--- title: "Mitochondrial Eve: original footnote citation map" description: "One compact record for every footnote definition in the original mitochondrial-Eve article, preserving IDs, source identities, links, local keys, locators, and verification or disposition notes." theme: common/themes/berean/theme.php --- # Original footnote citation map This ledger preserves all 173 original footnote-definition IDs. Sub-IDs such as colon-a and colon-b are retained as separate records and point back to their parent source definition. The first sentence is a navigation summary, not a replacement for the original footnote. Long quotations are deliberately not copied here. Before publication, verify wording and locators against source bytes; a WebFetch result is never sufficient. - [^cann-1987] — **verification/access flag; source identity or source-level note.** **Local key:** `cann-1987`; **file:** `web/cann-1987_mitochondrial-dna-and-human-evolution-transcription.html`. **Locator recorded:** 25:31. **Original-note summary:** Cann, Rebecca L.; Stoneking, Mark; and Wilson, Allan C. "Mitochondrial DNA and human evolution." *Nature* 325:31-36 (1 January 1987). doi:10.1038/325031a0 The *Nature* page is paywalled; a full transcription is hosted by Memorial University of Newfoundland at That transcription carries visible… Links: https://www.mun.ca/biology/scarr/Cann,%20et_%20al_%20Mitochondrial%20DNA%20and%20Human%20Evolution.htm. - [^cann-1987:a] — **retained source note; quote/data note; parent [^cann-1987].** **Local key:** `cann-1987`; **file:** `web/cann-1987_mitochondrial-dna-and-human-evolution-transcription.html`. **Original-note summary:** "Mitochondrial DNAs from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa." No URL was recorded in the original definition. - [^cann-1987:b] — **retained source note; quote/data note; parent [^cann-1987].** **Local key:** `cann-1987`; **file:** `web/cann-1987_mitochondrial-dna-and-human-evolution-transcription.html`. **Original-note summary:** "Each purified mtDNA was subjected to high resolution mapping with 12 restriction enzymes… In this way, we identified 467 independent sites, of which 195 were polymorphic (that is, absent in at least one individual). An average of 370 restriction sites per individual were surveyed, representing… No URL was recorded in the original definition. - [^cann-1987:c] — **retained source note; quote/data note; parent [^cann-1987].** **Local key:** `cann-1987`; **file:** `web/cann-1987_mitochondrial-dna-and-human-evolution-transcription.html`. **Original-note summary:** "The minimum-length tree requires fewer changes at 22 of the 93 phylogenetically-informative restriction sites than does the population-specific tree, while the latter tree required fewer changes at four sites… The minimum-length tree is thus favoured by a score of 22 to 4." No URL was recorded in the original definition. - [^cann-1987:d] — **retained source note; quote/data note; parent [^cann-1987].** **Local key:** `cann-1987`; **file:** `web/cann-1987_mitochondrial-dna-and-human-evolution-transcription.html`. **Original-note summary:** "Only two of the 20 Africans in our sample, those bearing mtDNA types I and 81 (see below) were born in sub-Saharan Africa. The other 18 people in this sample are Black Americans, who bear many non-African nuclear genes probably contributed mainly by Caucasian mates." Their defence, in the same… No URL was recorded in the original definition. - [^tierney-1988] — **retained source note; source identity or source-level note.** **Local key:** `tierney-1988`; **file:** `papers/tierney-1988_search-for-adam-and-eve.pdf`. **Original-note summary:** Tierney, John. "The Search for Adam and Eve." *Newsweek* 111 (11 January 1988): 46-52. PDF reprint from a University of Virginia course page: The original UVa URL is dead. Worth noting for accuracy: the misleading part of this famous story was the cover painting — a garden, a serpent, one couple… Links: https://i.b5z.net/i/u/736324/i/IN_SEARCH_FOR_ADAM___EVE.pdf. - [^tierney-1988:a] — **retained source note; quote/data note; parent [^tierney-1988].** **Local key:** `tierney-1988`; **file:** `papers/tierney-1988_search-for-adam-and-eve.pdf`. **Locator recorded:** p. 5 of the PDF: "There must be one lucky mother," Wilson says. **Original-note summary:** Wilson, quoted at p. 5 of the PDF: "There must be one lucky mother," Wilson says. "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. We're saying that in her generation there was some unknown number of… No URL was recorded in the original definition. - [^avise-1984] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Avise, John C.; Neigel, Joseph E.; and Arnold, Jonathan. "Demographic influences on mitochondrial DNA lineage survivorship in animal populations." *Journal of Molecular Evolution* 20(2):99-105 (1984). doi:10.1007/BF02257369 Abstract retrieved via NCBI (PMID 6433037); full text not obtained. From… No URL was recorded in the original definition. - [^barinaga-1992] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Barinaga, Marcia. "'African Eve' backers beat a retreat." *Science* 255(5045):686-687 (7 February 1992). doi:10.1126/science.1738842 Paywalled; cited here for the existence and framing of the retraction, which is not in dispute. The technical papers behind it are Maddison, D. R., "African origin… No URL was recorded in the original definition. - [^richards-2001] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Richards, Martin, and Macaulay, Vincent. "The Mitochondrial Gene Tree Comes of Age." *American Journal of Human Genetics* 68(6):1315-1320 (2001). Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC1226117/. - [^richards-2001:a] — **retained source note; quote/data note; parent [^richards-2001].** **Local key:** —; **file:** —. **Original-note summary:** "The high (average) mutation rate there, in conjunction with considerable variation in rate between sites, means that some sites mutate very fast indeed and that many have mutated many times in the genealogy. The result is that many tree topologies are equally plausible, and there may be no… No URL was recorded in the original definition. - [^mendez-2013] — **retained source note; source identity or source-level note.** **Local key:** `mendez-2013`; **file:** `papers/mendez-2013_african-american-paternal-lineage-a00.html`. **Original-note summary:** 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(3):454-459 (2013). A single previously unsampled lineage, found in one man, moved the estimated Y-chromosome… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC3591855/. - [^parsons-1997] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Parsons, Thomas J., et al. "A high observed substitution rate in the human mitochondrial DNA control region." *Nature Genetics* 15(4):363-368 (April 1997). doi:10.1038/ng0497-363 Paywalled at The quoted passages below were transcribed independently from three sources that agree word for word, one… Links: https://www.nature.com/articles/ng0497-363. - [^parsons-1997:a] — **retained source note; quote/data note; parent [^parsons-1997].** **Local key:** —; **file:** —. **Original-note summary:** "Thus, our observation of the substitution rate, 2.5/site/Myr, is roughly 20-fold higher than would be predicted from phylogenetic analyses. Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the… No URL was recorded in the original definition. - [^parsons-1997:b] — **retained source note; quote/data note; parent [^parsons-1997].** **Local key:** —; **file:** —. **Original-note summary:** "Sequences derived from blood samples detected eight substitutions within 153 generations, whereas sequences derived from cell lines revealed two substitutions in 174 generations." Note for anyone working from Eric's older notes: those record the sequenced region as "~60bp total." The correct… No URL was recorded in the original definition. - [^gibbons-1998] — **retained source note; source identity or source-level note.** **Local key:** `gibbons-1998`; **file:** `papers/gibbons-1998_calibrating-the-mitochondrial-clock.pdf`. **Original-note summary:** Gibbons, Ann. "Calibrating the Mitochondrial Clock." *Science* 279(5347):28-29 (2 January 1998). doi:10.1126/science.279.5347.28 AAAS licensed a verbatim reprint to Cold Spring Harbor's DNA Interactive teacher guide, which carries the AAAS permission line: That reprint is byte-for-byte identical… Links: https://www.dnai.org/teacherguide/pdf/reference_romanovs.pdf. - [^gibbons-1998:a] — **retained source note; quote/data note; parent [^gibbons-1998].** **Local key:** `gibbons-1998`; **file:** `papers/gibbons-1998_calibrating-the-mitochondrial-clock.pdf`. **Original-note summary:** The passage in full, with the paragraph break as printed: "Regardless of the cause, evolutionists are most concerned about the effect of a faster mutation rate. For example, researchers have calculated that 'mitochondrial Eve'--the woman whose mtDNA was ancestral to that in all living… No URL was recorded in the original definition. - [^gibbons-1998:b] — **retained source note; quote/data note; parent [^gibbons-1998].** **Local key:** `gibbons-1998`; **file:** `papers/gibbons-1998_calibrating-the-mitochondrial-clock.pdf`. **Original-note summary:** The article opens on the discrepancy as a live problem: mitochondrial DNA "mutates much more often than previously estimated — as much as 20-fold faster, according to two studies that are causing a stir." It also records the dissent: "'This is all a fuss about nothing,' says Oxford University… No URL was recorded in the original definition. - [^gibbons-1998:c] — **retained source note; quote/data note; parent [^gibbons-1998].** **Local key:** `gibbons-1998`; **file:** `papers/gibbons-1998_calibrating-the-mitochondrial-clock.pdf`. **Original-note summary:** "Therefore, Parsons and Holland, in their work identifying 220 soldiers' remains from World War II to the present, now have new guidelines--adopted by the FBI as well—to account for a faster mutation rate. When a missing soldier's or criminal suspect's mtDNA comes up with a single difference from… No URL was recorded in the original definition. - [^gibbons-1998:d] — **retained source note; quote/data note; parent [^gibbons-1998].