRCA was not. Creationist retellings that stop at Barinaga's "beat a retreat" without this sequel are quoting half the story. Not read. (This is the same author as the 1998 Science news item that generated the long-running "Calibrating the Mitochondrial Clock" quote trail — a separate matter, catalogued elsewhere on this page.)

Templeton 1993, "The 'Eve' Hypotheses"

Templeton, A. R. "The 'Eve' Hypotheses: A Genetic Critique and Reanalysis." American Anthropologist 95(1):51-72 (1993). doi:10.1525/aa.1993.95.1.02a00030 [paywalled], Wiley/AnthroSource returns 403, not read

topic critique · camp mainstream · type model · access paywalled · region HVR1+2 · calibration none · direction mixed

What it measured. A book-length critique and reanalysis of the whole Eve programme, separating the several distinct claims bundled under the name.

Why it matters here. The most substantive published critique of the mainstream position, and the article is currently unable to quote its author's own words. Not read; obtaining it is an outstanding research task.

Stoneking 1994, "In Defense of 'Eve'"

Stoneking, M. "In Defense of 'Eve' — A Response to Templeton's Critique." American Anthropologist 96(1):131-141 (1994). [paywalled], not read

topic critique · camp mainstream · type review · access paywalled · region HVR1+2 · calibration none · direction mixed

What it measured. Nothing new; the original author's published reply to Templeton 1993.

Why it matters here. Fairness requires the reply as well as the critique, and this pair is the fullest published exchange on what the 1987 and 1991 papers did and did not establish. Not read.

Ayala 1995, "The Myth of Eve"

Ayala, F. J. "The Myth of Eve: Molecular Biology and Human Origins." Science 270(5244):1930-1936 (1995). doi:10.1126/science.270.5244.1930 https://escholarship.org/content/qt93c199ck/qt93c199ck.pdf [verified]

topic bottleneck · camp mainstream · type review · access OA · region n/a · calibration n/a · direction mixed

What it measured. Coalescence times of HLA-DRB1 allelic lineages, which trace to a common ancestor about 60 million years ago — before the ape/Old World monkey split — implying a human ancestral effective population size of 100,000 or greater sustained throughout. Also states the coalescent expectation E[T] ≈ 2Nf generations and back-calculates Nf ≈ 5,000 from a 200,000-year mtDNA TMRCA at 20 years per generation.

Why it matters here. It cuts both ways, hard. Against the young-earth reading it is the strongest single argument on this page: a balanced nuclear locus retaining trans-species polymorphism cannot pass through a two-person bottleneck, and Ayala's own arithmetic sets a floor of roughly 1,000 individuals even with balancing selection at s = 0.01. For it, Ayala is equally clear that "the mitochondrial Eve hypothesis emanates from a confusion between gene genealogies and individual genealogies," that mtDNA is "a four-hundred-thousandth part" of a person's DNA, and that coalescence estimates "have large variances" — his own note that the standard deviation exceeds N/2 is why single-locus dates are soft. Note the circularity in his Nf = 5,000: it is derived from the 200,000-year date, so "2Nf = 200,000 years" is not independent confirmation of anything.

Library. key: ayala-1995. File: papers/ayala-1995_myth-of-eve.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Ingman et al. 2000, complete mitochondrial genomes

Ingman, M., Kaessmann, H., Pääbo, S. & Gyllensten, U. "Mitochondrial genome variation and the origin of modern humans." Nature 408:708-713 (2000). doi:10.1038/35047064 https://www.nature.com/scitable/content/12631/10.1038_35047064.pdf [verified]

topic founding-papers · camp mainstream · type measurement · access OA · region coding · calibration ape-divergence · direction mixed

What it measured. 53 complete human mitochondrial genomes with 657 segregating sites — the first full-genome attack on the problem, deliberately excluding the D-loop to escape the saturation that wrecked the hypervariable-region trees. Measured mean human–chimpanzee distance 0.17 substitutions per site, maximum human–human distance 5.82 × 10^-3 substitutions per site (the Africans Mkamba and San).

Rate as published / normalised. Published as 1.70 × 10^-8 substitutions per site per year, excluding the D-loop, obtained by dividing the 0.17 human–chimp distance by an assumed 5 Myr divergence. Per site per year: 1.70 × 10^-8. Across 16,569 bp at 25 years per generation: 7.04 × 10^-3 mutations per genome per generation (8.45 × 10^-3 at 30 years) — i.e. one mutation per ~142 generations, about 3,550 years — but that conversion assumes the coding-region rate applies genome-wide, which it does not.

Why it matters here. This is where the African root was genuinely re-established, on complete genomes rather than on the discredited restriction-site parsimony, so the article cannot treat the 1991-92 collapse as the last word on topology. It is also the textbook case of the measurement/model distinction: 0.17 substitutions per site is a measurement, 5 Myr is an assumption, 1.70 × 10^-8 is a model output, and the resulting TMRCA of 171,500 ± 50,000 years is a model output twice over. The creationist circularity charge is correct as applied to this paper.

Library. key: ingman-2000c, was: ingman-2000, was: ingman-2000b, was: ingman-2000d. File: papers/ingman-2000c_mitochondrial-genome-variation.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Richards & Macaulay 2001, the gene tree comes of age

Richards, M. & Macaulay, V. "The Mitochondrial Gene Tree Comes of Age." American Journal of Human Genetics 68(6):1315-1320 (2001). https://pmc.ncbi.nlm.nih.gov/articles/PMC1226117/ [verified]

topic saturation · camp mainstream · type review · access OA · region control-region · calibration none · direction mixed

What it measured. Nothing new; a retrospective diagnosis of why the 1987-1992 analyses failed. Their explanation is site-rate heterogeneity in the control region: "some sites mutate very fast indeed and … many have mutated many times in the genealogy," so "many tree topologies are equally plausible" and "the genealogy can remain unresolvable."

Why it matters here. It is the mainstream's own statement that hypervariable-region data cannot carry a phylogeny, which is worth having in the article's own words, and it is the source for "there were millions of plausible alternative trees, many of which did not show the same pattern of an African root." It also records what replaced parsimony (network methods, Watson et al. 1997), so it cannot be quoted as a wholesale retraction.

Library. key: richards-2001b, was: richards-2001c, was: richards-2001d. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Rosenberg & Nordborg 2002, coalescent theory

Rosenberg, N. A. & Nordborg, M. "Genealogical trees, coalescent theory and the analysis of genetic polymorphisms." Nature Reviews Genetics 3:380-390 (2002). doi:10.1038/nrg795 https://rosenberglab.stanford.edu/papers/coalnrg.pdf [verified]

topic method · camp mainstream · type review · access OA · region n/a · calibration n/a · direction mixed

What it measured. Nothing; a review of coalescent theory, whose Box 3, "The meaning of 'mitochondrial Eve'" (p. 385) is the cleanest published statement of what the mtDNA tree does and does not show.

Why it matters here. It concedes the 1991-92 criticism in the mainstream's own voice — "the estimated tree was by no means the only possible one, as several equally plausible trees had a non-African root" — and then states the deeper limitation: "a more fundamental problem is that the mtDNA tree itself actually tells us very little about human origins," and "a single gene tree will almost never suffice to choose among demographic models." That is a two-edged sentence: it restrains creationist over-reading of "Eve" and mainstream over-reading alike. It also notes what the tree does refute — the candelabra model.

Library. key: rosenberg-2002. File: papers/rosenberg-2002_genealogical-trees-coalescent-theory.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Rohde, Olson & Chang 2004, recent common ancestry

Rohde, D. L. T., Olson, S. & Chang, J. T. "Modelling the recent common ancestry of all living humans." Nature 431:562-566 (30 September 2004). doi:10.1038/nature02842 http://www.stat.yale.edu/~jtc5/papers/CommonAncestors/NatureCommonAncestors-Article.pdf [verified]; supplements at http://www.stat.yale.edu/~jtc5/papers/CommonAncestors/ [verified]

topic method · camp mainstream · type model · access OA · region n/a · calibration n/a · direction supports

What it measured. Simulations of human genealogy — not genetics — under substantial population substructure, with towns, countries, continents and migration ports. Under conservative parameters (5% of individuals leaving their home town, 0.05% leaving their country) the mean genealogical MRCA of all living humans dates to 1415 BC and the mean identical-ancestors point to 5353 BC; under higher migration, AD 55 and 2158 BC. A simpler ten-node graph extrapolated to 250 million people gives 76 generations (~300 BC) and 169 generations (~3000 BC).

Why it matters here. It is mainstream, in Nature, and it puts a universal common ancestor of all living people inside recorded history and an identical-ancestors point in the third-to-sixth millennium BC — biblical-era numbers reached with no biblical input. It is the honest answer to "everyone descending from one recent couple is absurd." It is not evidence about mtDNA and not evidence that a single couple were the only ancestors; the authors themselves note that "an individual will receive little or no actual genetic inheritance from the vast majority of the ancestors living at the IA point," and warn that "the date of the MRCA … cannot be identified with great precision."

Library. key: rohde-2004. File: papers/rohde-2004_modelling-recent-common-ancestry.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Hein 2004, News & Views on Rohde et al.

Hein, J. "Human evolution: Pedigrees for all humanity." Nature 431:518-519 (2004). http://www.stat.yale.edu/~jtc5/papers/CommonAncestors/Nature_NewsAndViews.pdf [verified]

topic method · camp mainstream · type news · access OA · region n/a · calibration n/a · direction mixed

What it measured. Nothing; the commentary accompanying Rohde et al., and the clearest short statement of the genealogical/genetic distinction.

Why it matters here. It is the fence around the previous entry, and it should be cited wherever the article uses Rohde: a universal pedigree ancestor "does not imply that an individual makes a significant genetic contribution to the present population. In fact, that individual might have contributed nothing." Hein also gives the scaling that explains why the two ancestries differ so wildly — pedigree MRCA time grows as log₂n, genetic MRCA time in proportion to n — and notes that going back only about six generations, members of our pedigree exist who contributed no DNA to us. His remark that ancestors calculated in 1700 would have dated further back is also the published support for the point that MRCA dates move with time.

Library. key: hein-2004. File: papers/hein-2004_pedigrees-for-all-humanity.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Gitschier 2010, interview with Rebecca Cann

Gitschier, J. "All About Mitochondrial Eve: An Interview with Rebecca Cann." PLoS Genetics 6(5):e1000959 (2010). https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000959 [verified]

topic history · camp mainstream · type popular · access OA · region n/a · calibration n/a · direction background

What it measured. Nothing; a retrospective interview with the first author of the 1987 paper, twenty-three years on.

Why it matters here. Two uses. Cann lists the sampling objection among the attacks she faced — "or that I had studied African Americans, not real Africans…" — confirming that the criticism was live and not invented afterwards. And Gitschier describes the Newsweek cover: "an Eden, replete with apple tree and serpent, but with the iconic blonde couple of Dürer now supplanted by an Adam and Eve of African descent." Used with Tierney 1988, it lets the article say precisely which part of the press coverage was misleading.

Library. No library record. used: no. Considered and not used: background or method source, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft. The library's gitschier-2015 is a different paper (an interview with Ford Doolittle), so it is not this source.

Behar et al. 2012, the "Copernican" reassessment (RSRS)

Behar, D. M., van Oven, M., Rosset, S., Metspalu, M., Loogväli, E.-L., Silva, N. M., Kivisild, T., Torroni, A. & Villems, R. "A 'Copernican' reassessment of the human mitochondrial DNA tree from its root." American Journal of Human Genetics 90(4):675-684 (2012). doi:10.1016/j.ajhg.2012.03.002 https://pmc.ncbi.nlm.nih.gov/articles/PMC3322232/ [verified]; supplement (Table S5) https://web.archive.org/web/2020/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322232/bin/mmc1.pdf [verified]

topic tree-topology · camp mainstream · type measurement · access OA · region whole-genome · calibration ape-divergence · direction undercuts

What it measured. Rebuilt the whole human mtDNA phylogeny from thousands of complete mitogenomes and reconstructed its root sequence, the RSRS. The root is a two-way split between L0 and L1'2'3'4'5'6, the two branches separated by 14 coding and 4 control-region mutations (18 total). Mean distance from the reconstructed root to a modern mitogenome: 57.1 substitutions (SD 5.9, range 41-77). Root age from the supplement: 176,689 ± 11,340 years.

Why it matters here. The 57.1 root-to-tip figure is the cleanest raw number in the whole subject and the quantity every clock argument on this page has to divide. The bifurcating root is also the direct test of the young-earth Flood prediction of up to three surviving maternal lineages: the data show two basal branches, not three. Its date, by contrast, is not independent — it inherits Soares et al. 2009's ape-calibrated rate, so the 176.7 ka figure is a model output, and the paper's own documented clock violations (four substitutions in one lineage versus thirty-two in another from the same node) argue that no published interval here should be taken at face value. Flag: the research notes give the sample size as 8,216 mitogenomes in one place and 18,843 in another; check the paper before printing a number.

Library. key: behar-2012. File: papers/behar-2012_copernican-reassessment-rsrs.pdf (also .md, behar-2012_copernican-reassessment-rsrs-supplement.md, behar-2012_copernican-reassessment-rsrs-supplement.pdf). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

van Oven & Kayser, PhyloTree Build 17

van Oven, M. & Kayser, M. PhyloTree mtDNA tree Build 17 (18 February 2016). Cite as Human Mutation 30(2):E386-E394 (2009). https://www.phylotree.org/builds/mtDNA_tree_Build_17.zip [verified, in the source library]

topic tree-topology · camp mainstream · type database · access database · region whole-genome · calibration none · direction background

What it measured. The reference human mtDNA phylogeny: every named haplogroup with the explicit list of mutations defining each branch, rooted on the RSRS. Build 17 is the standard against which haplogroup assignments and internode distances are counted.

Why it matters here. It makes the disputes on this page checkable by hand rather than by authority. Counting on this file confirms Behar's 18-mutation, two-branch root (L0 = 10 mutations, L1'2'3'4'5'6 = 8), confirms Carter's 12-difference rCRS-to-consensus list exactly, and puts the root of macrohaplogroup R — where Carter, Criswell & Sanford 2008 place "Eve1.0" — 42 mutational steps from the mainstream root. A reader who wants to referee the three-nodes-versus-two-branch question can download it and count.

Library. key: van-oven-2009. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: considered, not used in current draft. EVE2's index.md nevertheless cites it. The Build 17 file itself is stored under the library key vanoven-2016.

The pedigree measurements

There is no such thing as "the pedigree mutation rate." The phrase covers at least four different quantities, measured on different things, differing from each other by up to 300-fold, and both creationist and mainstream writers slide between them without saying so. In ascending order they are: (i) the bottleneck-corrected substitution rate, ~0.004–0.008 mutations per genome per generation (Rebolledo-Jaramillo 2014 gives 0.0045, Zaidi 2019 gives 0.0078); (ii) mutations directly observed to reach homoplasmy in whole-genome pedigrees, 0.006–0.026 per genome per generation (Connell 2022 gives 0.0058 counting only fixed changes, 0.026 counting heteroplasmies too; Guo 2013 observed zero in 26 transmissions); (iii) all mutations detected in deep matrilines, 0.070 per genome per transmission (Árnadóttir 2024, 8,199 mutations in 116,663 transmissions); (iv) new heteroplasmies appearing above a 1% detection threshold, 0.31–1.31 per genome per generation (Wei 2019 gives 0.313, Rebolledo-Jaramillo's observed μ₀ gives 1.31). Quantity (iv) is roughly 300× quantity (i), and both are real published measurements. The distinction that separates them is whether a study counted new heteroplasmies arising or variants reaching homoplasmy, so every entry below states which one it counted in so many words. A second trap runs alongside: most pre-2013 studies sequenced only the control region or a hypervariable segment of it, and their per-site rates cannot be multiplied by 16,569 to get a genome rate. Where a study measured only part of the molecule, the normalised figures below are given per that region, and no whole-genome figure is offered.

Howell, Kubacka & Mackey 1996 — the LHON pedigree that started it

Howell N, Kubacka I, Mackey DA. "How rapidly does the human mitochondrial genome evolve?" Am J Hum Genet 59(3):501–509 (1996). PMID 8751850 https://pubmed.ncbi.nlm.nih.gov/8751850/

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region control-region · calibration n/a · direction mixed

What it measured. Counted new germline substitutions reaching detectable levels, not fixation events specifically: 45 members of one large matrilineal Leber hereditary optic neuropathy pedigree, D-loop sequenced by Sanger, scored by Howell's own later pooling as 2 mutations in 88 transmissions. The paper reports two germline mutations producing "triplasmic descendants with three mitochondrial genotypes" — that is, heteroplasmic, not fixed — plus one somatic D-loop mutation in another family member.

Rate as published / normalised. Howell's later pooled table scores this study at a divergence rate of 1.90 mutations/bp/Myr for the control region. Normalised: 2/88 transmissions over 1,122 bp = 2.02 × 10^-5 per site per generation, and at the 20-year generation Howell assumed, 1.01 × 10^-6 per site per year for the control region. Per control region per 25-year generation that is 0.028 mutations. No whole-genome figure: only the D-loop was sequenced.

Why it matters here. This is the origin of the whole "pedigree rates are ten times phylogenetic rates" claim, and it rests on two events in one disease pedigree, both heteroplasmic. Read only as an abstract here; the full text was not obtained.

Library. key: howell-1996. Folder: papers/howell-1996_human-mitochondrial-genome-evolve/. Cited by the first draft and EVE2. EVE2 register: cited in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

Parsons et al. 1997 — the load-bearing citation

Parsons TJ et al. "A high observed substitution rate in the human mitochondrial DNA control region." Nat Genet 15(4):363–368 (1997). PMID 9090380 https://pubmed.ncbi.nlm.nih.gov/9090380/

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region HVR1+2 · calibration n/a · direction supports

What it measured. Counted substitutions observed between close maternal relatives in two control-region hypervariable segments — 10 substitutions across 134 lineages spanning 327 generational events. The abstract does not say how many were heteroplasmic and how many homoplasmic, and the full text is closed, so which quantity this is cannot be settled from the published abstract. Howell 2003, pooling this dataset, states that heteroplasmic and homoplasmic substitutions were both counted.

Rate as published / normalised. Published as "1/33 generations, or 2.5/site/Myr," described as "roughly twenty-fold higher than estimates derived from phylogenetic analyses." That is 2.5 × 10^-6 per site per year across HV1+HV2. Reverse-engineering the arithmetic — 10/(327 × 610 bp)/20 y = 2.51 × 10^-6 — recovers a sequenced length of ~610 bp and a 20-year generation; both are derivations from their own numbers, not quotes. Per 610 bp segment per 25-year generation: 0.038 mutations. Multiplying 2.5 × 10^-6 by 16,569 to get a genome rate is not licensed and is the single commonest error made with this paper.

Why it matters here. Every young-earth argument from a "20-fold faster" mtDNA clock traces to this abstract. It is a real measurement of a real quantity, but the quantity is a hypervariable-segment substitution rate over 327 transmissions, and its authors' own caveat — "this disparity cannot be accounted for simply by substitutions at mutational hot spots" — was directly contradicted four years later by Heyer et al.

Library. key: parsons-1997, was: parsons-1997b, was: parsons-1997c. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Cavelier et al. 2000 — 292 transmissions, zero fixed changes

Cavelier L, Jazin E, Jalonen P, Gyllensten U. "MtDNA substitution rate and segregation of heteroplasmy in coding and noncoding regions." Hum Genet 107(1):45–50 (2000). PMID 10982034 https://pubmed.ncbi.nlm.nih.gov/10982034/

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region control-region · calibration n/a · direction undercuts

What it measured. Counted homoplasmic (fixed) nucleotide substitutions specifically, in the full control region plus 500 bp of coding sequence (positions 5550–6050), across 194 individuals in 33 maternal lineages. Verbatim: "No homoplasmic nucleotide substitutions were detected in a total of 292 transmissions." Length heteroplasmy was seen at three poly-C sites (65, 309, 16189), all heteroplasmic.

Rate as published / normalised. Published rate is zero observed fixed substitutions; the paper's estimated per-nucleotide rates are given as >0.21 mutations/site/Myr for the control region (95% CI 0–0.6) and >0.54 for the coding region (95% CI 0–1.0), i.e. 2.1 × 10^-7 and 5.4 × 10^-7 per site per year. Per control region per 25-year generation: 0.006 mutations. Abstract only; the Springer full text was not obtained.

Why it matters here. It is the study that gets left out of pedigree-rate compilations on both sides, and it is the earliest direct constraint on the fixation rate rather than the heteroplasmy-appearance rate. 292 transmissions with zero fixed changes is hard to reconcile with any per-generation fixation rate near 0.1.

Library. key: cavelier-2000, was: cavelier-2000b. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Sigurðardóttir et al. 2000 — the Icelandic pedigrees

Sigurðardóttir S, Helgason A, Gulcher JR, Stefansson K, Donnelly P. "The mutation rate in the human mtDNA control region." Am J Hum Genet 66(5):1599–1609 (2000). PMC1378010 https://pmc.ncbi.nlm.nih.gov/articles/PMC1378010/

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region HVR1+2 · calibration n/a · direction mixed

What it measured. Counted base substitutions across the two hypervariable regions in 272 individuals related by 705 transmission events in 26 large Icelandic pedigrees, and reported 3. The authors' own count is of substitutions between relatives; Howell 2003 re-scored the same dataset as 5, because Howell counted newly arising heteroplasmic substitutions as well. The 3-vs-5 gap is exactly the arising-versus-fixing distinction showing up inside a single dataset.

Rate as published / normalised. Published as "3/705 = .0043 per generation (95% CI .00088–.013), or .32/site/1 million years (95% CI .065–.97)." That is 3.2 × 10^-7 per site per year across ~660 bp of hypervariable sequence, at a 20-year generation. Per that region per 25-year generation: 0.0053 mutations. No whole-genome figure.

Why it matters here. It is the largest pre-genomic pedigree study and its rate is lower than Parsons's by a factor of ~8, which is the first sign that the "20-fold faster" figure was not a stable measurement. Madrigal 2012's Table 3 then pairs Howell's count (5/705) with Sigurðardóttir's rate (0.32, which corresponds to 3/705) — an internal inconsistency worth knowing about before quoting either. Full text not retrievable; read at abstract level.

Library. key: sigurdardottir-2000. Folder: papers/sigurdardottir-2000_mtdna-control-region-rate/. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Heyer et al. 2001 — the hot-spot answer

Heyer E, Zietkiewicz E, Rochowski A, Yotova V, Puymirat J, Labuda D. "Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees." Am J Hum Genet 69(5):1113–1126 (2001). PMC1274355 https://pmc.ncbi.nlm.nih.gov/articles/PMC1274355/

topic saturation · camp mainstream · type measurement · access OA · region control-region · calibration internal · direction undercuts

What it measured. Counted substitutions between relatives in French-Canadian deep-rooting pedigrees: 4 in 508 maternal transmissions over 673 bp. Then pooled with earlier familial studies for 18 substitutions in 1,729 transmissions, and — the key measurement — found that only 12 of those 18 were at independent sites; three positions had each mutated twice.

Rate as published / normalised. Published as "0.0079 per generation per 673 bp (95% CI 0.0023–0.186)," and for the pooled set 18/1,729 = 0.0104 per generation. Normalised: 4/508/673 bp = 1.17 × 10^-5 per site per generation, and at 30 years 3.9 × 10^-7 per site per year for the control region. Per 673 bp per 25-year generation: 0.0066 mutations. Their fitted fast-site model gives 40 hypermutable sites in the whole control region (95% CI 27–54) mutating at 274 per site per million generations (95% CI 138–410) — a model output, not a count.

Why it matters here. This is the direct empirical rebuttal of Parsons's claim that hot spots cannot explain the pedigree-phylogeny gap. Three sites mutating twice in 1,729 transmissions is only possible if a small subset of sites is hypermutable, and hypermutable sites saturate — verbatim, they "are expected to be of no or little informativity for the evaluation of mutational distances at the phylogenetic time scale." Their fast:moderate:slow site ratio of 1:2:13 is the mechanism by which a fast pedigree rate and a slow phylogenetic rate are both correct. It undercuts any young-earth clock built by extrapolating a control-region pedigree rate backwards.

Library. key: heyer-2001. File: papers/heyer-2001_familial-mtdna-substitution-rates-deep-rooting-pedigrees.html. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Forster et al. 2002 — natural radioactivity in Kerala

Forster L, Forster P, Lutz-Bonengel S, Willkomm H, Brinkmann B. "Natural radioactivity and human mitochondrial DNA mutations." PNAS 99(21):13950–13954 (2002). PMC129803 https://pmc.ncbi.nlm.nih.gov/articles/PMC129803/

topic pedigree-rate · camp mainstream · type measurement · access OA · region control-region · calibration n/a · direction mixed

What it measured. Counted new heteroplasmies, explicitly and exclusively: "we observed 22 partial (heteroplasmic) mutations in 595 high-radiation transmissions, and only 1 mutation in 200 low-radiation transmissions, significantly more at P < 0.01." 248 pedigrees, 988 individuals, 579 nucleotides of control region (positions 16093–16390 and 35–315). None of the 23 mutations was fixed.

Rate as published / normalised. Low-radiation control: 1/200 = 0.005 per control region per transmission = 8.6 × 10^-6 per site per generation = 4.3 × 10^-7 per site per year at an assumed 20-year generation, or 0.0063 per 579 bp segment per 25-year generation. High-radiation: 22/595 = 0.037 per region per transmission = 6.4 × 10^-5 per site per generation = 3.2 × 10^-6 per site per year, or 0.046 per segment per 25-year generation.

Why it matters here. Two results, cutting opposite ways. A 7-fold environmental effect on the mutation rate means a single universal human rate is not obviously safe — which helps the young-earth argument that ancient rates may have differed. But the radiation-associated mutations hit "nucleotide positions that mutate, on average, 12 times faster during evolution," which is Heyer's hot-spot result again, and the low-radiation baseline (0.005 per control region per transmission) agrees with Sigurðardóttir and Howell rather than with Parsons.

Library. key: forster-2002. File: papers/forster-2002_natural-radioactivity-mtdna-mutations.html (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Howell et al. 2003 — the canonical pooled control-region rate

Howell N, Smejkal CB, Mackey DA, Chinnery PF, Turnbull DM, Herrnstadt C. "The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates." Am J Hum Genet 72(3):659–670 (2003). PMC1180241 https://pmc.ncbi.nlm.nih.gov/articles/PMC1180241/

topic pedigree-rate · camp mainstream · type compilation · access OA · region control-region · calibration n/a · direction supports

What it measured. 1 new germline control-region mutation in 185 transmissions from five LHON pedigrees, then pooled with eight published studies for 28 mutations in 2,633 transmissions. It counted everything newly arising, fixed or not — verbatim: "All newly arising substitutions, both heteroplasmic and homoplasmic, were included in our divergence-rate estimates." So this is an arising rate, not a fixation rate.

Rate as published / normalised. Published as a divergence rate of "0.95 mutations/bp/Myr for the control region … 99.5% confidence interval of 0.53–1.57," at 20 years per generation. Divergence rate is twice the mutation rate, which is verifiable from Howell's own table (Heyer 4/508 ÷ 1,122 bp ÷ 20 y × 2 = 0.70 ✓; Parsons & Holland 10/306 ÷ 1,122 ÷ 20 × 2 = 2.91 ✓). So the mutation rate is 4.72 × 10^-7 per site per year over 1,122 bp of control region, i.e. 0.0106 mutations per control region per 20-year generation, or 0.0132 per control region per 25-year generation. Summing his own table confirms it: 28/2,633 = 0.0106. No whole-genome figure is available from this study, and multiplying 0.53–1.57 × 10^-6 by 16,569 sites — as Carter 2025 endnote 10 does — inflates the result about 15-fold, then doubles an already-doubled divergence rate on top.

Why it matters here. It is the most-cited pedigree rate in the popular literature and the source of the biggest unit errors on both sides. Correctly decoded — divergence rate, control region only, 1,122 bp, heteroplasmies included, 20-year generations — it is consistent with the later whole-genome work rather than in conflict with it.

Quote from the paper added by Eric: "the pedigree divergence rate for the control region is approximately 10-fold higher than that obtained with phylogenetic analyses"

Library. key: howell-2003. File: papers/howell-2003_pedigree-rate-sequence-divergence-mtdna.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. If the merged tables add Howell 2003's Table 2 rows with their primary citations (Bendall 1996, Mumm 1997, Parsons and Holland 1998, Soodyall 1997), those four have no library record yet and need one first; otherwise cite Howell 2003 Table 2 alone.

Santos et al. 2005 — the Azores, and the first explicit arising→fixing correction

Santos C, Montiel R, Sierra B, Bettencourt C, Fernandez E, Alvarez L, Lima M, Abade A, Aluja MP. "Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal)." Mol Biol Evol 22(6):1490–1505 (2005). PMID 15814829 https://pubmed.ncbi.nlm.nih.gov/15814829/

topic rate-gap · camp mainstream · type model · access paywalled · region HVR1+2 · calibration n/a · direction undercuts

What it measured. Counted new point substitutions and classified each as somatic or germinal, and found every one of them heteroplasmic: "Eleven new point substitutions were found, all of them in heteroplasmy, from which five appear to be somatic mutations and six can be considered germinal." Zero reached homoplasmy. Length and/or point heteroplasmies appeared in at least one member of 72% of families.

Rate as published / normalised. Published corrected rate 0.2415 mutations/site/Myr = 2.415 × 10^-7 per site per year for HVRI and HVRII, after correcting "for gender (assuming that the mutations present in men have the same evolutionary weight of somatic mutations because they will inevitably be lost) and for the probability of intraindividual fixation." Per ~610 bp of hypervariable sequence per 25-year generation: 0.0037 mutations. Madrigal's Table 3 records the raw data as 6 germinal mutations in 321 transmissions. The corrected figure is a model, not a raw count. Abstract only; OUP full text was Cloudflare-blocked.

Why it matters here. This is a pedigree study from 2005 that performs the arising→fixing correction and lands "in the upper end of the values provided by phylogenetic estimations," concluding in as many words that the pedigree-phylogeny discrepancy "can be minimized" once fixation probability and sex of offspring are accounted for. Its 45% somatic fraction (5 of 11) is also the best per-mutation somatic estimate in the pre-sequencing literature, and it is the direct answer to any claim that somatic contamination is a minor effect on heteroplasmy counts.

Library. key: santos-2005, was: santos-2005b. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Stewart et al. 2008 — purifying selection in mutator mice

Stewart JB, Freyer C, Elson JL, Wredenberg A, Cansu Z, Trifunovic A, Larsson N-G. "Strong purifying selection in transmission of mammalian mitochondrial DNA." PLoS Biol 6(1):e10 (2008). PMC2214808 https://pmc.ncbi.nlm.nih.gov/articles/PMC2214808/

topic selection · camp mainstream · type measurement · access OA · region coding · calibration n/a · direction undercuts

What it measured. Measured which mutations survive transmission, not a rate: in mtDNA mutator mice, the ratio of nonsynonymous to synonymous substitutions per site in protein-coding regions was 0.6035, falling to 0.4617 once mutations confined to one individual or litter were excluded. Of 343 observed mutations, 90 were at the first codon position (19 synonymous, 71 nonsynonymous), 70 at the second, and 183 at the third (165 synonymous, 18 nonsynonymous). The bias "is evident as early as the N2 generation."

Why it matters here. It is a direct experimental demonstration that the germline removes protein-coding mutations within one or two generations, so the rate at which mutations arise cannot be equated with the rate at which they persist. Their own honest caveat is that these mice "have been exposed to the effects of purifying selection for only a few generations," at most six.

Library. key: stewart-2008. File: papers/stewart-2008_purifying-selection-mtdna.html. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. DOI added from EVE2's register and the library record: 10.1371/journal.pbio.0060010 (PMC2214808).

Fan et al. 2008 — severe mutations eliminated during oogenesis

Fan W, Waymire KG, Narula N, Li P, Rocher C, Coskun PE, Vannan MA, Narula J, MacGregor GR, Wallace DC. "A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations." Science 319(5865):958–962 (2008). PMC3049809 https://pmc.ncbi.nlm.nih.gov/articles/PMC3049809/

topic selection · camp mainstream · type measurement · access OA · region coding · calibration n/a · direction undercuts

What it measured. Tracked the fate of two known mutations across generations of the female mouse germline, not a mutation rate. A severe ND6 mutation fell from 47% heteroplasmy in F1 to 14% in F2, 6% in F3, and 0% by F4 — "selectively eliminated during oogenesis within four generations." A milder COI mutation "was retained throughout multiple generations even though the offspring consistently developed mitochondrial myopathy and cardiomyopathy."

Why it matters here. It answers the specific creationist objection that selection cannot be invoked to slow the pedigree rate because sampled adults are already healthy. This selection happens during oogenesis, before any adult exists to be sampled. The COI result is the honest limit: selection is strong on severe mutations and weak on mild ones, so it cannot explain the entire pedigree-phylogeny gap on its own.

Library. key: fan-2008, was: fan-2008b, was: fan-2008c. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Goto et al. 2011 — the two-tissue design

Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. "Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study." Genome Biol 12(6):R59 (2011). PMC3218847 https://pmc.ncbi.nlm.nih.gov/articles/PMC3218847/

topic method · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction background

What it measured. Counted heteroplasmic sites in blood and buccal tissue from nine individuals in three families, six maternal transmissions: four heteroplasmic sites total. Too few transmissions to yield a rate. Their conclusion: "the incidence of heteroplasmy may be lower than estimated in some other recent re-sequencing studies, and … mtDNA allelic frequencies differ significantly both between tissues and between individuals."

Why it matters here. Methodological ancestry. This introduced the blood-plus-buccal design that later let Rebolledo-Jaramillo 2014 and Zaidi 2019 separate germline heteroplasmy from somatic heteroplasmy — the separation that drops the measured rate by an order of magnitude.

Freyer et al. 2012 — heteroplasmy set prenatally, selection one generation later

Freyer C, Cree LM, Mourier A, Stewart JB, Koolmeister C, Milenkovic D, Wai T, Floros VI, Hagström E, Chatzidaki EE, Wiesner RJ, Samuels DC, Larsson N-G, Chinnery PF. "Variation in germ line mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission." Nat Genet 44(11):1282–1285 (2012). PMC3492742 https://pmc.ncbi.nlm.nih.gov/articles/PMC3492742/

topic selection · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Tracked heteroplasmy levels of a single base-pair deletion in the mitochondrial tRNA^Met gene through generations of mice. Verbatim: "mammalian mtDNA heteroplasmy levels are principally determined prenatally within the developing female germ line. Although we saw no evidence of mtDNA selection prenatally, skewed heteroplasmy levels were observed in the offspring of the next generation, consistent with purifying selection."

Why it matters here. It marks the boundary of the selection argument. Protein-coding mutations "were subject to a filter of purifying selection and preferentially eliminated within a few generations. Yet, mitochondrial tRNA genes evaded the selection." Anyone using germline selection to explain the whole pedigree-phylogeny gap is overstating what has been measured.