** **Local key:** `gibbons-1998`; **file:** `papers/gibbons-1998_calibrating-the-mitochondrial-clock.pdf`. **Original-note summary:** The same article reports the two contemporaneous studies that found no elevated rate — Stoneking's work on Tristan da Cunha and Gyllensten's on 33 Swedish families. Most creationist citations of this source omit them. No URL was recorded in the original definition. - [^budowle-1999] — **retained source note; source identity or source-level note.** **Local key:** `budowle-1999`; **file:** `papers/budowle-1999_mtdna-interpretation-guidelines.pdf`. **Original-note summary:** Budowle, Bruce; DiZinno, Joseph A.; and Wilson, Mark R. (FBI Laboratory Division). "Interpretation Guidelines for Mitochondrial DNA Sequencing." *Proceedings of the Tenth International Symposium on Human Identification* (Promega). "If the questioned and known samples differ by a single… Links: https://www.promega.ro/~/media/files/resources/conference%20proceedings/ishi%2010/oral%20presentations/37budowle.pdf. - [^humphreys] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Humphreys, D. Russell. "Evidence for a Young World." Institute for Creation Research. Item 8 states that measurements "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. No researcher… Links: https://www.icr.org/article/evidence-for-young-world/. - [^bechard] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** p. 28 for the "6,000 to 12,000 years" line, p. **Original-note summary:** Bechard, Paul. "Mutation Rates as a Creationist Clock." University of South Dakota, UHON 390 (2005). The live host refuses TLS; use A student page that caught the Humphreys error in 2005 and gives the only page-level citations within the Gibbons article that could be located: p. 28 for the "6,000… Links: http://web.archive.org/web/20151104025418/http://apps.usd.edu:80/esci/creation/age/content/creationist_clocks/mutations.html. - [^thomas-2010] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Thomas, Brian. "Mother of All Humans Lived 6,000 Years Ago." Institute for Creation Research, 7 September 2010. Quotes the Gibbons passage *including* "No one thinks that's the case." Cited here as the counter-example to the claim that creationists uniformly truncate this source. Links: https://www.icr.org/content/mother-all-humans-lived-6000-years-ago. - [^macandrew] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** MacAndrew, Alec. "Misconceptions Around Mitochondrial Eve." evolutionpages.com. The standard online rebuttal. It states four separate times that Parsons et al. and Howell et al. used RFLP analysis and builds a conclusion on it. They did not; Parsons directly sequenced 610 bp, as Gibbons states… Links: http://www.evolutionpages.com/Mitochondrial%20Eve.htm. - [^ingman-2000] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** table for dating evolutionary events. **Original-note summary:** Ingman, Max; Kaessmann, Henrik; Pääbo, Svante; and Gyllensten, Ulf. "Mitochondrial genome variation and the origin of modern humans." *Nature* 408(6813):708-713 (2000). The landing page is paywalled; the full PDF is free at 53 complete mitochondrial genomes. Mean pairwise difference over the… Links: https://www.nature.com/scitable/content/12631/10.1038_35047064.pdf. - [^ingman-2000:a] — **retained source note; quote/data note; parent [^ingman-2000].** **Local key:** —; **file:** —. **Original-note summary:** "From the mean genetic distance between all the humans and the one chimpanzee sequence (0.17 substitutions per site) and the assumption, based on palaeontological and genetic evidence, of a divergence time between humans and chimpanzees of 5 Myr, the mutation rate (μ) for the mitochondrial… No URL was recorded in the original definition. - [^soares-2009] — **retained source note; source identity or source-level note.** **Local key:** `soares-2009`; **file:** `papers/soares-2009_purifying-selection-mtdna-clock.pdf`. **Original-note summary:** Soares, Pedro, et al. "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock." *American Journal of Human Genetics* 84(6):740-759 (2009). 1.665 × 10^-8^ substitutions per nucleotide per year for the whole molecule — "one mutation every 3624 years." Calibrated on an… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC2694979/. - [^kimura-1968] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** 17:62. **Original-note summary:** Kimura, Motoo. "Evolutionary rate at the molecular level." *Nature* 217:624-626 (1968). The neutral result invoked here 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… No URL was recorded in the original definition. - [^howell-2003:a] — **retained source note; quote/data note; parent [^howell-2003].** **Local key:** —; **file:** —. **Original-note summary:** All verbatim from the paper. The comparison: "A control-region divergence rate of 0.95 mutations/bp/Myr is ∼10 times higher than the phylogenetically derived divergence rates for this region of the human mitochondrial genome. For example, estimates of 0.118 mutations/bp/Myr (Stoneking et al.… No URL was recorded in the original definition. - [^madrigal-2012] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** Table 2, which give 2. **Original-note summary:** Madrigal, Lorena, et al. "High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees." *American Journal of Physical Anthropology* 148(3):327-333 (2012). 19 deep-rooting genealogies, 289 meioses, 7 HVR-I mutations. The paper uses a measured female generation interval of… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC3377850/. - [^madrigal-2012:a] — **retained source note; quote/data note; parent [^madrigal-2012].** **Local key:** —; **file:** —. **Original-note summary:** "Our results confirm that mutation rates observed in pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution. We argue that, until the cause of these discrepancies will be fully understood, both lower estimates (i.e., those derived from phylogenetic… No URL was recorded in the original definition. - [^rebolledo-2014] — **retained source note; source identity or source-level note.** **Local key:** `rebolledo-jaramillo-2014`; **file:** `papers/rebolledo-jaramillo-2014_maternal-age-germline-bottleneck.pdf`. **Original-note summary:** Rebolledo-Jaramillo, Boris, et al. "Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA." *PNAS* 111(43):15474-15479 (2014). 39 mother-child pairs, blood and buccal tissue, 20,000-fold coverage, 1% detection threshold. Germline bottleneck estimated at… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC4217420/. - [^rebolledo-2014:b] — **retained source note; quote/data note; parent [^rebolledo-2014].** **Local key:** `rebolledo-jaramillo-2014`; **file:** `papers/rebolledo-jaramillo-2014_maternal-age-germline-bottleneck.pdf`. **Original-note summary:** Both quotations verified verbatim against the publisher PDF. The first, from the Results: "For mothers we found a significant positive association (P = 0.039, 0.049, and 0.055 for combined, buccal, and blood heteroplasmies, respectively, Poisson regression)… Thus, older mothers accumulate more… No URL was recorded in the original definition. - [^maternal-extrapolation] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** table are the same formula at other ages. **Original-note summary:** **The eighteen-fold is arithmetic done for this article. No source contains it, and two of its three inputs are choices rather than measurements.** The one measured input is Rebolledo's sentence, "the number of point heteroplasmies tripling over 30 y of life."[^rebolledo-2014:b] Poisson… No URL was recorded in the original definition. - [^rebolledo-2014:c] — **verification/access flag; quote/data note; parent [^rebolledo-2014].** **Local key:** `rebolledo-jaramillo-2014`; **file:** `papers/rebolledo-jaramillo-2014_maternal-age-germline-bottleneck.pdf`. **Original-note summary:** Figure 2 of the paper, "Maternal age effect", which is the direct evidence for the distinction drawn here: . The caption, verbatim: "The dependence of the total number of heteroplasmies (blue) in mothers on their age at collection and (red) in children on maternal age at fertilization. Poisson… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC4217420/figure/fig02/. - [^zaidi-2019:a] — **retained source note; quote/data note; parent [^zaidi-2019].** **Local key:** —; **file:** —. **Original-note summary:** Two separate findings, both verbatim. From the Discussion: "We found a significant positive association with maternal age for putative de novo germline mtDNA mutations. This parallels previous studies showing an increase in de novo germline nuclear mutations with paternal and maternal ages." From… No URL was recorded in the original definition. - [^rebolledo-2014:a] — **retained source note; quote/data note; parent [^rebolledo-2014].** **Local key:** `rebolledo-jaramillo-2014`; **file:** `papers/rebolledo-jaramillo-2014_maternal-age-germline-bottleneck.pdf`. **Original-note summary:** The correction stated as an equation: a new mutation is present in one of *N* bottleneck units, so "only 1/N of them will go to fixation, leading to μ = α/N." Their measured arising rate α is 0.143 mutations per genome per generation; their fixing rate μ is 0.0045. Jeanson's published young-earth… No URL was recorded in the original definition. - [^wei-2019] — **verification/access flag; source identity or source-level note.** **Local key:** `wei-2019`; **file:** `papers/wei-2019_germline-selection-mtdna-diversity.pdf`. **Locator recorded:** Table S2 lists 13 de novo D-loop variants, but the rate printed on the same row requires 131. **Original-note summary:** Wei, Wei, et al. "Germline selection shapes human mitochondrial DNA diversity." *Science* 364(6442):eaau6520 (2019). doi:10.1126/science.aau6520 The published version is paywalled; the accepted manuscript with the supplementary tables is free at 1,526 mother-offspring pairs. Note one error in the… Links: https://www.repository.cam.ac.uk/handle/1810/293282. - [^wei-2019:a] — **retained source note; quote/data note; parent [^wei-2019].