Madrigal et al. 2012 — deep-rooting Costa Rican pedigrees

Madrigal L, Melendez-Obando M, Villegas-Palma R, Barrantes R, Raventos H, Pereira R, Luiselli D, Pettener D, Barbujani G. "High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees." Am J Phys Anthropol 148(3):327–333 (2012). PMC3377850 https://pmc.ncbi.nlm.nih.gov/articles/PMC3377850/

topic pedigree-rate · camp mainstream · type measurement · access OA · region HVR1 · calibration n/a · direction supports

What it measured. Counted substitutions between relatives in 19 deep-rooting pedigrees from Atenas, Costa Rica, genealogies "each included at least seven generations, sometimes extending all the way back to the 1500s." 53 subjects typed, HVR-I only, 360 bp, 289 meioses, 7 mutations. The paper does not state how many were heteroplasmic. Its generation time is measured, not assumed: 28.3 years, from the actual ages at reproduction of the women in the sample.

Rate as published / normalised. Table 2: maximum 7/273 = 0.0256 per HVR-I per generation → 2.51 × 10^-6 per site per year; minimum 2/220 = 0.0091 → 0.89 × 10^-6 per site per year (95% CI 0.27–3.17 × 10^-6). Per 360 bp HVR-I per 25-year generation: 0.023 (max) and 0.008 (min) mutations. There is no whole-genome figure and none can be derived: only 360 bp of the fastest segment of the molecule was sequenced. Flagged errors inside the paper: the abstract's headline "1.24 × 10^-6 per site per year" appears nowhere in the Results or Table 2 and could not be reconstructed from any combination in the paper; Table 2's minimum denominator (2/220) and Table 3's (2/212) disagree, with 220 the arithmetically correct one; and Table 3 pairs Howell's count for Sigurðardóttir with Sigurðardóttir's own rate.

Why it matters here. It is the second load-bearing citation for a fast human mtDNA clock, and Carter 2025 converts its headline rate to "1.2 mutations per generation" by multiplying by 16,569 sites — a rate measured on 360 bp. Madrigal herself flags the hot-spot problem (three of the mutated sites are Bandelt's "speedy" sites 16311, 16335, 16362) and states plainly that "the process through which a mutation initially occurring in a single mtDNA molecule reaches fixation in an individual's cells is far from being understood."

Library. key: madrigal-2012. File: papers/madrigal-2012_deep-rooting-costa-rican-pedigrees.pdf. Cited by the first draft and EVE2. EVE2 register: cited in current draft. DOI added from EVE2's register and the library record: 10.1002/ajpa.22052 (PMC3377850).

Guo et al. 2013 — zero homoplasmic changes at 3,981× depth

Guo Y, Li CI, Sheng Q, Winther JF, Cai Q, Boice JD, Shyr Y. "Very low-level heteroplasmy mtDNA variations are inherited in humans." J Genet Genomics 40(12):607–615 (2013). PMC4149221 https://pmc.ncbi.nlm.nih.gov/articles/PMC4149221/

topic bottleneck · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Counted both homoplasmic and heteroplasmic differences across the whole mtDNA genome in 44 individuals from 18 families — 26 mother–child pairs and 9 sibling pairs — at a median depth of 3,981×. The homoplasmic result is a flat zero: "Homoplasmic SNPs were inherited without exception within each family, and all maternally related individuals within the same family shared the same detailed sub-haplogroup." Twelve heteroplasmic mutations above 1% were shared between mother and offspring. Inheritance of very low-level variants down to ~0.1%, falling off around 0.5%, implies "a bottleneck of about 200 mtDNA."

Rate as published / normalised. Published rate: 0 homoplasmic mutations in 26 whole-genome transmissions. A Poisson 95% upper bound is 3.0/26 = 0.115 mutations per genome per generation, i.e. under 6.9 × 10^-6 per site per generation, or under 2.3 × 10^-7 per site per year at a 30-year generation. Per genome per 25-year generation the upper bound is 0.096.

Why it matters here. Jeanson 2015 lists this study in his own Table 1 with 0 mutations in 26 pedigrees, then derives a pooled rate of 0.158 mutations per genome per generation from a different dataset. That rate predicts 4.1 homoplasmic changes in Guo's 26 transmissions; Guo observed zero, P(≤0) = 0.016. The sampling caveat cuts the same way: "all of the mothers in this study were survivors of childhood cancer who underwent radiation therapy including radiation of the uterus," which would bias the count upward, not down. Guo's bottleneck of ~200 is the high outlier against 3, 10.3 and 30–35 elsewhere.

Library. key: guo-2013. File: papers/guo-2013_very-low-level-heteroplasmy.pdf. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. DOI added from EVE2's register and the library record: 10.1016/j.jgg.2013.10.003 (PMC4149221).

Rebolledo-Jaramillo et al. 2014 — the arising-versus-fixing paper

Rebolledo-Jaramillo B, Su MS-W, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. "Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA." PNAS 111(43):15474–15479 (2014). PMC4217420 https://pmc.ncbi.nlm.nih.gov/articles/PMC4217420/ (full PDF also at https://escholarship.org/uc/item/61n5b3pc)

topic bottleneck · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Counted new heteroplasmies appearing above a 1% minor-allele threshold — 51 germline heteroplasmies across 39 mother–child pairs, blood and buccal from each (156 samples), ~20,000× per site — and then converted that arising count into a fixation rate using a measured bottleneck size. One de novo germline mutation was validated by droplet PCR (site 4191, family M500, absent from both maternal tissues, present in both child tissues at 4.7% and 5.6%). Of 98 classified heteroplasmy quartets, 38 (39%) showed tissue-specific patterns, i.e. were somatic rather than germline.

Rate as published / normalised. Three distinct numbers, and confusing them is the crux of this whole article. (a) Observed heteroplasmy appearance μ₀ = 51/(39 × 16,569) = 7.9 × 10^-5 per site per transmission = 1.31 per genome per generation. This is a measurement. (b) Arising rate α = μ₀/(2 ln(1/θ − 1)) with θ = 0.01 → 8.6 × 10^-6 per site per generation = 0.143 per genome per generation. (c) Fixation rate μ = α/N with N = 32.3 → 2.7 × 10^-7 per site per generation (IQR 8.3 × 10^-8 – 8.2 × 10^-7), or 1.3 × 10^-8 per site per year at their 20-year generation. Per genome per 25-year generation: 0.0056 mutations. Steps (b) and (c) are model, not measurement. D-loop-only rate: 1.5 × 10^-6 per site per generation = 7.7 × 10^-8 per site per year. Bottleneck 30–35, IQR 9 to 141.

Why it matters here. This paper states the conversion in one line — "only 1/N of them will go to fixation, leading to μ = α/N" — and its α of 0.143 mutations per genome per generation is numerically almost identical to Jeanson's published young-earth rate of 0.158, which Jeanson uses as a fixation rate. The gap between (a) and (c) is a factor of ~290, and it is the whole argument. Note also the authors' own caution: strict filtering means their rate "should therefore be seen as a 'lower bound'," and the two-tissue design is why it sits an order of magnitude below other pedigree studies. Their maternal-age result is the empirical ceiling on Carter's "Patriarchal Drive": mothers conceiving under 20 transmitted zero to one heteroplasmies, those in their late 30s two to three — a factor of two or three, not orders of magnitude.

Library. key: rebolledo-jaramillo-2014b, was: rebolledo-2014, was: rebolledo-2014b. File: papers/rebolledo-jaramillo-2014b_maternal-age-germline-bottleneck-mtdna.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. The library holds two copies of this paper with different md5 sums, rebolledo-jaramillo-2014 and rebolledo-jaramillo-2014b; the merged key is the b copy, which the plan names (see Library housekeeping). The 51 heteroplasmies this entry uses are 51 germ-line point heteroplasmies among 39 mothers, not 51 new mutations (see Checks made during the merge, item 1).

Ding et al. 2015 — SardiNIA, the dataset Jeanson's rate rests on

Ding J, Sidore C, Butler TJ, Wing MK, Qian Y, Meirelles O, Busonero F, Tanaka T, Lopez ME, Schlessinger D, Cucca F, Abecasis GR, Ferrucci L. "Assessing mitochondrial DNA variation and copy number in lymphocytes of ~2,000 Sardinians using tailored sequencing analysis tools." PLoS Genet 11(7):e1005306 (2015). PMC4501845 https://pmc.ncbi.nlm.nih.gov/articles/PMC4501845/

topic pedigree-rate · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Counted both homoplasmic and heteroplasmic variants in 333 parent–child trios from ~2,000 Sardinians, lymphocytes only, whole-genome sequencing at a median mtDNA depth of only ~180×, with a 4% minor-allele threshold (at 1.6% the false-discovery rate was 30%). Table 1: 7,273 homoplasmic sites in children, of which 7,238 (99.5%) also in the mother; 7,266 in the mothers, same 7,238 shared. 207 heteroplasmic sites in children, 66 (31.9%) shared with the mother.

Rate as published / normalised. The authors publish no mutation rate; they read the 0.5% homoplasmic discordance as noise, writing that "children and their mothers share essentially all homoplasmies." Derived figures: 141 heteroplasmies in children not in mothers = 0.423 per genome per transmission at ≥4% MAF = 2.55 × 10^-5 per site per generation = 8.5 × 10^-7 per site per year at an assumed 30-year generation, or 0.35 per genome per 25-year generation. 35 homoplasmies in children not in mothers = 0.105 per transmission; 28 in mothers not in children = 0.084; the sum, 63, is Jeanson's count and gives 0.189 per transmission.

Why it matters here. Everything in the young-earth mtDNA clock traces back to these 63 discordances. Twenty-eight of them are variants present in the mother and absent in the child, which under strict maternal inheritance require back-mutation to the reference allele at a homoplasmic site in one generation. At 180× depth with a 4% cutoff, a site at 90% in one relative and 97% in another is scored homoplasmic in one and heteroplasmic in the other, producing a spurious discordance. Nobody has yet gone back to the SardiNIA alignments to test which reading is right; that is the single most tractable open check in this literature.

Library. key: ding-2015. File: papers/ding-2015_sardinian-mtdna-variation.pdf. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Floros et al. 2018 — selection inside human primordial germ cells

Floros VI, Pyle A, Dietmann S, Wei W, Tang WCW, Irie N, Payne B, Capalbo A, Noli L, Coxhead J, Hudson G, Crosier M, Strahl H, Khalaf Y, Saitou M, Ilic D, Surani MA, Chinnery PF. "Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos." Nat Cell Biol 20(2):144–151 (2018). PMC6551220 https://pmc.ncbi.nlm.nih.gov/articles/PMC6551220/

topic selection · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Single-cell deep mtDNA sequencing of primordial germ cells inside healthy female human embryos — not a pedigree and not a rate. It measured mtDNA content per cell (a profound reduction, with discrete mitochondria containing ~5 mtDNA molecules), the rise of rare variants to higher heteroplasmy in later PGCs, and "the signature of selection against non-synonymous protein-coding, tRNA gene and D-loop variants."

Why it matters here. It is the physical substrate of the germline bottleneck, measured directly in humans: ~5 mtDNA molecules per mitochondrion in the cells that become eggs. And it is the human counterpart to Fan 2008 and Stewart 2008 — selection acting during germ-cell development, "preventing the relentless accumulation of mtDNA mutations in the human population predicted by Muller's ratchet." This is the evidence Carter's "selection has already done its work" argument does not reach, since it is measured before any sampled individual exists.

Library. key: floros-2018, was: floros-2018b, was: floros-2018c. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Wei et al. 2019 — 1,526 transmissions, and the fixation rate measured directly

Wei W et al. "Germline selection shapes human mitochondrial DNA diversity." Science 364(6442):eaau6520 (2019). doi:10.1126/science.aau6520 https://www.repository.cam.ac.uk/handle/1810/293282 (accepted manuscript with supplementary tables; published version paywalled)

topic heteroplasmy · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Both quantities, in the same dataset, which is why it is decisive. It counted new heteroplasmies arising above 1% variant allele frequency — 477 de novo variants in 1,526 mother–offspring pairs, whole blood, ~1,900× mean depth — and separately counted de novo variants that reached near-homoplasmy: only 3 above 80% heteroplasmic fraction (m.57T>C at 99.3%, m.8993T>G at 82.1%, m.14459G>A at 93.6%), two of which the authors attribute to ascertainment bias from recruiting childhood neurodegenerative disease. It also counted losses: 614 maternal heteroplasmies lost against 477 gained.

Rate as published / normalised. New heteroplasmies: 477/1,526 = 0.313 per genome per transmission = 1.887 × 10^-5 per site per generation = 6.3 × 10^-7 per site per year at an assumed 30-year generation, or 0.26 per genome per 25-year generation. Near-homoplasmic de novo variants: 3/1,526 = 0.00197 per genome per transmission (0.00066 if only the one not attributable to ascertainment counts) = 4.0 × 10^-9 per site per year, or 0.0016 per genome per 25-year generation. Regional rates from Table S2, per base per genome per transmission: D-loop 7.64 × 10^-5 (highest of any region), coding genes 9.51 × 10^-6 to 2.35 × 10^-5. Documented error in the source: Table S2's D-loop row prints "13" de novo variants, but the rate on the same row requires 131 at N = 1,526; every other row in the table is exactly consistent with N = 1,526 while the D-loop row implies N = 151, and 131 makes the loci sum to 475 against the 477 total in Table S1. The "13" is a dropped digit.

Why it matters here. The gap between arising and fixing is 159:1 to 477:1 within a single dataset, measured, not modelled. Jeanson's 0.158 per genome per generation predicts 242 near-homoplasmic de novo events in these 1,526 transmissions; three were seen, probably one. The selection results are equally direct: nonsynonymous-to-synonymous ratio higher in heteroplasmic than homoplasmic variants (P = 4 × 10^-24), higher in de novo and lost variants than in transmitted ones, and novel variants 4.7-fold less likely to be transmitted than known ones (P = 3.6 × 10^-13).

Library. key: wei-2019. File: papers/wei-2019_germline-selection-mtdna-diversity.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Zaidi et al. 2019 — 96 families, two tissues, a bottleneck of 10

Zaidi AA, Wilton PR, Su MSW, Paul IM, Arbeithuber B, Anthony K, Nekrutenko A, Nielsen R, Makova KD. "Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees." PNAS 116(50):25172–25178 (2019). PMC6911200 https://pmc.ncbi.nlm.nih.gov/articles/PMC6911200/

topic bottleneck · camp mainstream · type model · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Counted germline heteroplasmies, defined as those shared by two somatic tissues — 668 heteroplasmies across 690 samples from 345 individuals in 96 families, at least two siblings per mother, 249 mother–child transmissions, blood and buccal per person, mean depth ~11,400×, threshold ≥1% MAF. It then measured the bottleneck independently in different oocyte lineages from the same mother and converted the arising count to a fixation rate.

Rate as published / normalised. Published: germline bottleneck 10.3 mtDNA segregating units (95% HPD 8.5–12.3), oogenic bottleneck 13.4 (10.2–17.3), and from a median 71 germline heteroplasmies among 96 unrelated individuals, a germline mutation rate of 4.72 × 10^-7 mutations per site per generation (95% bootstrap CI 3.93–5.52 × 10^-7). At a 30-year generation that is 1.57 × 10^-8 per site per year, i.e. 0.0078 per genome per generation, or 0.0065 per 16,569 bp genome per 25-year generation. The bottleneck correction is a model; the heteroplasmy count is a measurement.

Why it matters here. This is a completely independent replication of Rebolledo-Jaramillo's corrected rate — different families, a bottleneck three times smaller (10.3 vs 32.3), a different generation time — landing within 16% of it and within 6% of Soares's phylogenetic 1.665 × 10^-8. Two independent pedigree datasets reproducing the phylogenetic rate without any human–chimpanzee calibration is what makes that rate hard to dismiss as circular. Its selection measurement is equally direct: relative nonsynonymous-to-synonymous heteroplasmy occurrence of 0.43, P < 0.001, i.e. germline selection removing more than half of protein-coding mutations before they are ever seen.

Library. key: zaidi-2019. File: papers/zaidi-2019_bottleneck-selection-maternal-age-mtdna.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Arbeithuber et al. 2020 — duplex sequencing of mouse oocytes

Arbeithuber B, Hester J, Cremona MA, Stoler N, Zaidi A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. "Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues." PLoS Biol 18(7):e3000745 (2020). PMC7363077 https://pmc.ncbi.nlm.nih.gov/articles/PMC7363077/

topic method · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction background

What it measured. Measured low-frequency de novo mutations directly in oocytes, bypassing pedigrees entirely, using duplex sequencing on oocytes, brain and muscle from 36 mice in two pedigrees. Result: "mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo," plus more pronounced drift of variants in older germlines, arguing for mtDNA turnover during oocyte meiotic arrest.

Why it matters here. It is the closest anyone has come to measuring the per-molecule mutation rate without the selection filter, and the authors say so: their design "minimized selection effects present in pedigree studies." It is also a mouse. Until someone duplex-sequences human oocytes, the arising→fixing conversion remains a model on both sides of this argument.

Arbeithuber et al. 2025 — duplex sequencing of human oocytes, and the maternal-age effect measured where it counts

Arbeithuber B, Ebner T, Makova KD, et al. "Allele frequency selection and no age-related increase in human oocyte mitochondrial mutations." Science Advances 11(32):eadw4954 (6 August 2025). doi:10.1126/sciadv.adw4954 https://pmc.ncbi.nlm.nih.gov/articles/PMC12327460/ CC BY-NC. Library key arbeithuber-2025.

topic pedigree-rate · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Duplex sequencing, error rate below 10^-7, on 80 single oocytes from 22 women aged 20 to 42, with blood and saliva from the same donors — the human version of the same laboratory's 2020 mouse and 2022 macaque studies. Two results. The age result: "with age, mutations increased in blood and saliva but not in oocytes." Mixed model Z-test P = 2.7 × 10^-3 (blood), 5.7 × 10^-2 (saliva), 0.688 (oocytes); permutation test on old versus young oocytes P = 0.550, a 0.99-fold decrease. The selection result: high-allele-frequency mutations are depleted in coding relative to non-coding regions while low-frequency ones are spread evenly, which they read as frequency-dependent purifying selection.

Rate as published / normalised. From 52 de novo mutations at MAF >= 1% over 70 mother-to-oocyte transmissions: 3.95 × 10^-4 per site per generation in the D-loop and 1.95 × 10^-5 in the coding region, 20.2-fold apart. Over the regions covered that is 0.443 + 0.300 = 0.743 mutations per genome per generation (computed here, not published in that form; their coding region is 15,359 bp — genes, rRNA, tRNA — with 88 bp of other non-coding sequence reported separately), i.e. 4.5 × 10^-5 per site per generation and 1.8 × 10^-6 per site per year at 25 years. This is the fastest human mtDNA rate ever measured — 2.4x Wei's arising rate, 4.7x Jeanson's published rate, 10.6x deCODE raw, 128x Connell's fixed-only rate.

Why it matters here, and it cuts both ways. It removes the article's top-ranked young-earth rescue: the maternal age effect is measured directly in the germ line and is null, so Rebolledo's somatic "tripling over 30 y" cannot be carried across to transmission. Quote the limits — 22 women, and the same lab found 2-3x in mouse oocytes and ~2.5x in macaque oocytes to age nine — so the human null is not the last word. And it hands the other side its best-looking number ever: read as a clock, 0.743 per generation dates Eve to ~1,900 years, which overshoots even a young-earth requirement. The answer is the article's own thesis at maximum resolution — this is an arising rate counted inside the germ cell before bottleneck, drift or transmission, and it is exactly what Árnadóttir predicted in print ("the true rate of mutation in the mtDNA germline must be substantially higher than reported here").

Library. key: arbeithuber-2025. File: papers/arbeithuber-2025_human-oocyte-mtdna-no-age-increase.html (also .md, arbeithuber-2025_human-oocyte-mtdna-no-age-increase/). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Connell et al. 2022 — Norfolk Island, the cleanest whole-genome pedigree rate

Connell JR, Benton MC, Lea RA, Sutherland HG, Chaseling J, Haupt LM, Wright KM, Griffiths LR. "Pedigree derived mutation rate across the entire mitochondrial genome of the Norfolk Island population." Sci Rep 12:6827 (2022). PMC9042960 https://pmc.ncbi.nlm.nih.gov/articles/PMC9042960/

topic pedigree-rate · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Counted both quantities separately across the entire mitochondrial genome by Sanger sequencing — 225 individuals, 45 maternal lineages, 345 generational events, heteroplasmy threshold 20% MAF. Nine mutations total: 2 fixed transitions and 7 cases of heteroplasmy. Because it reports the fixed changes on their own, it gives a fixation rate with no bottleneck model anywhere in the derivation.

Rate as published / normalised. Published: "Assuming a generation time of 26.9 years, the mutation rate for the entire mtGenome would be 0.058 mutations/site/Myr when including heteroplasmy (95% CI 0.031–0.108), and 0.013 mutations/site/Myr when excluding heteroplasmy (95% CI 0.003–0.047)." Normalised: including heteroplasmy, 5.85 × 10^-8 per site per year = 9/345 = 0.026 per genome per generation = 0.024 per genome per 25-year generation; excluding heteroplasmy, 1.30 × 10^-8 per site per year = 2/345 = 0.0058 per genome per generation = 0.0054 per genome per 25-year generation. Regional rates (mutations/site/Myr): HVI 1.201, HVII 0.343, control region 0.469, coding region 0.028. Wording error in the source: the sentence "1.57 × 10^-6 mutations occur … in the mtGenome in each generation" is per site per generation, not per genome; as written it is off by a factor of 16,569.

Why it matters here. This is the hardest single fact in this dimension for the young-earth reading. The fixed-change-only rate, 1.30 × 10^-8 per site per year, is 0.78× the standard phylogenetic rate — the pedigree clock, counting only mutations that actually stuck, is if anything slower than the phylogenetic clock, with no bottleneck correction applied. Its abstract's headline claim of rates "approximately 16 times higher than estimates derived from phylogenetic analysis" applies only to the heteroplasmy-inclusive figure. Note too that its control-region estimate, 0.469 mutations/site/Myr, is essentially identical to Howell 2003's pooled 0.475 — independent confirmation that the control-region excess is real and that it does not carry over to the whole genome. Jeanson's 0.158 per genome per generation predicts 54.6 fixed changes in these 345 transmissions; two were observed, P(≤2) ≈ 3 × 10^-21.

Library. key: connell-2022. File: papers/connell-2022_norfolk-island-mtgenome-mutation-rate.pdf (also .md, connell-2022_norfolk-island-mtgenome-mutation-rate-readable.txt). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Árnadóttir et al. 2024 — deCODE, 116,663 transmissions

Árnadóttir ER, Moore KHS, Guðmundsdóttir VB, Ebenesersdóttir SS, Guity K, Jónsson H, Stefánsson K, Helgason A. "The rate and nature of mitochondrial DNA mutations in human pedigrees." Cell 187(15):3904–3918.e8 (2024). doi:10.1016/j.cell.2024.05.022 https://pubmed.ncbi.nlm.nih.gov/38851187/ (deCODE summary: https://www.decode.com/the-rate-nature-and-transmission-of-mitochondrial-dna-mutations-in-humans/)

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region whole-genome · calibration n/a · direction mixed

What it measured. Counted 8,199 mutations across 116,663 mother–child transmissions from 64,806 contemporary Icelanders in 2,548 matrilines — by far the largest direct measurement ever made. Which quantity it counted cannot be determined from the abstract: the split between heteroplasmic and homoplasmic events, the detection threshold, and the tissue are all in the full text, which is paywalled and could not be obtained by any route tried. What the abstract does state is that the paper documents "the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants," the impact of negative selection on viable deleterious mutations, "pre-natal selection that most likely occurs during the development of oocytes," and a bottleneck of "an average of 3 mtDNA units effectively transmitted from mother to child."

Rate as published / normalised. From the deCODE summary: "2.87 × 10^-6 and 2.38 × 10^-5 mutations per position per generation for the coding and control regions of mtDNA, respectively, around 5 times greater than previous phylogenetic estimates." Those two figures reconstruct the headline count to within 1%: 2.87 × 10^-6 × 15,447 + 2.38 × 10^-5 × 1,122 = 0.0710 per genome per generation, against 8,199/116,663 = 0.0703. Normalised at an assumed 30-year generation: 1.41 × 10^-7 per site per year whole genome (coding 9.6 × 10^-8, control region 7.9 × 10^-7), or 0.059 mutations per 16,569 bp genome per 25-year generation.

Why it matters here. This is the strongest datum in the whole article for a young mitochondrial Eve, and it is a measurement rather than a model. Run as a star-phylogeny clock against the observed worldwide mean pairwise difference of 39.8 bp, 0.0703 per generation puts the mtDNA common ancestor at ~283 generations, about 8,500 years at 30-year generations or 7,100 at 25 — roughly 20× younger than the standard 150–200 ka. Its own abstract carries the counter-argument: the mutations are heavily concentrated at hypermutable sites that recur and revert, so the count cannot be extrapolated linearly, and the paper reports both negative selection and pre-natal oocyte selection. The internal test is decisive on that point: applying the study's own coding rate to the observed coding-region diversity gives ~10,100 years, while its control-region rate against control-region diversity gives ~5,560 — the faster-mutating region yielding the younger age, which is the signature of saturation, exactly as Heyer 2001 predicted. The full text was not read. Anything cited from this paper beyond the abstract and the deCODE press page needs institutional access first.

Library. key: arnadottir-2024. File: papers/arnadottir-2024_rate-nature-mtdna-mutations.html (also .md, arnadottir-2024_rate-nature-mtdna-mutations-readable.txt). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

Phylogenetic rates, and the ancient-DNA calibration

Take the most-cited date for mitochondrial Eve apart and it comes in four layers. The sequence difference between a human and a chimpanzee mitochondrial genome is a measurement — Ingman counted it at 0.17 substitutions per site, and anyone can recount it. The claim that those two lineages parted 5 million years ago is an assumption, imported from the fossil record and given no error bar in most of these papers. Dividing the first by the second yields a mutation rate, which is a model output. Dividing human mitochondrial diversity by that rate yields a date for Eve, which is a model output twice over. Ingman's famous 171,500 years is exactly this arithmetic and nothing more: (5.82 × 10⁻³ ÷ 0.17) × 5,000,000 = 171,176 years. The only empirical content is the ratio 1 : 29; the age scale is the assumption. Change the assumed split to 6.5 Myr and the same data give Mishmar's 198,000 years. A young-earth reader is entitled to say those numbers are worth nothing to him, because he denies the common ancestor they are pinned to.

He is not entitled to say it about the rest of the block. After 2013 four groups measured the same rate with no ape, no hominin fossil, and no assumed migration date — only radiocarbon-dated bones used as calibrated tips on the tree. Fu 2013 (10 tips), Rieux 2014 (26), Posth 2016 (66) and Brotherton 2013 (Holocene samples only) get 2.1–2.8 × 10⁻⁸ substitutions per site per year, and a most recent common ancestor at 143,000–157,000 years. Dropping the ape calibration entirely moves the answer by 20–25 %, not by a factor of twenty-five. The calibration field below records, for every rate, what set the clock. Read down it and the circularity charge sorts itself: it lands squarely on Horai, Ingman, Mishmar, Kivisild, Soares and Behar, and it misses Fu, Brotherton, Rieux, Posth, Cabrera and Översti completely.

Horai 1995 — complete hominoid mitochondrial genomes

Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N. "Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs." PNAS 92(2):532–536 (1995). doi:10.1073/pnas.92.2.532 https://pmc.ncbi.nlm.nih.gov/articles/PMC42775/ — PMC has no OCR text for this article, only page images; the readable full text is the Wayback copy of the publisher PDF, https://web.archive.org/web/2019/http://www.pnas.org/content/92/2/532.full.pdf . The live publisher PDF at pnas.org returns HTTP 403 to scripted requests.

topic phylogenetic-rate · camp mainstream · type model · access OA · region whole-genome · calibration ape-divergence · direction mixed

What it measured. Complete mitochondrial sequences of three humans and four apes, then a substitution rate fixed by assuming the orangutan / African ape split at 13 Myr. Human–chimpanzee at 4.87 ± 0.23 Myr is an output of that calibration, not an input, so the human date sits two calibration steps away from anything datable. The paper's own data give two irreconcilable ages for the human ancestor: 450,000 ± 70,000 years from nonsynonymous and RNA-gene sites, and 143,000 ± 18,000 years from synonymous sites plus the D-loop. Only the second is ever quoted; the authors explain the first away as saturation in Ala↔Thr and Ile↔Val changes.

Rate as published / normalised. Synonymous sites 3.89 × 10⁻⁸ per site per year. D-loop 7.00 × 10⁻⁸ per site per year — and note this is derived, not measured, by assuming the D-loop runs 1.8× faster than synonymous sites. Hypervariable segment I 10.3 × 10⁻⁸, segment II 7.39 × 10⁻⁸. Over the 1,143 bp control region the D-loop figure is 2.0 × 10⁻³ mutations per control region per 25-year generation. No whole-genome rate is published here, and multiplying the D-loop rate across all 16,569 sites is not licensed — it would inflate the answer roughly fourfold.

Why it matters here. The 143,000-year figure is the lowest classic number and gets quoted approvingly in young-earth material, but it is fossil-calibrated to the hilt, and the same paper's other clock gives triple the age from the same sequences. It cannot be used as an independent check on anything.

Library. key: horai-1995. File: papers/horai-1995_hominoid-mtdna-african-origin.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Ingman 2000 — the 171,500-year figure

Ingman M, Kaessmann H, Pääbo S, Gyllensten U. "Mitochondrial genome variation and the origin of modern humans." Nature 408:708–713 (2000). doi:10.1038/35047064 https://www.nature.com/scitable/content/12631/10.1038_35047064.pdf

topic phylogenetic-rate · camp mainstream · type model · access paywalled · region coding · calibration ape-divergence · direction mixed

What it measured. 53 complete human mitochondrial genomes, 657 segregating sites (141 in the D-loop, 516 outside), mean pairwise distance 3.8 × 10⁻³ substitutions per site, maximum human pairwise distance 5.82 × 10⁻³, mean human–chimpanzee distance 0.17. It also ran a relative-rates test and found the D-loop rejects clocklike evolution at P < 0.001 while the rest of the molecule does not (P = 0.094), which is why they dropped the D-loop from all dating.

Rate as published / normalised. 1.70 × 10⁻⁸ substitutions per site per year for the molecule excluding the D-loop, obtained by dividing 0.17 by an assumed 5-Myr split. Over the 15,426 non-D-loop bases that is 6.6 × 10⁻³ mutations per generation at 25 years; scaled to all 16,569 bases it would be 7.0 × 10⁻³. The ±50,000 on the published date is sampling error on the genetic distance only and contains no calibration uncertainty at all.

Why it matters here. This is the source of the "Eve at 170,000 years" citation that circulates everywhere, and the article should say plainly that the number is one division by an assumed ape date. It also supplies the cleanest evidence that the control region is not clocklike — a point that cuts against control-region-based clock arguments from either camp.

Mishmar 2003 — the 1.26 × 10⁻⁸ coding-region rate

Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, Brandon M, Easley K, Chen E, Brown MD, Sukernik RI, Olckers A, Wallace DC. "Natural selection shaped regional mtDNA variation in humans." PNAS 100(1):171–176 (2003). doi:10.1073/pnas.0136972100 https://pmc.ncbi.nlm.nih.gov/articles/PMC140917/

topic phylogenetic-rate · camp mainstream · type model · access OA · region coding · calibration ape-divergence · direction mixed

What it measured. 104 complete genomes; distance to the human–chimp ancestor 818.05 ± 0.75 × 10⁻⁴ substitutions per nucleotide, human tree depth 24.88 ± 0.90 × 10⁻⁴, ratio 1 : 32.8. Fixing the denominator at 6.5 Myr gives 198 ± 19 kyr. Separately it compared kₐ/kₛ by climate zone and reported ATP6 variability in the arctic — on counts as small as 3 versus 7 nonsynonymous changes.

Rate as published / normalised. 1.26 ± 0.08 × 10⁻⁸ base substitutions per nucleotide per year (HKY85). Across 16,569 bp at a 25-year generation that is 5.22 × 10⁻³ mutations per genome per generation, or one mutation per 4,790 years.

Why it matters here. Two things a skeptic should see side by side. The Methods state outright that the standard errors "do not include any uncertainty in the calibration point," so the famous ±19 kyr excludes the dominant error term. And the Discussion's last line concedes that if selection matters, "the rate of mtDNA molecular clock may not have been constant throughout human history" — the same paper supplying the field's most-used strict-clock rate.

Library. key: mishmar-2003. File: papers/mishmar-2003_natural-selection-regional-mtdna.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Kivisild 2006 — the synonymous clock, and a failure to replicate

Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, Passarino G, Underhill PA, Scharfe C, Torroni A, Scozzari R, Modiano D, Coppa A, de Knijff P, Feldman M, Cavalli-Sforza LL, Oefner PJ. "The role of selection in the evolution of human mitochondrial genomes." Genetics 172(1):373–387 (2006). doi:10.1534/genetics.105.043901 https://pmc.ncbi.nlm.nih.gov/articles/PMC1456166/

topic selection · camp mainstream · type measurement · access OA · region coding · calibration ape-divergence · direction mixed

What it measured. 1,758 mutations at 1,292 coding-region sites across 277 complete genomes. It also re-ran Ruiz-Pesini and Mishmar's climate-selection test and could not reproduce it: "we did not observe any significant regional (climatic) differences in the rate of nonsynonymous changes," attributing the earlier result to comparing old African paragroups with young Arctic haplogroups.

Rate as published / normalised. Average transition rate at 4,212 synonymous positions 3.5 ± 0.1 × 10⁻⁸ per year per position, equivalent to one synonymous transition per 6,764 ± 140 years genome-wide — that is 3.7 × 10⁻³ synonymous transitions per genome per 25-year generation, not a total mutation rate. Calibrated on 6 Myr for the species split and 6.5 Myr for the mitochondrial coalescence, giving a tree age of 160,000 ± 22,000 years. Kivisild avoids a whole-molecule interspecies clock deliberately, because of "saturation of transitions at silent positions and the effect of selection on the fixation rate of amino acid replacement mutations."

Why it matters here. It is the counterweight to any claim that selection on mitochondrial DNA is strong and climate-driven. A creationist argument that leans on Mishmar's selection result to discredit the clock has to reckon with the fact that the next group to look could not find it.

Library. key: kivisild-2006. File: papers/kivisild-2006_role-of-selection-human-mitochondrial-genomes.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

Briggs 2007 — the damage model for ancient DNA

Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. "Patterns of damage in genomic DNA sequences from a Neandertal." PNAS 104(37):14616–14621 (2007). doi:10.1073/pnas.0704665104 https://pmc.ncbi.nlm.nih.gov/articles/PMC1976210/

topic method · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction background

What it measured. The quantitative model of post-mortem cytosine deamination: 68 % deamination in single-stranded overhangs versus 0.97 % in double-stranded DNA, 21 % C→T at terminal positions, overhangs of 1.6–1.8 nucleotides, nicks at 2.4 % of positions.

Why it matters here. It settles the direction of the damage artifact, which is the natural objection to every tip-calibrated rate below. Damage adds spurious derived alleles to the ancient tip, which makes an ancient genome look more different from the root, shortening the apparent branch shortening and slowing the inferred rate. It cannot manufacture the signal; it can only suppress it. The artifact makes Eve look older, not younger.

Endicott & Ho 2008 — the calibration swap

Endicott P, Ho SYW. "A Bayesian evaluation of human mitochondrial substitution rates." American Journal of Human Genetics 82(4):895–902 (2008). doi:10.1016/j.ajhg.2008.01.019 https://pmc.ncbi.nlm.nih.gov/articles/PMC2427281/

topic phylogenetic-rate · camp mainstream · type model · access OA · region whole-genome · calibration archaeological · direction supports

What it measured. The cleanest head-to-head experiment in the subject: the same 177 genomes, the same 11,940 bp four-partition alignment, the same Bayesian relaxed-clock software, run twice with only the calibration swapped. Internal calibration (Sahul settlement at 40–55 ka for haplogroup P, H1 and H3 at 18 ± 3.5 ka) gives a human mitochondrial ancestor at 108 kyr (82–134). External calibration (human–chimp at 5–7.5 Myr) gives 162 kyr (122–213). On first-and-second codon positions alone the same swap gives 79 kyr versus 310 kyr — a fourfold disagreement from one methodological choice.

Rate as published / normalised. Concatenated rate 9.66 × 10⁻⁸ internal, 6.81 × 10⁻⁸ external. Unit trap: those are not per-site rates of the alignment. Their partition rates were normalised to an unweighted mean of 1 across four partitions of very unequal length, so the length-weighted per-site rate over their 11,940 bp is 5.36 × 10⁻⁸ (internal) and 3.76 × 10⁻⁸ (external). Anyone comparing the headline 9.66 × 10⁻⁸ with Soares' 1.665 × 10⁻⁸ is out by about sixfold. The safe comparable numbers are the coding first-and-second-position rates: 1.30 × 10⁻⁸ internal and 3.82 × 10⁻⁹ external, which over 7,198 bp per 25-year generation are 2.3 × 10⁻³ and 6.9 × 10⁻⁴ mutations per generation. Their footnote also warns these are gamma-model rates and "should not be used for analyses of uncorrected genetic distances."

Why it matters here. This is the strongest mainstream statement of the young-earth side's methodological complaint, and it comes with numbers: "The use of a human-chimpanzee calibration appears to be generally inappropriate for mitochondrial studies of human evolution." The 108 kyr estimate is genuinely free of any ape date — though it substitutes archaeological dates that Soares 2009 disputes in detail.

Library. key: endicott-2008. File: papers/endicott-2008_bayesian-evaluation-human-mitochondrial-substitution-rates.html (and .txt beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft. The first draft cited this paper only as two claims filed under the Henn 2009 footnote (henn-2009b:endicott-2008), so it never had a source footnote of its own. The PMC page was stored in the library on 2026-10-27, and its Table 3 shows the internal-calibration concatenated row at 108 kyr (82-134), as this entry reports. Do not use library key endicott-2008b for this paper (see Library housekeeping). Verified: full (stored PMC HTML and text).

Ho & Endicott 2008 — what calibration choice does to the peopling of the Americas

Ho SYW, Endicott P. "The crucial role of calibration in molecular date estimates for the peopling of the Americas." American Journal of Human Genetics 83(1):142–146 (2008). doi:10.1016/j.ajhg.2008.06.005 https://pmc.ncbi.nlm.nih.gov/articles/PMC2443849/ — note that Unpaywall returns a different article for this DOI; use the PMC record.

topic phylogenetic-rate · camp mainstream · type model · access OA · region coding · calibration archaeological · direction supports

What it measured. A reanalysis of Fagundes 2008 and Achilli 2008, the same sequences rerun with an internally calibrated rate. Their point about the original papers is sharp: both "calibration methods" used there were the human–chimp split at 6.5 Myr, once directly and once through Mishmar's rate, "which is not surprising given that they were effectively based on the same calibration."

Rate as published / normalised. 2.038 × 10⁻⁸ ± 2.064 × 10⁻⁹ substitutions per site per year for the coding region — 7.9 × 10⁻³ mutations across 15,447 coding bases per 25-year generation. Applying it moves the American population expansion from 15–19 kyr to 10–12 kyr.

Why it matters here. A ~40 % shift in a published date from changing nothing but the clock's anchor, in a mainstream journal, by mainstream authors who call the alternative "an unsettling trivialization of the effect of calibration choice."

Henn 2009 — fourteen archaeological calibrations, one dataset

Henn BM, Gignoux CR, Feldman MW, Mountain JL. "Characterizing the time dependency of human mitochondrial DNA mutation rate estimates." Molecular Biology and Evolution 26(1):217–230 (2009). doi:10.1093/molbev/msn244 https://web.archive.org/web/2017/http://mbe.oxfordjournals.org/content/26/1/217.full.pdf — the live OUP page returns 403 to scripted requests; the Wayback PDF is the working route.

topic rate-gap · camp mainstream · type compilation · access paywalled · region HVR1 · calibration archaeological · direction mixed

What it measured. Fourteen independent hypervariable-region-1 rates, each calibrated on a different archaeological settlement date, plus ten coding-region rates the same way, plus a compilation table putting sixteen published rates into one unit system.

Rate as published / normalised. Published as divergence rates 2λ in mutations per bp per Myr; per-lineage, the HVR1 rates run from 1.10 × 10⁻⁷ per site per year (Japan, calibrated at 32 ka) to 5.47 × 10⁻⁷ (Marianas, 4.3 ka) — a fivefold spread that decreases monotonically with calibration age. Over 359 bp of HVR1 the extremes are 9.9 × 10⁻⁴ and 4.9 × 10⁻³ mutations per generation at 25 years; these are hypervariable-segment rates and must not be scaled to 16,569 sites. Their ten coding-region rates span only 1.33–2.68 × 10⁻⁸ per site per year, which over the whole genome is 5.5 × 10⁻³ to 1.11 × 10⁻² mutations per generation.

Why it matters here. It cuts both ways, hard. The fivefold HVR1 spread shows that internal calibration is a menu — pick your archaeological event, pick your rate — which supports the young-earth complaint about clock softness. But the coding-region rates from the same exercise vary only twofold and land at 1.3–2.7 × 10⁻⁸, right on top of the radiocarbon-tip values obtained years later by entirely different means. Their proposed explanation for the time dependency is demographic: "serial bottlenecks prior to the Holocene."

Used in the article as of 2026-09-04, in ### The genuine time-dependency, and how big it is — footnotes was: henn-2009 and was: henn-2009:a, now keyed henn-2009b. It had been catalogued here since the first pass and never cited, which left the article's "about twofold" verdict resting on no human-specific measurement of the decay. Working route is the Wayback PDF; live OUP serves a Cloudflare interstitial. PDF now in the library as henn-2009b.

Library. key: henn-2009b, was: henn-2009. File: papers/henn-2009b_time-dependency-human-mtdna-rate.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft. The library also holds this paper's PDF under henn-2009, and the library key endicott-2008b holds this Henn paper, not Endicott & Ho 2008 (see Library housekeeping). The first draft's footnote filed Endicott & Ho 2008 as two claims of this source by mistake.

Soares 2009 — the purifying-selection correction

Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB. "Correcting for purifying selection: an improved human mitochondrial molecular clock." American Journal of Human Genetics 84(6):740–759 (2009). doi:10.1016/j.ajhg.2009.05.001 https://pmc.ncbi.nlm.nih.gov/articles/PMC2694979/ — supplement with Tables S1–S5 (including the mtEve age) at https://ueaeprints.uea.ac.uk/id/eprint/31812/2/Soares_calibration_SOM.pdf

topic selection · camp mainstream · type model · access OA · region whole-genome · calibration ape-divergence · direction mixed

What it measured. More than 2,000 complete genomes. For every node in the global tree they computed the synonymous fraction of the mutations on the path to it, found that fraction rising from about 25 % near the tips to a plateau deep in the tree, fitted a Gompertz curve, and read the asymptote at 47.94 %. Two independent checks — the modern-human/Neanderthal split (55 %, corrected to 51.0 %) and the bonobo–chimp split (56.1 %, corrected to 46.6 %) — land near the same plateau.

Rate as published / normalised. Whole molecule 1.665 × 10⁻⁸ ± 1.479 × 10⁻⁹ substitutions per nucleotide per year, "or one mutation every 3624 years," calibrated on a 6.5-Myr species split plus 0.5 Myr of lineage coalescence. Across 16,569 bp at 25 years per generation that is 6.90 × 10⁻³ mutations per genome per generation. Region rates from their eight-partition ML fit: HVS-I 1.64 × 10⁻⁷, HVS-II 2.30 × 10⁻⁷, whole control region 9.883 × 10⁻⁸, protein-coding first-and-second positions 8.88 × 10⁻⁹, third positions 1.93 × 10⁻⁸. Their mtEve age, in Supplemental Table S5 and not in the main text, is 192,400 years (151,600–233,600).

Why it matters here. This is the paper usually cited to say "purifying selection explains the pedigree/phylogeny gap," and its own Table S4 says it does not. The correction factor is 1.501× for nodes under 1,000 years, falling to 1.128× at 50,000–100,000 years. The authors write that "the extent of this overestimation is less than has generally been asserted." A correction of at most 1.5× cannot close a gap of 12–14×, let alone 26×. That is a mainstream admission the article should quote in both directions: it undercuts the standard reply to the creationist argument, and it also removes selection as a rescue for the young-earth clock. Note also that the much-quoted line about "a severe shortage of such uncontroversial episodes" is Soares criticising Endicott & Ho, not a concession by the calibration critics — an attribution error present in the article owner's own older notes.

Library. key: soares-2009. File: papers/soares-2009_purifying-selection-mtdna-clock.pdf (also .md, soares-2009_purifying-selection-mtdna-clock-supplement.md, soares-2009_purifying-selection-mtdna-clock-supplement.pdf). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Endicott, Ho, Metspalu & Stringer 2009 — the review

Endicott P, Ho SYW, Metspalu M, Stringer C. "Evaluating the mitochondrial timescale of human evolution." Trends in Ecology & Evolution 24(9):515–521 (2009). doi:10.1016/j.tree.2009.04.006 https://pubmed.ncbi.nlm.nih.gov/19682765/

topic critique · camp mainstream · type review · access paywalled · region whole-genome · calibration n/a · direction supports

What it measured. Nothing new; it is a review. Read in abstract only. The full text is closed at Elsevier, HAL holds a metadata-only record with no file, and no Wayback capture of the body was found. Nothing beyond the abstract should be quoted from it.

Why it matters here. For one sentence, verbatim from the abstract: "we contend that some of the most widely-cited mitochondrial rate estimates have several significant shortcomings, including a reliance on a human-chimpanzee calibration, and highlight the pressing need for revised rate estimates." That is the circularity charge, made in a mainstream review by four mainstream authors including Chris Stringer. For the same argument with numbers attached and full text available, use Endicott & Ho 2008 and Rieux 2014 instead.

Briggs 2010 — UDG treatment removes deaminated cytosines

Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S. "Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA." Nucleic Acids Research 38(6):e87 (2010). doi:10.1093/nar/gkp1163 https://pmc.ncbi.nlm.nih.gov/articles/PMC2847228/

topic method · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction background

What it measured. Uracil-DNA-glycosylase plus endonuclease VIII treatment cuts the per-base error rate in ancient mitochondrial sequence from 2.20 % to 0.40 %, and to 0.09 % with multi-pass consensus — a 22-fold reduction. It also showed that CpG-methylation damage residue is absent in mitochondrial DNA specifically.

Why it matters here. It is the direct answer to "the ancient sequences are too damaged to trust." Every tip-calibrated genome used by Fu, Rieux and Posth was produced on treated libraries, and the residual error is an order of magnitude smaller than the branch shortening being measured.

Sawyer 2012 — the authenticity criterion

Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S. "Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA." PLoS ONE 7(3):e34131 (2012). doi:10.1371/journal.pone.0034131 https://pmc.ncbi.nlm.nih.gov/articles/PMC3316601/

topic method · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction background

What it measured. How misincorporation and fragmentation patterns scale with specimen age, producing the ≥20 % 5′ C→T threshold used as an authenticity test.

Why it matters here. It is the criterion Fu 2013 used to reject one of its own samples (Paglicci Str. 4b). Worth citing because it shows the tip-calibration studies discarding data that fails a stated test, rather than accepting everything that helps.

Behar 2012 — the RSRS, and 57.1 substitutions

Behar DM, van Oven M, Rosset S, Metspalu M, Loogväli E-L, Silva NM, Kivisild T, Torroni A, Villems R. "A 'Copernican' reassessment of the human mitochondrial DNA tree from its root." American Journal of Human Genetics 90(4):675–684 (2012). doi:10.1016/j.ajhg.2012.03.002 https://pmc.ncbi.nlm.nih.gov/articles/PMC3322232/ — supplement (Table S5, the root age) at https://web.archive.org/web/2020/https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322232/bin/mmc1.pdf

topic tree-topology · camp mainstream · type measurement · access OA · region whole-genome · calibration ape-divergence · direction mixed

What it measured. 18,843 complete genomes, with the root sequence reconstructed using six Neanderthal genomes as outgroup. The headline number is the distance from that reconstructed root to a living person: mean 57.1 substitutions, median 56, standard deviation 5.9, range 41 to 77. Known hotspots (16519, the 309/315 C-insertions, 16182/16183, the 515–522 repeat) were excluded first, so 57.1 slightly undercounts. It estimates no rate of its own; its dates are Soares' clock, and therefore Soares' 6.5/7-Myr ape calibration, inherited whole. Its own root age, in Supplemental Table S5 and not the main text, is 176,689 ± 11,340 years.

Why it matters here. Two uses. First, 57.1 is the cleanest raw number either side can work from: divide it by any published rate and you get that rate's date for Eve — Soares 207 ka, Rieux 161 ka, Fu 129 ka, Posth 126 ka. Getting 6,000 years requires 0.238 mutations per genome per 25-year generation. Second, Behar documents clock violations it cannot explain (χ² p ≈ 1.5–3 × 10⁻⁴ within haplogroup M), including two M genomes with 43 substitutions and two with 71 — where the path from the root to M already contains 39, so one descendant lineage accumulated 4 changes while another accumulated 32. Under a Poisson clock with mean 32, observing 4 is astronomically unlikely. That damages the precision claims of every estimate in this block.

Fu 2013 — the founding tip calibration

Fu Q, Mittnik A, Johnson PLF, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, Krause J. "A revised timescale for human evolution based on ancient mitochondrial genomes." Current Biology 23(7):553–559 (2013). doi:10.1016/j.cub.2013.02.044 https://pmc.ncbi.nlm.nih.gov/articles/PMC5036973/ — the Cell Press page returns 403 to scripted clients but loads in a browser.

topic ancient-dna · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction undercuts

What it measured. Ten radiocarbon-dated ancient modern-human mitochondrial genomes spanning 40,000 years (Dolní Věstonice 13 and 14, Tianyuan, Boshan, Oberkassel 998, Kostenki, the Iceman, Saqqaq, Loschbour and one since withdrawn) plus 311 modern genomes, measuring branch shortening — the substitutions a dead lineage did not have time to acquire. No ape, no fossil hominin, no migration date. Their own reason for the method: "no fossil has yet been identified to represent the uncontested MRCA for humans and chimpanzees."

Rate as published / normalised. Linear regression: 1.92 × 10⁻⁸ per site per year (1.16–2.68) whole molecule, 1.25 ± 0.68 × 10⁻⁸ coding. Bayesian, constant-size relaxed clock: 2.67 × 10⁻⁸ (2.16–3.16 HPD) whole molecule, 1.57 × 10⁻⁸ coding. Across 16,569 bp at 25 years per generation the Bayesian value is 1.11 × 10⁻² mutations per genome per generation, one mutation every 2,260 years. That is about 1.6× the fossil-calibrated rate. Human mitochondrial MRCA 157 ka (120–197).

Why it matters here. This is the single strongest paper against the circularity charge, and the article must engage it head-on rather than around it. Its robustness check matters too: each sample older than 4,000 years used alone as the calibration gives rates from 1.14 × 10⁻⁸ (Kostenki) to 4.5 × 10⁻⁸ (Boshan), all overlapping the pooled value, so no one specimen drives the result. Incidentally the team re-dated its own Cro-Magnon 1 sample, found it medieval (~700 years), and had it removed from the Musée de l'Homme collection — the field does catch its own dating errors.

Library. key: fu-2013f, was: fu-2013b, was: fu-2013c, was: fu-2013d. File: papers/fu-2013f_revised-timescale-ancient-mitogenomes.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Brotherton 2013 — the Holocene-only calibration

Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Der Sarkissian C, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SYW, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A, and the Genographic Consortium. "Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans." Nature Communications 4:1764 (2013). doi:10.1038/ncomms2656 https://pmc.ncbi.nlm.nih.gov/articles/PMC3978205/

topic ancient-dna · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction undercuts

What it measured. 39 complete haplogroup H genomes from Central European skeletons dated 5500–2000 BC (about 7,450–3,950 cal BP). No Pleistocene sample, no ape split, no Out-of-Africa node — every calibration point sits inside the dendrochronologically anchored part of the radiocarbon curve. A date-randomization test run on the Holocene samples alone confirmed the dates carry enough signal to calibrate the tree.

Rate as published / normalised. 2.4 × 10⁻⁸ substitutions per site per year (1.7–3.2 × 10⁻⁸ HPD) for the entire genome, which the authors note is 1.45× the human/chimp-calibrated 1.66 × 10⁻⁸. Across 16,569 bp at 25 years that is 9.9 × 10⁻³ mutations per genome per generation, one mutation every 2,515 years. Haplogroup H coalescence 10.9–19.1 ka.

Why it matters here. This is the version a young-earth reader can least easily dismiss. Reject radiocarbon beyond 40,000 years and Fu, Posth and Rieux go with it — but Brotherton's oldest calibration point is 7,450 years and tree-ring-anchored, and it still yields a rate within 10 % of theirs, and a coalescence for one European sub-branch alone exceeding 10,000 years. Its honest weakness: only 18 of the 39 individuals carry direct radiocarbon dates, the other 21 being assigned mean archaeological dates for their culture.

Library. key: brotherton-2013, was: brotherton-2013b, was: brotherton-2013c. The library has a YAML record only; no file is stored. Cited by the first draft, EVE2 and ASTRA. EVE2 register: considered, not used in current draft. EVE2's index.md nevertheless cites it.

Rieux 2014 — root, node and tip calibration on one dataset

Rieux A, Eriksson A, Li M, Sobkowiak B, Weinert LA, Warmuth V, Ruiz-Linares A, Manica A, Balloux F. "Improved calibration of the human mitochondrial clock using ancient genomes." Molecular Biology and Evolution 31(10):2780–2792 (2014). doi:10.1093/molbev/msu222 CC-BY. https://pmc.ncbi.nlm.nih.gov/articles/PMC4166928/ and https://academic.oup.com/mbe/article/31/10/2780/1015730

topic ancient-dna · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction mixed

What it measured. 30 high-quality ancient plus 320 contemporary complete genomes (26 ancient retained after damage screening), and — uniquely — root, internal-node and tip calibration run on the same data so the three approaches can be compared directly. Its root-to-tip regression against sample age gives R² = 0.7524, P < 2.2 × 10⁻¹⁶. Its Table S13 uses each of 21 ancient samples alone as the sole calibration point: rates run 2.268–2.517 × 10⁻⁸, an 11 % spread across a 15.6-fold range of sample age (2,535 to 39,464 cal BP). Modelling post-mortem damage raised the rate by 4.2 %.

Rate as published / normalised. Whole molecule 2.143 × 10⁻⁸ per site per year (1.580–2.706 HPD) = 8.9 × 10⁻³ mutations per 16,569 bp genome per 25-year generation, one mutation every 2,816 years. Partitions: coding first-and-second positions 0.756 × 10⁻⁸, third positions 3.323 × 10⁻⁸, HVS1+HVS2 31.434 × 10⁻⁸ — the control region runs about 15× the whole-molecule rate, which is the whole reason control-region and whole-genome rates cannot be compared without conversion. Human MRCA 143 ka (112–180); Neanderthal split 389 ka; human–chimpanzee 4.14 Ma (2.99–5.45) as an output.

Why it matters here. It undercuts the circularity charge by producing 143 ka with no ape date, and its tip-calibrated clock returns an ape split 40 % younger than the fossil-based 6–7 Myr everybody else assumes — proof that the rate is not being tuned to reproduce the fossil record. But it supports the charge that internal calibration is unreliable: the pooled internal-node estimate overlaps only four of ten individual node estimates, with 11× the variance of tip calibration, and it finds rate declining with calibration age (r = −0.53). Its Table 2 is also the least flattering thing in the block: run the tip-calibrated clock forward onto clades with known archaeology and New Zealand comes out 6.6× too old, Remote Oceania 4.9×, the Canaries 3.9×, Madagascar 3.3×. The standard defence — a clade's coalescence necessarily predates the migration that carried it — is legitimate but absorbs any overestimate, and every check with a genuinely known date errs in the same direction. Error to carry forward: its Table S3 lists the six Blätterhöhle sample ages in cal BC while labelling the column "Age (CalBP)," so each is exactly 2,000 years too young.

Library. key: rieux-2014d, was: rieux-2014, was: rieux-2014b, was: rieux-2014c. File: papers/rieux-2014d_improved-calibration-human-mitochondrial-clock.pdf (also rieux-2014d_improved-calibration-human-mitochondrial-clock/, .md). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PLF, Aximu-Petri A, Prüfer K, de Filippo C, Meyer M, Zwyns N, Salazar-García DC, Kuzmin YV, Keates SG, Kosintsev PA, Razhev DI, Richards MP, Peristov NV, Lachmann M, Douka K, Higham TFG, Slatkin M, Hublin J-J, Reich D, Kelso J, Viola TB, Pääbo S. "Genome sequence of a 45,000-year-old modern human from western Siberia." Nature 514:445–449 (2014). doi:10.1038/nature13810 https://pmc.ncbi.nlm.nih.gov/articles/PMC4753769/

topic ancient-dna · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction undercuts

What it measured. A single femur, radiocarbon-dated twice (41,400 ± 1,300 and 41,400 ± 1,400 BP, calibrating to 46,880–43,210 cal BP), whose mitochondrial genome was sequenced at 4,439-fold average coverage with 0.50 % contamination. The mitochondrial sequence carries the twelve substitutions defining haplogroup R, one private substitution at 16150, and nothing else — it differs from a panel of 311 living people at only one site.

Rate as published / normalised. 2.53 × 10⁻⁸ substitutions per site per year (95 % HPD 1.76–3.23 × 10⁻⁸), from BEAST tip calibration on the single dated specimen plus 311 moderns. Across 16,569 bp at 25 years that is 1.05 × 10⁻² mutations per genome per generation, one mutation every 2,386 years. Note that the abstract's "1.8 to 3.2 × 10⁻⁸" is the rounded HPD, not a point estimate, and it has been miscopied as such in secondary summaries. Error to carry forward: the paper's own Supplementary Information §8 cites Fu 2013's whole-mtDNA rate as 2.47 × 10⁻⁸ when the published value is 2.67 × 10⁻⁸ — the quoted HPD (2.16–3.16) matches Fu 2013 exactly, so it is a digit transposition, still uncorrected.

Why it matters here. Its best argument is the one run backwards. Using the other nine dated genomes to calibrate, the clock predicted Ust'-Ishim's own age blind at 48,741 BP (HPD 31,177–65,907). Radiocarbon says 46,880–43,210 cal BP. Two unrelated physical systems — ¹⁴C decay and mitochondrial mutation — agreeing on one bone's date with no shared assumption. It is also the direct refutation of Jeanson 2015's one-sentence dismissal that "DNA sequences from fossils are too degraded to be useful." The paper's own honest caveat, on the autosomal side, is that branch shortening "must be interpreted with caution in samples with differing qualities" — a 2× spread in the same measurement driven by the quality of the modern comparison genome. That problem is real for nuclear data and much smaller for mitochondrial DNA sequenced at thousands-fold coverage.

Library. key: fu-2014. Folder: papers/fu-2014_ust-ishim-45000-year-old-genome/. Cited by the first draft and EVE2. EVE2 register: considered, not used in current draft. EVE2's index.md nevertheless cites it.

Rohland 2015 — partial-UDG treatment

Rohland N, Harney E, Mallick S, Nordenfelt S, Reich D. "Partial uracil–DNA–glycosylase treatment for screening of ancient DNA." Philosophical Transactions of the Royal Society B 370(1660):20130624 (2015). doi:10.1098/rstb.2013.0624 https://pmc.ncbi.nlm.nih.gov/articles/PMC4275898/

topic method · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction background

What it measured. A protocol that removes deaminated cytosines from the interiors of ancient molecules while deliberately leaving the terminal damage signal intact, demonstrated on 60 ancient human samples.

Why it matters here. It is why "cleaned" ancient sequences can still be authenticated as ancient: the damage signature used to prove the DNA is old is preserved at the fragment ends while the errors that would corrupt a mutation count are removed from the middle.

Posth 2016 — 66 dated tips

Posth C, Renaud G, Mittnik A, Drucker DG, Rougier H, Cupillard C, Valentin F, Thevenet C, Furtwängler A, Wißing C, Francken M, Malina M, Bolus M, Lari M, Gigli E, Capecchi G, Crevecoeur I, Beauval C, Flas D, Germonpré M, van der Plicht J, Cottiaux R, Gély B, Ronchitelli A, Wehrberger K, Grigorescu D, Svoboda J, Semal P, Caramelli D, Bocherens H, Harvati K, Conard NJ, Haak W, Powell A, Krause J. "Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a Late Glacial population turnover in Europe." Current Biology 26(6):827–833 (2016). doi:10.1016/j.cub.2016.01.037 Free author PDF: https://www.eva.mpg.de/documents/Elsevier/Posth_Pleistocene_CurrBiol_2016_2583534.pdf

topic ancient-dna · camp mainstream · type measurement · access paywalled · region whole-genome · calibration radiocarbon-tip · direction undercuts

What it measured. 66 radiocarbon-dated ancient genomes used as tip calibrations alongside 311 modern ones — the largest such set of its generation, spanning 3,600 cal BP (Saqqaq) to 46,880 cal BP (Ust'-Ishim), with roughly a third of the calibration points Holocene. All but one sample (Stuttgart, archaeologically dated) carry radiocarbon dates.

Rate as published / normalised. Four model combinations give 2.62, 2.67, 2.74 and 2.77 × 10⁻⁸ substitutions per site per year; the preferred Bayesian-skyline/strict-rate model gives 2.74 × 10⁻⁸ (2.44–3.01 HPD). Across 16,569 bp at 25 years that is 1.14 × 10⁻² mutations per genome per generation, one mutation every 2,203 years. Haplogroup M coalesces at ~49 ka and N at ~51 ka; no whole-tree TMRCA is reported.

Why it matters here. It shows the tip-calibrated rate is not an artifact of model choice: swapping the demographic and clock models moves it by 6 %. Any argument that the ancient-DNA rate is soft has to explain that.

Library. key: posth-2016. File: papers/posth-2016_pleistocene-mitochondrial-genomes.pdf (also .md, posth-2016_pleistocene-mitochondrial-genomes-supplement.pdf). Cited by the first draft, EVE2 and ASTRA. EVE2 register: considered, not used in current draft. EVE2's index.md nevertheless cites it.

Cabrera 2021 — mutation counts against radiocarbon age, no phylogenetic model

Cabrera VM. "Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes." Scientific Reports 11:5036 (2021). doi:10.1038/s41598-021-84583-1 CC-BY. https://www.nature.com/articles/s41598-021-84583-1

topic ancient-dna · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction mixed

What it measured. 423 radiocarbon-dated ancient genomes against 784 modern ones, binned into ten age periods, counting mutation differences directly with no phylogenetic model at all. Mean differences rise monotonically with radiocarbon age: 0.63 at 1,119 BP, 1.63 at 4,294, 3.28 at 8,504, 6.50 at 15,977, 11.07 at 29,638, 14.39 at 40,160. That table is arguably the single cleanest dataset in the subject.

Rate as published / normalised. 4.33 × 10⁻⁸ per site per year (3.90–4.82) for the most recent bin, falling to 1.91 × 10⁻⁸ (1.72–2.10) for the oldest — a 2.27-fold decay. Across 16,569 bp at 25 years that is 1.79 × 10⁻² and 7.9 × 10⁻³ mutations per genome per generation respectively. Flagged discrepancy: Table 2's rates cannot be reproduced from Table 1 by the paper's own stated formula. Period 1 gives 3.40 × 10⁻⁸, not 4.33; period 10 gives 2.16 × 10⁻⁸, not 1.91. Reverse-engineering implies sequence lengths of ~13,000 bp and ~18,800 bp for the two periods — mutually inconsistent, and the length is never stated. The direction and monotonicity of Table 1 are not in doubt; the exact Table 2 rates are not reproducible from published numbers.

Why it matters here. It cuts hard both ways and should be presented that way. The measured near-present rate of 4.33 × 10⁻⁸ is the fastest tip-based figure in the mainstream literature and supports the claim that the clock runs faster over short windows. But Cabrera's own conclusion is that tree-based methods undercount by missing generations with no mutation, and he pushes mtEve older, to 211 ka on the ancient-DNA rate and 312 ka on Soares' — the oldest published estimates in this block. His Table 3 is also the most convenient one-stop comparison of published TMRCAs across Soares, Fu, Rieux and himself.

Library. key: cabrera-2021. File: papers/cabrera-2021_mtdna-rate-time-dependency.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Översti & Palo 2022 — 234 dated genomes, non-circular regressions, and lineage rate variation

Översti S, Palo JU. "Variation in the substitution rates among the human mitochondrial haplogroup U sublineages." Genome Biology and Evolution 14(7):evac097 (2022). doi:10.1093/gbe/evac097 CC-BY. https://pmc.ncbi.nlm.nih.gov/articles/PMC9250076/ and https://academic.oup.com/gbe/article/14/7/evac097/6613373 (HEAD requests return 403; the page loads in a browser)

topic ancient-dna · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction mixed

What it measured. 234 radiocarbon-dated ancient genomes from haplogroups U2, U4, U5a and U5b, plus 301 contemporary genomes and two outgroups — 212 of the 234 Holocene, and 84 younger than 4,500 cal BP. Twelve TempEst root-to-tip regressions run on non-clock trees, so unlike Rieux's Figure S10 the linearity test is not conditioned on a clock-calibrated tree. All twelve slopes are positive, with R² from 0.10 to 0.84.

Rate as published / normalised. TempEst slopes range 1.55–8.80 × 10⁻⁸ per site per year by haplogroup and scenario. Bayesian means by sublineage: ancient-only 3.38–5.65 × 10⁻⁸, ancient plus contemporary 2.13–4.43 × 10⁻⁸. The extreme case is U4 ancient-only — 42 genomes, every one Holocene (1,475–8,374 cal BP), no modern sequences — giving 8.80 × 10⁻⁸ per site per year, which over 16,569 bp at 25 years is 3.6 × 10⁻² mutations per genome per generation, one mutation every 686 years. That is 3.3× the tip-calibrated consensus and the best single number in the mainstream literature for the young-earth side. Its x-intercept still puts the U4 root at 12,723 years, and R² for that regression is only 0.37.

Why it matters here. Two findings pull opposite ways. Ancient-only datasets run 1.2–1.6× faster than ancient-plus-modern, and U2, U4 and U5a run up to about 2× faster than U5b in the same analysis — real, published, mainstream evidence that mitochondrial lineages do not all tick at one rate, which is the young-earth side's "the clock is not constant" argument made by people with no stake in it. The authors attribute the heterogeneity to demography (range expansion during the Bronze Age Yamnaya spread) rather than to mutation rate, and note the HPD intervals largely overlap. The magnitude is the point: about 2×, against the roughly 26× a 6,000-year Eve requires. Their supplementary tables — 234 samples with raw ¹⁴C dates and GenBank accessions, and the twelve published regressions — are extracted to research/data/ and contain everything needed to redo the regression from primary sequence.

Library. key: oversti-2022d, was: oversti-2022, was: oversti-2022b, was: oversti-2022c. File: papers/oversti-2022d_substitution-rate-variation-haplogroup-u.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

The young-earth literature

Three things in this body of work are right, and they should be said before anything else. First, the gap between pedigree mutation rates and phylogenetic substitution rates is real, it is large, and mainstream researchers say so in print — Howell et al. 2003 titled their paper "there is a difference between phylogenetic and pedigree rates," and Madrigal et al. 2012 declined to resolve it. Second, every phylogenetic rate published before Rieux et al. 2014 was calibrated on an assumed human–chimpanzee divergence date, which means it is a model output and cannot be offered as independent evidence for that date. Carter and Jeanson both identify this correctly, and critics who answer them by quoting Soares' 1.665 × 10^-8 as "the measured rate" have walked into the error. Third, the arithmetic in the technical papers mostly checks out: Jeanson's 2015b Table 1 reproduces exactly from his own inputs (63 / 6,594,462 = 9.5535 × 10^-6; 63 / 398 = 0.158291; the 95% CI bounds recompute to 0.1192 and 0.1974), his 2016 post-Flood figure of 115 nucleotides is exact, and Carter's rCRS-to-consensus list of 12 differences verifies position by position against PhyloTree Build 17.

Where the work goes wrong, it goes wrong in units, in the conversion of ranges into point predictions, and in claims that outran the sample they came from. Carter converts control-region-only per-site rates to whole-genome per-generation rates by multiplying by 16,569 sites instead of the ~1,122 bp control region, and then doubles a figure that was already a divergence rate — a ~30x overstatement he has published for eighteen years, and the load-bearing number of the whole CMI case. His "84.1% of the genome is invariant" is a property of his 827-sequence sample; at 56,434 individuals in gnomAD it is 46.9%. Jeanson's 2015b comparison mislabels two of its three "non-African" targets, which are global figures. Brian Thomas turns Jeanson's 2–8 and 121–137 ranges into the point values 8 and 123 and calls the result "a spectacular confirmation." D. Russell Humphreys asserts that researchers "revised" Eve's age down to 6,000 years, which no researcher ever did. And two of the movement's own load-bearing claims have now been retracted by their authors: Jeanson abandoned the D-loop and the three-node "three wives of Noah's sons" root in 2025, and Carter conceded in 2024 and 2025 that there is no three-way split in either the mtDNA or the Y tree.

A shrinking date for Eve

Carl Wieland. "A shrinking date for 'Eve'." Creation Ex Nihilo Technical Journal (Journal of Creation) 12(1):1–3 (1998). https://creation.com/a-shrinking-date-for-eve (original 1998–2000 AiG posting archived at http://web.archive.org/web/20000414044227/http://www.answersingenesis.org:80/docs/4055.asp)

topic yec-clock · camp creationist · type popular · access web · region HVR1+2 · calibration none · direction supports

What it measured. Nothing of its own. It relays Parsons et al. 1997's control-region pedigree rate of ~2.5 substitutions per site per Myr and Gibbons' 1998 Science news report of it, and concludes: "If correct, it means that mitochondrial Eve lived 6,000 to 6,500 years ago." Wieland never read Parsons — his reference 5 says so explicitly, "as cited in ref. 4," which is the Gibbons news story.

Rate as published / normalised. Parsons' rate as relayed: 2.5 × 10^-6 per site per year, measured on 610 bp of HVR1 and HVR2. (a) Per site per year: 2.5 × 10^-6, control region only. (b) Not convertible to a whole-genome per-generation figure; the measurement covers 610 bp of the fastest-mutating sequence in the molecule, and multiplying it by 16,569 is the error this catalogue exists to prevent.