** **Local key:** `wei-2019`; **file:** `papers/wei-2019_germline-selection-mtdna-diversity.pdf`. **Original-note summary:** 477 de novo heteroplasmies above a 1% threshold across 1,526 transmissions, against only 3 de novo variants above 80% heteroplasmic fraction — two of which the authors attribute to ascertainment bias. A 160-fold to 470-fold gap between mutations appearing and mutations approaching permanence,… No URL was recorded in the original definition. - [^connell-2022] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** 12:68. **Original-note summary:** Connell, Jennifer R.; Benton, Miles C.; Lea, Rodney A.; Sutherland, Heidi G.; Chaseling, Janet; Haupt, Larisa M.; Wright, Kim M.; and Griffiths, Lyn R. "Pedigree derived mutation rate across the entire mitochondrial genome of the Norfolk Island population." *Scientific Reports* 12:6827 (2022).… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC9042960/. - [^connell-2022:a] — **retained source note; quote/data note; parent [^connell-2022].** **Local key:** —; **file:** —. **Locator recorded:** Table 2 gives the fixed-only figure as 0. **Original-note summary:** Abstract, verified verbatim against the publisher PDF at `sources/papers/connell-2022_norfolk-island-mtgenome-mutation-rate.pdf`. The 0.058 figure is the all-inclusive rate; the paper's Table 2 gives the fixed-only figure as 0.013 mutations per site per million years (95% CI 0.003-0.047) in the… No URL was recorded in the original definition. - [^connell-2022:b] — **retained source note; quote/data note; parent [^connell-2022].** **Local key:** —; **file:** —. **Locator recorded:** Table 3's footnote key labels every row by inclusion criterion — footnote e, "All the substitutions (including heteroplasmy) that were detected were considered," is the one attached to every Norfolk Island row. **Original-note summary:** Discussion, "Mutation rate," verbatim. The full sentence pair matters: "In this study, the rates calculated for the NI population included all mutations (heteroplasmy, germline, somatic). In contrast, for the HVI region, Santos et al. reported a mutation rate of 0.074 mutations/site/Myr … however… No URL was recorded in the original definition. - [^connell-2022:c] — **retained source note; quote/data note; parent [^connell-2022].** **Local key:** —; **file:** —. **Locator recorded:** Table 2 gives the Norfolk Island hypervariable-region-1 rate as 1. **Original-note summary:** Discussion, verbatim, and the arithmetic checks: Table 2 gives the Norfolk Island hypervariable-region-1 rate as 1.201 and Table 3 gives Santos's as 0.074, so 1.201 ÷ 0.074 = 16.2. Santos et al. 2005 is a pedigree study of Azorean families,[^santos-2005] not a phylogenetic analysis. A coincidence… No URL was recorded in the original definition. - [^connell-2022:d] — **retained source note; quote/data note; parent [^connell-2022].** **Local key:** —; **file:** —. **Locator recorded:** Table 3, standardised to a 25-year generation, contains: Norfolk Island 0. **Original-note summary:** Conclusion, verbatim. Their complete-mtGenome block in Table 3, standardised to a 25-year generation, contains: Norfolk Island 0.063, Fu 2013 (ancient DNA) 0.019, Rieux 2014 (ancient DNA) 0.021, Brotherton 2013 (ancient DNA) 0.024, and Rebolledo-Jaramillo 2014's fixation rate 0.011 — and no… No URL was recorded in the original definition. - [^guo-2013] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Guo, Yan; Li, Chung-I; Sheng, Quanhu; Winther, Jeanette F.; Cai, Qiuyin; Boice, John D.; and Shyr, Yu. "Very low-level heteroplasmy mtDNA variations are inherited in humans." *Journal of Genetics and Genomics* 40(12):607-615 (2013). 26 mother-child pairs at a median depth of 3,981-fold — more… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC4149221/. - [^ding-2015] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Ding, Jun; Sidore, Carlo; Butler, Thomas J.; et al. "Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools." *PLoS Genetics* 11(7):e1005306 (2015). CC-BY. This is the study Jeanson's whole-genome rate rests on. It… Links: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005306. - [^ding-2015:a] — **retained source note; quote/data note; parent [^ding-2015].** **Local key:** —; **file:** —. **Original-note summary:** Mitochondrial genome copy number per lymphocyte: mean 111.5, standard deviation 25.0, range 50-350. Estimates for other tissues run into the thousands. No URL was recorded in the original definition. - [^ding-2015:b] — **verification/access flag; quote/data note; parent [^ding-2015].** **Local key:** —; **file:** —. **Locator recorded:** Table 1). **Original-note summary:** "Children and their mothers share essentially all homoplasmies. We observed 7,273 homoplasmic sites in 333 children, among which 7,238 (99.5%) were also observed in their mothers (Table 1)." Their Table 1 also gives 7,266 homoplasmic variants in the mothers. The young-earth rate is built by… No URL was recorded in the original definition. - [^jeanson-2015b] — **verification/access flag; source identity or source-level note.** **Local key:** `jeanson-2015`; **file:** `papers/jeanson-2015_mtdna-clock-whole-genome.pdf`. **Locator recorded:** 8:37. **Original-note summary:** Jeanson, Nathaniel T. "A Young-Earth Creation Human Mitochondrial DNA 'Clock': Whole Mitochondrial Genome Mutation Rate Confirms D-Loop Results." *Answers Research Journal* 8:375-378 (2015). Supplemental Table 1, with formulas intact, at Every figure in his Table 1 reproduces exactly when… Links: https://answersresearchjournal.org/mitochondrial-genome-mutation-rate/; https://assets.answersresearchjournal.org/doc/articles/arj/v8/mitochondrial-genome-mutation-rate-supplemental-table.xlsx. - [^jeanson-2015b:a] — **retained source note; quote/data note; parent [^jeanson-2015b].** **Local key:** `jeanson-2015`; **file:** `papers/jeanson-2015_mtdna-clock-whole-genome.pdf`. **Locator recorded:** Table 1 pools Guo et al. **Original-note summary:** Table 1 pools Guo et al. 2013 (26 pedigrees, 0 mutations), Rebolledo-Jaramillo et al. 2014 (39 pedigrees, 0), and Ding et al. 2015 (333 pedigrees, 63): 63 / 6,594,462 bp-generations = 9.55 × 10^-6^ per base pair per generation, or 1.58 × 10^-1^ per genome per generation, 95% CI 0.119-0.197. On the… No URL was recorded in the original definition. - [^jeanson-2015b:b] — **retained source note; quote/data note; parent [^jeanson-2015b].** **Local key:** `jeanson-2015`; **file:** `papers/jeanson-2015_mtdna-clock-whole-genome.pdf`. **Original-note summary:** "The only remaining caveat to the present results is whether the mutation rate reported in Ding et al. (2015) represents a germline rate rather than a somatic mutation rate. To confirm germline transmission in the future, the DNA sequences from at least three successive generations must be… No URL was recorded in the original definition. - [^jeanson-2016] — **retained source note; source identity or source-level note.** **Local key:** `jeanson-2016`; **file:** `papers/jeanson-2016_generation-time-out-of-africa.pdf`. **Locator recorded:** 9:12. **Original-note summary:** Jeanson, Nathaniel T. "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). Note his own account of how the headline figure… Links: https://answersresearchjournal.org/origin-human-mitochondrial-dna-differences/. - [^jeanson-2016:a] — **retained source note; quote/data note; parent [^jeanson-2016].** **Local key:** `jeanson-2016`; **file:** `papers/jeanson-2016_generation-time-out-of-africa.pdf`. **Original-note summary:** "Going back to the time of the Flood, modern ethnic groups would have all traced their maternal ancestry back to the three wives of Noah's sons (Jeanson 2015a). Consistent with this historical record, three major nodes were visible in human mtDNA trees (Fig. 1)." The figure is an unrooted radial… No URL was recorded in the original definition. - [^jeanson-2016:b] — **retained source note; quote/data note; parent [^jeanson-2016].** **Local key:** `jeanson-2016`; **file:** `papers/jeanson-2016_generation-time-out-of-africa.pdf`. **Original-note summary:** Jeanson's own footnote 3, verified verbatim 2026-08-24 against the paper: "Again, note that male generation times are virtually irrelevant since mtDNA lineages stop with the men who inherit them. The only generation times historically relevant to mtDNA analyses are from females." He wrote it to… No URL was recorded in the original definition. - [^jeanson-2017] — **retained source note; source identity or source-level note.** **Local key:** `jeanson-2017`; **file:** `papers/jeanson-2017_response-frello-mtdna.pdf`. **Locator recorded:** 10:18. **Original-note summary:** Jeanson, Nathaniel T. "Response to 'On the Creationist View on mtDNA'." *Answers Research Journal* 10:183-186 (2017). Links: https://answersresearchjournal.org/creationist-view-mtdna-response/. - [^jeanson-2017:a] — **retained source note; quote/data note; parent [^jeanson-2017].** **Local key:** `jeanson-2017`; **file:** `papers/jeanson-2017_response-frello-mtdna.pdf`. **Original-note summary:** "Second, even if we assume that Neanderthal and Denisovan DNA sequences are reliable, they don't fit any scientific model (YEC or evolution)—when we assume that rates of mtDNA mutation have been constant. With respect to the evolutionary timescale, current rates of mutation are much too high to… No URL was recorded in the original definition. - [^jeanson-2017:b] — **retained source note; quote/data note; parent [^jeanson-2017].** **Local key:** `jeanson-2017`; **file:** `papers/jeanson-2017_response-frello-mtdna.pdf`. **Original-note summary:** Jeanson's answer to Frello's internal-diversity test, from the same paper, section "Examining Frello's Criticisms," verified verbatim 2026-08-24 at : "The problem with Frello's argument is that he implicitly assumes a particular genealogical relationship among the Neanderthal individuals—and does… Links: https://answersresearchjournal.org/creationist-view-mtdna-response/. - [^jeanson-degraded] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Jeanson's stated reason for excluding ancient DNA, from *Answers Research Journal* 8 (2015): "DNA sequences from fossils are too degraded to be useful for comparative DNA analyses today," and, in the same body of work, "Because DNA is such a labile molecule, it seems unlikely that reliable… No URL was recorded in the original definition. - [^frello-2017] — **retained source note; source identity or source-level note.** **Local key:** `frello-2017`; **file:** `papers/frello-2017_creationist-view-mtdna.pdf`. **Locator recorded:** 10:18. **Original-note summary:** Frello, Stefan. "On the Creationist View on mtDNA." *Answers Research Journal* 10:181-182 (2017). A working Danish biologist, not a creationist, publishing a critique inside the creationist journal. His BLAST-derived figures, with GenBank accessions given in the paper: maximum modern human to… Links: https://answersresearchjournal.org/creationist-view-mtdna/. - [^green-2008] — **retained source note; source identity or source-level note.** **Local key:** `green-2008`; **file:** `papers/green-2008_complete-neandertal-mtdna-genome.html`. **Original-note summary:** Green, Richard E.; Malaspinas, Anna-Sapfo; Krause, Johannes; et al. "A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing." *Cell* 134(3):416-426 (8 August 2008). doi:10.1016/j.cell.2008.06.021 The Vindija 33.16 genome, at 34.9-fold average coverage, and… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC2602844/. - [^green-2008:a] — **retained source note; quote/data note; parent [^green-2008].** **Local key:** `green-2008`; **file:** `papers/green-2008_complete-neandertal-mtdna-genome.html`. **Original-note summary:** The branch-length result, in full, with the caveat the authors attach to it: "A tantalizing finding is that when all substitutions in the mtDNA are analyzed, the Neandertal mtDNA lineage is shorter than the human lineage by approximately 20% (Supp. Fig. 3B). It is tempting to speculate that this… No URL was recorded in the original definition. - [^green-2008:b] — **retained source note; quote/data note; parent [^green-2008].** **Local key:** `green-2008`; **file:** `papers/green-2008_complete-neandertal-mtdna-genome.html`. **Locator recorded:** Table 3), we consistently observed the highest dN/dS on the Neandertal lineage and this value was significantly higher than background rates in all comparisons (all P < 0. **Original-note summary:** The one Neanderthal-specific rate elevation that is real: "While lineage-specific estimates of dN/dS were sensitive to both the underlying model of sequence evolution and the number of outgroups considered (see Supp. Fig. 6 and Supp. Table 3), we consistently observed the highest dN/dS on the… No URL was recorded in the original definition. - [^cserhati-2024] — **retained source note; source identity or source-level note.** **Local key:** `jordan-2024`; **file:** `web/jordan-2024_neanderthals-denisovans-line-ham.html`. **Original-note summary:** Cserháti, Matthew. "Ancient DNA Shows Neanderthals and Denisovans Descending from Noah in the Line of Ham." *Answers Research Journal* (2024). 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… Links: https://answersresearchjournal.org/neanderthal/ancient-dna/. - [^cserhati-2024:a] — **verification/access flag; quote/data note; parent [^cserhati-2024].** **Local key:** `jordan-2024`; **file:** `web/jordan-2024_neanderthals-denisovans-line-ham.html`. **Original-note summary:** Verified verbatim 2026-08-24. On the Y chromosome: "If sequencing errors did not cause the excessive number of Neanderthal Y chromosome variant alleles, the only other option is hypermutation. So, what caused the high mutation rate found in Neanderthal Y chromosomes? One possibility is patriarchal… No URL was recorded in the original definition. - [^carter-2019-drive] — **retained source note; source identity or source-level note.** **Local key:** `carter-2019`; **file:** `web/carter-2019_patriarchal-drive.html`. **Original-note summary:** Carter, Robert W. "Patriarchal drive in the early post-Flood population." *Journal of Creation* 33(1):110-118 (2019). The source Cserháti cites for the mechanism: "It has already been established that the number of mutations passed to children scales with the age of the father. Yet, the oldest… Links: https://creation.com/patriarchal-drive. - [^carter-2009] — **retained source note; source identity or source-level note.** **Local key:** `carter-2009`; **file:** `papers/carter-2009_neandertal-mtdna-not-evolution.pdf`. **Original-note summary:** Carter, Robert W. "The Neandertal mitochondrial genome does not support evolution." *Journal of Creation* 23(1):40-43 (2009). The most substantial young-earth treatment of this question in print, and the source of every mechanism discussed above except patriarchal drive. It also gives Green's… Links: https://creation.com/images/pdfs/tj/j23_1/j23_1_40-43.pdf. - [^criswell-2009] — **retained source note; source identity or source-level note.** **Local key:** `criswell-2009`; **file:** `papers/criswell-2009_neandertal-dna-and-modern-humans.pdf`. **Original-note summary:** Criswell, Daniel. "Neandertal DNA and Modern Humans." *Creation Research Society Quarterly* 45(4):246-254 (Spring 2009). The detailed young-earth case that the archaic gap is post-mortem damage, and the source both Habermehl 2010 and Carter 2009 defer to on this question. Worth reading for its… Links: https://crsq.creationresearch.org/id/eprint/1062/1/Neandertal%20DNA%20and%20Modern%20Humans.pdf. - [^criswell-2009:a] — **verification/access flag; quote/data note; parent [^criswell-2009].** **Local key:** `criswell-2009`; **file:** `papers/criswell-2009_neandertal-dna-and-modern-humans.pdf`. **Original-note summary:** The test and his own verdict on it: "The alignment identifies 40 transition sites between the nine Neandertal HVRI sequences and the Eve1.0 HVRI. Of these 40 sites, 16 are Type 1 transitions and 24 are Type 2 transitions." And: "A chi-square test for the difference between Type 1: Type 2… No URL was recorded in the original definition. - [^criswell-2009:b] — **retained source note; quote/data note; parent [^criswell-2009].** **Local key:** `criswell-2009`; **file:** `papers/criswell-2009_neandertal-dna-and-modern-humans.pdf`. **Original-note summary:** On the thymine trimer: "Neandertal AF142095 has a thymine trimer inserted into the middle of what is called the poly-cytosine tract (polyC 309). A thymine trimer has not been identified for any of the 4300 modern human sequences… and none of the 21 primates have this insertion." His own… No URL was recorded in the original definition. - [^sanchez-contreras-2021] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** 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(19):11103-11118 (2021). Duplex sequencing of naturally occurring somatic… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC8565317/. - [^sanchez-contreras-2021:a] — **verification/access flag; quote/data note; parent [^sanchez-contreras-2021].** **Local key:** —; **file:** —. **Locator recorded:** table in principle by position rather than by rate: a Neanderthal population running a proofreading-deficient polymerase should show a flattened gradient, not merely a longer branch. **Original-note summary:** From the abstract: "We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity…… No URL was recorded in the original definition. - [^vandervalk-2021] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** van der Valk, Tom, et al. "Million-year-old DNA sheds light on the genomic history of mammoths." *Nature* 591(7849):265-269 (2021). doi:10.1038/s41586-021-03224-9 And Kjær, Kurt H., et al. "A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA." *Nature* 612(7939):283-291… No URL was recorded in the original definition. - [^carter-2009:b] — **retained source note; quote/data note; parent [^carter-2009].** **Local key:** `carter-2009`; **file:** `papers/carter-2009_neandertal-mtdna-not-evolution.pdf`. **Original-note summary:** On environmental stress: "It has been suggested by several creationists that the Neandertal population lived in Europe under less-than-ideal conditions and was subjected to nutrient limitations, specifically vitamin D deficiency due to the perpetually cloudy weather during the post-Flood Ice Age.… No URL was recorded in the original definition. - [^carter-2009:c] — **verification/access flag; quote/data note; parent [^carter-2009].** **Local key:** `carter-2009`; **file:** `papers/carter-2009_neandertal-mtdna-not-evolution.pdf`. **Original-note summary:** The polymerase mechanism, in full: "Neutral theory does not allow for mutations in DNA polymerase or in anything that affects DNA copying or repair to occur in only a single subpopulation. That would destroy the very notion of a molecular clock, for then mutations would not be expected to… No URL was recorded in the original definition. - [^carter-2009:d] — **retained source note; quote/data note; parent [^carter-2009].** **Local key:** `carter-2009`; **file:** `papers/carter-2009_neandertal-mtdna-not-evolution.pdf`. **Original-note summary:** The category slip: "The accumulation of non-synonymous mutations in important genes is evidence for a high mutation rate acting on a small population under threat of extinction." The finding he is reading is Green's, and Green attributes it to *reduced purifying selection* — less removal — not to… No URL was recorded in the original definition. - [^trifunovic-2004] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Trifunovic, Aleksandra, et al. "Premature ageing in mice expressing defective mitochondrial DNA polymerase." *Nature* 429(6990):417-423 (2004). doi:10.1038/nature02517 PMID 15164064. The mtDNA mutator mouse, and the only measurement of what a broken mitochondrial polymerase actually does to the… No URL was recorded in the original definition. - [^trifunovic-2004:a] — **retained source note; quote/data note; parent [^trifunovic-2004].** **Local key:** —; **file:** —. **Original-note summary:** From the abstract: "we created homozygous knock-in mice that express a proof-reading-deficient version of PolgA, the nucleus-encoded catalytic subunit of mtDNA polymerase. Here we show that the knock-in mice develop an mtDNA mutator phenotype with a threefold to fivefold increase in the levels of… No URL was recorded in the original definition. - [^stewart-2008] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Stewart, James B., et al. "Strong purifying selection in transmission of mammalian mitochondrial DNA." *PLoS Biology* 6(1):e10 (2008). Maternal transmission of randomly generated mtDNA mutations in the Trifunovic mutator mice — the direct experimental test of what happens to a raised mutation… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC2214808/. - [^stewart-2008:a] — **retained source note; quote/data note; parent [^stewart-2008].