Why it matters here. This is patient zero for the whole creationist argument, and — importantly — its arithmetic is control-region-internal: a control-region rate applied to control-region diversity does give roughly 6,500 years, so Wieland does not commit Carter's later unit error. Its real weakness is different: HVR1 and HVR2 are precisely the hypermutable, saturating, homoplasy-prone sites where recurrent mutation makes a fast pedigree count compatible with a slow tree. Wieland's own hedge, "If correct," should be quoted whenever the claim is.

Library. key: wieland-1998. File: web/wieland-1998_shrinking-date-for-eve.html (and .txt beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Evidence for a Young World, item 8

D. Russell Humphreys. "Evidence for a Young World." Impact #384, Institute for Creation Research (2005; current web version undated). https://www.icr.org/article/evidence-for-young-world/

topic yec-clock · camp creationist · type popular · access web · region control-region · calibration none · direction undercuts

What it measured. Nothing. Item 8 asserts, citing Gibbons 1998: "Measurements of the mutation rate of mitochondrial DNA recently forced researchers to revise the age of 'mitochondrial Eve' from a theorized 200,000 years down to possibly as low as 6,000 years."

Why it matters here. No researcher revised anything. Gibbons' next sentence is "No one thinks that's the case." This is not a truncation but an invented claim, and it was caught by a University of South Dakota honours-seminar page in 2005 — twenty-one years ago and still uncorrected. It is also filed under "Biological material decays too fast," which confuses a fast mutation rate with molecular decay. The article should print this beside Gibbons' disclaimer as the clearest single failure on the young-earth side.

Library. key: humphreys-2005d, was: humphreys. File: web/humphreys-2005d_evidence-for-a-young-world.html (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft. Plan section 5.2 D names humphreys-2006b for this work, but that library record is the Creation Ministries International version of 27 January 2006 (twelve items, no mitochondrial sentence), a different text. The ICR page held here (Acts & Facts 34(6), June 2005, fourteen items) carries item 8 with the sentence about mitochondrial Eve and its Gibbons footnote, so this is the key to use.

Mitochondrial Eve and biblical Eve are looking good

Carl Wieland. "Mitochondrial Eve and biblical Eve are looking good: criticism of young age is premature." creation.com (2006). https://creation.com/en/articles/cmi-responds-to-sceptics-criticism-of-mitochondrial-eve-article

topic critique · camp creationist · type popular · access web · region HVR1+2 · calibration none · direction mixed

What it measured. Nothing; it is Wieland's reply to Alec MacAndrew's rebuttal. It correctly insists that CMI never claimed mtEve was the only woman alive, and correctly presses the point that the phylogenetic rate is calibrated on assumed divergence dates — a point MacAndrew conceded for the control region.

Why it matters here. It also contains a claim that does not survive comparison with the 1998 article: "Not only did I not imply it" that the MRCA lived 6,500 years ago, against his own 1998 sentence "it means that mitochondrial Eve lived 6,000 to 6,500 years ago." Print both and let the reader judge. The concession-and-overreach pattern here is the same one the article documents on both sides.

Carter 2007 (Nucleic Acids Research)

Robert W. Carter. "Mitochondrial diversity within modern human populations." Nucleic Acids Research 35(9):3039–3045 (2007). doi:10.1093/nar/gkm207 https://pmc.ncbi.nlm.nih.gov/articles/PMC1888801/

topic diversity · camp creationist · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. A consensus sequence built from 827 curated full-length human mitogenomes (disease, HeLa, patent and unpublished sequences excluded). The 827 sequences contain 2,631 variant positions and differ from the consensus by 21.6 ± 10.0 nucleotides on average; 84.1% of the molecule is invariant in that sample; 43.8% of variable sites are private; only 36 positions have a majority allele below p = 0.90.

Why it matters here. This is genuine peer-reviewed work by a creationist in a mainstream journal, and it does not say what the popular literature says it says. It contains no reference to creation, a young earth, Noah or the Flood; it locates the consensus at the root of macrohaplogroup R, a node mainstream work dates at ~59 kya; and it states that there are "perhaps as few as 30 differences between the macrohaplogroup R consensus and the root node of all extant human mitochondrial sequences." At Soares' rate, 59.1 kyr × 1.665 × 10^-8 × 16,569 = 16.3 expected differences from the R node — so Carter's measured 21.6 is what the mainstream model predicts for the node he chose, not a surprise. The 84.1% invariant figure is a sample artefact: at 56,434 individuals (gnomAD) it falls to 46.9%.

The "Eve" mitochondrial consensus sequence (ICC 2008)

Robert W. Carter, Daniel Criswell, and John Sanford. "The 'Eve' Mitochondrial Consensus Sequence." In A. A. Snelling (ed.), Proceedings of the Sixth International Conference on Creationism, pp. 111–116 (2008). https://www.icr.org/i/pdf/technical/The-Eve-Mitochondrial-Consensus-Sequence.pdf (record: https://cedarville.tind.io/record/21036)

topic yec-clock · camp creationist · type model · access OA · region whole-genome · calibration none · direction mixed

What it measured. Re-presents the 2007 consensus for a creationist audience ("more than 83%" invariant; 21.6 nt mean divergence, printed as 22.6 in the Results — a 1.0 nt internal contradiction) and adds a Mendel's Accountant simulation: 16,500-nucleotide genome, one linkage block, N = 1,000, 2.20 offspring per female, mutation rate 0.050000 per individual per generation, run for 150 versus 10,000 generations, comparing allele-frequency spectra.

Rate as published / normalised. Mendel parameter 0.05 mutations per genome per generation, unsourced in the paper. (a) Per site per year, assuming their 30-year generation: 1.01 × 10^-7. (b) Per 16,569 bp genome per 25-year generation: 0.042. For scale, that sits between the measured whole-genome pedigree rates of Connell 2022 (0.029/gen) and Árnadóttir 2024 (0.070/gen), so the value is defensible — but the paper never says where it came from, and it is 6x the Soares phylogenetic rate.

Why it matters here. This is the source of "Eve1.0 = root of macrohaplogroup R" and of the three-daughters-in-law model that Jeanson later hardened into a prediction. It is also honest about two things the popularisations drop: "the main difficulty comes from the mtDNA clades from sub-Saharan Africa," and the admission that the consensus method cannot detect fixed mutations at all ("any 'mutation' at greater than 50% would have automatically been assigned to the ancestral state"), which truncates the very allele-frequency spectrum being compared to the untruncated Mendel output. Its "we did not expect to find the original human mitochondrial sequence to be so well preserved" has no quantified basis — nobody expected more than ~16 differences from the R node.

Library. key: carter-2008. File: papers/carter-2008_eve-mitochondrial-consensus-sequence.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Vardiman, Mitochondrial DNA and a recent human origin

Larry Vardiman. "Mitochondrial DNA and a Recent Human Origin." Acts & Facts, Institute for Creation Research, 1 May 2008. https://www.icr.org/content/mitochondrial-dna-and-recent-human-origin

topic yec-clock · camp creationist · type popular · access web · region whole-genome · calibration none · direction undercuts

What it measured. Nothing; it reports the ICC 2008 results, crediting Daniel Criswell and Mendel's Accountant, and naming neither Carter nor Sanford.

Why it matters here. It restates Carter's sample statistic as a species-level fact: "more than 83 percent of the mitochondrial genome had not changed in all of human history." That is false. Roughly half the genome carries observed variation once 56,434 people are sequenced (Laricchia 2022), and even that is unsaturated — only 55% of possible synonymous variants have been seen. This is the cleanest example of a sample-dependent measurement being promoted into a claim about the species.

Thomas 2010, Mother of all humans

Brian Thomas. "Mother of All Humans Lived 6,000 Years Ago." Institute for Creation Research, 7 September 2010. https://www.icr.org/content/mother-all-humans-lived-6000-years-ago

topic yec-clock · camp creationist · type popular · access web · region whole-genome · calibration none · direction mixed

What it measured. Nothing; it popularises Carter/Criswell/Sanford 2008 (quoting the 21.6 nt figure) and Gibbons 1998.

Why it matters here. Credit where it is due: this is the one creationist source in the whole quote trail that prints Gibbons' disclaimer — "No one thinks that's the case, but at what point should models switch from one mtDNA time zone to the other?" — in full. His argument is then that the disclaimer is itself evidence of assumption-driven dating, which is a real argument and should be answered on its merits rather than on quotation ethics. The headline nevertheless states as fact what the body only argues.

Library. key: thomas-2010j, was: thomas-2010k. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Jeanson 2013, metazoan mitochondrial genes

Nathaniel T. Jeanson. "Recent, Functionally Diverse Origin for Mitochondrial Genes from ~2700 Metazoan Species." Answers Research Journal 6:467–501 (2013). https://answersresearchjournal.org/origin-mitochondrial-genes-metazoan/ (PDF: https://assets.answersresearchjournal.org/doc/v6/mitochondrial-genes.pdf)

topic yec-clock · camp creationist · type model · access OA · region control-region · calibration none · direction mixed

What it measured. Pools homoplasmic D-loop mutations from seven human pedigree studies — 16 mutations across 1,486,027 bp·generations — and uses the resulting rate, with a 10,000-year creation date and the divergence equation (differences = 2μt), to predict present-day diversity in Homo, Caenorhabditis, Drosophila and Daphnia. Table 6 gives years-until-one-mutation as Evolution / Creation / Actual: Homo 36,364 / 2,020 / 1,244–2,915; Caenorhabditis 21,752 / 12 / 6–11; Drosophila 34,247 / 17 / 9–202; Daphnia 23,259 / 31 / 48–62.

Rate as published / normalised. 16 / 1,486,027 = 1.08 × 10^-5 mutations per site per generation, control region only. (a) Per site per year, at a 25-year generation: 4.31 × 10^-7 at control-region sites. (b) Per whole 16,569 bp genome: not licensed by this measurement — over a 1,122 bp control region it is 0.012 mutations per control region per generation. Jeanson himself applies it only within the D-loop in this paper.

Why it matters here. Every published number recomputes from his own supplemental spreadsheets, with one digit-transposition typo (Daphnia "23,259" where his formula gives 23,529). But the cross-species test is weaker than it reads: Daphnia fails outright (predicted 31 years per mutation against a measured 48–62), Caenorhabditis misses by 9%, and the Drosophila "actual" range spans a factor of 22, so it cannot discriminate anything. His own 2025 paper then rejects the D-loop entirely because of back mutation, which removes the basis of this paper's human result.

Library. key: jeanson-2013. File: papers/jeanson-2013_metazoan-mtdna-origin.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Jeanson 2015a, linear speciation rates

Nathaniel T. Jeanson. "Mitochondrial DNA Clocks Imply Linear Speciation Rates Within 'Kinds'." Answers Research Journal 8:273–304 (2015). https://answersresearchjournal.org/mitochondrial-clocks-speciation-rates/ (Supplemental Table 8: https://assets.answersresearchjournal.org/doc/articles/arj/v8/mitochondrial-dna-clocks/supplemental-table-8.xlsx)

topic yec-clock · camp creationist · type model · access OA · region control-region · calibration none · direction mixed

What it measured. Re-runs the 2013 D-loop clock at a 6,000-year creation date, using differences = 2μt for humans, C. elegans and Drosophila and differences = μt for D. pulex, and introduces the three-node / three-wives-of-Noah's-sons reading of the human tree.

Rate as published / normalised. Same pooled D-loop rate as 2013: 1.08 × 10^-5 per site per generation in the control region; (a) 4.31 × 10^-7 per site per year at 25-year generations; (b) not extrapolable to the whole genome.

Why it matters here. The D-loop point prediction over 6,000 years is 5.8 differences (range 4.1–9.7) against an observed non-African mean of 12.78 ± 3.61 — the prediction overlaps the standard deviation, which is what the text claims, but the point estimate is 2.2x low. His supplemental file also contains a second, unpublished weighting scheme giving 1.967 × 10^-5 per bp per generation, 1.8x the published figure. And Jeanson himself retracted this paper's root model in 2025: "the original Carter, Criswell, and Sanford (2008) model was correct, whereas the Jeanson (2015a) model was incorrect."

Library. key: jeanson-2015e. File: papers/jeanson-2015e_mtdna-clocks-speciation.pdf (and .md beside it). Cited by the first draft only. EVE2 register: considered, not used in current draft. The first draft reached this paper only through its was: jeanson-2015g footnote, whose title was missing. That footnote joined two quotations from two different papers of ARJ volume 8: "Because DNA is such a labile molecule, it seems unlikely that reliable sequences will ever be obtained from samples older than just a few years or decades, unless remarkable care is taken to preserve them" is in this paper (stored text found in jeanson-2015e_mtdna-clocks-speciation.md, where the PDF's two-column text interleaves), while "DNA sequences from fossils are too degraded to be useful for comparative DNA analyses today" is in the whole-genome clock paper (key jeanson-2015). Cite each sentence to its own paper. Verified from stored bytes for the wording; the page is not pinned (ARJ 8:273-304).

Jeanson 2015b, the whole-genome clock

Nathaniel T. Jeanson. "A Young-Earth Creation Human Mitochondrial DNA 'Clock': Whole Mitochondrial Genome Mutation Rate Confirms D-Loop Results." Answers Research Journal 8:375–378 (2015). https://answersresearchjournal.org/mitochondrial-genome-mutation-rate/ (PDF: https://assets.answersresearchjournal.org/doc/v8/mitochondrial-dna-clock-d-loop-results.pdf; Supplemental Table 1: https://assets.answersresearchjournal.org/doc/articles/arj/v8/mitochondrial-genome-mutation-rate-supplemental-table.xlsx)

topic yec-clock · camp creationist · type model · access OA · region whole-genome · calibration none · direction supports

What it measured. Pools three whole-mitogenome trio studies — Guo et al. 2013 (26 pedigrees, 0 homoplasmic mutations), Rebolledo-Jaramillo et al. 2014 (39, scored 0), Ding et al. 2015 (333, 63) — for 63 mutations across 6,594,462 bp·generations. The 63 comes from Ding's Table 1: 7,273 homoplasmic sites in the children of which 7,238 are shared with the mother (35 gains), and 7,266 in the mothers of which 7,238 are shared with the child (28 losses).

Rate as published / normalised. 9.55 × 10^-6 per bp per generation; 1.58 × 10^-1 per mtDNA genome per generation (95% CI 0.119–0.197). (a) Per site per year, at a 25-year generation: 3.82 × 10^-7 (CI 2.88–4.77 × 10^-7). (b) Per 16,569 bp genome per 25-year generation: 0.1583 by construction, since the published figure is already per genome per generation. That is 22.5x the Ingman 2000 rate and 23.0x the Soares 2009 rate.

Why it matters here. This is the load-bearing paper of the young-earth case, and its arithmetic is clean: every cell of Table 1 reproduces exactly, including the CI, and the two null studies lower the pooled rate by 16%, so the "cherry-picking" charge is quantitatively small and runs against him. Four problems are real. (i) Rebolledo-Jaramillo was scored 0 because it did not report the quantity — Jeanson says so, verbatim: "Since none were reported, I assumed that none occurred." (ii) 28 of the 63 are variants present in the mother and absent in the child, i.e. reversions to reference; under his own rate the expected number among 7,266 maternal variant instances in one generation is 7,266 × 9.5535 × 10^-6 = 0.069, and he observed 28 — 403x too many, and the near-symmetry of 35 gains and 28 losses is the signature of genotype-calling discordance at ~180x coverage, not of mutation. (iii) The paper drops the factor of 2 it uses in 2013, 2015a and 2016; restore it and the headline 37.99 becomes 75.98 against an observed 35–40. (iv) The comparison targets are mislabelled: Kim & Schuster's 39.8 and 39.3 are global mean pairwise differences, not non-African; the true non-African values are 35.4 and 34.9, which moves the target from 39.2 to 36.3. Jeanson also flags the unresolved caveat himself — Ding sequenced lymphocytes cross-sectionally, so germline transmission is unconfirmed, and "the DNA sequences from at least three successive generations must be sequenced" to fix that. Read at its strongest, the trio-derived rate puts the mtDNA root at 4,674–18,057 years (central cell, 25-year generations and the point rate: 9,713 years) — an order of magnitude below the conventional figure, and also outside a strict 6,000 years unless you take short generations, the high CI, or both.

Library. key: jeanson-2015, was: jeanson-2015b, was: jeanson-2015c, was: jeanson-2015d. File: papers/jeanson-2015_mtdna-clock-whole-genome.pdf. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. The first draft's was: jeanson-2015g footnote (title missing) quotes "DNA sequences from fossils are too degraded to be useful for comparative DNA analyses today" from this paper (stored PDF text found in the closing discussion, which cites Criswell 2009, Jeanson 2015 and Thomas and Tomkins 2014; the printed page, 377 or 378, is not pinned). The html and supplement are stored as jeanson-2015f.

Jeanson & Lisle 2016, eukaryotic diversity

Nathaniel T. Jeanson and Jason Lisle. "On the Origin of Eukaryotic Species' Genotypic and Phenotypic Diversity." Answers Research Journal 9:81–122 (2016). https://answersresearchjournal.org/origin-eukaryotic-species-diversity/

topic yec-clock · camp creationist · type model · access OA · region whole-genome · calibration none · direction undercuts

What it measured. Extends the 6,000-year mtDNA clock to yeast, and runs the identical method on nuclear DNA in humans, Drosophila, Daphnia pulex and yeast as a control.

Why it matters here. Both controls fail, and the authors report it honestly. The yeast mtDNA prediction is worse than a near miss: "the current rate of mtDNA change predicted a maximum DNA difference in excess of the yeast mtDNA genome size" — over 100% divergence. The nuclear runs "severely underestimated existing nuclear SNV diversity… by nearly an order of magnitude or more" in all four species, and their own figure captions read "Contradiction between mtDNA and nuclear DNA SNV clocks." Their resolution — that more than 75% of nuclear diversity was created rather than mutational — makes the method unfalsifiable in both directions: matches confirm the timescale, misses are created diversity or a rate anomaly. This is the strongest self-inflicted problem in the young-earth clock literature.

Library. key: jeanson-2016d. File: web/jeanson-2016d_origin-eukaryotic-species-diversity.html (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Jeanson 2016, generation time and the African excess

Nathaniel T. Jeanson. "On the Origin of Human Mitochondrial DNA Differences, New Generation Time Data Both Suggest a Unified Young-Earth Creation Model and Challenge the Evolutionary Out-of-Africa Model." Answers Research Journal 9:123–130 (2016). https://answersresearchjournal.org/origin-human-mitochondrial-dna-differences/ (PDF: https://assets.answersresearchjournal.org/doc/v9/out_of_africa_model.pdf)

topic yec-clock · camp creationist · type model · access OA · region whole-genome · calibration none · direction mixed

What it measured. Two things. (i) The percentage of women married by ages 15–19 by region in the UN World Marriage Data 2012, earliest survey per country (mean assessment year 1976): 32.8% in African nations, about three times the non-African figure. (ii) A realignment of 369 mtDNA genomes giving a maximum pairwise difference of 117 nucleotides (a San / Taiwanese-Aborigine pair), with three visible "nodes" and connecting branches estimated algebraically at 2–8 nucleotides.

Rate as published / normalised. Uses the 2015b upper 95% bound, 0.19738 mutations per genome per generation at a 15-year generation = 0.0131586 per genome per year. (a) Per site per year: 7.94 × 10^-7. (b) Per 16,569 bp genome per 25-year generation: 0.329. Applied over 4,365 years with the divergence equation: 0.0131586 × 4,365 × 2 = 114.9, published as 115. That arithmetic is exact.

Why it matters here. This paper is Jeanson at his most defensible and his most vulnerable at once. Defensible: it anchors on the maximum pairwise difference rather than the sample-dependent mean, which is the right statistic. Vulnerable: a marriage-age distribution is not a generation interval — Jeanson concedes the limitation himself — and the direction of the measured effect is the reverse of what he needs. Wang et al. 2023 infer an African sex-averaged generation interval of 26.9 ± 3.5 years against 20.1–21.0 for East Asian, European and South Asian populations, and Madrigal et al. 2012 use a female interval of 28.3 years from actual genealogies. Nothing in the literature supports 15 years, and he needs it unbroken for 291 consecutive mother–daughter links. A further problem he does not address: the 123-difference maximum in Kim & Schuster is a within-African pair, so in his own three-node tree all 123 differences must be post-Flood, requiring 0.2113 mutations per generation at 15 years — above his own upper 95% bound of 0.1974. He is also candid that the figure was drawn by hand: the calculation gave 121–137, but "I simply reported the maximum YEC predictions as 123," the observed value.

Library. key: jeanson-2016. File: papers/jeanson-2016_generation-time-out-of-africa.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Thomas 2016, DNA trends confirm Noah's family

Brian Thomas. "DNA Trends Confirm Noah's Family." Acts & Facts, Institute for Creation Research, 30 June 2016. https://www.icr.org/article/dna-trends-confirm-noahs-family (identical text at https://www.icr.org/content/dna-trends-confirm-noahs-family)

topic yec-clock · camp creationist · type popular · access web · region whole-genome · calibration none · direction mixed

What it measured. Nothing; it popularises Jeanson 2016.

Why it matters here. It is the clearest case in this literature of a range being converted into a point prediction on our own side, and the article should say so plainly. Jeanson wrote "about 2–8 nucleotides in length (calculation not shown)"; Thomas prints "eight DNA differences." Jeanson wrote "a total of 121–137 mutations"; Thomas prints 123 as the biblical prediction and then reports the match to the observed 123 as "a spectacular confirmation… Check, check, and check." ICR later appended an editor's note adjudicating which visual clusters in Jeanson's figure count as "nodes" — a structural prediction that needs post-hoc adjudication of its own figure is not a strong test.

Library. key: thomas-2016b. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Jeanson 2017, response to Frello

Nathaniel T. Jeanson. "Response to 'On the Creationist View on mtDNA'." Answers Research Journal 10:183–186 (2017). https://answersresearchjournal.org/creationist-view-mtdna-response/

topic archaics · camp creationist · type review · access OA · region whole-genome · calibration none · direction undercuts

What it measured. Nothing; it is his one published reply to a critic (Stefan Frello, ARJ 10:181–182, who reported BLAST distances of 180–240 nt between Neanderthals and modern humans against a maximum of ~80 nt among Neanderthals).

Why it matters here. It contains Jeanson's own statement that his clock fails on archaic DNA in both directions: "With respect to the YEC timescale, current rates of mtDNA mutation are too low to explain the differences between ancient DNA samples and modern human mtDNA sequences." At his point rate and 25-year generations, 240 differences need 18,950 years; even at his upper CI with 15-year generations, 9,120 years. Both are past creation, let alone the Flood. His only two options — declare the ancient sequences unreliable, or invoke a lineage-specific acceleration — are the ones he names. The exchange ended unresolved: Frello's counter-reply (ARJ 10:237–238) abandons the technical argument and tells Jeanson to publish in mainstream journals.

Library. key: jeanson-2017. File: papers/jeanson-2017_response-frello-mtdna.pdf. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft. The last round of the exchange is a separate source, jeanson-2017b (see the entry for it in the section added in the merge).

Carter, Lee & Sanford 2018 (ICC)

Robert W. Carter, Stephen S. Lee, and John C. Sanford. "An overview of the independent histories of the human Y chromosome and the human mitochondrial chromosome." Proceedings of the Eighth International Conference on Creationism, pp. 133–151 (2018). doi:10.15385/jpicc.2018.8.1.15 https://digitalcommons.cedarville.edu/icc_proceedings/vol8/iss1/7/ (PDF: https://core.ac.uk/download/301493764.pdf)

topic yec-clock · camp creationist · type model · access OA · region whole-genome · calibration none · direction mixed

What it measured. Internode distances between mtDNA haplogroup ancestors reconstructed from 1000 Genomes data (Table 2: L1↔R = 25, L1↔L5 = 5, L3↔M = 0, N↔R = 2) and derived founder ages for ten mtDNA haplogroups (Table 5), with the minimum column based on Madrigal 2012 and the maximum on Sigurðardóttir 2000. Values run from L1 at 4,603–37,336 years to R at 2,013–16,324 years, averaging 3,020 minimum and 24,500 maximum.

Rate as published / normalised. The dating uses a hypervariable-region rate scaled to the whole genome by an empirically measured ratio: "We found 25.3 times more mutations genome-wide than in HVSII and 8.5 times more mutations genome-wide than in the control region," yielding "approximately 1 mutation every-other generation." (a) Per site per year, re-deriving their stated method at 30-year generations: ~6 × 10^-7. (b) Per 16,569 bp genome per 25-year generation: ~0.25–0.30. This method is defensible in principle, unlike the 2025 version. The paper misidentifies the region, though: Madrigal 2012 sequenced HVR-I (16024–16383), not "HVSII."

Why it matters here. Notable for its candour: the paper's own minimum estimate puts L1 at 4,603 years, older than the 4,500-year Flood, and its maximum column runs to 37,000 years, with the caption conceding "these estimates cover a huge range." It also moves Eve off the R node — "Eve is most likely to be located along the long branch that connects macrohaplogroup L/M to macrohaplogroup N" — which is the second of three positions Carter has taken. One unresolved check: their Table 2 internode distances are ~40% shorter than PhyloTree Build 17 (their L1↔R = 25 against 40 counted directly), plausibly from low-coverage 1000 Genomes Phase 1 calls plus their missing-data filter. If so, every age in Table 5 is biased young by about 40%.

Library. key: carter-2018. File: papers/carter-2018_independent-histories-y-and-mtdna.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Sanford et al. 2018, designed diversity and allele frequencies (ICC)

John Sanford, Robert Carter, Wesley Brewer, John Baumgardner, Bruce Potter, and Jon Potter. "Adam, Eve, designed diversity, and allele frequencies." Proceedings of the Eighth International Conference on Creationism, pp. 200–216 (2018).

topic yec-clock · camp creationist · type model · access OA · region whole-genome · calibration none · direction background

What it measured. Forward population-genetic simulations (Mendel's Accountant) of allele-frequency spectra under created heterozygosity plus accumulated mutation. Not retrieved and read in full for this catalogue; listed because it is the framework Carter's 2023 mitochondrial modelling sits inside, and because a reader tracing the genetic-entropy argument needs the reference.

Why it matters here. Sanford's genetic-entropy framework supplies the reason young-earth authors expect mutation counts to be informative at all, but it does not itself measure a mitochondrial rate. Cite it as background, not as evidence for a young mtDNA root, and note that this catalogue read it only at the citation level.

Library. key: sanford-2018. File: papers/sanford-2018_adam-eve-designed-diversity.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Sanders 2018, AiG summary of Jeanson

Harry F. Sanders III. "Origin of Mitochondrial DNA Differences." Answers in Depth, Answers in Genesis, 10 October 2018. https://answersingenesis.org/genetics/mitochondrial-dna/origin-of-mitochondrial-dna-differences/

topic yec-clock · camp creationist · type popular · access web · region whole-genome · calibration none · direction supports

What it measured. Nothing; it summarises Jeanson 2016 for a lay audience.

Why it matters here. Included as the fair-dealing contrast to Thomas 2016: Sanders reports the 137 maximum and the 121–137 range rather than collapsing them to a point, and concludes only that "the observed difference in nucleotide bases in mitochondrial DNA is well within the creationist expectation." That is true, and it is a much weaker claim than "a spectacular confirmation." The difference between these two popularisations of the same paper is worth showing.

Carter 2019, patriarchal drive

Robert W. Carter. "Patriarchal drive in the early post-Flood population." Journal of Creation 33(1):110–118 (2019). https://creation.com/patriarchal-drive

topic yec-clock · camp creationist · type model · access web · region whole-genome · calibration none · direction background

What it measured. Three models of paternal-age-driven mutation accumulation on the Y chromosome, given the long lifespans and late fatherhood recorded in Genesis 11. Conclusion: "the 'molecular clock' would have ticked much faster in the first few centuries after the Flood than it does today."

Why it matters here. The mechanism is explicitly paternal, and Carter says why: sperm-producing cells divide continuously from puberty while oocytes are arrested. That asymmetry is the reason the argument does not transfer to maternally inherited mtDNA, yet the 2025 popular article generalises it anyway — "all molecular clocks would be messed up!" — without a mitochondrial model. Checking it would need a quantified maternal-age effect on the mtDNA de novo rate, which nobody has published. This is a genuine open question rather than a settled point against Carter, but as published it is a Y-chromosome argument applied to mtDNA by assertion.

Library. key: carter-2019. File: web/carter-2019_patriarchal-drive.html (and .txt, .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Tomkins 2020, Out of Babel — not Africa

Jeffrey Tomkins. "Out of Babel—not Africa." Journal of Creation 34(1):79–85 (2020). https://creation.com/en/articles/genetics-supports-a-biblical-model-of-human-origins

topic yec-clock · camp creationist · type popular · access web · region whole-genome · calibration none · direction mixed

What it measured. Nothing; it summarises the creationist case for a general audience.

Rate as published / normalised. Relays "an empirical estimate of human mitochondrial DNA mutation of about 0.5 per generation, as reported in the literature," used to argue that "200 generations would be needed to accumulate 100 mutations—a time of less than 6,000 years." (a) Per site per year, at 30-year generations: 1.01 × 10^-6. (b) Per 16,569 bp genome per 25-year generation: 0.42. That figure is not a measured whole-genome rate. The measured ones are 0.029/gen (Connell 2022, Norfolk Island) and 0.070/gen (Árnadóttir 2024, Iceland) — 7x to 17x lower.

Why it matters here. This is where Carter's unit error enters the popular literature as a bare number with no derivation attached, and it is also where Jeanson's three-wives mapping gets attributed as settled. A reader who encounters "0.5 mutations per generation" anywhere in creationist writing should trace it back to this chain and then to Carter's footnote 10.

Library. key: tomkins-2020. File: web/tomkins-2020_out-of-babel-not-africa.html (and .txt, .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Carter 2021, replying to his critics

Robert W. Carter. "Robert Carter gets everything wrong?" creation.com (2021). https://creation.com/everything-wrong

topic critique · camp creationist · type popular · access web · region whole-genome · calibration n/a · direction supports

What it measured. Nothing; it is Carter's reply to Dan Stern-Cardinale and "Gutsick Gibbon."

Why it matters here. Carter states the neutral-theory identity correctly — the long-run substitution rate equals the mutation rate, r = Nμ/N = μ — and critics who argue that drift or selection can slow long-term accumulation enough to bridge a large pedigree–phylogeny gap are wrong on the population genetics. The article should concede this point to him before pressing the ones where he is wrong.

Library. key: carter-2023c. File: web/carter-2023c_robert-carter-gets-everything-wrong.txt. used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft. The key's year does not match the page, which the library dates 2021-06-07 (see Library housekeeping).

Carter 2023, genealogical vs phylogenetic rates (ICC)

Robert W. Carter. "Genealogical vs Phylogenetic Mutation Rates: Answering a Challenge." Proceedings of the Ninth International Conference on Creationism, pp. 168–180 (2023). doi:10.15385/jpicc.2023.9.1.10 https://cedarville.tind.io/record/21178/files/10_Carter_1514_Genealogical_vs_phylogenetic_mutation_rates.pdf

topic rate-gap · camp creationist · type model · access OA · region whole-genome · calibration none · direction mixed

What it measured. Mendel's Accountant runs on a mitochondrial-sized genome, reporting how much of the deleterious load selection can remove (≤ ~8–60%) and finding that the simulated population survives only at a mutation rate "below 0.005" per generation — "about two orders of magnitude below genealogical estimates."

Rate as published / normalised. Three incompatible numbers appear in one paper. (i) The asserted rate, p. 178: "approximately 60 in the nuclear genome, 1 in the Y chromosome, and 0.5 in the mitochondrial genome" → (a) 1.01 × 10^-6 per site per year at 30-year generations, (b) 0.42 per genome per 25-year generation. (ii) The measured rate he himself quotes on p. 168: Connell 2022's "only 0.029 mutations per generation" → (a) 5.83 × 10^-8, (b) 0.024. (iii) The rate his own model needs to keep the population alive: 0.005/gen → (a) 1.01 × 10^-8, (b) 0.0042. No reconciliation is offered between (i) and (ii), a 17x internal contradiction inside a single paper.

Why it matters here. The abstract's headline claim — "Genealogical mutation rates are several orders of magnitude faster than phylogenetic estimates" — does not survive contact with the numbers. Normalised to whole genome per 30-year generation: Árnadóttir 0.070, Howell (correctly converted) 0.030, Connell 0.029, Rieux 0.0106, Soares 0.0083. The real ratio is 2.7x to 8.5x, not orders of magnitude. Note also the direction of the genetic-entropy result: it needed a rate below the measured one, which is 100x below Carter's asserted 0.5 but only 6–14x below the correctly measured 0.029–0.070.

Library. key: carter-2023. File: papers/carter-2023_genealogical-vs-phylogenetic-mutation-rates.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Carter 2024, sons of Noah on the Y tree

Robert W. Carter. "Where are the sons of Noah on the Y chromosome tree?" creation.com, 29 October 2024. https://creation.com/en/articles/sons-of-noah-y-chromosome-tree

topic tree-topology · camp creationist · type popular · access web · region whole-genome · calibration n/a · direction undercuts

What it measured. Nothing new; it enumerates nine hypotheses for reconciling three sons of Noah with the observed Y phylogeny.

Why it matters here. It abandons the three-branch expectation from inside CMI, in print: "Just look at figure 2. Do you see 'three' branches? I can force my brain to see them, but this does not mean what I am seeing is correct." And: "If there was little mutation prior to the Flood, the three sons of Noah could have had identical Y chromosomes… There would not be 'three' founding branches, there would only be 'one'." That is a fair and honest retreat, but it means the structural prediction Jeanson still makes for mtDNA has been dropped by the movement's other principal researcher.

Library. key: carter-2024. File: web/carter-2024_sons-of-noah-y-chromosome-tree.html (and .txt beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Jeanson 2025, mtDNA lineages in the Americas

Nathaniel T. Jeanson. "Y-Chromosome-Guided Analysis of Mitochondrial DNA Lineages in the Americas: New Evidence for a Mitochondrial DNA Root, for a Mitochondrial DNA Clock, and for at Least One Migration from Asia into the Americas in the First Millennium BC." Answers Research Journal 18:347–375 (2025). https://answersresearchjournal.org/genetics/analysis-mitochondrial-dna-lineages-americas/

topic yec-clock · camp creationist · type model · access OA · region coding · calibration internal · direction mixed

What it measured. Branch-length structure in American mtDNA lineages against Y-haplogroup Q and documented post-Contact population history. No mutation rate is used: the young-earth timescale is an input — "I used an overall timeframe of 4,441 and 4,026 years from the node that joins haplogroup L and mtDNA macrohaplogroup M, rather than the 4,636 and 4,206 years that I employed for the rest of the haplogroups" — and branch lengths are scaled within it.

Why it matters here. This paper contains two self-retractions of load-bearing earlier claims. It abandons the D-loop: "due to the frequency of back mutation in the D-loop… I eventually rejected the D-loop from analyses," which is the entire basis of the 2013 paper. And it abandons the three-node root: "it appears that the original Carter, Criswell, and Sanford (2008) model was correct, whereas the Jeanson (2015a) model was incorrect." It also concedes that "we don't yet know whether mtDNA acts like a simple biological clock." Because the timescale is assumed rather than derived, this paper cannot be cited as independent confirmation of a young mtDNA root, whatever its title says; its internal consistency test is legitimate but tests something else.