** **Local key:** —; **file:** —. **Original-note summary:** From the abstract: "We experimentally addressed this issue by studying the maternal transmission of random mtDNA mutations in mtDNA mutator mice expressing a proofreading-deficient mitochondrial DNA polymerase. We report a rapid and strong elimination of nonsynonymous changes in protein-coding… No URL was recorded in the original definition. - [^endicott-2008] — **retained source note; source identity or source-level note.** **Local key:** `henn-2009`; **file:** `papers/henn-2009_time-dependency-mtdna-rate.pdf`. **Original-note summary:** Endicott, Phillip, and Ho, Simon Y. W. "Characterizing the Time Dependency of Human Mitochondrial DNA Mutation Rate Estimates." *Molecular Biology and Evolution* 26(1):217-230 (2008). doi:10.1093/molbev/msn244 CC-BY-NC. The publisher's copy sits behind a bot wall that refuses every automated… No URL was recorded in the original definition. - [^endicott-2008:a] — **retained source note; quote/data note; parent [^endicott-2008].** **Local key:** `henn-2009`; **file:** `papers/henn-2009_time-dependency-mtdna-rate.pdf`. **Locator recorded:** Table 1 coding-region rates for five Sahul and Oceanic lineages, in substitutions per base per million years: New Britain M28 0. **Original-note summary:** Their Table 1 coding-region rates for five Sahul and Oceanic lineages, in substitutions per base per million years: New Britain M28 0.0265, Australian O 0.0317, Papua New Guinean P1 0.0327, Australian M42 0.0336, Oceanic P 0.0401 — a 1.51-fold spread. Verbatim: "The coding region estimates from… No URL was recorded in the original definition. - [^rieux-2014:e] — **retained source note; quote/data note; parent [^rieux-2014].** **Local key:** —; **file:** —. **Original-note summary:** Appendix S13 again, read as a test of rate constancy rather than of calibration. Thirteen radiocarbon-dated ancient genomes, each used alone as the sole calibration point, give thirteen rate estimates with mean 2.391 × 10^-8^ per site per year, standard deviation 0.077, **coefficient of variation… No URL was recorded in the original definition. - [^jeanson-2017-final] — **verification/access flag; source identity or source-level note.** **Local key:** `jeanson-2017b`; **file:** `web/jeanson-2017b_second-response-frello-mtdna.html`. **Original-note summary:** Jeanson, Nathaniel T. "Response to 'Reply to Response to "On the Creationist View on mtDNA"'." *Answers Research Journal* 10 (2017). The fourth and last round of the exchange. Jeanson treats Frello's withdrawal as a surrender — "Since Frello has refused to respond to the errors that I documented,… Links: https://answersresearchjournal.org/creationist-view-mtdna-second-response/. - [^carter-2025] — **verification/access flag; source identity or source-level note.** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Original-note summary:** Carter, Robert W. "When did Eve live? An evaluation of the data." Creation Ministries International, 18 September 2025. Note for anyone checking links mechanically: the server returns 403 to a HEAD request but 200 to a GET, so automated link checkers will falsely flag it. Carter's peer-reviewed… Links: https://creation.com/when-did-eve-live; https://pmc.ncbi.nlm.nih.gov/articles/PMC1888801/. - [^carter-2025:a] — **retained source note; quote/data note; parent [^carter-2025].** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Locator recorded:** table variants *in an individual*, and for mitochondrial DNA a new variant must first take over inside the mother's own germline before it is one. **Original-note summary:** Both concessions verbatim from the article text on disk at `sources/web/carter-2025c_when-did-eve-live.txt`. In full: "Ten years later, a study done on the population of Norfolk Island calculated a rate closer to 0.03 mutations per generation. This equates to one mutation every 33 generations, or… No URL was recorded in the original definition. - [^carter-2023] — **retained source note; source identity or source-level note.** **Local key:** `carter-2023`; **file:** `papers/carter-2023_genealogical-vs-phylogenetic-mutation-rates.pdf`. **Locator recorded:** pp. 168-180 (2023). **Original-note summary:** Carter, Robert W. "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 On disk at `sources/papers/carter-2023_genealogical-vs-phylogenetic-mutation-rates.pdf`.… No URL was recorded in the original definition. - [^carter-2023:a] — **retained source note; quote/data note; parent [^carter-2023].** **Local key:** `carter-2023`; **file:** `papers/carter-2023_genealogical-vs-phylogenetic-mutation-rates.pdf`. **Original-note summary:** Verbatim. Carter's own summary of Connell in the same paragraph reports the Norfolk Island study accurately, including the transmission count, and flags the tension between the small absolute rate and the paper's headline ratio. He does not resolve it, and he does not cite the fixed-only figure. No URL was recorded in the original definition. - [^jeanson-2025] — **retained source note; source identity or source-level note.** **Local key:** `jeanson-2025`; **file:** `papers/jeanson-2025_mtdna-lineages-americas.pdf`. **Locator recorded:** 18:34. **Original-note summary:** Jeanson, Nathaniel T. "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." *Answers Research Journal* 18:347-375 (2025). Checked directly:… Links: https://answersresearchjournal.org/genetics/analysis-mitochondrial-dna-lineages-americas/. - [^jeanson-2026] — **retained source note; source identity or source-level note.** **Local key:** `jeanson-2026`; **file:** `media/jeanson-2026_standing-for-truth-interview.en.vtt`. **Locator recorded:** 1:00. **Original-note summary:** Jeanson, Nathaniel T., interviewed on *Standing For Truth*. "Does Modern Genetics Confirm the Bible? | Dr. Nathaniel Jeanson Explains." YouTube, uploaded 10 March 2026, 1:00:25. The host puts the mutation-versus-substitution objection to him at 46:05–47:20 and he answers through 53:40. Quotations… Links: https://www.youtube.com/watch?v=SWWd4K0FFj8. - [^jeanson-2026:a] — **retained source note; quote/data note; parent [^jeanson-2026].** **Local key:** `jeanson-2026`; **file:** `media/jeanson-2026_standing-for-truth-interview.en.vtt`. **Locator recorded:** 48:02. **Original-note summary:** At 48:02–48:44: "Mutation rate is how fast or slow does mom mutate the DNA to daughter? … And it came out to be about an average of one mistake every five to ten generations. Way too fast for evolution … I had been assuming that rate had been consistent in the past. It's basically… No URL was recorded in the original definition. - [^jeanson-2026:b] — **verification/access flag; quote/data note; parent [^jeanson-2026].** **Local key:** `jeanson-2026`; **file:** `media/jeanson-2026_standing-for-truth-interview.en.vtt`. **Locator recorded:** 49:50. **Original-note summary:** At 49:50: "The biggest gift though from Dan has been arguing that I'm wrong on mutation versus substitution rate because the textbooks say otherwise." At 50:20: "It's a fundamentalist atheistic religion or agnostic religion, whatever you want to call it." At 51:05: "What we should be saying… No URL was recorded in the original definition. - [^jeanson-2026:c] — **retained source note; quote/data note; parent [^jeanson-2026].** **Local key:** `jeanson-2026`; **file:** `media/jeanson-2026_standing-for-truth-interview.en.vtt`. **Locator recorded:** 53:33. **Original-note summary:** At 53:33: "So, I'm conflating substitution rate and mitochondrial [sic]. No, I'm equating substitution rate and mutation rate because the data says so." No URL was recorded in the original definition. - [^jeanson-2022-clip] — **retained source note; source identity or source-level note.** **Local key:** `creation-myths-2022`; **file:** `media/creation-myths-2022_jeanson-mutation-substitution-clip.en.vtt`. **Locator recorded:** 4:30. **Original-note summary:** From the clip Dan Stern Cardinale posted of their conversation on the *Apologetics Live* show of 2 June 2022: Creation Myths, "Bad Creationist Genetics: 'I'm treating the mutation rate as a substitution rate' – Dr. Jeanson." YouTube, 3 June 2022, 4:30. Jeanson's words, from the clip's automatic… Links: https://www.youtube.com/watch?v=sUPHNeL9wFk. - [^jeanson-2025:b] — **retained source note; quote/data note; parent [^jeanson-2025].** **Local key:** `jeanson-2025`; **file:** `papers/jeanson-2025_mtdna-lineages-americas.pdf`. **Original-note summary:** Verified against the text of the paper's methods note on time frames: "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 in the tree." Both… No URL was recorded in the original definition. - [^jeanson-2025:c] — **retained source note; quote/data note; parent [^jeanson-2025].** **Local key:** `jeanson-2025`; **file:** `papers/jeanson-2025_mtdna-lineages-americas.pdf`. **Original-note summary:** Verified against the text: "In short, we don't yet know whether mtDNA acts like a simple biological clock. How could we find out whether mtDNA does?" His own framing, in the same paper the interview offers as the confirmation. No URL was recorded in the original definition. - [^carter-2025:d] — **retained source note; quote/data note; parent [^carter-2025].** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Locator recorded:** Table 2 pooled row "28/2633 / . **Original-note summary:** Endnote 10 of Carter 2025, quoted in full and verbatim; endnote 11 applies the identical formula to Madrigal 2012, "1.24e-6 µ/site/year x 16,569 sites x 30 years/generation x 2 … They also only studied the control region." Read from the page bytes, not through a summariser. Howell's figures are… No URL was recorded in the original definition. - [^carter-2025:e] — **verification/access flag; quote/data note; parent [^carter-2025].** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Original-note summary:** "The reported 'genealogical' mtDNA mutation rates are a bit too slow for the creationists." He then proposes a mechanism he calls "Patriarchal Drive" to close the gap. Diagnosed as the unit error described above, the gap he is trying to close does not exist. No URL was recorded in the original definition. - [^carter-2025:b] — **verification/access flag; quote/data note; parent [^carter-2025].** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Original-note summary:** "Importantly, they had no way of predicting Eve's existence before they discovered her. Instead, once the concept of a single human female ancestress became obvious (from various genomics analyses), a 'bottleneck' was added to the evolutionary model, post facto." Against this: Avise, Neigel &… No URL was recorded in the original definition. - [^carter-2025:c] — **verification/access flag; quote/data note; parent [^carter-2025].** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Original-note summary:** "Option 3 raises an interesting question. How many lines would we expect to see? Depending on how closely related they were, there could have been 1, 2, or 3 mitochondrial lines among Noah's daughters-in-law. Thus, it is entirely possible that every mutation in the tree occurred post-Flood. The… No URL was recorded in the original definition. - [^carter-selection] — **verification/access flag; source identity or source-level note.** **Local key:** `carter-2025c`; **file:** `web/carter-2025c_when-did-eve-live.html`. **Original-note summary:** Carter, Robert W., on why selection cannot bridge the pedigree and phylogenetic rates: "It must be emphasized that lethal mutations cannot appear in the studies listed above. The people sampled were all healthy adults. The scientists would also have avoided people with mtDNA mutations that cause… Links: https://creation.com/when-did-eve-live. - [^wieland-1998] — **retained source note; source identity or source-level note.** **Local key:** `wieland-1998`; **file:** `web/wieland-1998_shrinking-date-for-eve.html`. **Original-note summary:** Wieland, Carl. "A shrinking date for 'Eve'." *Journal of Creation* 12(1):1-3 (April 1998), reposted 29 January 2006. See also his 2006 reply to MacAndrew, Links: https://creation.com/a-shrinking-date-for-eve; https://creation.com/en/articles/cmi-responds-to-sceptics-criticism-of-mitochondrial-eve-article. - [^wieland-1998:a] — **verification/access flag; quote/data note; parent [^wieland-1998].** **Local key:** `wieland-1998`; **file:** `web/wieland-1998_shrinking-date-for-eve.html`. **Original-note summary:** "Evolutionists do not claim, nor can it be fairly stated, that this evidence proves that there was only one woman alive at any point in the past. Holders to the 'Eve' theory certainly insist that all modern humans are indeed descended from one woman. However, they believe that there were other… No URL was recorded in the original definition. - [^wieland-1998:b] — **retained source note; quote/data note; parent [^wieland-1998].** **Local key:** `wieland-1998`; **file:** `web/wieland-1998_shrinking-date-for-eve.html`. **Locator recorded:** table populations three years before Cann et al. **Original-note summary:** "And it was not something that was expected by evolutionists." Avise, Neigel & Arnold 1984 predicted exactly this outcome for stable populations three years before Cann et al. 1987. No URL was recorded in the original definition. - [^kim-2013] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** 4:13. **Original-note summary:** Kim, Hie Lim, and Schuster, Stephan 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). The observed comparator for every clock calculation in this article.… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC3584485/. - [^arnadottir-2024] — **verification/access flag; source identity or source-level note.** **Local key:** `arnadottir-2024`; **file:** `papers/arnadottir-2024_rate-nature-mtdna-mutations.html`. **Original-note summary:** Árnadóttir, Erna R.; Moore, Kristjan H. S.; Guðmundsdóttir, Valdís B.; Ebenesersdóttir, S. Sunna; Guity, Kamran; Jónsson, Hákon; Stefánsson, Kári; and Helgason, Agnar. "The rate and nature of mitochondrial DNA mutations in human pedigrees." *Cell* 187(15):3904-3918.e8 (2024).… Links: https://pubmed.ncbi.nlm.nih.gov/38851187/; https://www.decode.com/the-rate-nature-and-transmission-of-mitochondrial-dna-mutations-in-humans/. - [^arnadottir-2024:b] — **retained source note; quote/data note; parent [^arnadottir-2024].** **Local key:** `arnadottir-2024`; **file:** `papers/arnadottir-2024_rate-nature-mtdna-mutations.html`. **Original-note summary:** Both quotations verbatim from the rendered full text. The detection rule, from the Results: "we used a minimum read frequency threshold of 0.05 for detecting mutations in individuals, requiring at least one carrier to have a read frequency of ≥0.1." The comparison with Connell, from the same… No URL was recorded in the original definition. - [^arnadottir-2024:c] — **retained source note; quote/data note; parent [^arnadottir-2024].** **Local key:** `arnadottir-2024`; **file:** `papers/arnadottir-2024_rate-nature-mtdna-mutations.html`. **Original-note summary:** Verbatim, from the Discussion and from the section headed "Limitations of the study" respectively. The second sentence is the more important of the two: a study reporting 0.0703 mutations per transmission, telling its readers that the true germline mutation rate is higher than that, is telling… No URL was recorded in the original definition. - [^arnadottir-2024:d] — **verification/access flag; quote/data note; parent [^arnadottir-2024].** **Local key:** `arnadottir-2024`; **file:** `papers/arnadottir-2024_rate-nature-mtdna-mutations.html`. **Locator recorded:** table positions are evidently missed in phylogenies such as the one from Soares et al. **Original-note summary:** Verbatim from the Results, on the comparison against Soares 2009: "In the control region, mutations involved markedly fewer (19.7%, p 1 × 10^-5^) positions in matrilines than in the phylogeny and were more likely to affect the same positions multiple times (p ID 65.3% higher, p 1 × 10^-5^). This… No URL was recorded in the original definition. - [^arnadottir-2024:e] — **retained source note; quote/data note; parent [^arnadottir-2024].** **Local key:** `arnadottir-2024`; **file:** `papers/arnadottir-2024_rate-nature-mtdna-mutations.html`. **Locator recorded:** Table S2). **Original-note summary:** Verbatim, from the Discussion: "Previous studies of humans, based on the same methodology, but many fewer transmissions (typically across a single generation), have produced estimates of N e ranging from 2 to 32, with an average of 8.1 (Table S2). Even after excluding the outlying estimate of 32… No URL was recorded in the original definition. - [^arnadottir-2024:a] — **verification/access flag; quote/data note; parent [^arnadottir-2024].** **Local key:** `arnadottir-2024`; **file:** `papers/arnadottir-2024_rate-nature-mtdna-mutations.html`. **Locator recorded:** table sites which recur and revert, so the count cannot be extrapolated linearly, and reports negative selection and pre-natal (oocyte) selection operating inside ordinary pedigrees. **Original-note summary:** The same paper documents that the mutations are heavily concentrated at hypermutable sites which recur and revert, so the count cannot be extrapolated linearly, and reports negative selection and pre-natal (oocyte) selection operating inside ordinary pedigrees. Both findings cut against using this… No URL was recorded in the original definition. - [^kivisild-2006] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Kivisild, Toomas; Shen, Peidong; Wall, Dennis P.; et al. "The role of selection in the evolution of human mitochondrial genomes." *Genetics* 172(1):373-387 (2006). 1,758 mutations at 1,292 coding-region sites across 277 genomes. The ratio of amino-acid-changing to silent variation declines with… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC1456166/. - [^laricchia-2022] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Laricchia, Kristen M., et al. "Mitochondrial DNA variation across 56,434 individuals in gnomAD." *Genome Research* 32(3):569-582 (2022). Of all possible variants, 55% of synonymous, about 10% of missense and RNA, and about 1% of stop-gain variants are actually observed across 56,434 people. The… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC8896463/. - [^fan-2008] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Fan, Weiwei, et al. "A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations." *Science* 319(5865):958-962 (2008). A severe ND6 mutation was eliminated during oogenesis within four generations (47% → 14% → 6% → 0%) while a mild COI mutation was retained.… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC3049809/. - [^floros-2018] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Floros, Vasileios I., et al. "Segregation of mitochondrial DNA heteroplasmy through a developmental genetic bottleneck in human embryos." *Nature Cell Biology* 20(2):144-151 (2018). Single-cell deep sequencing of human primordial germ cells, showing a signature of selection against… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC6551220/. - [^fu-2013] — **retained source note; source identity or source-level note.** **Local key:** `fu-2013e`; **file:** `papers/fu-2013e_revised-timescale-ancient-mitochondrial-genomes/`. **Original-note summary:** Fu, Qiaomei; Mittnik, Alissa; Johnson, Philip L. F.; et al. "A revised timescale for human evolution based on ancient mitochondrial genomes." *Current Biology* 23(7):553-559 (2013). Ten radiocarbon-dated ancient mitochondrial genomes spanning 40,000 years, used as tip calibrations. Whole-genome… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC5036973/. - [^fu-2013:a] — **retained source note; quote/data note; parent [^fu-2013].** **Local key:** `fu-2013e`; **file:** `papers/fu-2013e_revised-timescale-ancient-mitochondrial-genomes/`. **Original-note summary:** On the Cro-Magnon 1 sample, archaeologically assumed to be about 30,000 years old but carrying the derived haplogroup T2b1: "Since the radiocarbon date for this specimen was obtained from an associated shell, we AMS dated the sample itself. Surprisingly, the sample had a much younger age of about… No URL was recorded in the original definition. - [^fu-2014] — **retained source note; source identity or source-level note.** **Local key:** `fu-2014`; **file:** `papers/fu-2014_ust-ishim-45000-year-old-genome/`. **Original-note summary:** Fu, Qiaomei; Li, Heng; Moorjani, Priya; et al. "Genome sequence of a 45,000-year-old modern human from western Siberia." *Nature* 514(7523):445-449 (2014). Two independent radiocarbon dates on the Ust'-Ishim femur, 41,400 ± 1,300 and 41,400 ± 1,400 BP, calibrating to 46,880-43,210 cal BP.… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC4753769/. - [^rieux-2014] — **verification/access flag; source identity or source-level note.** **Local key:** `rieux-2014c`; **file:** `papers/rieux-2014c_improved-calibration-ancient-genomes.xml`. **Locator recorded:** Table S3 lists the six Blätterhöhle samples' ages in calibrated BC while labelling the column "Age (CalBP)," so each is exactly 2,000 years too young. **Original-note summary:** Rieux, Adrien; Eriksson, Anders; Li, Mingkun; et al. "Improved calibration of the human mitochondrial clock using ancient genomes." *Molecular Biology and Evolution* 31(10):2780-2792 (2014). CC-BY. 30 high-quality ancient plus 320 contemporary whole mitochondrial genomes, 26 ancient retained… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC4166928/. - [^rieux-2014:a] — **retained source note; quote/data note; parent [^rieux-2014].** **Local key:** `rieux-2014c`; **file:** `papers/rieux-2014c_improved-calibration-ancient-genomes.xml`. **Original-note summary:** The tip-calibrated clock returns a human-chimpanzee mitochondrial split of 4.14 Ma (2.99-5.45) — *younger* than the 6-7 Ma the fossil evidence is usually taken to support. The two calibration systems disagree with each other, which is the clearest evidence that tip calibration is not being quietly… No URL was recorded in the original definition. - [^rieux-2014:b] — **retained source note; quote/data note; parent [^rieux-2014].** **Local key:** `rieux-2014c`; **file:** `papers/rieux-2014c_improved-calibration-ancient-genomes.xml`. **Locator recorded:** Table S13: each ancient sample used alone as the single calibration point. **Original-note summary:** Appendix S13, Table S13: each ancient sample used alone as the single calibration point. Twenty-one estimates across samples from 2,535 to 39,464 years old — a 15.6-fold range of age — give rates from 2.268 to 2.517 × 10^-8^, mean 2.391, standard deviation 0.077, coefficient of variation 3.2%.… No URL was recorded in the original definition. - [^rieux-2014:c] — **verification/access flag; quote/data note; parent [^rieux-2014].** **Local key:** `rieux-2014c`; **file:** `papers/rieux-2014c_improved-calibration-ancient-genomes.xml`. **Original-note summary:** "Accounting for PMD had a limited influence on the rate estimation. We obtained a value of 2.23 × 10^-8^ μ/site/year (95% HPD: 1.71-2.75 × 10^-8^) for the whole molecule, which is 1.04× (4.2%) higher than when not accounting for PMD." The estimated damage rate was 1.03 × 10^-9^ errors per site per… No URL was recorded in the original definition. - [^rieux-2014:d] — **retained source note; quote/data note; parent [^rieux-2014].** **Local key:** `rieux-2014c`; **file:** `papers/rieux-2014c_improved-calibration-ancient-genomes.xml`. **Original-note summary:** Appendix S6: among the 30 ancient sequences, 156 A/T and 36 G/C singleton SNPs were observed against 84.8 and 107.2 expected under no deamination; four Swedish sequences carried the excess and were dropped from the analysis. Four of thirty ancient genomes failed a damage screen — the screening is… No URL was recorded in the original definition. - [^oversti-2022] — **retained source note; source identity or source-level note.** **Local key:** `oversti-2022d`; **file:** `papers/oversti-2022d_substitution-rate-variation-haplogroup-u.pdf`. **Original-note summary:** Översti, Sanni, and Palo, Jukka U. "Variation in the substitution rates among the human mitochondrial haplogroup U sublineages." *Genome Biology and Evolution* 14(7):evac097 (2022). CC-BY. 234 radiocarbon-dated ancient mitochondrial genomes, of which 212 are Holocene and 84 are younger than 4,500… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC9250076/. - [^oversti-2022:a] — **retained source note; quote/data note; parent [^oversti-2022].** **Local key:** `oversti-2022d`; **file:** `papers/oversti-2022d_substitution-rate-variation-haplogroup-u.pdf`. **Locator recorded:** table S5, Supplementary Material online). **Original-note summary:** On lineage-to-lineage rate variation, verified verbatim 2026-08-24 against the PDF: "The largest differences are seen in scenario B, where the rates for U2 and U5a are 2.1 and 1.9 times higher than for U5b, respectively (fig. 3 and supplementary table S5, Supplementary Material online). However,… No URL was recorded in the original definition. - [^behar-2012] — **retained source note; source identity or source-level note.** **Local key:** `behar-2012`; **file:** `papers/behar-2012_copernican-reassessment-rsrs.pdf`. **Original-note summary:** Behar, Doron M.; van Oven, Mannis; Rosset, Saharon; et al. "A 'Copernican' Reassessment of the Human Mitochondrial DNA Tree from its Root." *American Journal of Human Genetics* 90(4):675-684 (2012). Two sample sizes appear in discussions of this paper and they refer to different things; the… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC3322232/. - [^phylotree] — **retained source note; source identity or source-level note.** **Local key:** `vanoven-2016`; **file:** `data/vanoven-2016_phylotree-mtdna-build-17.zip`. **Original-note summary:** van Oven, Mannis, and Kayser, Manfred. "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation." *Human Mutation* 30(2):E386-E394 (2009). PhyloTree mtDNA tree Build 17 (18 February 2016), built from 24,275 complete sequences. The Build 17 archive was downloaded and… Links: https://www.phylotree.org/. - [^icr-note] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Thomas, Brian. "DNA Trends Confirm Noah's Family." *Acts & Facts*, Institute for Creation Research, 30 June 2016. The editor's note appended after readers objected: "Some readers have contacted us about what they perceive to be a fourth node in the lower right of the figure from Dr. Jeanson's… Links: https://www.icr.org/article/dna-trends-confirm-noahs-family. - [^meyer-2014] — **verification/access flag; source identity or source-level note.** **Local key:** `meyer-2014b`; **file:** `papers/meyer-2014b_sima-de-los-huesos-mtdna.pdf`. **Original-note summary:** Meyer, Matthias, et al. "A mitochondrial genome sequence of a hominin from Sima de los Huesos." *Nature* 505(7483):403-406 (2014). doi:10.1038/nature12788 Dated the specimen from its mitochondrial branch length alone to roughly 400,000 years. A later paper by the same group (Meyer et al. 2016)… No URL was recorded in the original definition. - [^arnold-2014] — **retained source note; source identity or source-level note.** **Local key:** `arnold-2014`; **file:** `papers/arnold-2014_sima-luminescence-dating.pdf`. **Locator recorded:** 67:85. **Original-note summary:** Arnold, Lee 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). doi:10.1016/j.jhevol.2013.12.001 A minimum age of 427,000 ± 12,000 years for the deposit, from two physical methods… No URL was recorded in the original definition. - [^howell-1996] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Howell, Neil; Kubacka, Iwona; and Mackey, David A. "How rapidly does the human mitochondrial genome evolve?" *American Journal of Human Genetics* 59(3):501-509 (1996). The study that opened the pedigree-rate literature. Two germline mutations in 88 transmissions through one large Leber hereditary… Links: https://pubmed.ncbi.nlm.nih.gov/8751850/. - [^cavelier-2000] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Cavelier, Lucia; Jazin, Elena; Jalonen, Pia; and Gyllensten, Ulf. "MtDNA substitution rate and segregation of heteroplasmy in coding and noncoding regions." *Human Genetics* 107(1):45-50 (2000). The forgotten null result, and the first study to count fixed changes specifically. Verbatim: "No… Links: https://pubmed.ncbi.nlm.nih.gov/10982034/. - [^sigurdardottir-2000] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Sigurðardóttir, Sigrún; Helgason, Agnar; Gulcher, Jeffrey R.; Stefansson, Kari; and Donnelly, Peter. "The mutation rate in the human mtDNA control region." *American Journal of Human Genetics* 66(5):1599-1609 (2000). 26 large Icelandic pedigrees, 705 transmissions, 3 substitutions. Howell 2003… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC1378010/. - [^heyer-2001] — **retained source note; source identity or source-level note.** **Local key:** `heyer-2001`; **file:** `papers/heyer-2001_familial-mtdna-substitution-rates-deep-rooting-pedigrees.html`. **Locator recorded:** table sites "are expected to be of no or little informativity for the evaluation of mutational distances at the phylogenetic time scale. **Original-note summary:** Heyer, Evelyne; Zietkiewicz, Ewa; Rochowski, Anna; Yotova, Vania; Puymirat, Jack; and Labuda, Damian. "Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees." *American Journal of Human Genetics* 69(5):1113-1126 (2001).… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC1274355/. - [^xia-2024] — **retained source note; source identity or source-level note.** **Local key:** `xia-2024`; **file:** `papers/xia-2024_denisovan-subsistence-baishiya.html`. **Locator recorded:** 32:10. **Original-note summary:** 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 CC-BY. The elevation, verbatim from the Methods: "Baishiya Karst Cave (BKC; 35.45° N, 102.57° E, 3,280 metres above sea level) is located in… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC11291277/. - [^cosmic-dose] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** table is built in Forster's currency rather than mixing the two. **Original-note summary:** The cosmic figures are computed here from UNSCEAR's own altitude formulas rather than taken from any single measurement, so the working is given in full. UNSCEAR 2008, Annex B, paragraphs 61-66. Sea-level cosmic dose is 31 nGy/h in free air, or about 0.27 mSv per year effective; the… No URL was recorded in the original definition. - [^kennedy-2013] — **retained source note; source identity or source-level note.** **Local key:** `kennedy-2013`; **file:** `papers/kennedy-2013_ultrasensitive-mtdna-somatic-mutations.pdf`. **Original-note summary:** Kennedy, Scott R.; Salk, Jesse J.; Schmitt, Michael W.; and Loeb, Lawrence A. "Ultra-Sensitive Sequencing Reveals an Age-Related Increase in Somatic Mitochondrial Mutations That Are Inconsistent with Oxidative Damage." *PLoS Genetics* 9(9):e1003794 (2013). doi:10.1371/journal.pgen.1003794 CC-BY.