Library. key: jeanson-2025. File: papers/jeanson-2025_mtdna-lineages-americas.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Carter 2025, When did Eve live?

Robert W. Carter. "When did Eve live?" creation.com, 18 September 2025. https://creation.com/when-did-eve-live (the server returns 403 to HEAD requests, so link-checkers will falsely flag this URL; it returns 200 to GET)

topic yec-clock · camp creationist · type popular · access web · region whole-genome · calibration none · direction mixed

What it measured. Nothing new; it is the current canonical CMI statement, working through six "appeals" that critics use to explain away fast pedigree rates.

Rate as published / normalised. Footnote 10 converts Howell et al. 2003 as "0.53–1.57e-6 μ/site/year × 16,569 sites × 30 years/generation × 2," giving "about 0.5 to 1.5 per generation." Footnote 11 does the same to Madrigal 2012: "1.24e-6 μ/site/year × 16,569 sites × 30 years/generation × 2," giving 1.2 per generation. Both are wrong three ways. Howell's 0.95 (CI 0.53–1.57) mutations/bp/Myr is already a divergence rate — 2μ, as Howell's own Table 2 footnote states — so doubling it double-counts; it is a control-region per-site rate, and the rCRS control region is 1,122 bp, not 16,569, so multiplying by 16,569 inflates by 14.8x; and Madrigal's rate is narrower still, covering only HVR-I (16024–16383, 360 bp). Converted correctly from Howell's own two figures: control region 4.75 × 10^-7 /site/yr × 1,122 bp × 30 yr = 0.0160 per generation, plus coding region 3.0 × 10^-8 × 15,447 × 30 = 0.0139, total 0.0299 mutations per genome per 30-year generation = (a) 6.01 × 10^-8 per site per year = (b) 0.0249 per genome per 25-year generation. Carter's published figure is ~30x too high at the midpoint. The correctly converted 2003 pooled figure of 0.030/gen is essentially identical to Connell 2022's directly measured whole-genome 0.029/gen — the "estimates vary widely" framing is an artefact of the conversion.

Why it matters here. This is simultaneously the most important error in the young-earth literature and, in places, its most honest document. The error: the unit slip above is the load-bearing quantitative claim of the CMI case, repeated in one form or another since 2007, and Carter has converted the same Madrigal study three incompatible ways across 2018, 2023 and 2025 (0.3, 0.5 and 1.2 per generation). His claim that "the mutations that remain are, by definition, not subject to selection" is contradicted by gnomAD, where 55% of possible synonymous variants but only 10% of possible missense and 1% of possible stop-gain variants are observed across 56,434 healthy people, and by Árnadóttir 2024, which observes negative selection operating inside ordinary pedigrees. The honesty: he reports the measured rates against himself — "a study done on the population of Norfolk Island calculated a rate closer to 0.03 mutations per generation… one every 1,000 years," the Icelandic "0.07 mutations per generation," and then, verbatim, "These rates are a bit too slow for the creationist… and a bit too fast for the evolutionist." He also concedes the structural prediction: "The fact that there is no obvious three-way split in the tree tells us something important." Both the error and the concession belong in the article.

Library. key: carter-2025c, was: carter-2025d, was: carter-2025e. File: web/carter-2025c_when-did-eve-live.html (and .txt beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Critiques, archaic hominins, and the shape of the tree

There is no rebuttal of the young-earth mitochondrial clock in any mainstream peer-reviewed journal. The only peer-reviewed exchange that engages it directly ran inside the creationist journal: Stefan Frello, a working Danish biologist, published a two-page comment in Answers Research Journal in 2017, Jeanson replied in the same volume, and Frello answered again. Everything else in the critical literature is a blog post, a forum thread, a YouTube video, or a peer-reviewed paper aimed at a different target — Duff, Beatman & MacMillan 2020 is genuinely peer-reviewed and does cite Jeanson, but it attacks hyper-rapid speciation and baraminology, not the human mtDNA rate.

That matters in both directions. It means the young-earth clock has never had to survive expert review, and it also means several of the most-circulated rebuttals carry errors that no referee ever caught. Three are documented below. Stern Cardinale's central premise — that the substitution rate is always slower than the mutation rate — is false for neutral sites, where Kimura's result gives k = μ independent of population size; Carter is right on that point and the critic is wrong. Sterley's "cherry-picking" charge is self-refuting by his own sentence, since the studies he says Jeanson added lowered the rate. And the standard online rebuttal of the Parsons result (Alec MacAndrew's page, catalogued in the quote-trail block) states four times that Parsons and Howell used RFLP analysis and builds a conclusion on it; they did not — Parsons directly sequenced 610 bp of HVR1 and HVR2, and the Science news piece critics cite alongside it says so.

The archaic-hominin sources cut mostly against a young mitochondrial Eve, and hard: the Sima de los Huesos branch-length date and the luminescence date of the same deposit agree to within 7% from methods with nothing in common. But three results in this block cut the other way and are given their full weight here — the chimpanzee within-species mtDNA divergence figures, which reach and exceed the human–Neanderthal distance inside a single living species; the steady downward movement of the published human–Neanderthal mtDNA split date from 550–690 kyr in 1997 to 413 kyr in 2017, tracking the calibration source rather than any new sequence; and the two documented cases where mtDNA gave the wrong population history outright.

Mismatch distributions as a signature of population growth

Rogers, A.R., Harpending, H. "Population growth makes waves in the distribution of pairwise genetic differences." Molecular Biology and Evolution 9(3):552–569 (1992). PMID 1316531 https://pubmed.ncbi.nlm.nih.gov/1316531/

topic method · camp mainstream · type model · access paywalled · region restriction-map · calibration n/a · direction background

What it measured. Nothing; this is the derivation of the method. It shows that a population expansion leaves a unimodal "wave" in the histogram of pairwise differences between individuals, and gives the expressions θ = 2Nu and τ = 2tu used by everyone downstream. Read in abstract only in the research sweep: "Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals."

Why it matters here. It supplies the statistic behind the young-earth "star-like expansion" prediction. The important structural point for the article is visible already in the equations: τ is read off the histogram and needs no clock, while the expansion date is τ divided by an assumed rate.

Mismatch distributions in 17 human populations

Sherry, S.T., Rogers, A.R., Harpending, H., Soodyall, H., Jenkins, T., Stoneking, M. "Mismatch Distributions of mtDNA Reveal Recent Human Population Expansions." Human Biology 66(6):761–775 (1994). https://collections.lib.utah.edu/dl_files/18/59/18591292ec923bb21975ff69237cd1b3cc47bdf4.pdf

topic diversity · camp mainstream · type measurement · access OA · region HVR1 · calibration ape-divergence · direction mixed

What it measured. τ and inferred expansion times for 17 human populations plus pooled samples, from HVS-I sequence. World sample τ = 4.26 ± 0.56, giving T = 53.3 ka (95% range 30.4–95.0). Individual populations run from Herero τ = 0.43 (5.4 ka) to East Asian 1 τ = 4.99 (62.4 ka), on a stated 25-year generation.

Rate as published / normalised. Not a rate measurement — the paper uses a divergence rate of 0.41 ± 0.06 per site per Myr for HVS-I (0.25 ± 0.03 for HVS-I and HVS-II together). As a divergence rate that is 4.1 × 10^-7 per site per year across HVS-I only; it must not be carried to the whole genome, and the paper's own dates would move with it.

Why it matters here. It is the actual data behind "human mtDNA shows a recent expansion." It supports the young-earth reading in that the expansion is real and its τ values are clock-free; it undercuts it in that the expansion dates are not synchronous across populations, which a single Babel dispersal predicts they should be. The research notes flag that the τ → T conversion could not be reproduced from the stated HVS-I length and rate (~14 ka came out where 53.3 ka is published), so quote the published T values as published and do not re-derive them.

Library. key: sherry-1994. File: papers/sherry-1994_mismatch-distributions-mtdna-expansions.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

The first Neanderthal mtDNA sequence

Krings, M., Stone, A., Schmitz, R.W., Krainitzki, H., Stoneking, M., Pääbo, S. "Neandertal DNA Sequences and the Origin of Modern Humans." Cell 90(1):19–30 (1997). doi:10.1016/S0092-8674(00)80310-4 https://www.cell.com/fulltext/S0092-8674(00)80310-4

topic archaics · camp mainstream · type measurement · access OA · region HVR1 · calibration ape-divergence · direction mixed

What it measured. 379 bp of control region from Feldhofer 1, rebuilt from 123 clones across 13 amplifications, with 27 differences from the human reference outside the heteroplasmic homopolymer (24 transitions, 2 transversions, 1 insertion). Against 994 modern human lineages over 360 bp: humans differ among themselves by 8.0 ± 3.1 (range 1–24) and from the Neanderthal by 27.2 ± 2.2 (range 22–36); humans differ from chimpanzees by 55.0 ± 3.0.

Why it matters here. Two things at once. The famous result is much weaker than its reputation — Krings says in his own sentence that the largest human–human difference (24) exceeds the smallest human–Neanderthal difference (22), and recomputation on modern data shows 47.5% of human pairs exceed the minimum human–Neanderthal HVR1 distance. And the divergence estimate of 550,000–690,000 years is a model whose input was an assumed 4–5 Myr human–chimp split, so it cannot be offered as evidence for deep time. Note the access flag: Cell blocks automated agents with HTTP 403 but the article is free to read in a browser; the PubMed record is at https://pubmed.ncbi.nlm.nih.gov/9230299/.

Ape mtDNA diversity compared with human

Gagneux, P. et al. "Mitochondrial sequences show diverse evolutionary histories of African hominoids." PNAS 96(9):5077–5082 (1999). https://pmc.ncbi.nlm.nih.gov/articles/PMC21819/

topic other-species · camp mainstream · type measurement · access OA · region control-region · calibration n/a · direction mixed

What it measured. Average transversional differences within clades, normalised to sequence length: 811 human sequences average 0.41, eastern chimpanzees 1.14, central chimpanzees 2.36, western chimpanzees 3.40, bonobos 3.43, Nigerian chimpanzees 6.47, gorillas 12.37. Also: the 19 chimpanzee haplotypes from a single Taï forest breeding community show greater diversity than the entire human clade.

Why it matters here. It is the strongest form of the "humans are genetically uniform" argument, and it is a real measurement, not an inference. It also undercuts the Flood-model expansion argument in the same paper: "The narrow unimodal mismatch distributions of humans and eastern chimpanzees are typical of rapidly expanding populations." The expansion signature is not unique to us. Region matters here — these are control-region transversions, and the ratio shrinks sharply on whole mitogenomes (see Zsurka 2010).

African matrilineal structure from 624 complete L-clade genomes

Behar, D.M. et al. "The Dawn of Human Matrilineal Diversity." American Journal of Human Genetics 82(5):1130–1140 (2008). https://pmc.ncbi.nlm.nih.gov/articles/PMC2427203/

topic diversity · camp mainstream · type measurement · access OA · region whole-genome · calibration ape-divergence · direction undercuts

What it measured. 624 complete African L mitogenomes. Khoisan matrilineal ancestry diverges from the rest of the human pool at 90,000–150,000 ybp with at least five additional extant lineages present in parallel at that depth; a minimum of 40 evolutionarily successful sub-Saharan lineages existed at 60,000–70,000 ybp; L0d and L0k account for over 60% of the contemporary Khoisan mtDNA pool. (The calibration source was not recorded in the research sweep; the coalescence figures are model output either way.)

Why it matters here. Deep, geographically structured African lineage diversity is the hardest single observation for a Babel-dispersal model. Every non-African lineage descends from L3, which sits 35 mutations inside the African clade — mutations that a Babel model has to produce along one maternal line in about 101 years, roughly 146× the measured deCODE rate.

The first complete Neanderthal mitochondrial genome

Green, R.E. et al. "A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing." Cell 134(3):416–426 (2008). https://pmc.ncbi.nlm.nih.gov/articles/PMC2602844/

topic archaics · camp mainstream · type measurement · access OA · region whole-genome · calibration ape-divergence · direction undercuts

What it measured. Vindija 33.16, 16,565 nt at 34.9-fold average coverage, with 206 differences from the rCRS (195 transitions, 11 transversions). Against 53 human genomes, human–human differences run 2–118 and are bimodal, while human–Neanderthal differences run 201–234 and are unimodal, with no overlap. Contamination best estimate 0.5% (upper 95% limit 0.87%).

Why it matters here. This is the paper that made the archaic distances unavoidable, and it also states the caveat that kills the 1997 headline: "when the comparisons are restricted to only the HVRI or HVRII, the distributions of pairwise differences among extant humans and between humans and the Neandertal overlap." Two further items cut for the young-earth side. Green concedes that if the human–chimp divergence date or current assumptions about mtDNA evolution "would be incorrect, the estimates in calendar years … would need to be revised." And the Neanderthal mtDNA lineage is about 20% shorter than the human lineage — the opposite of what hypermutation in the Neanderthal line would produce, and a reduction the paper itself calls about three times larger than fossil age can explain.

Library. key: green-2008. File: papers/green-2008_complete-neandertal-mtdna-genome.html (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

The Denisova mitochondrial genome

Krause, J. et al. "The complete mitochondrial DNA genome of an unknown hominin from southern Siberia." Nature 464:894–897 (2010). doi:10.1038/nature08976 https://www.nature.com/articles/nature08976

topic archaics · camp mainstream · type measurement · access paywalled · region whole-genome · calibration ape-divergence · direction undercuts

What it measured. Denisova 3, aligned against 54 present-day human mtDNAs: Neanderthals differ from modern humans at an average of 202 positions, the Denisovan at 385, the chimpanzee at 1,462. Authenticity: 14,961 of 15,008 fragments spanning 276 diagnostic positions carry the Denisovan base, and a second extract sequenced by a different method gave an identical assembly.

Why it matters here. A second archaic lineage roughly twice as far from us as Neanderthals, which doubles the arithmetic problem for a 6,000-year mtEve. Its dates — 465,700 years for the human–Neanderthal mtDNA ancestor and about 1.04 Myr for the three-way ancestor — are again model output from an assumed 6 Myr human–chimp split, and the 465,700 figure is already 30% below Green's 660,000 two years earlier. Note the fetch quirk: Nature's redirect to its identity provider is a bot check, not a paywall.

Bonobo mitogenome diversity

Zsurka, G., Kudina, T., Peeva, V., Hallmann, K., Elger, C.E., Khrapko, K., Kunz, W.S. "Distinct patterns of mitochondrial genome diversity in bonobos (Pan paniscus) and humans." BMC Evolutionary Biology 10:270 (2010). https://pmc.ncbi.nlm.nih.gov/articles/PMC2942848/

topic other-species · camp mainstream · type measurement · access OA · region whole-genome · calibration ape-divergence · direction mixed

What it measured. 22 complete bonobo mitogenomes against 4,902 human ones. The bonobo mismatch distribution is multimodal — one set of pairs under 95 differences and a sharper peak at 145–175 — indicating a stable demographic history with no expansion. The maximum bonobo pairwise difference is 1.5× the human maximum, which the authors note is "somewhat closer to the distance between modern humans and the extinct Neandertal." Bonobo mtDNA MRCA 540,000 years (430,000–660,000), on a 6–8 Ma calibration.

Why it matters here. It is the honest whole-genome version of the Gagneux comparison, and it shrinks the human-uniformity claim from 8× (control region, bonobo/human) to 1.5×. It cuts for the young-earth side on one point: a living species carries whole-mitogenome distances approaching the human–Neanderthal gap. It cuts against on another: bonobos show no expansion signature, so the signature humans show is not simply what small ape populations look like.

Great ape nuclear diversity

Prado-Martinez, J. et al. "Great ape genetic diversity and population history." Nature 499:471–475 (2013). https://pmc.ncbi.nlm.nih.gov/articles/PMC3822165/

topic diversity · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Genome-wide nuclear heterozygosity across the great apes. Non-African humans, eastern lowland gorillas, bonobos and western chimpanzees all sit at about 0.8 × 10^-3 heterozygotes/bp; central chimpanzees, western lowland gorillas and both orangutan species sit at 1.6–2.4 × 10^-3.

Why it matters here. It breaks the uniqueness form of the low-diversity argument. Humans are in a four-way tie for lowest, not anomalously low, and three of the four species tied with us never passed through an Ark. ("Humans have uniquely low genetic diversity" needs the qualifier "in the mtDNA control region.") Note that the region vocabulary here has no nuclear value; this is nuclear data, not mtDNA.

Library. key: prado-martinez-2013. File: papers/prado-martinez-2013_great-ape-genetic-diversity.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

7,098 human mitogenomes and the maximum pairwise difference

Kim, H.L., Schuster, S.C. "Poor Man's 1000 Genome Project: Recent Human Population Expansion Confounds the Detection of Disease Alleles in 7,098 Complete Mitochondrial Genomes." Frontiers in Genetics 4:13 (2013). https://pmc.ncbi.nlm.nih.gov/articles/PMC3584485/

topic diversity · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Mean pairwise difference Π = 39.8 and a maximum of 123 across 7,098 GenBank human mtDNA genomes, with Table A2 breaking this down by region: African Π = 64.0, non-African Π = 35.4.

Why it matters here. The number 123 is the observed quantity the whole young-earth clock argument has to reach, and this is where it comes from. The regional breakdown is what makes the entry mixed: the "any two humans differ by about 40" figure that creationist writers quote is a sampling artifact of a mostly non-African database, and the African value is 64.

Library. key: kim-2013, was: kim-2013b. The library has a YAML record only; no file is stored. Cited by the first draft and ASTRA. EVE2 register: considered, not used in current draft.

Blog critique of creationist "kinds" and mtDNA distances

Duff, R.J. "Of Kinds and Common Ancestors: Comparing Mitochondrial Genomes of Mammals." Naturalis Historia, 26 February 2013. https://thenaturalhistorian.com/2013/02/26/kinds-baramins-creationism-mtdna-genomes-compared/

topic critique · camp counter-apologetics · type blog · access web · region whole-genome · calibration n/a · direction undercuts

What it measured. BLAST-derived whole-mtDNA pairwise differences across mammal pairs, human–chimp among them, presented as a single comparable table.

Why it matters here. The first version of the double-standard argument, superseded by the 2016 revision below, which carries the Neanderthal comparison and the numbers worth quoting.

Sima de los Huesos mtDNA and the branch-length date

Meyer, M. et al. "A mitochondrial genome sequence of a hominin from Sima de los Huesos." Nature 505:403–406 (2014). doi:10.1038/nature12788 https://www.eva.mpg.de/documents/Nature/Meyer_Mitochondrial_Nature_2014_1896606.pdf

topic archaics · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction undercuts

What it measured. About 98% of the mtDNA of Femur XIII from Sima de los Huesos — 16,302 positions at 31.6× coverage from 1.95 g of bone across 77 libraries — showing a Denisovan affinity. Using 13 directly dated ancient mtDNA sequences for calibration, the age of the specimen estimated from the length of its own mtDNA branch alone is 0.37–0.40 Myr (95% HPD spanning 0.15–0.64).

Why it matters here. This is the single most damaging item in the archaic literature for a young-earth clock, and its force does not depend on the human–chimp calibration: the clock was set by radiocarbon-dated tips, and the molecular date then matched an independent physical date of the same deposit (Arnold et al. 2014, below) to within 7%. There is no young-earth answer to it on file.

Library. key: meyer-2014b. File: papers/meyer-2014b_sima-de-los-huesos-mtdna.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Neanderthal admixture in living non-Africans

Prüfer, K. et al. "The complete genome sequence of a Neanderthal from the Altai Mountains." Nature 505:43–49 (2014). doi:10.1038/nature12886

topic archaics · camp mainstream · type measurement · access paywalled · region whole-genome · calibration n/a · direction mixed

What it measured. Read only at second hand. The figure carried through the creationist literature is that all humans outside Africa today carry Neanderthal sequence in their autosomal DNA at 1.5–2.1%. The research sweep reached this only through Cserhati's 2024 ARJ paper and flags it for direct verification before it is printed.

Why it matters here. Interbreeding at that level is the strongest support for treating Neanderthals as one kind with us, which is exactly what makes the 200-substitution mtDNA gap between us a problem rather than a curiosity for a young-earth model.

Library. key: prufer-2014. File: papers/prufer-2014_altai-neanderthal-genome.md. used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Luminescence dating of the Sima de los Huesos deposit

Arnold, L.J. et al. "Luminescence dating and palaeomagnetic age constraint on hominins from Sima de los Huesos, Atapuerca, Spain." Journal of Human Evolution 67:85–107 (2014). https://cir.cenieh.es/bitstream/20.500.12136/315/1/Luminescence%20dating%20and%20palaeomagnetic%20age%20constraint%20on%20hominins%20from%20Sima%20de%20los%20Huesos,%20Atapuerca,%20Spain_Arnold_et_al_2014.pdf

topic archaics · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Single-grain TT-OSL and pIR-IR ages of sedimentary horizons overlying the hominin-bearing clay breccia: weighted means of 433 ± 15 ka and 416 ± 19 ka, six reproducible replicates, giving a combined minimum age of 427 ± 12 ka for the underlying hominin. (Physical dating; the region field does not apply and is filled for form only.)

Why it matters here. It is the independent half of the Sima agreement. A molecular branch-length estimate near 400 kyr and a physical minimum of 427 ± 12 kyr, arrived at by methods sharing no assumptions, is a successful prediction of the long-age clock.

Library. key: arnold-2014. File: papers/arnold-2014_sima-luminescence-dating.pdf. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

"Creationists invent their own mutation rate!"

Sterley, S. ("AceOfSpades25"). evoanth.net / Filthy Monkey Men, 23 May 2016. Live URL [dead — domain parked] http://www.evoanth.net/2016/05/23/invent-mutation-rate/ Archive: https://web.archive.org/web/20171029161135/http://www.evoanth.net:80/2016/05/23/invent-mutation-rate/

topic critique · camp counter-apologetics · type blog · access web · region whole-genome · calibration n/a · direction mixed

What it measured. Nothing new; it recomputes Jeanson's published rate in other units and compares it to Soares et al. 2009. It is the origin of the widely repeated "35× too fast" figure and of the claim that only about two germline mutations should have been seen in 333 pedigrees rather than 63. Its comment thread also carries Jeanson's full point-by-point reply (13 February 2017) and the "Onlycurious" catch that Jeanson's model actually predicted a maximum of 137 differences and that he reported 123 instead.

Rate as published / normalised. Published as 5.94 × 10^-7 mutations per nucleotide per year, from 0.197 per genome per generation at a 20-year generation — "a new mitochondrial mutation every 100 years." Per 16,569 bp per 25-year generation that is 0.246. The arithmetic is right but the generation time is wrong: Jeanson used 15 years for that calculation, which gives 7.93 × 10^-7 per site per year and a ratio to Soares of 47.6×, not 35×. Jeanson's point estimate of 0.158 at 25 years is 3.82 × 10^-7 per site per year, 22.9× Soares. The honest range is 23–48×, and Sterley's headline lands inside it by accident.

Why it matters here. It is the source of most downstream criticism, and two of its three claims fail. The "about 2 expected mutations" figure is derived from the phylogenetic rate, which is the very quantity in dispute — at the largest direct pedigree measurement now available the expectation is 23, not 2. The cherry-picking charge is self-refuting: Sterley's own sentence says the added null studies lowered Jeanson's rate, which moves it against Jeanson's interest. What survives is the somatic-versus-germline objection, which is real.

Testing hyper-evolution with mammal mitogenome diversity

Duff, R.J. "Testing YEC Hyper-Evolution from Common Ancestors: Comparisons of mtDNA Genome Diversity in Mammals." Naturalis Historia, 7 April 2016. https://thenaturalhistorian.com/2016/04/07/testing-yec-hyper-evolution-from-common-ancestors-comparisons-of-mtdna-genome-diversity-in-mammals/

topic critique · camp counter-apologetics · type blog · access web · region whole-genome · calibration n/a · direction undercuts

What it measured. BLAST pairwise whole-mtDNA differences: human–chimp 1,462 (8.8%); human–Neanderthal about 200 against a human–human maximum near 100; red fox versus dog/wolf 2,269; domestic cat versus cheetah 1,765; lion versus tiger 1,373; brown versus polar bear 295.

Why it matters here. This is the strongest counter-apologetic argument in the whole critical literature, and it is arithmetic rather than assertion. The same clock that puts human mtEve at 6,000 years requires 2,269 differences inside the canid "kind" in 4,350 years — 0.52 mutations per genome per generation at a 2-year canid generation, or 1.57 × 10^-5 per site per year. That is about 25× the rate a 6,000-year human mtEve needs and about 945× the Soares phylogenetic rate. The bill is real and a creationist has already seen it: Todd Wood's 2013 ICC paper concluded from the same class of data that an accelerated rate near the Flood must be postulated. One caution — Duff's citation of Soares et al. 2009's "10,683 separate mutation events" across 2,196 human genomes is not by itself a problem for a young-earth star phylogeny, and the article should not treat it as one.

Sima de los Huesos nuclear DNA overturns the mtDNA grouping

Meyer, M. et al. "Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins." Nature 531:504–507 (2016). doi:10.1038/nature17405 https://www.eva.mpg.de/documents/Nature/Meyer_Nuclear_Nature_2016_2259387.pdf

topic tree-topology · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Nuclear sequence from two Sima specimens showing that these hominins were related to Neanderthals, not Denisovans — while the mtDNA from one of the same specimens retains its Denisovan affinity. The paper is candid about how hard this was: initial human contamination in the nuclear fraction exceeded 63% in all five specimens, dropping to 21% or less in three after filtering for terminal C→T deamination, leaving 189 kb–2.0 Mb of usable sequence.

Why it matters here. This is the first of the two documented cases where mtDNA gave the wrong population history, and it is a mainstream result, not a creationist complaint. The mtDNA tree said Denisovan; the nuclear tree said Neanderthal; the nuclear tree won. A skeptic of the mitochondrial clock can fairly cite it — with the qualification that the same contamination arithmetic the argument leans on is also a fair target for a young-earth critic of the nuclear result.

Library. key: meyer-2016. File: papers/meyer-2016_sima-de-los-huesos-nuclear-dna.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

"On the Creationist View on mtDNA"

Frello, S. "On the Creationist View on mtDNA." Answers Research Journal 10:181–182 (2017). https://answersresearchjournal.org/creationist-view-mtdna/

topic critique · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Frello ran BLAST comparisons and reports three numbers: the largest difference between two modern human mtDNAs is about 120 nt, human–Neanderthal differences run 180–240 nt, and the largest difference between two Neanderthals is about 80 nt. He lists the accessions used, which makes the claim re-runnable: HM771221 vs KJ669164 (human–human), JN655834 vs KC879692 and FJ770968 vs KX198083 (human–Neanderthal), KX198083 vs KC879692 (Neanderthal–Neanderthal).

Why it matters here. This is the strongest criticism of the young-earth mtDNA clock anywhere in print, and it appeared inside the creationist journal. Its logic is an internal-consistency test: if the archaic sequences were degraded or produced by a hypermutating lineage, Neanderthals should differ from each other at least as much as they differ from us. They differ about three times less. Independent recomputation on the full 36-genome GenBank corpus confirms the direction and sharpens it — within-Neanderthal mean distance 32.1 against within-modern-human 60.4. Jeanson's published reply (ARJ 10:183–186) answers with a "close genealogical relationship" among the Neanderthal specimens, which comes with no number and no test, and it concedes in the same paper that "current rates of mtDNA mutation are too low to explain the differences between ancient DNA samples and modern human mtDNA sequences." Frello also has one point scored against him: Jeanson never offered differing generation times as a reason to exclude fossil DNA, and Frello attributes it to him. Frello's BLASTs were not re-run in the research sweep; re-running them is cheap and would let the article state the numbers first-hand.

Library. key: frello-2017. File: papers/frello-2017_creationist-view-mtdna.pdf. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Frello's rejoinder

Frello, S. "Reply to 'Response to On the Creationist View on mtDNA'." Answers Research Journal 10:237–238 (2017). https://answersresearchjournal.org/creationist-view-mtdna-reply-response/

topic critique · camp mainstream · type review · access OA · region whole-genome · calibration n/a · direction mixed

What it measured. Nothing. Frello does not defend the Neanderthal-diversity argument against Jeanson's reply; he changes the subject to venue: "As long as Dr. Jeanson insists only to publish in the safe haven of Answers Research Journal, his ideas will never be confronted by experts … Confront them, Dr. Jeanson!"

Why it matters here. It is the closing move of the only peer-reviewed exchange on this subject, and it is a retreat. Having made a specific, quantitative, testable objection that Jeanson had not answered on the data, Frello fell back on an argument from authority — which leaves Jeanson's opening complaint, that critics rarely respond in peer-reviewed venues, factually accurate. The article should say this plainly even though the underlying scientific point in the first comment stands.

Library. key: frello-2017b. File: papers/frello-2017b_reply-to-jeanson-mtdna.pdf. used: no. Considered and not used: no footnote in the first draft, EVE2 or ASTRA cites it, although EVE2's register lists it as cited. Cite it if the article reports Frello's reply (ARJ 10:237-238), or leave it marked.

The Hohlenstein-Stadel Neanderthal and the introgression rescue

Posth, C. et al. "Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals." Nature Communications 8:16046 (2017). https://pmc.ncbi.nlm.nih.gov/articles/PMC5500885/

topic tree-topology · camp mainstream · type measurement · access OA · region whole-genome · calibration radiocarbon-tip · direction mixed

What it measured. The HST Neanderthal mtDNA at ~35× coverage. Adding it nearly doubles Neanderthal Watterson's θ to 2.50 × 10^-3, and it sits an average of 104 (89–111) positions from other Neanderthal mtDNAs — greater than any Denisovan pair and in the upper range of the modern human worldwide distribution. Divergence of HST from other Neanderthals ~270 ka; Altai branch TMRCA ~160 ka; Neanderthal–modern human mtDNA divergence dated to 413 ka (95% HPD 468–360 ka).

Why it matters here. Two things. First, 413 ka is 37% below Green's 660 ka, and the trend across Krings 1997 (550–690 kyr), Green 2008 (660 ± 140 kyr), Krause 2010 (466 kyr) and this paper tracks the calibration source moving from an assumed ape split to radiocarbon-dated tips — evidence that the number is model output, not measurement. Second, this is the second documented case where mtDNA misrepresents population history: to reconcile mtDNA with nuclear DNA the paper posits that an introgressing African mtDNA lineage replaced the earlier Denisovan-like Neanderthal mtDNA more than 270 kyr ago. That is an unobserved auxiliary hypothesis — though a testable one, and Sima de los Huesos is the prediction it makes.

Library. key: posth-2017. Folder: papers/posth-2017_deeply-divergent-archaic-mtdna/. Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

"Adam and Eve: a tested hypothesis?"

Buggs, R. Personal blog, 29 October 2017. https://richardbuggs.com/2017/10/29/adam-and-eve-a-tested-hypothesis/

topic critique · camp unaffiliated · type blog · access web · region whole-genome · calibration n/a · direction supports

What it measured. Nothing directly; a point-by-point methodological critique of chapter 3 of Venema's Adam and the Genome. Its load-bearing citations are measurements by others: two individuals drawn at random from a large population carry on average 75% of its heterozygosity (Slatkin & Excoffier 2012), a single-pair bottleneck followed by rapid growth does not cause massive diversity loss (Nei, Maruyama & Chakraborty 1975), and Tenesa et al. 2007's own discussion opens "Overall, the estimates of Ne appear to be much lower than the usually quoted value of 10,000." His central point: "None of the studies above set out to explicitly test the hypothesis that humans could have passed through a single-couple bottleneck."

Why it matters here. Buggs largely won this exchange and Venema conceded in 2019 — but the concession is that a single-couple bottleneck is undetectable only before about 500,000 years ago, and it is about nuclear effective population size, not mtDNA. It does nothing for a 6,000-year mitochondrial Eve, and citing it as though it did would be exactly the overstatement this article criticises elsewhere. (Nuclear data; the region value is filled for form.)

Library. key: buggs-2017. File: web/buggs-2017_adam-and-eve-tested-hypothesis.html (and .txt beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

The BioLogos reply thread and the 2019 concession

Venema, D. et al. "Adam, Eve and Population Genetics: A Reply to Dr. Richard Buggs (Part 1)." BioLogos forum, 2017–2018. https://discourse.biologos.org/t/adam-eve-and-population-genetics-a-reply-to-dr-richard-buggs-part-1/37039/print — with the later concession quoted in Craig, W.L., "What Became of the Genetic Challenge to Adam and Eve?", Peaceful Science, https://peacefulscience.org/articles/wlc-genetic-challenge/

topic critique · camp counter-apologetics · type forum · access web · region whole-genome · calibration n/a · direction mixed

What it measured. Nothing; a 500-post exchange. Two items are load-bearing. Buggs records Venema's walk-back on the strength of the claim: "I am happy to take your point that you do not believe that science has DISPROVEN that a bottleneck of two individuals could have happened in the human lineage." And Venema names the young-earth model on the table: "Robert Carter is an example of a YEC who tries to get around the bottleneck/founding with 2 problem this way. The challenge for YECs (and Richard) is explaining the patterns we see in the present day with reasonable recombination events." Swamidass' positive result from the same exchange is a TMR4A of 495 ± 100 kya.

Why it matters here. It is the exchange most often cited by young-earth writers as a mainstream retreat, and the retreat is real but bounded at half a million years. Two quotations in this cluster are unverified at source: Venema's November 2019 "we would be able to detect it if it happened more recently than 500,000 years ago" (BioLogos returned HTTP 429 on three attempts — https://biologos.org/articles/adam-once-more-with-feeling) and the "the sun is at the center of our solar system, humans evolved" line from Adam and the Genome, quoted via Craig without the book being consulted. Both should be verified before printing.

Library. No library record. used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft. EVE2 register flag: the primary text, quotation or locator remains unverified, so keep it as a lead until checked against source bytes.

"mtEve was not 6000 years ago"

Stern Cardinale, D. ("DarwinZDF42"). r/debatecreation, 14 February 2018. https://www.reddit.com/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/ [unfetchable by automated agent; recovered via the Arctic Shift Pushshift mirror, https://arctic-shift.photon-reddit.com/api/posts/ids?ids=7xnjdv and https://arctic-shift.photon-reddit.com/api/comments/search?link_id=7xnjdv&limit=100]

topic critique · camp counter-apologetics · type forum · access web · region whole-genome · calibration n/a · direction mixed

What it measured. Nothing; it is the clearest statement of the mutation-versus-substitution objection, arguing that Jeanson's rate came from lymphocyte data that cannot separate germline from somatic change and that the correct approach gives a substitution rate "30-something times slower," putting the TMRCA near 200 kya.

Why it matters here. The core objection lands, and Jeanson concedes the premise in print — "The only remaining caveat … is whether the mutation rate reported in Ding et al. (2015) represents a germline rate rather than a somatic mutation rate." But three of the supporting claims are wrong, and the article should say so. (i) "It's always the case that the substitution rate is slower than the mutation rate" is false for neutral sites: under Kimura's neutral theory the 1/(2N) fixation probability exactly cancels the 2Nμ input, so k = μ and drift alone cannot produce a 10–30× gap; Carter makes this correction and is right. (ii) "Jeanson counted all of the differences found between parents and offspring" is inaccurate — Jeanson wrote "I ignored all mutations reported as heteroplasmic," and the reframing offered later was never a withdrawal. (iii) The definition of homoplasmy as "same within a cell" misdescribes bulk lymphocyte sequencing, though the broader point survives on a different mechanism.

"Jeanson's Fulcrum Fails"

evograd. "Reviewing Replacing Darwin — Part 6: Jeanson's Fulcrum Fails." 30 October 2018. https://evograd.wordpress.com/2018/10/30/reviewing-replacing-darwin-part-6-jeansons-fulcrum-fails/

topic critique · camp counter-apologetics · type blog · access web · region whole-genome · calibration n/a · direction undercuts

What it measured. Nothing new, but it is the best-argued online critique and makes two points the others miss. First, the rate inflation is two-step: "By applying the D-loop mutation rate across the entire mitochondrial genome … Jeanson immediately inflates the overall mutation rate by an order of magnitude (about 10×)," on top of the genuine ~10× pedigree-versus-phylogenetic gap, turning an accepted 10× discrepancy into one of order 100×. Second, the alleged circularity of Jeanson's corroboration: Jeanson cites Li et al. 2016 as independent confirmation, Li et al. 2016 use per-site rates from Li et al. 2010, and those come from Soares et al. 2009 — the paper Jeanson rejects.

Why it matters here. The region-extrapolation charge is the same unit error this catalogue flags on both sides, and here it is aimed at the young-earth clock's foundation. The circularity chain was not independently traced in the research sweep; it is a serious accusation and should be checked link by link before the article repeats it. The reported in-person Q&A concession from Jeanson is second-hand testimony about an oral exchange, not evidence.

"Dissent with modification"

Duff, R.J., Beatman, T.R., MacMillan, D. "Dissent with modification: how postcreationism's claim of hyperrapid speciation opposes yet embraces evolutionary theory." Evolution: Education and Outreach 13:14 (2020). https://link.springer.com/article/10.1186/s12052-020-00124-w

topic critique · camp counter-apologetics · type review · access OA · region whole-genome · calibration n/a · direction undercuts

What it measured. Nothing; a peer-reviewed critique of creationist hyper-rapid speciation and baraminology that cites Jeanson 2015 and Jeanson & Lisle 2016.

Why it matters here. It is the closest thing to a peer-reviewed mainstream engagement with Jeanson, and it does not touch the human mtDNA rate — which is the point. Its most useful item for this article is its citation of Todd Wood's 2013 ICC paper, whose title alone says a leading creationist biologist concluded from mtDNA that the measured rate is insufficient and an acceleration near the Flood must be postulated. Wood's paper itself could not be retrieved: both Cedarville digital-commons URLs now serve a repository-migration page.

Reasons to Believe on the age of mitochondrial Eve

Rana, F. "When Did Mitochondrial Eve and Y Chromosomal Adam Live?" RTB 101, Reasons to Believe. https://reasons.org/explore/publications/rtb-101/rtb-101-post-9-age-of-adam

topic critique · camp old-earth-christian · type popular · access web · region whole-genome · calibration radiocarbon-tip · direction undercuts

What it measured. Nothing; it adopts Fu et al. 2013's calibration on ten radiocarbon-dated ancient human genomes spanning about 40,000 years and lands on a mitochondrial Eve at 157,000 ± 40,000 years ago, converging with Y-chromosomal Adam near 150 kya. Rana explicitly disavows the human–chimp calibration: "This comparison assumes that humans and chimps share a common evolutionary ancestor, a notion that I reject."

Why it matters here. It is the third position, and it is hard to dismiss as naturalistic bias — an explicitly Christian, anti-common-descent author reaching 157 kya on a clock calibrated by radiocarbon rather than by an ape split. His stated reason for rejecting pedigree rates is weak and should be answered rather than adopted: stochasticity affects a clock's variance, not its expectation, and pedigree studies are the only direct measurement of the mutation rate that exists. RTB's real strength here is the calibration, not that argument.

Report of Jeanson's current response to the substitution-rate objection

Duff, R.J. "How Dr. Jeanson's Rhetoric Substitutes Mockery for Methodology." Naturalis Historia, 17 March 2026. https://thenaturalhistorian.com/2026/03/17/how-dr-jeansons-rhetoric-substitutes-mockery-for-methodology/

topic critique · camp counter-apologetics · type blog · access web · region whole-genome · calibration n/a · direction undercuts

What it measured. Nothing; a secondary report of the current Jeanson–Stern Cardinale exchange, documenting Jeanson framing the mutation-versus-substitution objection as "fundamentalist atheistic religion."

Why it matters here. It is the most recent state of the dispute and shows where it now sits — on YouTube rather than in print. The primary video was obtained on 2026-09-02 (YouTube auto-captions) and is worked up in the next entry; the article quotes the video, not this post. Duff is R. Joel Duff.

Library. key: duff-2026b. File: web/duff-2026b_jeanson-rhetoric-substitutes-mockery-for-methodology.html (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Jeanson 2026, the interview answer to the substitution-rate objection

Jeanson, N.T., interviewed on Standing For Truth. "Does Modern Genetics Confirm the Bible? | Dr. Nathaniel Jeanson Explains." YouTube, uploaded 10 March 2026, 1:00:25. https://www.youtube.com/watch?v=SWWd4K0FFj8 Library key jeanson-2026 (auto-caption VTT plus transcript).

topic young-earth · camp young-earth · type interview · access web · region whole-genome · calibration n/a · direction supports

What it says. His newest statement on the mutation-versus-substitution objection, given at 46:05–53:40 in answer to the host's request for "the best way to just shut it down." He defines the mutation rate as "how fast or slow does mom mutate the DNA to daughter," gives "about an average of one mistake every five to ten generations," and concedes the extrapolation outright: "I had been assuming that rate had been consistent in the past. It's basically uniformitarianism." Three replies to the objection: evolutionists use uniformitarianism in geology and so cannot object to it in genetics; the textbook distinction is "a fundamentalist atheistic religion or agnostic religion"; and the assumption is a tested hypothesis — "the predictions have been confirmed … last summer with mitochondrial DNA." Closing: "I'm equating substitution rate and mutation rate because the data says so." Nowhere in the hour does he mention Connell, Norfolk Island, Árnadóttir, deCODE, heteroplasmy, a bottleneck or fixation.

Why it matters here. It is the newest primary statement and it does not engage the measurement. The "confirmation" is the 2025 Americas paper, whose dating scales branch lengths inside an assumed young-earth span (4,441/4,026 or 4,636/4,206 years, Methods) rather than applying a measured rate. The 2 June 2022 origin of the exchange, on Apologetics Live, survives only as the critic's clip (Creation Myths, 3 June 2022, 4:30, https://www.youtube.com/watch?v=sUPHNeL9wFk; library key creation-myths-2022), in which Jeanson says "I'm treating the mutation rate as a substitution rate, that this rate is consistent. That's what I'm doing." Both are cited in the article's "How the young-earth literature reads Norfolk Island" section. Caveat: both transcripts are YouTube auto-captions with no punctuation, so every printed sentence carries editorial punctuation and stutters removed; timestamps are given in the footnotes so anyone can check the audio.

Library. key: jeanson-2026, key: creation-myths-2022 (the 2022 clip, a separate source this entry compares). Files: media/jeanson-2026_standing-for-truth-interview.en.vtt (also jeanson-2026_standing-for-truth-interview.md) and media/creation-myths-2022_jeanson-mutation-substitution-clip.en.vtt (also .md). Cited by the first draft only, as the footnotes for both sources. EVE2 register: considered, not used in current draft. Both are machine captions, not Jeanson's checked words: EVE2's quarantine.md lists both as unverified (the audio was not checked, and the caption at 53:33 includes a garbled phrase). Before the article prints either as a quotation, a verifier should check the audio (download with yt-dlp -x, then listen or transcribe locally) and record the route in this entry; until then keep the quotations in quarantine.md and paraphrase with the timestamp.

Clocks tested elsewhere, and the quote trail

The strongest possible check on a molecular clock is to run it against a history that is already known from somewhere else. A pedigree with birth records. A colony of bones that can be radiocarbon-dated one by one. An island whose age is fixed by potassium-argon. A domestication event fixed by archaeology. In those cases the clock is not being asked to produce a date — it is being asked to reproduce one, and it can fail in public. The sources below are those tests, run in penguins, bison, bears, horses, cattle, chickens, nematodes, fruit flies, Hawaiian honeycreepers, and in human populations whose founding is a matter of parish record.

Two results dominate them. First, the short-term-fast / long-term-slow pattern is real and it is universal. Molak & Ho's meta-analysis of 239 metazoan rate estimates finds a significant negative rate-versus-calibration-age slope in every group tested — mammals, birds, reptiles, insects, coding and non-coding — and Ho et al. 2011 document the same inflation in nuclear DNA, in bacteria and in viruses. That generality cuts both ways, and it cuts harder against the young-earth reading than for it: a pattern that appears in every organism ever tested is a property of rate estimation, not evidence that any one species is young. Applied consistently to Drosophila, the same reasoning would date the melanogaster/simulans split at a few thousand years, which nobody defends. Second, where the correction has actually been modelled rather than assumed — Millar et al.'s Adélie penguins, the best-controlled test in existence — the short-term and long-term rates turn out to be statistically indistinguishable, and almost the entire apparent inflation was heteroplasmy accounting.

One argument in this site's own older notes does not survive and is retracted here. The claim that cattle have a "mitochondrial Eve at 200,000 years" while domestication is only 10,000 years old, and that this proves the clock fails, is wrong. Loftus et al., who produced the 200,000-year figure, read it as the divergence between two wild aurochs lineages that were domesticated separately — not as a post-domestication coalescence. Bollongino et al. later estimated roughly 80 founding females for taurine cattle. Domestication sampled standing wild variation; there was never a one-female cattle bottleneck to date, so there is no clock failure to point at. The honest young-earth question about cattle is a different and harder one — how two deeply divergent aurochs lineages, or ~80 founding females, fit a Flood bottleneck of one pair a few thousand years earlier — and it should be argued as that, not repackaged as a clock test.

The second half of this block is the paper trail behind the single most-quoted sentence in the whole subject: Ann Gibbons' "using the new clock, she would be a mere 6000 years old." The sentence is real, the reprint is public, and the next sentence is "No one thinks that's the case." The entries below record who quotes it fairly and who does not, in both directions.

Romanov identification

Gill P, Ivanov PL, Kimpton C, Piercy R, Benson N, Tully G, Evett I, Hagelberg E, Sullivan K. "Identification of the remains of the Romanov family by DNA analysis." Nature Genetics 6(2):130–135 (1994). PMID 8162066 https://pubmed.ncbi.nlm.nih.gov/8162066/

topic forensics · camp mainstream · type measurement · access paywalled · region control-region · calibration n/a · direction background

What it measured. STR and mtDNA typing of nine skeletons from a 1991 grave in Ekaterinburg; the putative Tsarina and three children matched a living maternal relative exactly, and cloned mtDNA from the putative Tsar showed heteroplasmy at a single base in the control region, one of the two sequences matching two living maternal relatives. Abstract read via PubMed; full text not obtained.

Why it matters here. This is where the whole story starts. The Tsar's single-base "mismatch" is the anomaly that drove the 1997 workshop, the Parsons pedigree study, the forensic rule change, and eventually the 6,000-year sentence.

Two cattle domestications

Loftus RT, MacHugh DE, Bradley DG, Sharp PM, Cunningham P. "Evidence for two independent domestications of cattle." PNAS 91(7):2757–2761 (1994). doi:10.1073/pnas.91.7.2757 https://pubmed.ncbi.nlm.nih.gov/8146187/

topic other-species · camp mainstream · type measurement · access OA · region control-region · calibration none · direction undercuts

What it measured. Mitochondrial control-region sequences from European, African and Indian cattle breeds, which fell into two sharply distinct geographic lineages that do not follow the taurine/zebu split. Applying a molecular clock, the authors put the divergence of the two clades at "at least 200,000, and possibly as much as 1 million, years ago." Abstract read via PubMed; PMC holds only a page scan, and the research notes do not record which external calibration produced the 200,000-year figure.

Why it matters here. This is the actual source of the popular "cattle mitochondrial Eve is 200,000 years old but cattle were domesticated 10,000 years ago" argument, and it kills it. The authors read the 200,000 years as a divergence between two already-separate wild aurochs subspecies domesticated independently — never as a coalescence after domestication. No clock failed. The argument should be dropped from this article's case.

Grand Duke Georgij and the Tsar's heteroplasmy

Ivanov PL, Wadhams MJ, Roby RK, Holland MM, Weedn VW, Parsons TJ. "Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II." Nature Genetics 12(4):417–420 (1996). PMID 8630496 https://pubmed.ncbi.nlm.nih.gov/8630496/

topic heteroplasmy · camp mainstream · type measurement · access paywalled · region control-region · calibration n/a · direction background

What it measured. Exhumed the Tsar's brother and found the same point heteroplasmy at the same control-region position, in a different ratio — confirming the heteroplasmy was inherited, not artefact. The position is 16169: Coble et al. 2009 report the Tsar as mostly C/t and Georgij as mostly T/c, with maternal references fixed for T. Abstract read via PubMed; full text not obtained.

Why it matters here. The paper's own explanation of the two brothers' different ratios is "a 'bottleneck' mechanism of mtDNA segregation" — the germline bottleneck that later work quantified at N ≈ 30–35. Note also the unit trap Coble et al. expose: point heteroplasmy at np 16169 specifically occurs in 0.016% of 18,788 AFDIL haplotypes, which is not the same quantity as the "10 to 20% of humans" whole-molecule heteroplasmy figure quoted in Gibbons.

Parsons 1997, the fast control-region rate

Parsons TJ, Muniec DS, Sullivan K, Woodyatt N, Alliston-Greiner R, Wilson MR, Berry DL, Holland KA, Weedn VW, Gill P, Holland MM. "A high observed substitution rate in the human mitochondrial DNA control region." Nature Genetics 15(4):363–368 (1997). doi:10.1038/ng0497-363 https://www.nature.com/articles/ng0497-363

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region HVR1+2 · calibration n/a · direction mixed

What it measured. Direct comparison of ~610 bp of HV1 plus HV2 between close maternal relatives, across 134 independent lineages and 327 mother-to-child transmission events: ten substitutions observed, "an empirical rate of 1/33 generations, or 2.5/site/Myr," roughly twenty-fold higher than phylogenetic estimates, and explicitly not explainable by hot spots alone. Abstract publisher-verified; the discussion paragraph containing the 6,500-year sentence is reconstructed from three independent web transcriptions (one of them a hostile critic's) that agree word for word, and is not publisher-verified.

Rate as published / normalised. As published: 2.5 substitutions per site per Myr, or 1 mutation per 33 generations over 610 bp. (a) 2.5 × 10^-6 per site per year. (b) 1.04 mutations per 16,569 bp per 25-year generation — ‡ a naive extrapolation of a hypervariable control-region rate across the whole molecule, which is physically invalid and is given only for unit comparison. A recount by Heyer et al. 2001 gives nine substitutions rather than ten, which would lower the rate to 2.26/site/Myr.

Why it matters here. This is the measurement behind the entire "6,500-year Eve" claim, and it is a real, published, forensic-laboratory measurement. It is also the paper whose own authors wrote that using their rate "would result in an age of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the known age of modern humans." Two corrections to this site's older notes: the wording is "an age," not "an average age," and the segment is ~610 bp, not ~60 bp — at 60 bp the paper's own arithmetic would not yield 2.5/site/Myr.

Tristan da Cunha and the Swedish families — the null results

Soodyall H et al. (Tristan da Cunha, 1997) and Cavelier L et al. (33 Swedish families, 2000), as reported in Gibbons 1998 and tabulated in Jeanson 2013, Answers Research Journal 6:467–501. https://www.dnai.org/teacherguide/pdf/reference_romanovs.pdf

topic pedigree-rate · camp mainstream · type measurement · access paywalled · region control-region · calibration n/a · direction undercuts

What it measured. Two documented-founding pedigrees sequenced specifically to replicate the Parsons and Howell result. Tristan da Cunha traces to five female founders in the early 19th century: 0 substitutions in 108 transmissions over 698 bp. The Swedish study: 0 substitutions in 292 transmissions over 792 bp. Gyllensten, quoted by Gibbons: "After we read Howell's study, we looked in vain for mutations in our families." Neither primary paper was obtained; the counts come from Jeanson's own pooled table, which was read verbatim, and the existence of the null results from Gibbons.

Why it matters here. Documented-founding human populations do not uniformly show a fast clock — the two studies designed as replications found nothing at all. Any article that says "whenever we check the clock against a known history it runs fast" has to print these two rows.

Hawaiian honeycreepers on a volcanic conveyor belt

Fleischer RC, McIntosh CE, Tarr CL. "Evolution on a volcanic conveyor belt: using phylogeographic reconstructions and K-Ar-based ages of the Hawaiian Islands to estimate molecular evolutionary rates." Molecular Ecology 7(4):533–545 (1998). doi:10.1046/j.1365-294x.1998.00364.x https://pubmed.ncbi.nlm.nih.gov/9628004/

topic other-species · camp mainstream · type model · access paywalled · region coding · calibration internal · direction undercuts

What it measured. Calibrated mtDNA cytochrome b divergence in Hawaiian drepanidine honeycreepers against potassium-argon ages of the islands they live on — Kauai 5.1 Ma, Hawaii 0.43 Ma — obtaining 0.016 sequence divergence per Myr, with parallel figures for Hawaiian Drosophila (0.019/Myr) and Laupala crickets (0.024–0.102/Myr). Abstract only; the authors list seven assumptions in the abstract itself, which is unusually candid.

Rate as published / normalised. As published: 0.016 divergence per Myr, which is 0.8% per Myr per lineage. (a) 8.0 × 10^-9 per site per year per lineage. (b) 3.3 × 10^-3 mutations per 16,569 bp per 25-year generation, using the 25-year normalisation of this catalogue rather than a bird's real generation time.

Why it matters here. Over a 0.43–5.1 Myr window, with no fossils involved, the recovered rate is essentially the conventional 2%/Myr avian standard. If mtDNA clocks were inflated 10–100x everywhere, Hawaii would show it and does not. The honest caveat: the calibration is radiometric, so a reader who rejects K-Ar dating rejects this test — but then the dispute is about K-Ar, not about mtDNA.

Library. key: fleischer-1998. File: papers/fleischer-1998_volcanic-conveyor-belt.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Gibbons 1998 — where "a mere 6000 years old" comes from

Gibbons A. "Calibrating the Mitochondrial Clock." Science 279(5347):28–29 (1998). doi:10.1126/science.279.5347.28 Publisher page returns HTTP 403 to automated fetch; the AAAS-licensed verbatim reprint is at https://www.dnai.org/teacherguide/pdf/reference_romanovs.pdf

topic history · camp mainstream · type news · access paywalled · region control-region · calibration ape-divergence · direction mixed

What it measured. Nothing of its own — it is a Research News report on the October 1997 First International Workshop on Human Mitochondrial DNA. It reports Parsons' 610 bp / 357 individuals / 134 families / 327 generational events / 10 substitutions, Howell's "one mutation every 25 to 40 generations," the pooled cross-laboratory rate of one mutation per 1,200 years, the Tristan da Cunha and Swedish null results, and the FBI guideline change. Full text read from the reprint, which is byte-identical to a Wayback capture from 10 January 2004.

Rate as published / normalised. Pooled cross-laboratory rate, as published: "one mutation per 1200 years" across ~610 bp of control region. (a) 1.37 × 10^-6 per site per year. (b) 0.57 mutations per 16,569 bp per 25-year generation — ‡ naive control-region extrapolation. Gibbons' phylogenetic baseline, attributed to Stoneking, is "one mutation every 300 to 600 generations, or one every 6000 to 12,000 years," i.e. 0.137–0.273 per site per Myr.

Why it matters here. Two things, pulling opposite ways. The famous line — "Using the new clock, she would be a mere 6000 years old" — is followed immediately, at the start of the next paragraph, by "No one thinks that's the case, but at what point should models switch from one mtDNA time zone to the other?" Any use of the first sentence without the second is a misquote by omission. But Gibbons also contains the single cleanest mainstream admission of what the standard rate rests on: "The most widely used mutation rate for noncoding human mtDNA relies on estimates of the date when humans and chimpanzees shared a common ancestor, taken to be 5 million years ago." That sentence is almost never the one quoted, and it is the strongest thing in the article for the young-earth side.

Library. key: gibbons-1998. File: papers/gibbons-1998_calibrating-the-mitochondrial-clock.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Wieland 1998 — patient zero of the quote trail

Wieland C. "A shrinking date for 'Eve'." CEN Technical Journal / Journal of Creation 12(1):1–3 (1998). https://creation.com/a-shrinking-date-for-eve

topic critique · camp creationist · type popular · access web · region control-region · calibration n/a · direction supports

What it measured. Nothing; it is a two-page commentary on Gibbons. Its two Gibbons fragments are verbatim-correct and its ellipsis is legitimate. It never read Parsons: its reference 5 cites Parsons "as cited in ref. 4," and ref. 4 is Gibbons. Its "lived about 6500 years ago" quotation is not from Gibbons at all but from Loewe & Scherer, Trends in Ecology and Evolution 12(11):422–423 (1997) — which the original 1998/2000 Answers in Genesis HTML footnoted to Gibbons and the current creation.com HTML silently corrected. The Loewe & Scherer text itself has not been obtained, and the DOI in circulation for it resolves to a different TREE article, so that quote should not be printed yet.

Why it matters here. This is the article every later creationist citation traces back to, and its own conclusion carries a hedge that later repeaters drop: "If correct, it means that mitochondrial Eve lived 6,000 to 6,500 years ago." It omits "No one thinks that's the case" and omits the two studies that found no elevated rate. Worth stating plainly: Siegfried Scherer, co-author of the "review of the data" Wieland relies on, is himself a German creationist.

Library. key: wieland-1998. File: web/wieland-1998_shrinking-date-for-eve.html (and .txt beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

FBI mtDNA interpretation guidelines

Budowle B, DiZinno JA, Wilson MR. "Interpretation Guidelines for Mitochondrial DNA Sequencing." Proceedings of the Tenth International Symposium on Human Identification (1999). https://www.promega.ro/~/media/files/resources/conference%20proceedings/ishi%2010/oral%20presentations/37budowle.pdf

topic forensics · camp mainstream · type review · access OA · region control-region · calibration n/a · direction background

What it measured. Codifies the rule Gibbons describes, verbatim: "If the questioned and known samples differ by a single nucleotide, and no evidence of heteroplasmy is present, the comparison should be reported as inconclusive." Authors are FBI Laboratory Division. Full PDF read.

Why it matters here. It independently confirms that Gibbons' account of the forensic rule change is accurate to the letter, which is the strongest verifiable real-world consequence in the whole episode and depends on no one's origins position. It also refutes a specific creationist claim: the guideline is a rule for identity comparison between two specimens. It has nothing to do with the age of mitochondrial Eve, and ICR's Tomkins, Genesis Apologetics and The Creation Club all misstate it as having been driven by "faster mutation rates pointing to mitochondrial Eve about 6,000 years ago."

Library. key: budowle-1999. File: papers/budowle-1999_mtdna-interpretation-guidelines.pdf. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

C. elegans mutation-accumulation lines

Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK. "High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans." Science 289(5488):2342–2344 (2000). doi:10.1126/science.289.5488.2342 https://pubmed.ncbi.nlm.nih.gov/11009418/

topic other-species · camp mainstream · type measurement · access paywalled · region whole-genome · calibration none · direction supports

What it measured. Screened long-term mutation-accumulation lines across ~75% of the C. elegans mitochondrial genome and found "a mutation rate that is two orders of magnitude higher than previous indirect estimates," with a strongly biased spectrum and hotspots at homopolymeric runs. Abstract only — the full text is paywalled at Science and was not obtained.

Rate as published / normalised. The rate is usually quoted as 1.6 × 10^-7 per site per generation (this is Konrad et al. 2017's rendering of it; Haag-Liautard et al. 2008 describe Denver's figure as only ~1.5x their own 6.2 × 10^-8, i.e. ~9.3 × 10^-8, and Konrad's own re-measurement gives 4.32 × 10^-8). (a) 1.5 × 10^-5 per site per year, assuming the ~4-day laboratory generation. (b) 2.7 × 10^-3 mutations per 16,569 bp per nematode generation — the 25-year human generation is meaningless here, and C. elegans mtDNA is ~13.8 kb, so this figure is an arithmetic normalisation only.

Why it matters here. This is the measurement that made "mtDNA mutates far faster than phylogenies say" a general claim rather than a human one, and it is the rate Jeanson 2013 converts to years using laboratory culture times. Flag honestly: three incompatible values for this one paper circulate, and the headline figure has since come down ~3.7x (see Konrad et al. 2017 below). Do not quote 1.6 × 10^-7 as "the C. elegans mtDNA mutation rate" without the paper in hand.

Iceland — 705 documented transmissions

Sigurðardóttir S, Helgason A, Gulcher JR, Stefansson K, Donnelly P. "The mutation rate in the human mtDNA control region." American Journal of Human Genetics 66(5):1599–1609 (2000). doi:10.1086/302902 https://pubmed.ncbi.nlm.nih.gov/10756141/

topic pedigree-rate · camp mainstream · type measurement · access OA · region HVR1+2 · calibration n/a · direction mixed

What it measured. Sequenced the mtDNA control region in 272 people from 26 large Icelandic pedigrees, related by 705 documented transmission events, using deCODE's genealogical records. Three base substitutions observed: 3/705 = 0.0043 per generation (95% CI 0.00088–0.013). Abstract read via PubMed; PMC1378010 holds the full text.

Rate as published / normalised. As published: 0.32 substitutions per site per Myr (95% CI 0.065–0.97) across HVI+HVII (~675 bp), implying a ~20-year generation. (a) 3.2 × 10^-7 per site per year. (b) 0.13 mutations per 16,569 bp per 25-year generation — ‡ naive control-region extrapolation.

Why it matters here. It is the largest pedigree study of its era and it lands eight times below Parsons' 2.5/site/Myr on the same region. That eightfold spread among pedigree studies of the same 600-odd base pairs is the single most important caution against treating "the pedigree rate" as one number, in either direction. Note also that Carter 2025 reports a much larger deCODE dataset — 8,199 mutations among 116,663 mother-child transmissions, ~0.07 mutations per generation — which this catalogue has not independently traced to its primary paper.

Library. key: sigurdardottir-2000. Folder: papers/sigurdardottir-2000_mtdna-control-region-rate/. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Adélie penguins, ancient DNA

Lambert DM, Ritchie PA, Millar CD, Holland B, Drummond AJ, Baroni C. "Rates of Evolution in Ancient DNA from Adélie Penguins." Science 295(5563):2270–2273 (2002). doi:10.1126/science.1068105 https://pubmed.ncbi.nlm.nih.gov/11910113/ — publisher page and the figshare copy both return HTTP 403; abstract also at https://api.semanticscholar.org/graph/v1/paper/DOI:10.1126/science.1068105

topic other-species · camp mainstream · type measurement · access paywalled · region HVR1 · calibration radiocarbon-tip · direction supports

What it measured. Sequenced hypervariable region I from 96 individually radiocarbon-dated subfossil Adélie penguin bones, some over 7,000 years old, against 380 living birds, and estimated the rate by MCMC and by least-squares regression. Result: rates "approximately two to seven times higher than previous indirect phylogenetic estimates." Abstract only — the full text could not be obtained.

Rate as published / normalised. Contested, and this must be flagged. Millar et al. 2008 report the Lambert median as 0.96 substitutions/site/Myr (CI 0.53–1.43) and Peterson & Masel give 0.95; Ho et al. 2005 render it as "95% per million years"; Molak & Ho's Table S1 enters 2.3054 × 10^-6 per site per year (= 2.31/site/Myr) for the d-loop at a 6,424-year calibration. (a) 9.6 × 10^-7 or 2.31 × 10^-6 per site per year depending on which is taken. (b) 0.40 or 0.96 mutations per 16,569 bp per 25-year generation — ‡ naive HVR extrapolation. Do not cite a Lambert 2002 rate without obtaining the paper.

Why it matters here. It is the first properly radiocarbon-anchored ancient-DNA rate in any species, and it does come out 2–7x above the phylogenetic estimate. It is also, at 2.31 × 10^-6, the fastest non-coding rate in Molak & Ho's entire 239-estimate compilation — and the same laboratory, extending the same 344 bp to 37,600-year-old bones six years later, got a rate 2.7x lower. The rate falls as the calibration window lengthens, within one species and one region.

Library. key: lambert-2002, was: lambert-2002b. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Beringian steppe bison — 220 radiocarbon dates

Shapiro B et al. "Rise and Fall of the Beringian Steppe Bison." Science 306(5701):1561–1565 (2004). doi:10.1126/science.1101074 Publisher https://www.science.org/doi/10.1126/science.1101074 [dead to automated fetch — HTTP 403]; working copy at the SFU repository https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/15088/11A.pdf

topic other-species · camp mainstream · type measurement · access OA · region control-region · calibration radiocarbon-tip · direction undercuts

What it measured. Sequenced a 685 bp fragment of the bison mitochondrial control region from fossils with 220 accelerator-mass-spectrometry radiocarbon dates spanning 960,000 years, and derived the rate directly from the dated tips: 32% per Myr (95% HPD 23–41%). Full text read.

Rate as published / normalised. As published: 32% per Myr, with a supporting-table range of 2.30 × 10^-7 to 4.13 × 10^-7 substitutions/site/year. (a) 3.2 × 10^-7 per site per year. (b) 0.13 mutations per 16,569 bp per 25-year generation — ‡ control-region rate, human generation used only for unit comparison.

Why it matters here. This is the clearest case in the literature where an independent, radiocarbon-anchored clock check came out right: the authors state their estimate "is independent of paleontological calibrations but agrees with fossil-calibrated rates for cattle of 30.1% per My and 38% per My." A ~6% agreement across 960,000 years of dated samples is a direct answer to the claim that the mtDNA clock always fails when tested. The counter — Ho, Shapiro et al. 2007's reslicing of the same data by sample age — is contested; see below.

Library. key: shapiro-2004. File: papers/shapiro-2004_beringian-steppe-bison.pdf (and .md beside it). Cited by the first draft and EVE2. EVE2 register: cited in current draft.

MacAndrew's rebuttal

MacAndrew A. "Misconceptions Around Mitochondrial Eve: A Critique of Carl Wieland's AiG article on Mitochondrial Eve." evolutionpages.com, n.d. (before Wieland's 2006 reply). http://www.evolutionpages.com/Mitochondrial%20Eve.htm

topic critique · camp counter-apologetics · type blog · access web · region control-region · calibration ape-divergence · direction undercuts

What it measured. Nothing; it is the standard online rebuttal to the creationist use of Parsons and Gibbons. Full page read. It prints the Parsons abstract and the key discussion paragraph in full — including the sentences creationists cut — and concedes explicitly that the standard rate "is calibrated, as Wieland correctly says, by counting mutations in great ape and human mitochondria and regressing back to the age of their divergence as determined by fossils dated by radiometric dating."

Why it matters here. It is the best-known counter-argument and it contains two errors this article should name. First, it states four separate times, including in a concluding bullet, that Parsons and Howell used RFLP analysis; they did not — Parsons directly sequenced 610 bp of HV1 and HV2, as his own abstract and Gibbons both say. One of MacAndrew's nine conclusions is therefore void. Second, it resolves the dispute by citing Ingman et al. 2000's 1.7 × 10^-8 per site per year to "confirm" a 150,000–200,000-year MRCA, when that rate is itself derived from an assumed 5 Myr human–chimp split — the circularity he had granted two sections earlier for the control-region rate.

Library. key: macandrew. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Bechard's student page catches the ICR error

Bechard P. "Mutation Rates as a Creationist Clock." Honors Seminar UHON 390 (Prof. Timothy Heaton), University of South Dakota (2005). Live host refuses TLS; use http://web.archive.org/web/20151104025418/http://apps.usd.edu:80/esci/creation/age/content/creationist_clocks/mutations.html

topic critique · camp counter-apologetics · type web · access web · region control-region · calibration n/a · direction undercuts

What it measured. Nothing; an undergraduate seminar page. It quotes Humphreys' Impact #384 sentence and answers it: "the article from which that information was taken directly states that no one believes that the mitochondrial Eve is truly only 6,000 years old (Gibbons 1998:29)."

Why it matters here. A student caught the ICR misstatement in 2005 and it is still on ICR's website twenty-one years later. This page is also the only source found that assigns page numbers within Gibbons — "6000 to 12,000 years" at p. 28, "No one thinks that's the case" at p. 29 — so it is the sole support if this article prints page-level citations. One slip of its own: it merges Howell's "25 to 40 generations" rate with the pooled "one every 1,200 years" rate, which are different numbers.

Library. key: bechard-2005. The library has a YAML record only; no file is stored. Cited by the first draft only. EVE2 register: considered, not used in current draft.

Humphreys, "Evidence for a Young World," item 8

Humphreys DR. "Evidence for a Young World." ICR Impact #384 (2005), current web version at https://www.icr.org/article/evidence-for-young-world/

topic yec-clock · camp creationist · type popular · access web · region control-region · calibration n/a · direction supports

What it measured. Nothing. Item 8 reads: "Measurements of the mutation rate of mitochondrial DNA recently forced researchers to revise the age of 'mitochondrial Eve' from a theorized 200,000 years down to possibly as low as 6,000 years," citing Gibbons 1998. Page read in full.

Why it matters here. This is the worst single error in the creationist citation trail, and it is not a truncation but an invented claim: no researcher revised anything, and Gibbons says so in the following sentence. It is also filed under "Biological material decays too fast," alongside DNA-in-amber claims, which confuses a mutation rate with molecular decay. This article should print it next to "No one thinks that's the case" and disown it.

Ho et al. 2005 — the time-dependency curve

Ho SYW, Phillips MJ, Cooper A, Drummond AJ. "Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times." Molecular Biology and Evolution 22(7):1561–1568 (2005). doi:10.1093/molbev/msi145 https://academic.oup.com/mbe/article/22/7/1561/974191

topic rate-gap · camp mainstream · type model · access paywalled · region whole-genome · calibration internal · direction mixed

What it measured. Fitted an exponential decay curve to published avian and primate mtDNA rate estimates plotted against the age of the calibration used, and tested competing explanations for the decline. Conclusion: "purifying selection offers the most convincing explanation," with sequencing error ruled out and mutational saturation judged unlikely at these depths.

Rate as published / normalised. Its avian protein-coding phylogenetic baseline is 0.5% per Myr per lineage. (a) 5.0 × 10^-9 per site per year. (b) 2.1 × 10^-3 mutations per 16,569 bp per 25-year generation.

Why it matters here. This is the paper that made "time-dependent rates" a named phenomenon, and its headline conclusion — "it is invalid to extrapolate molecular rates of change across different evolutionary timescales" — is a mainstream statement that cuts at exactly the move the young-earth clock argument makes. It is tagged mixed because the same sentence also concedes that recent divergence times have been systematically overestimated.

Library. key: ho-2005. File: papers/ho-2005_time-dependency-molecular-rate-estimates.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Ho et al. 2007 — the bison reslice

Ho SYW, Shapiro B, Phillips MJ, Cooper A, Drummond AJ. "Evidence for Time Dependency of Molecular Rate Estimates." Systematic Biology 56(3):515–522 (2007). doi:10.1080/10635150701435401 https://pubmed.ncbi.nlm.nih.gov/17562475/ (no abstract in PubMed; the OUP PDF link returns a landing page only)

topic rate-gap · camp mainstream · type model · access paywalled · region control-region · calibration radiocarbon-tip · direction mixed

What it measured. Reanalysed Shapiro's radiocarbon-dated bison sequences in sliding windows of sample age, reporting a higher rate from the 0–10,000 yr BP window than from wider windows. Not read — full text could not be obtained, and everything here is secondhand.

Why it matters here. It is the direct counter to the bison result above, so the article cannot avoid it. But both independent characterisations available are sceptical: Millar et al. 2008 write that the sliding-window rate distributions "are, however, not statistically different from each other and the likely effects of small sample sizes remain unresolved," and Peterson & Masel say it confirms elevated rates exist "without support for an exponentially decaying rate curve." Treat as contested and obtain the paper before relying on it.

Adélie penguins — the best-controlled clock test in existence

Millar CD, Dodd A, Anderson J, Gibb GC, Ritchie PA, Baroni C, Woodhams MD, Hendy MD, Lambert DM. "Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic." PLoS Genetics 4(10):e1000209 (2008). doi:10.1371/journal.pgen.1000209 https://pmc.ncbi.nlm.nih.gov/articles/PMC2546446/

topic other-species · camp mainstream · type measurement · access OA · region HVR1 · calibration radiocarbon-tip · direction undercuts

What it measured. Both halves of the clock, on the same 344 bp of the same species. The pedigree half: 508 families of parents plus chicks from Cape Bird, Ross Island, 2,618 individuals from 711 families, generation time 6.46 years, 62 heteroplasmies detected. The ancient-DNA half: 66 additional radiocarbon-dated bones up to 37,000 years old, analysed by MCMC over 20 million steps. Full text read.

Rate as published / normalised. Raw heteroplasmy rate μ₀ = 54.9 mutations/site/Myr (95% CI 41.2–68.6). Corrected mutation rate μ = 0.55/site/Myr (95% HPD 0.29–0.88) after modelling heteroplasmy persistence through a germline bottleneck estimated independently at N = 31.3 (fuller model, median 38.3). Ancient-DNA substitution rate k = 0.86 substitutions/site/Myr (95% HPD 0.53–1.17). (a) 5.5 × 10^-7, 8.6 × 10^-7, and 5.49 × 10^-5 per site per year respectively. (b) 0.23, 0.36 and 22.7 mutations per 16,569 bp per 25-year generation — ‡ HVR-only rates, human generation used for unit comparison only.

Why it matters here. This is the strongest single result in this whole block and it cuts against the young-earth reading. Short-term and long-term rates in the same 344 bp "cannot be distinguished statistically (p = 0.13)," and the test had power to reject agreement over a 2.6-fold range. The apparent 100-fold inflation was entirely an artefact of counting every heteroplasmy as a fixed mutation — and the authors say so about human work explicitly: "Howell estimated a mutation rate for the control region of the human mitochondrial genome assuming that each heteroplasmy contributes to the actual mutation rate. According to our model, this assumption over-estimates μ by a factor of 5." Two honest caveats: μ = 0.55 is model-corrected, not a raw count, and nobody has replicated the experiment; and Millar et al. never address that their own group's 6,400-year-calibrated rate is 2.7x their 37,600-year-calibrated rate in the same species.

Library. key: millar-2008. File: papers/millar-2008_adelie-penguin-mutation-evolutionary-rates.pdf (and .md beside it). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Drosophila mutation accumulation — mutation rate is not substitution rate

Haag-Liautard C, Coffey N, Houle D, Lynch M, Charlesworth B, Keightley PD. "Direct Estimation of the Mitochondrial DNA Mutation Rate in Drosophila melanogaster." PLoS Biology 6(8):e204 (2008). doi:10.1371/journal.pbio.0060204 https://pmc.ncbi.nlm.nih.gov/articles/PMC2517619/

topic other-species · camp mainstream · type measurement · access OA · region whole-genome · calibration none · direction mixed

What it measured. Screened 11,428 bp (59%) of the Drosophila mitochondrial genome across mutation-accumulation lines that had run for an average of 262 and 187 generations, detecting 28 point mutations and 8 indels. Full text read. The spectrum is extreme: of 24 single-nucleotide mutations in coding DNA, all but one were nonsynonymous, and 23 of 28 were major-strand G→A.

Rate as published / normalised. As published: 6.2 × 10^-8 per site per fly generation for single-nucleotide mutations (1.6 × 10^-8 for indels), and 4.2 × 10^-7 for major-strand G→A alone versus 1.2 × 10^-8 for all other changes. (a) 2.3 × 10^-6 per site per year assuming a ~10-day laboratory generation. (b) 1.0 × 10^-3 mutations per 16,569 bp per fly generation — a unit normalisation only; Drosophila mtDNA is ~19.5 kb and its generation is days, not 25 years.

Why it matters here. This is the cleanest demonstration anywhere that a high measured mutation rate does not imply a young divergence. The fly mitochondrial genome mutates ~10x faster per site per generation than the nuclear genome — yet the synonymous divergence between D. melanogaster and D. simulans is about 0.12 in both genomes. The excess mutations are nonsynonymous G→A changes that selection removes, so they never become substitutions. Running the 6.2 × 10^-8 rate back to date the melanogaster/simulans split would give an answer ~10x too young, and no one on either side defends that. The authors also address humans directly and conclude that mutation bias "is not therefore a strong candidate to explain the difference between pedigree and phylogenetic mtDNA mutation rate estimates."

Library. key: haag-liautard-2008b. File: papers/haag-liautard-2008b_mtdna-mutation-rate-drosophila.xml (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Penguin mitogenomes — synonymous sites do not speed up

Subramanian S, Denver DR, Millar CD, Heupink T, Aschrafi A, Emslie SD, Baroni C, Lambert DM. "High mitogenomic evolutionary rates and time dependency." Trends in Genetics 25(11):482–486 (2009). doi:10.1016/j.tig.2009.09.005 https://pubmed.ncbi.nlm.nih.gov/19836098/

topic selection · camp mainstream · type measurement · access paywalled · region whole-genome · calibration radiocarbon-tip · direction mixed

What it measured. Complete modern and ancient Adélie penguin mitochondrial genomes, the oldest up to 44,000 years, partitioned by site class. Overall rates came out two to six times greater than phylogenetic estimates; the rate at constrained sites — nonsynonymous positions and RNAs — varied more than twofold between shallow and deep nodes; but "the rate of evolution at synonymous sites remains the same." Abstract only.

Rate as published / normalised. Molak & Ho's Table S1 enters this study's mitogenome coding rate as 2.1 × 10^-8 substitutions/site/year at a 44,000-year calibration. (a) 2.1 × 10^-8 per site per year. (b) 8.7 × 10^-3 mutations per 16,569 bp per 25-year generation.

Why it matters here. This is the mechanistic discriminator between the two explanations of the rate gap. If short-term rates look fast because the true elapsed time is short, every site class inflates equally. If they look fast because purifying selection has not yet removed transient deleterious variants, only constrained sites inflate — which is what was observed. The young-earth reading predicts the first pattern and the data show the second.

Library. key: subramanian-2009, was: subramanian-2009b. File: papers/subramanian-2009_high-mitogenomic-evolutionary-rates-time-dependency.abstract.txt. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Peterson & Masel — the inflation, quantified from standard theory

Peterson GI, Masel J. "Quantitative Prediction of Molecular Clock and Ka/Ks at Short Timescales." Molecular Biology and Evolution 26(11):2595–2603 (2009). doi:10.1093/molbev/msp175 https://pmc.ncbi.nlm.nih.gov/articles/PMC2912466/

topic rate-gap · camp mainstream · type model · access OA · region coding · calibration internal · direction mixed

What it measured. Modelled the decay of the apparent divergence rate over time from segregating ancestral polymorphism, neutral and slightly deleterious, and fitted a single parameter — effective population size — to hominid mitochondrial data. Full text read. Result: Ne ≈ 300 for this process; "the observed divergence rate will decay to 2-fold elevation in approximately Ne generations… Assuming a generation time of 28 years, this corresponds to 8,400 years," and 3 Ne generations (~25,200 years) to reach 1.25x the long-term rate.

Rate as published / normalised. Their long-term baseline is the accepted 0.02 substitutions/site/Myr for mammalian and avian protein-coding mtDNA. (a) 2.0 × 10^-8 per site per year. (b) 8.3 × 10^-3 mutations per 16,569 bp per 25-year generation. They report the human control-region pedigree literature as spanning 0.32 to 2.5 substitutions/site/Myr — a 16x to 125x span against that coding baseline, though note those are different regions.

Why it matters here. It concedes the young-earth side's narrow point and denies the broad one, with numbers. The pedigree rate genuinely is the right rate for the last few thousand years — which is why it works on Icelandic pedigrees and Romanov genealogies. What the model forbids is running that rate back 150,000 years, because the elevation is predicted to decay on a timescale of ~8,400 years. It is a mainstream, single-parameter, non-ad-hoc account of exactly the gap the young-earth argument depends on.

Library. key: peterson-2009. File: papers/peterson-2009_quantitative-prediction-molecular-clock-short-timescales.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Ho et al. 2011 — the same inflation in nuclear DNA, bacteria and viruses

Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. "Time-dependent rates of molecular evolution." Molecular Ecology 20(15):3087–3101 (2011). doi:10.1111/j.1365-294X.2011.05178.x Wiley page returns HTTP 403; working copy at https://www.robertlanfear.com/publications/assets/Ho_etal_MolEcol_2011.pdf

topic rate-gap · camp mainstream · type review · access OA · region whole-genome · calibration internal · direction undercuts

What it measured. A review, not a measurement. Its Box 2 collects pedigree-versus-phylogenetic rate comparisons for nuclear genomes — Caenorhabditis, Drosophila, human — and states that "these estimates are far higher than substitution rates estimated in phylogenetic analyses." Box 3 reports that in Vibrio cholerae a heterochronously calibrated substitution rate came out 100-fold above the standard assumed rate.

Why it matters here. This is the hardest single fact in this block for the young-earth reading. The pedigree-versus-phylogenetic gap is not a mitochondrial peculiarity; it is the same size in nuclear DNA. If the gap proves a young mitochondrial MRCA, the identical argument on nuclear data proves a recent human–chimpanzee nuclear divergence — a conclusion the young-earth position rejects outright. Applied consistently, the argument does not deliver a young Eve.

Library. key: ho-2011. File: papers/ho-2011_time-dependent-rates-molecular-evolution.pdf (and .md beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

About eighty founding cows

Bollongino R, Burger J, Powell A, Mashkour M, Vigne J-D, Thomas MG. "Modern taurine cattle descended from small number of near-eastern founders." Molecular Biology and Evolution 29(9):2101–2104 (2012). doi:10.1093/molbev/mss092 https://pubmed.ncbi.nlm.nih.gov/22422765/

topic other-species · camp mainstream · type measurement · access paywalled · region control-region · calibration radiocarbon-tip · direction undercuts

What it measured. Sequenced mtDNA from 15 Neolithic to Iron Age Iranian domestic cattle and, with modern data, used serial coalescent simulation and approximate Bayesian computation to estimate "that around 80 female aurochs were initially domesticated." Abstract read via PubMed.

Rate as published / normalised. The rate derived from this dataset, as entered in Molak & Ho's Table S1, is 4.5 × 10^-7 substitutions/site/year for non-coding cattle mtDNA at an 8,451-year calibration. (a) 4.5 × 10^-7 per site per year. (b) 0.19 mutations per 16,569 bp per 25-year generation — ‡ non-coding rate, human generation for comparison only.

Why it matters here. It closes the cattle argument. Domestication sampled about eighty already-diverse wild females, so cattle mtDNA diversity was never expected to coalesce at the domestication date, and its failure to do so is not a clock failure. What the paper does contribute is a genuine same-taxon rate comparison: 4.5 × 10^-7 at an 8,451-year calibration against fossil-calibrated aurochs control-region rates of 2.0–2.4 × 10^-8 at 8.5–9 Myr — a ~20x gap in the same lineage and marker.

Library. key: bollongino-2012. The library has a YAML record only; no file is stored. Cited by EVE2 only. EVE2 register: cited in current draft. Verified: abstract (read via PubMed, per the entry above and EVE2's register). The first draft cites this paper nowhere, so its cattle argument rested on Molak & Ho's table alone; EVE2's footnote supplies the 80-founder result and the 23-452 interval. The citation line above drops an "a" from the title; the title as published, in EVE2 and in the library record, is "Modern taurine cattle descended from a small number of near-eastern founders."

A 50-generation chicken pedigree

Alexander M, Ho SYW, Molak M, Barnett R, Carlborg Ö, Dorshorst B, Honaker C, Besnier F, Wahlberg P, Dobney K, Siegel P, Andersson L, Larson G. "Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance." Biology Letters 11:20150561 (2015). doi:10.1098/rsbl.2015.0561 https://pmc.ncbi.nlm.nih.gov/articles/PMC4650172/

topic other-species · camp mainstream · type measurement · access OA · region whole-genome · calibration n/a · direction supports

What it measured. Whole mitochondrial genomes across a documented Virginia selection-line chicken pedigree: two novel mutations over 47 years and 385 transmissions in the ~16,000 bp genome. Full text read. The study also reports evidence of paternal mtDNA inheritance.

Rate as published / normalised. As published: 3.13 × 10^-7 mutations/site/year (95% CI 3.75 × 10^-8–1.12 × 10^-6). (a) 3.13 × 10^-7 per site per year. (b) 0.13 mutations per 16,569 bp per 25-year generation; at the chicken's own one-year generation it is 5.2 × 10^-3 per genome per generation. Against Ho et al. 2005's avian protein-coding phylogenetic rate this is 63x; against the conventional 2%/Myr avian standard, 31x.

Why it matters here. This is a whole-genome, documented-pedigree, domestic-animal measurement — no calibration assumption anywhere in it — and it comes out 31–63x the fossil-calibrated rate. It is the cleanest supports entry in this block. The honesty flag is severe, though: the estimate rests on two observed mutations and the 95% interval spans a factor of thirty. The direction survives at the lower bound (still 4–8x the fossil rate); the magnitude does not.

Molak & Ho — 239 rate estimates across the animal kingdom

Molak M, Ho SYW. "Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA." PeerJ 3:e821 (2015). doi:10.7717/peerj.821 https://pmc.ncbi.nlm.nih.gov/articles/PMC4358697/

topic rate-gap · camp mainstream · type compilation · access OA · region whole-genome · calibration internal · direction mixed

What it measured. Compiled 239 published metazoan mtDNA rate estimates with the age of the calibration used for each, and regressed rate against calibration age. Full text read and the supplementary spreadsheet parsed directly. Rates span 1.78 × 10^-10 (mammoth cytochrome b and tRNAs) to 2.31 × 10^-6 (Adélie penguin control region, Lambert et al. 2002) substitutions/site/year; calibration ages span 6 years to 4 × 10⁸ years. Log-log slopes: −0.28 for coding markers (p = 1.6 × 10^-12, R² = 0.24) and −0.43 for non-coding (p = 1.4 × 10^-12, R² = 0.60), with significant negative relationships in mammals, birds, reptiles and insects separately. A randomisation test was run against the obvious self-correlation objection and the regressions survived.

Rate as published / normalised. Range as published: 1.78 × 10^-10 to 2.31 × 10^-6 substitutions/site/year — already in per-site-per-year units. (b) 7.4 × 10^-5 to 0.96 mutations per 16,569 bp per 25-year generation across that whole range. Same-taxon same-marker ratios worth quoting from its Table S1: brown bear control region 9.1x (120 kyr aDNA vs 550 kyr fossil); cattle/aurochs control region ~20x; human control region 10.1x (pedigree vs 5.8 Myr fossil).

Why it matters here. It settles that the rate gap is real, quantitative and completely general — the −0.43 non-coding slope predicts a ~190x rate ratio between a 20-year and a 5-Myr calibration, the same order as the human pedigree-versus-phylogenetic gap. That generality is exactly why it cannot be used as evidence that humans are young: the same slope appears in insects and reptiles. The authors attribute it to purifying selection giving way to mutational saturation. Two cautions: the compilation genuinely conflicts with Millar et al.'s penguin null result, and its human coding-region rows are not monotonic in calibration age (1.57 × 10^-8 at a 40 kyr calibration against 2.83 × 10^-8 at 6 Myr), so individual cells should be checked against the underlying papers before publication.

Library. key: molak-2015. Folder: data/molak-2015_prolonged-decay-metazoan-mtdna/. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Tomkins, "Genetic Clocks Verify Recent Creation"

Tomkins JP. "Genetic Clocks Verify Recent Creation." Institute for Creation Research, 30 November 2015. https://www.icr.org/article/genetic-clocks-verify-recent-creation

topic yec-clock · camp creationist · type popular · access web · region control-region · calibration n/a · direction supports

What it measured. Nothing; a web commentary. Page read in full.

Why it matters here. It is the most-circulated modern version of the quote trail and it contains four distinct problems worth naming: it truncates the Parsons sentence exactly at the comma before "clearly incompatible with the known age of modern humans," without an ellipsis; it truncates the Gibbons paragraph exactly before "No one thinks that's the case"; it interpolates the gloss "[most recent common ancestor, or the first human woman]" into a quotation, which the mtDNA MRCA is not on any model — Answers in Genesis' own current position says so explicitly; and it misstates the FBI guideline change as driven by "faster mutation rates pointing to mitochondrial Eve about 6,000 years ago," when the guideline is about single-nucleotide mismatches between two specimens. Genesis Apologetics and The Creation Club repeat the same text with the gloss reduced to the bare "[the first human woman]."

Konrad et al. — the C. elegans rate revised down

Konrad A, Thompson O, Waterston RH, Moerman DG, Keightley PD, Bergthorsson U, Katju V. "Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size." Molecular Biology and Evolution 34(6):1319–1334 (2017). doi:10.1093/molbev/msx051 https://pmc.ncbi.nlm.nih.gov/articles/PMC5850408/

topic other-species · camp mainstream · type measurement · access OA · region whole-genome · calibration none · direction undercuts

What it measured. Re-measured the C. elegans mitochondrial base-substitution rate from mutation-accumulation lines maintained at different population sizes, obtaining μ_bs = 4.32 × 10^-8 per nucleotide site per generation, "a greater than two-fold difference" from Denver et al. 2000. Across five multicellular eukaryotes — D. melanogaster, D. pulex, C. elegans, C. briggsae, P. pacificus — the spontaneous mtDNA base-substitution rate "varies less than three-fold with a range of 3.75–9.7 × 10^-8." Read through the WebFetch summariser rather than raw text; quotations should be re-verified against the PDF before publication.

Rate as published / normalised. As published: 4.32 × 10^-8 per site per generation. (a) 3.9 × 10^-6 per site per year at the ~4-day laboratory generation. (b) 7.2 × 10^-4 mutations per 16,569 bp per nematode generation — normalisation only.

Why it matters here. The "two orders of magnitude" C. elegans headline that anchors part of the young-earth cross-species argument has come down by a factor of 3.7 with better methods, and the direct metazoan mtDNA mutation rate now clusters tightly at 4–10 × 10^-8 per site per generation. Jeanson 2013's conversions use the older Denver figure and laboratory culture generation times.

Library. key: konrad-2017. File: papers/konrad-2017_mtdna-mutation-rate-elegans-ma-lines.html (and .txt beside it). used: no. Considered and not used: catalogued for the record, and no claim in any of the three drafts rests on it. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

The derivative and fabricated citations

Multiple web sources, 2010–2024: Thomas B, "Mother of All Humans Lived 6,000 Years Ago," ICR (2010) https://www.icr.org/content/mother-all-humans-lived-6000-years-ago · beautiesofthetruth.org, "Science supports the Bible: The Mother of Us All – Mitochondrial Eve" https://beautiesofthetruth.org/science-supports-the-bible-the-mother-of-us-all-mitochondrial-eve/ · teotwministries.com, "Reevaluating Mutation Rates…", 6 February 2024 https://www.teotwministries.com/post/reevaluating-mutation-rates-the-misinterpretation-of-haplogroup-science-in-ancestral-studies

topic critique · camp creationist · type blog · access web · region control-region · calibration n/a · direction supports

What it measured. Nothing; all three were read in full and audited against the Gibbons reprint and the Parsons abstract.

Why it matters here. Because the audit's result is not uniform and the article should say so. Brian Thomas (ICR, 2010) quotes it fairly — he prints all four sentences including "No one thinks that's the case," and then argues, legitimately, that the disclaimer itself shows the dating is assumption-driven. That argument deserves engagement on its merits rather than a quotation complaint, though his headline overstates his body text. beautiesofthetruth.org puts four errors inside quotation marks, including "lived 10,000 to 200,000 years ago" where Gibbons wrote "100,000 to 200,000," but does keep the sentence "Other studies have not found such rapid mutation rates," which most omit. teotwministries.com prints a quotation-marked sentence attributed to Parsons that appears nowhere in the paper and then disclaims it in a parenthesis as "(Paraphrased from Parsons et al., 1997)" — a clean, citable example of a fabricated quote. Worth noting the other end: Jeanson's 2015 whole-mitogenome clock paper cites neither Gibbons nor Parsons, working instead from primary trio-sequencing studies, so the 1998 news story is a popular-level artefact rather than the load-bearing evidence for the modern young-earth argument.

Library. key: thomas-2010j, was: thomas-2010k. The library has a YAML record only; no file is stored. Cited by the first draft and EVE2. EVE2 register: cited in current draft.

Sources added in the 2026-10-27 merge

These entries cover sources that the second and third drafts cite, or that the merge plan names, and that the first draft's catalogue lacked. Two other sources the plan names were already catalogued above under other headings and only gained a key: the entry headed "Endicott & Ho 2008" and the entry headed "About eighty founding cows" (Bollongino et al. 2012). Each entry below carries a verified tag: full means the stored text was read for the point made, abstract means only the abstract was, and citation means only the bibliographic record was.

Subramanian & Lambert 2011, constrained sites vary and synonymous sites do not

Subramanian S, Lambert DM. "Time Dependency of Molecular Evolutionary Rates? Yes and No." Genome Biology and Evolution 3:1324–1328 (2011). doi:10.1093/gbe/evr108 PMC3236606 https://pmc.ncbi.nlm.nih.gov/articles/PMC3236606/

topic rate-gap · camp mainstream · type measurement · access OA · region whole-genome · calibration archaeological and ape-divergence · direction undercuts · verified full

What it measured. Mitochondrial genomes of 216 humans (83 European H1, 33 Australian, and 100 spread over 20 major haplogroups), plus the Neanderthal and the chimpanzee, split into synonymous sites, nonsynonymous sites, RNA genes and the D-loop. Each site class gets a rate at five calibration depths: 18 kyr (European H1), 45 kyr (Australians), 150 kyr (humans), 500 kyr (human–Neanderthal) and 6 Myr (human–chimpanzee).

Rate as published / normalised. Table 1 gives rates in 10^-8 substitutions per site per year. At synonymous sites the European H1 rate is 5.1 and the human–chimpanzee rate is 4.3, a ratio of 1.2. At nonsynonymous sites the same two rates are 2.2 and 0.2, a ratio of 10.8. The RNA and D-loop ratios are 3.8 and 2.8. Not converted to a per-genome figure, because each rate belongs to one site class.

Why it matters here. It is the human-primate test of where the time dependence lives. The abstract reports "an order of magnitude variation in the evolutionary rates at constrained sites (including nonsynonymous sites, D-loop, and RNA) and virtually an identical rate of evolution at synonymous sites, independent of the timescales over which they were estimated." That fits short-window rates being inflated by variants selection has not yet removed, and does not fit a clock that simply runs faster now. It is a separate 2011 test from the 2009 Adélie-penguin paper, so its site-class result should not be credited to that earlier source. Two cautions: the calibrations are archaeological and ape-divergence dates a young-earth reader will dispute, and EVE2's footnote adds that the ratios depend on the sequence model and on the correction for repeated changes at one site.

Library. key: subramanian-2011b, was: subramanian-2011c. File: papers/subramanian-2011b_time-dependency-molecular-rates.xml (and .md beside it). The library also holds a YAML-only record under the retired key. Cited by EVE2 only. EVE2 register: considered, not used in current draft. EVE2's index.md nevertheless cites it.

Trifunovic et al. 2004, a proofreading-deficient PolgA mutator mouse

Trifunovic A, Wredenberg A, Falkenberg M, Spelbrink JN, Rovio AT, Bruder CE, Bohlooly-Y M, Gidlöf S, Oldfors A, Wibom R, Törnell J, Jacobs HT, Larsson N-G. "Premature ageing in mice expressing defective mitochondrial DNA polymerase." Nature 429(6990):417–423 (2004). doi:10.1038/nature02517 PMID 15164064

topic archaics · camp mainstream · type measurement · access paywalled · region n/a (somatic mouse mtDNA) · calibration none · direction mixed · verified abstract

What it measured. Knock-in mice whose nucleus-encoded catalytic subunit of the mitochondrial polymerase, PolgA, lacks proofreading. The abstract says the mice "develop an mtDNA mutator phenotype with a threefold to fivefold increase in the levels of point mutations, as well as increased amounts of deleted mtDNA."

Why it matters here. It shows that a change in polymerase fidelity can alter mutation production in a mammal, which is the mechanism behind the proposal that a polymerase or repair defect sped up the Neanderthal and Denisovan lineages. It is also the limit of that suggestion: the measurement is somatic, in an engineered mouse, and says nothing about a human or archaic germline multiplier, inherited fixed substitutions, or a mitochondrial Eve date. The full-text wording and page locators were not obtained.

Library. key: trifunovic-2004. File: papers/trifunovic-2004_defective-mtdna-polymerase.txt (the PubMed XML abstract only). Cited by the first draft, EVE2 and ASTRA. EVE2 register: cited in current draft.

Farnum, Nurminen & Kaguni 2014, 136 POLG mutations mapped into functional modules

Farnum GA, Nurminen A, Kaguni LS. "Mapping 136 pathogenic mutations into functional modules in human DNA polymerase γ establishes predictive genotype-phenotype correlations for the complete spectrum of POLG syndromes." Biochimica et Biophysica Acta (2014). PMC4687743 https://pmc.ncbi.nlm.nih.gov/articles/PMC4687743/

topic archaics · camp mainstream · type review · access OA · region n/a (protein) · calibration none · direction mixed · verified citation

What it measured. ASTRA's footnote describes it as sorting 136 pathogenic POLG mutations into structural and biochemical functional modules that extend beyond the catalytic residues. It did not test L580P. Volume and pages are not recorded in the library, and the merge did not read the paper.

Why it matters here. ASTRA cites it for the point that a change outside the exonuclease active site does not rule out an effect on copying fidelity, which is why the first draft's "wrong part of the enzyme" argument against L580P does not hold. Merge plan section 4 item 9 says to check this paper against its text before citing it for the spacer-domain point, and that check has not been made.

Library. key: farnum-2014. The library has a YAML record only; no file is stored. Cited by ASTRA only. EVE2 register: no entry.

Qian, Ziehr & Johnson 2015, Alpers mutations tested in purified POLG

Qian Y, Ziehr JL, Johnson KA. "Alpers disease mutations in human DNA polymerase gamma cause catalytic defects in mitochondrial DNA replication by distinct mechanisms." Frontiers in Genetics 6:135 (published 9 April 2015). doi:10.3389/fgene.2015.00135

topic archaics · camp mainstream · type measurement · access OA · region n/a (protein) · calibration none · direction background · verified citation

What it measured. ASTRA's footnote says it used purified-enzyme and reconstructed-replication experiments to assess polymerization and fidelity for the Alpers-disease mutations S305R and P1073L. It did not test L580P. The footnote gave no authors; the author list and date here come from the Crossref record of the DOI, fetched as bytes on 2026-10-27, and the paper itself was not read.

Why it matters here. It shows that a purified-enzyme assay has been run for other POLG mutations, which is the kind of test that could settle whether L580P changes fidelity. Such a test still needs a specialist laboratory, and none has been published for L580P.

Library. key: polg-purified-assay. The library has a YAML record only; no file is stored, and the record lists no authors. Cited by ASTRA only. EVE2 register: no entry. The merged article's footnote for this paper is named qian-2015 (authors Yufeng Qian, Jessica L. Ziehr and Kenneth A. Johnson), while the library record is polg-purified-assay; one of the two should be renamed so that they agree.

Kaliszewska et al. 2015, yeast model of POLG variants

Kaliszewska M, et al. "Yeast model analysis of novel polymerase gamma variants found in patients with autosomal recessive mitochondrial disease." Human Genetics 134:951–966 (2015). doi:10.1007/s00439-015-1578-x

topic archaics · camp mainstream · type measurement · access paywalled · region n/a (protein) · calibration none · direction background · verified citation

What it measured. ASTRA's footnote says it tested human POLG-equivalent variants from patients with autosomal recessive mitochondrial disease in the yeast gene MIP1. The full author list is not recorded in the library, and the merge did not read the paper.

Why it matters here. It is an example of a yeast route to testing POLG variants. A yeast result cannot be assumed to transfer quantitatively to human germline transmission, so it would give a lead on L580P, not an answer.

Library. key: kaliszewska-2015. The library has a YAML record only; no file is stored. Cited by ASTRA only. EVE2 register: no entry.

UniProt P54098, the human POLG annotation

UniProt Consortium. "DPOG1_HUMAN (POLG), DNA polymerase subunit gamma-1," reviewed UniProtKB/Swiss-Prot entry P54098, entry version 238 (updated 2 September 2026). https://rest.uniprot.org/uniprotkb/P54098.txt

topic archaics · camp unaffiliated · type database · access database · region n/a (protein) · calibration none · direction mixed · verified full

What it measured. Nothing new; it is a curated annotation. The stored record (1,239 amino acids) puts the exonuclease active site at Asp198, and lists natural variants between residues 570 and 600 that include R574W, R579W and P587L, each tied to disease.

Why it matters here. The first draft used it to say that residues 570 to 600 sit beside working parts of the enzyme and carry only recessive disease variants. That "recessive" reading is withdrawn: ASTRA's text reports that dominant POLG alleles exist, and a nearby disease variant does not fix the phenotype of the Neanderthal change (merge plan section 4 item 9). The record still shows that L580P lies outside the annotated exonuclease motifs, and it does not show that L580P changes polymerase fidelity.

Library. key: uniprot-polg. The footnote key's own record is YAML only; the stored text is under the library key uniprot-2026 as data/uniprot-2026_polg-human.txt. Cited by the first draft and EVE2. EVE2 register: cited in current draft, under the key uniprot-2026.

POLG Foundation, a proposed variant-to-function map of POLG

The POLG Foundation. "A variant-to-function map of POLG via deep mutational scanning." Project page, undated. https://polgfoundation.org/research-projects/a-variant-to-function-map-of-polg-via-deep-mutational-scanning/ (checked 12 September 2026 according to the library record)

topic archaics · camp unaffiliated · type popular · access web · region n/a (protein) · calibration none · direction background · verified citation

What it measured. Nothing; it is a project page for a proposed deep mutational scan of POLG. ASTRA's footnote says the page names Vamsi Mootha and Anna Kotrys at the Broad Institute as leads, proposes a respiratory-function screen of POLG variants, states an aim, and publishes neither an L580P result nor a polymerase-fidelity measurement. The page was not archived, and the merge did not re-read it.

Why it matters here. ASTRA cites it to show that no published functional result for L580P was found, and that even a respiratory-function score would not directly measure DNA-copying fidelity. A reader who wants to check that claim has to look at the live page, since no copy is stored.

Library. key: polg-variant-map. The library has a YAML record only; no file is stored. Cited by ASTRA only. EVE2 register: no entry.

Sawyer et al. 2015, Denisova 4 and 8

Sawyer S, Renaud G, Viola B, Hublin J-J, Gansauge M-T, Shunkov MV, Derevianko AP, Pääbo S, Meyer M, et al. "Nuclear and mitochondrial DNA sequences from two Denisovan individuals." Proceedings of the National Academy of Sciences 112(51):15696–15700 (2015). doi:10.1073/pnas.1519905112 PMC4697428

topic archaics · camp mainstream · type measurement · access OA · region whole-genome · calibration none · direction background · verified full

What it measured. Nuclear DNA from the Denisovan molar Denisova 4, and mitochondrial and nuclear DNA from another molar, Denisova 8, both from Denisova Cave. The abstract says that "the mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period," and that nuclear diversity among the three Denisovans is comparable to that among six Neanderthals but lower than among present-day humans.

Why it matters here. It identifies the Denisovan specimens whose mitochondrial sequences enter archaic panels and shows that they span a long interval. It gives relative age information only, not a direct date for every sequence in the seven-record Denisovan panel, so it cannot anchor the arithmetic the way a dated layer can.

Library. key: sawyer-2015. File: papers/sawyer-2015_two-denisovan-individuals.xml. used: no. Considered and not used (EVE2 register's disposition note, kept as written): checked for the identity and context of Denisova 4 and 8 in the research report research/combined-root-anchor.md; that paper's relative age information does not provide direct individual dates for every sequence in the seven-record panel; the main article's explicit dated example uses Brown's Denisova-19 context instead; retained as supporting research, not used as a separate main-article citation. Cited by none of the first draft, EVE2 or ASTRA. EVE2 register: considered, not used in current draft.

Brown et al. 2021, Denisova 19 to 21 and the dated layer 15

Brown S, Massilani D, Kozlikin MB, Shunkov MV, Derevianko AP, et al. "The earliest Denisovans and their cultural adaptation." Nature Ecology & Evolution 6(1):28–35 (2021, issue 2022). doi:10.1038/s41559-021-01581-2 PMC7612221 https://pmc.ncbi.nlm.nih.gov/articles/PMC7612221/

topic archaics · camp mainstream · type measurement · access OA (author manuscript) · region whole-genome · calibration archaeological (Bayesian model of optical ages) · direction mixed · verified full

What it measured. Collagen fingerprinting identified five hominin bones in Denisova Cave (Denisova 17 to 21). Mitochondrial genomes were reconstructed for four of them. Denisova 17 is a Neanderthal, with a molecular age of about 134 ka (95% HPD 94 to 177 ka). Denisova 19, 20 and 21 carry Denisovan mtDNA and all come from layer 15 of the East Chamber, which the paper dates to about 200 ka (205 to 192 ka at 68.2%, 217 to 187 ka at 95.4%) by Bayesian modelling of existing optical ages. The mtDNAs of Denisova 19 and 21 are identical, which the authors say indicates they may belong to the same individual or be maternal relatives, and Denisova 20 differs from them by 4 substitutions.

Why it matters here. It supplies a dated context for Denisovan tips, which the archaic arithmetic needs. The date is a layer age from a mainstream luminescence chronology, not a direct radiocarbon date of any individual, and a young-earth reader will dispute it, so it should not be presented as a universal fossil calibration. The identical 19 and 21 sequences are a warning not to count them as two independent maternal tips.

Library. key: brown-2021. Folder: papers/brown-2021_earliest-denisovans-cultural-adaptation/ (primary.xml). Cited by EVE2 only. EVE2 register: cited in current draft.

Gupta R, Durham TJ, Chau G, Kanai M, Uddin MM, Lu W, Argentieri MA, Karczewski KJ, Howrigan D, Natarajan P, Zhou W, Neale BM, Mootha VK. "Mechanism of age-related accumulation of mtDNA mutations in human blood." Nature 656:140–148 (6 August 2026). doi:10.1038/s41586-026-10569-6 Open access, CC BY.

topic heteroplasmy · camp mainstream · type measurement · access OA · region whole-genome · calibration none · direction background · verified full

What it measured. Blood mtDNA from whole-genome sequence data of approximately 750,000 people in the UK Biobank and All of Us (736,038 individuals in the called set, 19,051,526 variants from 620,385 individuals after quality control). The abstract reports that mtDNA single-nucleotide variants "accumulate sharply at age 60 years, occur at low levels of heteroplasmy, exhibit little evidence of positive selection and are likely to be predominantly neutral," and that their spectrum "does not reflect oxidative lesions, as is commonly invoked, but is more consistent with mtDNA replication errors." High burden is associated with clonal haematopoiesis.

Why it matters here. It measures detectable somatic heteroplasmy in blood and the growth of existing mutant cell clones, not the maternal germline mutation rate, a transmission rate, or the age of mitochondrial Eve. It is a scope-control source: it limits what blood data can say about the clock, and the merged article uses it only for the difference between mutation production and age-related clonal detection.

Library. key: gupta-2026. File: papers/gupta-2026_age-related-mtdna-blood.pdf (and .md beside it). Cited by EVE2 only. EVE2 register: cited in current draft (listed under "New draft source added after the original register").

Jeanson 2017b, the last round of the Frello exchange

Nathaniel T. Jeanson. "Response to 'Reply to Response to On the Creationist View on mtDNA'." Answers Research Journal 10:239–241 (published 4 October 2017). https://answersresearchjournal.org/creationist-view-mtdna-second-response/

topic archaics · camp creationist · type review · access OA · region n/a · calibration none · direction mixed · verified full

What it measured. Nothing new on the sequences. It answers Frello's reply (ARJ 10:237–238), which changed the subject to venue and to experts in ancient DNA, and spends its length on whether the critic is an expert and where creationists should publish, with no new technical material. Its own summary of the exchange is "Since Frello has refused to respond to the errors that I documented, I conclude that he has conceded the points that I raised."

Why it matters here. It shows how the exchange ended: the technical question of Neanderthal internal diversity is neither answered nor settled, and neither of the last two rounds closes it. The first draft cited this page only as a claim filed under the Jeanson 2017 footnote (slug 2017-final), which also gave the wrong parent. Verified from the stored page text (the quoted sentence is in the first paragraph after the abstract).

Library. key: jeanson-2017b. File: web/jeanson-2017b_second-response-frello-mtdna.html (and .txt beside it). Cited by the first draft and EVE2, under the misfiled claim slug and with no source footnote of its own. EVE2 register: no separate entry (the register's Jeanson 2017 entry covers the first response only).

UNSCEAR 2008 Annex B, cosmic-ray dose rises with altitude

United Nations Scientific Committee on the Effects of Atomic Radiation. Sources and Effects of Ionizing Radiation, UNSCEAR 2008 Report, Volume I, Annex B: Exposures of the public and workers from various sources of radiation. United Nations, New York (2010). ISBN 978-92-1-142274-0 https://www.unscear.org/unscear/en/publications/2008_1.html

topic method · camp mainstream · type book · access OA · region n/a · calibration none · direction background · verified full

What it measured. Dose rates from natural and artificial radiation. In the stored PDF, paragraph 62 (printed page 232) says that "the ionizing component is, however, strongly dependent on altitude. For the same latitude, a variation by a factor of about 4 in the absorbed dose rate in free air was measured in China between sea level and 4,000 m altitude in Tibet," and paragraph 61 adopts an average dose rate in free air at sea level of 31 nGy/h.

Why it matters here. EVE2 uses it for the altitude dose figures behind its comparison with Baishiya Cave on the Tibetan Plateau, while noting that dose quantities and environments are not perfectly interchangeable. The first draft's footnote unscear-2008c credits UNSCEAR for numbers that this project calculated from UNSCEAR's formulas; where a figure is UNSCEAR's own it should cite this record, and the calculation should be a note- footnote of ours.

Library. key: unscear-2008. File: papers/unscear-2008_annex-b-exposures-public-workers.pdf (and .md beside it). Cited by EVE2 only. EVE2 register: no entry.

Library housekeeping

Defects in the source library found while merging, recorded here and not in the article. Keys are written as plain text so that the review tooling does not read them as sources.

The library key endicott-2008b holds Henn et al. 2009 (Molecular Biology and Evolution 26(1):217–230, "Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates"), not Endicott & Ho 2008 (American Journal of Human Genetics 82(4):895–902). Endicott & Ho is endicott-2008, whose PMC page was stored on 2026-10-27. Three keys (endicott-2008b, henn-2009 and henn-2009b) therefore hold one paper.
Two Rebolledo-Jaramillo 2014 PDFs with different md5 sums sit in the library, under rebolledo-jaramillo-2014 (4cd043dc...) and rebolledo-jaramillo-2014b (90085113...). The merged key is the b copy. The YAML-only records rebolledo-2014 and rebolledo-2014b name the same paper. Consolidation is pending.
jeanson-2015g has no title ("[title not given in the old footnote]") and no file. The footnote it served joined two papers of Answers Research Journal 8: the whole-genome clock paper (jeanson-2015, with html and supplement as jeanson-2015f) and the linear-speciation paper (jeanson-2015e). The record should be retired.
humphreys-2006b is the Creation Ministries International version of "Evidence for a Young World" (27 January 2006, twelve items, no mitochondrial sentence). The page the articles quote, with item 8 and its Gibbons footnote, is humphreys-2005d (ICR, Acts & Facts 34(6), June 2005). The YAML-only record humphreys_evidence-young-world has no year in its key.
carter-2023c is Carter's "Robert Carter gets everything wrong?", which the library dates 2021-06-07. The year in the key does not match the page.
unscear-2008c holds this project's own calculation, filed with the author "UNSCEAR". The cosmic-dose workings belong in a note footnote, and the report itself is unscear-2008. The YAML-only record unscear-2008b ("2008 report") belongs to a different article and carries an unchecked 2.4 mGy figure.
The 2026-10-13 conversion gave each of the three drafts its own record for the same work, so many works sit under two to five keys: avise-1984 (also b, c), barinaga-1992 (b, c), brotherton-2013 (b, c), carter-2025c (d, e), cavelier-2000 (b), fan-2008 (b, c), floros-2018 (b, c), fu-2013 (b to f), henn-2009 and henn-2009b, ingman-2000 (b to d, with c holding the PDF and text), jeanson-2015 (b, c, d), kim-2013 (b), lambert-2002 (b), laricchia-2022 (b), meyer-2012b and meyer-2012d, oversti-2022 (b to e, with d holding the PDF and text), parsons-1997 (b, c), richards-2001 (b, c, d), rieux-2014 (b to d, with d holding the PDF, text and supplement), santos-2005 (b), subramanian-2009 (b), subramanian-2011b and subramanian-2011c, thomas-2010j and thomas-2010k, vandervalk-2021 (b), zhang-2020 (b). The merged key for each is the one in the merge plan's section 5.2 D table, with humphreys-2005d replacing humphreys-2006b as item 4 explains.
Three POLG records carry thin metadata: polg-purified-assay has no authors (the authors are Qian Y, Ziehr JL and Johnson KA, from the Crossref record of the DOI), kaliszewska-2015 lists "Kaliszewska; et al." only, and polg-variant-map lists the organisation as author with no date. None has a file.
The footnote key uniprot-polg is a YAML-only record, while the stored UniProt text sits under uniprot-2026.
The keys macandrew and humphreys have no year; the plain "surname-year" form is not available for them without the page's date.

Checks made during the merge (2026-10-27)

Rebolledo-Jaramillo 2014, the 51. The paper says "Having observed 51 germ-line point heteroplasmies among 39 mothers, we estimated μ0 as 51/(39 × 16,569 bp) = 7.9 × 10−5 heteroplasmies per transmission per site" (stored text of rebolledo-jaramillo-2014b), with a detection threshold of θ = 0.01. The 51 are observed heteroplasmies above a 1% threshold, used as μ0. They include inherited variation and are not 51 new mutations, so the first draft's "51/39 = 1.31 new heteroplasmies" and the roughly 870-year Eve age built on it should go, and the merged article follows EVE2 (plan section 4 item 12).
Rieux 2014, Table S13. The stored table image (sources/papers/rieux-2014d_improved-calibration-human-mitochondrial-clock/rieux-2014-table-s13-individual-tip-rates.jpeg) lists 21 tip calibrations aged 2,535 to 39,464 years. The 21 mean rates, read off the image, have mean 2.391 × 10^-8, standard deviation 0.077 (a coefficient of variation of 3.2%) and a highest-to-lowest ratio of 1.11, and these figures were recomputed here. The first draft's other count, thirteen genomes aged 5,200 to 39,500 years, is not a figure in that table; use 21 and 2,535 to 39,464. The 21 runs share sequences, tree and model, so they are not 21 independent measurements.
Neanderthal and chimpanzee distances. Recomputed from research/data/archaic-pairwise.npz and the sequence inventory beside it. The 36 Neanderthal mitogenomes sit 169 to 209 substitutions from the human reference (mean 198.3; the lowest is Goyet Q57-1, the highest Les Cottes Z4-1514). Vindija 33.16 is 206 in the merge's own check; the recomputation here puts the panel's Vindija sequence (the same sequence as Vindija 33.16, according to research/archaic-hominin-mtdna.md) at 205, a one-substitution difference left unsettled. The 166 chimpanzees average 214.14 pairwise differences, with a maximum of 402, and 45.7% of chimpanzee pairs differ by more than 206.
Parsons 1997. The PubMed abstract (PMID 9090380, fetched as bytes) verifies "Ten substitutions were observed, resulting in an empirical rate of 1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than estimates derived from phylogenetic analyses." It does not contain the "~6,500 y.a." sentence, which is in the body of the paper; Eric's notes give it as "would result in an average age of the mtDNA MRCA of only ~6,500 y.a." at p. 364. The full text was not obtained (nature.com is paywalled and scholar.archive.org returned a challenge), so that sentence stays in quarantine.md and the entries for Parsons above rest on the abstract.
Humphreys. The stored CMI page (2006) has no mitochondrial text; item 8 with the mitochondrial Eve sentence is in the ICR page of June 2005, stored as humphreys-2005d. The merge plan's table names humphreys-2006b and should be corrected.
Jeanson, "DNA sequences from fossils are too degraded". The sentence is in the whole-genome clock paper (ARJ 8:375–378, stored PDF text), cited there to Criswell 2009, Jeanson 2015 and Thomas and Tomkins 2014. The first draft's footnote jeanson-2015g paired it with a sentence from a different paper (jeanson-2015e); the page of the first sentence, 377 or 378, is not pinned.
Jeanson 2017b. The stored page is "Response to 'Reply to Response to On the Creationist View on mtDNA'," ARJ 10:239–241, published 4 October 2017, and it contains the sentence "Since Frello has refused to respond to the errors that I documented, I conclude that he has conceded the points that I raised." It is the round the first draft's 2017-final claim describes.
Endicott & Ho 2008. Table 3 of the stored PMC text gives the internal-calibration concatenated row as 108 (82–134) kyr, matching the first entry for the paper above.
Authors of Frontiers in Genetics 6:135 (2015). Qian Y, Ziehr JL and Johnson KA, issued 2015-04-09, from the Crossref record of DOI 10.3389/fgene.2015.00135 fetched as JSON bytes with curl. The paper itself was not read.

Sources first entered here at the merge (2026-10-27)

These sources are cited by the merged article but had no entry in any of the three drafts' reviews. Each carries its library key.

Aneli 2024, Functional characterization of archaic-specific variants in mitonuclea

Aneli, Serena; Ceccatelli Berti, Camilla; Gilea, Alexandru Ionut; et al. "Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae." Human Molecular Genetics 33:1152–1163 (2024). doi:10.1093/hmg/ddae057

camp mainstream · type experiment · direction complicates · verified citation (no file in the library; details as the earlier drafts recorded them)

What it found, and why it matters here. A 2024 study that tested archaic-specific gene variants in yeast, rather than only predicting their effects. The authors searched mitochondria-related nuclear genes for non-synonymous, fixed, archaic-derived variants that are rare or absent in living humans, expressed the archaic and human versions in yeast, and measured the result. The article uses it as the nearest existing experiment, since nobody has yet run POLG Leu580Pro through a yeast assay. A yeast assay of an archaic YARS2 variant; the precedent for testing POLG Leu580Pro in a model organism.

Library. key: aneli-2024. YAML record only. Cited in the merged article.

Carter 2009, The Neandertal mitochondrial genome does not support evolution

Carter, Robert W.. "The Neandertal mitochondrial genome does not support evolution." Journal of Creation 23:40–43 (2009).

camp creationist · type model · direction supports · verified full

What it found, and why it matters here. A young-earth critique of Green's 2008 Neanderthal mitochondrial genome paper, and the most substantial young-earth treatment of this question in print. It is the source of every mechanism discussed above except patriarchal drive. It also gives Green's figures correctly, a year before the web article that miscounted them as 210: Carter's fullest treatment of Neanderthal mitochondrial DNA; source of the "harsh environment" and polymerase-fidelity proposals the article prices.

Library. key: carter-2009. Files: carter-2009_neandertal-mtdna-not-evolution.md, carter-2009_neandertal-mtdna-not-evolution.pdf. Cited in the merged article.

Castellano 2014, Patterns of coding variation in the complete exomes of three Neanderta

Castellano, Sergi; Parra, Genís; Sánchez-Quinto, Federico A.; et al. "Patterns of coding variation in the complete exomes of three Neandertals." PNAS 111:6666–6671 (2014). doi:10.1073/pnas.1405138111

camp mainstream · type measurement · direction undercuts · verified full

What it found, and why it matters here. A 2014 study that captured the protein-coding DNA of 17,367 genes from two Neandertals, one from El Sidrón Cave in Spain and one from Vindija Cave in Croatia, and compared it with the genome of a Neandertal from southern Siberia. It is the source of the amino-acid change catalogues the article uses. The article uses it for those catalogues, and for the enrichment test that its authors ran on them. The catalogue of amino-acid changes fixed on the Neanderthal and modern lineages, used for the 206-gene repair scan.

Library. key: castellano-2014. Files: castellano-2014_neandertal-exomes-coding-variation.md, castellano-2014_neandertal-exomes-coding-variation.pdf. Cited in the merged article.

Criswell 2009, Neandertal DNA and Modern Humans

Criswell, Daniel. "Neandertal DNA and Modern Humans." Creation Research Society Quarterly 45:246–254 (2009).

camp creationist · type measurement · direction complicates · verified full

What it found, and why it matters here. A detailed young-earth case, by a Ph.D. at the Institute for Creation Research, that the gap between Neanderthal and modern mtDNA is post-mortem damage. Habermehl 2010 and Carter 2009 both defer to it, and it is worth reading for its candour about its own statistics. Its evidence base is nine hypervariable-region-1 sequences and two hypervariable-region-2 sequences published up to 2007, PCR-amplified, from before enzymatic damage removal was routine. The article uses it as the older young-earth position on the archaic gap. Criswell's damage argument on nine short Neanderthal HVR1 sequences; re-run in the article at 154 times his data.

Library. key: criswell-2009. Files: criswell-2009_neandertal-dna-and-modern-humans.md, criswell-2009_neandertal-dna-and-modern-humans.pdf. Cited in the merged article.

Fotiadou 2026, Archaeogenetic insights into the demographic history of Late Neanderth

Fotiadou, Charoula M.; Pedersen, Jesper Borre; Rougier, Hélène; et al. "Archaeogenetic insights into the demographic history of Late Neanderthals." PNAS 123:e2520565123 (2026). doi:10.1073/pnas.2520565123

camp mainstream · type model · direction complicates · verified full

What it found, and why it matters here. A 2026 study that sequenced ten new Neanderthal mitochondrial genomes from six archaeological sites in Belgium, France, Germany and Serbia, and analysed them alongside 49 published ones. The authors date the diversification of the Late Neanderthal lineage to about 65 ka, and still use the modern human coding-region rate of 1.57 × 10^-8 per site per year. The article uses it for two sentences in which the authors concede the limits of their own dating, and quotes them as the other side's words. A recent dated Neanderthal mitochondrial analysis; it still assumes the human rate, the point the article concedes to the young-earth side.

Library. key: fotiadou-2026. Files: fotiadou-2026_late-neanderthal-demography.md, fotiadou-2026_late-neanderthal-demography.pdf. Cited in the merged article.

Cserháti 2024, Ancient DNA Shows Neanderthals and Denisovans Descending from Noah in

Cserháti, Matthew. "Ancient DNA Shows Neanderthals and Denisovans Descending from Noah in the Line of Ham." Answers Research Journal 17:43–61 (2024-01-31).

camp creationist · type model · direction supports · verified full

What it found, and why it matters here. A creationist paper that rebuilds the Neanderthal and Denisovan Y-chromosome tree on a "Noah" root instead of a root shared with chimpanzees, and explains the long branches with high mutation rates. The journal's disclaimer says the views are those of the writer, not necessarily those of the editor or Answers in Genesis, and the paper says its conclusions remain tenuous because only a few Neanderthal Y chromosomes have been sequenced. The article uses it because it is the current Answers in Genesis position on archaic hominin DNA: re-root the archaic Y-chromosome tree on a "Noah root," and explain the residual divergence by hypermutation. Marshall Jordan's ARJ paper proposing archaic hypermutation from a post-Flood repair defect. Earlier drafts named Matthew Cserhati as author; the stored page says "by Marshall Jordan" and thanks Cserhati in its acknowledgments.

Library. key: jordan-2024. Files: jordan-2024_neanderthals-denisovans-line-ham.html, jordan-2024_neanderthals-denisovans-line-ham.txt. Cited in the merged article.

Kennedy, Scott R.; Salk, Jesse J.; Schmitt, Michael W.; Loeb, Lawrence A.. "Ultra-Sensitive Sequencing Reveals an Age-Related Increase in Somatic Mitochondrial Mutations That Are Inconsistent with Oxidative Damage." PLoS Genetics 9:e1003794 (2013). doi:10.1371/journal.pgen.1003794

camp mainstream · type measurement · direction undercuts · verified full

What it found, and why it matters here. A laboratory method paper that applied Duplex Sequencing, which detects one mutation among more than 10⁷ wild-type molecules, to human brain mitochondrial DNA from young and old donors. The authors note that the mutation spectrum matches what is seen in population and phylogenetic data. The article uses it to show that the chemistry of oxidative damage is not what generates mitochondrial mutations, and the point is about which chemistry makes mitochondrial point mutations, not about the germline rate, since this is somatic brain tissue. Duplex sequencing of brain mtDNA across ages showing the spectrum is not oxidative; used against the altitude rescue.

Library. key: kennedy-2013. Files: kennedy-2013_ultrasensitive-mtdna-somatic-mutations.md, kennedy-2013_ultrasensitive-mtdna-somatic-mutations.pdf. Cited in the merged article.

Kimura 1968, Evolutionary rate at the molecular level

Kimura, Motoo. "Evolutionary rate at the molecular level." Nature 217:624–626 (1968-02-17). doi:10.1038/217624a0

camp mainstream · type model · direction complicates · verified citation

What it found, and why it matters here. A short theoretical paper in which Motoo Kimura estimated how fast DNA changes in mammals, from amino-acid differences in proteins such as haemoglobin, and found that one nucleotide pair is substituted in the population about every two years. He argued that a rate this fast could be sustained only if most such changes are almost neutral, meaning that selection neither helps nor harms them. The neutral result the article invokes is standard: for a strictly neutral variant, the long-run substitution rate equals the mutation rate independent of population size, because the N new mutants per generation and the 1/N fixation probability cancel. Robert Carter is right to insist on this against critics who answer the young-earth argument by gesturing at selection in general. The article uses it for this point, and says that mitochondrial sites are measurably not neutral, so the fixing rate can be measured directly anyway. The neutral-theory identity (substitution rate equals mutation rate) that Carter correctly invokes.

Library. key: kimura-1968. Files: kimura-1968_evolutionary-rate-at-molecular-level.md, kimura-1968_evolutionary-rate-at-molecular-level.pdf. Cited in the merged article.

Laricchia 2022, Mitochondrial DNA variation across 56,434 individuals in gnomAD

Laricchia, Kristen M.; et al. "Mitochondrial DNA variation across 56,434 individuals in gnomAD." Genome Research 32:569–582 (2022).

camp mainstream · type measurement · direction undercuts · verified citation (no file in the library; details as the earlier drafts recorded them)

What it found, and why it matters here. A survey of mitochondrial DNA in 56,434 people from the gnomAD genome database, counting which possible changes actually occur: about 55% of synonymous (silent) changes, about 10% of missense and RNA changes, and about 1% of stop-gain changes. The same data show 7,776 of 16,569 bases invariant (the same in everyone surveyed), 46.9%, not the 84.1% figure circulating in creationist literature, which is an artifact of an 827-sequence sample. The article uses it to show that protein-changing variants are still being removed from healthy living people. gnomAD mitochondrial variation in 56,434 people: missense and stop-gain variants are depleted, evidence of ongoing purifying selection in healthy people.

Library. key: laricchia-2022. YAML record only. Cited in the merged article.

Mendez 2013, An African American paternal lineage adds an extremely ancient root to

Mendez, Fernando L.; et al. "An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree." American Journal of Human Genetics 92:454–459 (2013). doi:10.1016/j.ajhg.2013.02.002

camp mainstream · type measurement · direction complicates · verified full

What it found, and why it matters here. A genetic study that sequenced about 240 kb of the Y chromosome, the male sex chromosome, from one African American man, a lineage that had not been sampled before. The sample came from a large database of consumer DNA tests of African Americans, and several authors work for Family Tree DNA, a commercial genealogy company. One lineage found in one man moved the estimated age of the Y-chromosome common ancestor from about 138,000 to 338,000 years (95% confidence interval 237,000–581,000 years), and the article cites it only to show that a single-locus common ancestor depends on the sample as much as on history. The A00 Y lineage, which deepened the male tree; used for the point that ancestors move as lineages are found or lost.

Library. key: mendez-2013. Files: mendez-2013_african-american-paternal-lineage-a00.html, mendez-2013_african-american-paternal-lineage-a00.md. Cited in the merged article.

Meyer 2012, A high-coverage genome sequence from an archaic Denisovan individual

Meyer, Matthias; Kircher, Martin; Gansauge, Marie-Theres; et al. "A high-coverage genome sequence from an archaic Denisovan individual." Science 338:222–226 (2012). doi:10.1126/science.1224344

camp mainstream · type measurement · direction undercuts · verified full

What it found, and why it matters here. A genome-sequencing paper that read a Denisovan genome at 30-fold coverage, meaning each position was read about 30 times, from a finger bone found in Denisova Cave in the Altai Mountains of southern Siberia. It compared the number of changes on the Denisovan and present-day human branches since their split from the human-chimpanzee ancestor, over roughly three billion base pairs, sharing no assumptions with any mitochondrial analysis. The article uses it as an independent nuclear-genome check that the archaic branch is shorter than ours, not longer. The high-coverage Denisovan genome; its nuclear branch is 1.16% shorter than ours, the opposite of hypermutation.

Library. key: meyer-2012b. Files: meyer-2012b_denisovan-high-coverage-genome.md, meyer-2012b_denisovan-high-coverage-genome.pdf. Cited in the merged article.

Ross 2013, Germline mitochondrial DNA mutations aggravate ageing and can impair b

Ross, Jaime M.; Stewart, James B.; Hagström, Erik; Brené, Stefan; Mourier, Arnaud; Coppotelli, Giuseppe; Freyer, Christoph; Lagouge, Marie; Hoffer, Barry J.; Olson, Lars; Larsson, Nils-Göran. "Germline mitochondrial DNA mutations aggravate ageing and can impair brain development." Nature 501:412–415 (2013). doi:10.1038/nature12474

camp mainstream · type experiment · direction complicates · verified abstract

What it found, and why it matters here. A mouse study from the laboratory that built the mutator mouse, breeding lines in which mitochondrial mutations made by a proofreading-dead polymerase were passed down the maternal line. The inherited mutations caused mild ageing in mice with normal nuclear genes and, in mice carrying one mutator copy, fertility that fell over the generations. The article uses it for the price a mutator burst would carry. Inherited mutator mutations aggravate ageing and reduce fertility in mice; the cost of a post-Flood mutator burst. Full text not read.

Library. key: ross-2013. Files: ross-2013_germline-mtdna-mutations-aggravate-ageing.abstract.txt. Cited in the merged article.

Sanchez-Contreras 2021, A replication-linked mutational gradient drives somatic mutation accum

Sanchez-Contreras, Monica; et al. "A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA." Nucleic Acids Research 49:11103–11118 (2021). doi:10.1093/nar/gkab901

camp mainstream · type measurement · direction undercuts · verified full

What it found, and why it matters here. A laboratory study that used Duplex Sequencing to map naturally occurring somatic mutations across mouse and human mitochondrial DNA. It shows that the normal mitochondrial mutation pattern looks like a damage pattern because it is one, produced in living cells rather than after death. The article uses it for that reason. The mitochondrial mutation spectrum in living tissue; used in the damage discussion.

Library. key: sanchez-contreras-2021. Files: sanchez-contreras-2021_replication-linked-mutational-gradient-mtdna.html, sanchez-contreras-2021_replication-linked-mutational-gradient-mtdna.md. Cited in the merged article.

van der Valk 2021, Million-year-old DNA sheds light on the genomic history of mammoths

van der Valk, Tom; et al. "Million-year-old DNA sheds light on the genomic history of mammoths." Nature 591:265–269 (2021). doi:10.1038/s41586-021-03224-9

camp mainstream · type measurement · direction complicates · verified citation (no file in the library; details as the earlier drafts recorded them)

What it found, and why it matters here. A study of the genomic history of mammoths from DNA more than a million years old. The same footnote also cites Kjær, Kurt H., et al., "A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA," Nature 612(7939):283-291 (2022), doi:10.1038/s41586-022-05453-y. The article uses these against the claim that DNA cannot survive tens of thousands of years, a reasonable inference from 1996 kinetic calculations that is no longer one. Million-year-old mammoth DNA; used against the claim that DNA cannot survive.

Library. key: vandervalk-2021. YAML record only. Cited in the merged article.

Wang 2023, Human generation times across the past 250,000 years

Wang, Richard J.; Al-Saffar, Samer I.; Rogers, Jeffrey; Hahn, Matthew W.. "Human generation times across the past 250,000 years." Science Advances 9:eabm7047 (2023). doi:10.1126/sciadv.abm7047

camp mainstream · type measurement · direction undercuts · verified full

What it found, and why it matters here. A genetics study that estimated how long human generations have been over the past 250,000 years, from the spectrum of de novo mutations (the new changes that appear in a child's DNA and are not inherited). Its African generation intervals are longer, not shorter, than those of East Asian, European and South Asian populations, which is the reverse of what a short-generation argument requires. The article uses it to answer a 2016 argument that needs fifteen-year generations. Generation intervals from the mutation spectrum: 26.9 years sex-averaged, 23.2 female, 30.7 male; used against 15-year maternal generations.

Library. key: wang-2023. Files: wang-2023_human-generation-times-250kyr.md, wang-2023_human-generation-times-250kyr.pdf, wang-2023_human-generation-times-250kyr.pdf.md. Cited in the merged article.

Wood 2013, Mitochondrial DNA Analysis of Three Terrestrial Mammal Baramins (Equid

Wood, Todd Charles. "Mitochondrial DNA Analysis of Three Terrestrial Mammal Baramins (Equidae, Felidae, and Canidae) Implies an Accelerated Mutation Rate Near the Time of the Flood." Proceedings of the Seventh International Conference on Creationism (2013).

camp creationist · type model · direction supports · verified full

What it found, and why it matters here. A creationist analysis by a leading young-earth biologist of published mitochondrial DNA from living and Pleistocene horses, cats and dogs, with the ancient specimens' radiocarbon dates recalibrated into a post-Flood chronology. It concludes that mutation ran fast just after the Flood and has been low since, and it tests and rejects the alternative that heteroplasmy on the Ark explains the diversity. The article uses it as the young-earth burst model in its author's own words. Todd Wood's mtDNA analysis of horses, cats and dogs, inferring a post-Flood burst of mutation and ruling out "relict" Ark heteroplasmy. Read in the stored PDF (no printed folios; quotations from the Discussion, PDF pp. 7-8). Found by the young-age research for the merge.

Library. key: wood-2013. Files: wood-2013_mtdna-three-baramins.md, wood-2013_mtdna-three-baramins.pdf. Cited in the merged article.

Xia 2024, Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Ca

Xia, Huan; et al. "Middle and Late Pleistocene Denisovan subsistence at Baishiya Karst Cave." Nature 632:108–113 (2024). doi:10.1038/s41586-024-07612-9

camp mainstream · type measurement · direction complicates · verified full

What it found, and why it matters here. A research paper on Denisovan subsistence at Baishiya Karst Cave, a cave on the northeastern Tibetan Plateau. Its Denisovan identifications rest on protein evidence and sediment: the new Xiahe 2 rib was assigned to the Denisovan lineage by shotgun proteomic analysis, and the Denisovan presence at the cave rests on the mandible, the rib and sedimentary mitochondrial DNA from layers 2, 3, 4 and 7. The article uses it for the cave's elevation and to show that the high-altitude Denisovan material is protein or sediment DNA rather than specimen genomes. Denisovans at Baishiya Karst Cave, 3,280 m, from at least 160,000 years ago; the premise of the altitude rescue.

Library. key: xia-2024. Files: xia-2024_denisovan-subsistence-baishiya.html, xia-2024_denisovan-subsistence-baishiya.md. Cited in the merged article.

Zhang 2020, Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave o

Zhang, Dongju; et al. "Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau." Science 370:584–587 (2020). doi:10.1126/science.abb6320

camp mainstream · type measurement · direction complicates · verified citation (no file in the library; details as the earlier drafts recorded them)

What it found, and why it matters here. A study that recovered Denisovan mitochondrial DNA from cave sediment, not from a bone. The point is what kind of evidence this is: sediment DNA establishes that Denisovans were present, but it is not a specimen genome, so it adds no branch to the mitochondrial phylogeny. The article uses it to show that the high-altitude mitochondrial sequences came from cave sediment. Denisovan mitochondrial DNA from Baishiya Karst Cave sediment; shows the high-altitude Denisovan sequences are sedimentary, not the divergent cave specimens.

Library. key: zhang-2020. YAML record only. Cited in the merged article.

How to read an entry

Field definitions

The founding papers, and the concept

Brown 1980, human mtDNA polymorphism

Anderson et al. 1981, the Cambridge Reference Sequence

Avise, Neigel & Arnold 1984, lineage survivorship

Cann, Stoneking & Wilson 1987, the paper itself

Wainscoat 1987, the News & Views that named her

Tierney 1988, the Newsweek cover story

Vigilant et al. 1991, the sequencing follow-up

Maddison 1991, the African root re-examined

Barinaga 1992, "'African Eve' backers beat a retreat"

Templeton 1992, technical comment

Hedges et al. 1992, technical comment

Maddison, Ruvolo & Swofford 1992, control-region topologies

Wills 1992, comment in Nature

Gibbons 1992, "wounded, but not dead yet"

Templeton 1993, "The 'Eve' Hypotheses"

Stoneking 1994, "In Defense of 'Eve'"

Ayala 1995, "The Myth of Eve"

Ingman et al. 2000, complete mitochondrial genomes

Richards & Macaulay 2001, the gene tree comes of age

Rosenberg & Nordborg 2002, coalescent theory

Rohde, Olson & Chang 2004, recent common ancestry

Hein 2004, News & Views on Rohde et al.

Gitschier 2010, interview with Rebecca Cann

Behar et al. 2012, the "Copernican" reassessment (RSRS)

van Oven & Kayser, PhyloTree Build 17

The pedigree measurements

Howell, Kubacka & Mackey 1996 — the LHON pedigree that started it

Parsons et al. 1997 — the load-bearing citation

Cavelier et al. 2000 — 292 transmissions, zero fixed changes

Sigurðardóttir et al. 2000 — the Icelandic pedigrees

Heyer et al. 2001 — the hot-spot answer

Forster et al. 2002 — natural radioactivity in Kerala

Howell et al. 2003 — the canonical pooled control-region rate

Santos et al. 2005 — the Azores, and the first explicit arising→fixing correction

Stewart et al. 2008 — purifying selection in mutator mice

Fan et al. 2008 — severe mutations eliminated during oogenesis

Goto et al. 2011 — the two-tissue design

Freyer et al. 2012 — heteroplasmy set prenatally, selection one generation later

Madrigal et al. 2012 — deep-rooting Costa Rican pedigrees

Guo et al. 2013 — zero homoplasmic changes at 3,981× depth

Rebolledo-Jaramillo et al. 2014 — the arising-versus-fixing paper

Ding et al. 2015 — SardiNIA, the dataset Jeanson's rate rests on

Floros et al. 2018 — selection inside human primordial germ cells

Wei et al. 2019 — 1,526 transmissions, and the fixation rate measured directly

Zaidi et al. 2019 — 96 families, two tissues, a bottleneck of 10

Arbeithuber et al. 2020 — duplex sequencing of mouse oocytes

Arbeithuber et al. 2025 — duplex sequencing of human oocytes, and the maternal-age effect measured where it counts

Connell et al. 2022 — Norfolk Island, the cleanest whole-genome pedigree rate

Árnadóttir et al. 2024 — deCODE, 116,663 transmissions

Phylogenetic rates, and the ancient-DNA calibration

Horai 1995 — complete hominoid mitochondrial genomes

Ingman 2000 — the 171,500-year figure

Mishmar 2003 — the 1.26 × 10⁻⁸ coding-region rate

Kivisild 2006 — the synonymous clock, and a failure to replicate

Briggs 2007 — the damage model for ancient DNA

Endicott & Ho 2008 — the calibration swap

Ho & Endicott 2008 — what calibration choice does to the peopling of the Americas

Henn 2009 — fourteen archaeological calibrations, one dataset

Soares 2009 — the purifying-selection correction

Endicott, Ho, Metspalu & Stringer 2009 — the review

Briggs 2010 — UDG treatment removes deaminated cytosines

Sawyer 2012 — the authenticity criterion

Behar 2012 — the RSRS, and 57.1 substitutions

Fu 2013 — the founding tip calibration

Brotherton 2013 — the Holocene-only calibration

Rieux 2014 — root, node and tip calibration on one dataset

Fu 2014 — Ust'-Ishim, and a blind prediction of a radiocarbon date

Rohland 2015 — partial-UDG treatment

Posth 2016 — 66 dated tips

Cabrera 2021 — mutation counts against radiocarbon age, no phylogenetic model

Översti & Palo 2022 — 234 dated genomes, non-circular regressions, and lineage rate variation

The young-earth literature

A shrinking date for Eve

Evidence for a Young World, item 8

Mitochondrial Eve and biblical Eve are looking good

Carter 2007 (Nucleic Acids Research)

The "Eve" mitochondrial consensus sequence (ICC 2008)