… No URL was recorded in the original definition. - [^zhang-2020] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Zhang, Dongju, et al. "Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau." *Science* 370(6516):584-587 (2020). doi:10.1126/science.abb6320 From the abstract: "We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand… No URL was recorded in the original definition. - [^forster-2002] — **retained source note; source identity or source-level note.** **Local key:** `forster-2002`; **file:** `papers/forster-2002_natural-radioactivity-mtdna-mutations.html`. **Original-note summary:** Forster, Lucy; Forster, Peter; Lutz-Bonengel, Sabine; Willkomm, Horst; and Brinkmann, Bernd. "Natural radioactivity and human mitochondrial DNA mutations." *PNAS* 99(21):13950-13954 (2002). 248 pedigrees in Kerala, 579 bp of control region. Counts new heteroplasmies explicitly and exclusively: 22… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC129803/. - [^howell-2003] — **retained source note; source identity or source-level note.** **Local key:** `howell-2003`; **file:** `papers/howell-2003_pedigree-rate-sequence-divergence-mtdna.pdf`. **Original-note summary:** Howell, Neil; Smejkal, Carolyn Bogolin; Mackey, David A.; Chinnery, Patrick F.; Turnbull, Douglass M.; and Herrnstadt, Corinna. "The pedigree rate of sequence divergence in the human mitochondrial genome: there is a difference between phylogenetic and pedigree rates." *American Journal of Human… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC1180241/. - [^santos-2005] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Santos, Cristina; Montiel, Rafael; Sierra, Beatriz; et al.; Aluja, María Pilar. "Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal)." *Molecular Biology and Evolution* 22(6):1490-1505 (2005). The first… Links: https://pubmed.ncbi.nlm.nih.gov/15814829/. - [^zaidi-2019] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Zaidi, Arslan A.; Wilton, Peter R.; Su, Marcia Shu-Wei; Paul, Ian M.; Arbeithuber, Barbara; Anthony, Kate; Nekrutenko, Anton; Nielsen, Rasmus; and Makova, Kateryna D. "Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees." *PNAS*… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC6911200/. - [^horai-1995] — **retained source note; source identity or source-level note.** **Local key:** `horai-1995`; **file:** `papers/horai-1995_hominoid-mtdna-african-origin.pdf`. **Original-note summary:** Horai, Satoshi; Hayasaka, Kenji; Kondo, Rumi; Tsugane, Kazuo; and Takahata, Naoyuki. "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 PMC carries page images without OCR text; the… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC42775/. - [^mishmar-2003] — **retained source note; source identity or source-level note.** **Local key:** `mishmar-2003`; **file:** `papers/mishmar-2003_natural-selection-regional-mtdna.pdf`. **Original-note summary:** Mishmar, Dan; Ruiz-Pesini, Eduardo; Golik, Pawel; et al.; Wallace, Douglas C. "Natural selection shaped regional mtDNA variation in humans." *PNAS* 100(1):171-176 (2003). doi:10.1073/pnas.0136972100 104 complete genomes. The measured quantity is a ratio — human tree depth to the human-chimpanzee… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC140917/. - [^brotherton-2013] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** 4:17. **Original-note summary:** Brotherton, Paul; Haak, Wolfgang; Templeton, Jennifer; et al.; Cooper, Alan; and the Genographic Consortium. "Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans." *Nature Communications* 4:1764 (2013). doi:10.1038/ncomms2656 39 complete haplogroup H genomes from… No URL was recorded in the original definition. - [^posth-2016] — **retained source note; source identity or source-level note.** **Local key:** `posth-2016`; **file:** `papers/posth-2016_pleistocene-mitochondrial-genomes.pdf`. **Original-note summary:** Posth, Cosimo; Renaud, Gabriel; Mittnik, Alissa; et al.; Krause, Johannes. "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 66… No URL was recorded in the original definition. - [^cabrera-2021] — **verification/access flag; source identity or source-level note.** **Local key:** `cabrera-2021`; **file:** `papers/cabrera-2021_mtdna-rate-time-dependency.pdf`. **Locator recorded:** 11:50. **Original-note summary:** Cabrera, Vicente M. "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. 423 radiocarbon-dated ancient genomes against 784… Links: https://www.nature.com/articles/s41598-021-84583-1. - [^branch-shortening] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Original to this article. Root-to-tip regression of substitution count against radiocarbon age, on 229 ancient haplogroup U mitochondrial genomes that passed quality control, ages 1,475 to 37,985 cal BP, 82 of them younger than 4,500 cal BP. The sequences and dates come from Översti & Palo's… No URL was recorded in the original definition. - [^control-region-age] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Original to this article. Pairwise distances were computed on the alignment described under the relative-rate test,[^rate-test] restricted to the control region and projected onto revised-Cambridge-Reference-Sequence coordinates, which drops positions inserted relative to that reference and… No URL was recorded in the original definition. - [^region-diversity] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Original to this article. Mean and maximum pairwise substitution counts by region, from the alignment described under the relative-rate test:[^rate-test] 54 modern human genomes (the revised Cambridge Reference Sequence plus Ingman's 53), 36 Neanderthal and 7 Denisovan mitogenomes, all projected… No URL was recorded in the original definition. - [^rate-test] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Original to this article. Tajima's (1993) one-degree-of-freedom relative-rate test, run on 54 modern human mitochondrial genomes (the revised Cambridge Reference Sequence plus the Ingman 53), 35 Neanderthal individuals (every near-complete GenBank record, minus the RefSeq duplicate, the partial… No URL was recorded in the original definition. - [^meyer-2012] — **verification/access flag; source identity or source-level note.** **Local key:** `meyer-2012b`; **file:** `papers/meyer-2012b_denisovan-high-coverage-genome.pdf`. **Original-note summary:** Meyer, Matthias; Kircher, Martin; Gansauge, Marie-Theres; et al. "A high-coverage genome sequence from an archaic Denisovan individual." *Science* 338(6104):222-226 (2012). doi:10.1126/science.1224344 Open copy at The nuclear-genome version of the branch-length test, on roughly three billion base… Links: https://pgl.soe.ucsc.edu/Meyer12.pdf. - [^posth-2017] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** 8:16. **Original-note summary:** Posth, Cosimo; Wißing, Christoph; Kitagawa, Keiko; et al. "Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals." *Nature Communications* 8:16046 (2017). CC-BY. The quoted admission is in Supplementary Note 4, "Mutation rate mtDNA," of… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC5500885/. - [^fotiadou-2026] — **verification/access flag; source identity or source-level note.** **Local key:** `fotiadou-2026`; **file:** `papers/fotiadou-2026_late-neanderthal-demography.pdf`. **Original-note summary:** Fotiadou, Charoula M.; Pedersen, Jesper Borre; Rougier, Hélène; et al.; Posth, Cosimo. "Archaeogenetic insights into the demographic history of Late Neanderthals." *PNAS* 123(13):e2520565123 (2026). doi:10.1073/pnas.2520565123 Open access. Ten new Neanderthal mitochondrial genomes analysed with 49… No URL was recorded in the original definition. - [^denisovan-repair] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Original to this article. The same 206-gene panel run against the Denisova 3 high-coverage genome VCF, then the surviving candidates re-genotyped in the MPI-EVA combined exome VCF (`19_3nt_1d_9human_exomes_hg19_1000g_LowQualDeamination.md.bam.annotated_1.3-14gatk.vcf.gz` and the chromosome-8… No URL was recorded in the original definition. - [^repair-scan] — **verification/access flag; source identity or source-level note.** **Local key:** `mpi-eva-2014`; **file:** `data/mpi-eva-2014_archaic-aa-change-catalog/`. **Original-note summary:** Original to this article. The gene panel, the scan and the verification are at `research/code/repair-genes/` with outputs at `research/data/repair-genes/`, and the full write-up with every candidate and its disposition is at `research/neanderthal-dna-repair-genes.md`. Sources: the Max Planck… Links: http://ftp.eva.mpg.de/neandertal/. - [^uniprot-polg] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** UniProt P54098 (DPOG1_HUMAN), DNA polymerase subunit gamma-1, 1,239 residues. Exonuclease active site Asp198; exonuclease motifs Exo I 196-200, Exo II 267-275, Exo III 395-403; polymerase motifs Pol A 887-896, Pol B 943-958, Pol C 1134-1141. Residue 579 is annotated as an RNA-primer binding… Links: https://www.uniprot.org/uniprotkb/P54098/. - [^aneli-2024] — **verification/access flag; source identity or source-level note.** **Local key:** `aneli-2024`; **file:** `-`. **Original-note summary:** Aneli, Serena; Ceccatelli Berti, Camilla; Gilea, Alexandru Ionut; et al.; Goffrini, Paola; Capelli, Cristian. "Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in *S. cerevisiae*." *Human Molecular Genetics* 33(13):1152-1163 (2024).… No URL was recorded in the original definition. - [^castellano-2014] — **retained source note; source identity or source-level note.** **Local key:** `castellano-2014`; **file:** `papers/castellano-2014_neandertal-exomes-coding-variation.pdf`. **Original-note summary:** Castellano, Sergi; Parra, Genís; Sánchez-Quinto, Federico A.; et al.; Pääbo, Svante; Lalueza-Fox, Carles. "Patterns of coding variation in the complete exomes of three Neandertals." *PNAS* 111(18):6666-6671 (2014). doi:10.1073/pnas.1405138111 Open copy at The source of the change catalogues used… Links: https://www.eva.mpg.de/documents/NatlAcadSciences/Castellano_Patterns_PNAS_2014_2019648.pdf. - [^lambert-2002] — **verification/access flag; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Lambert, David M.; Ritchie, Peter A.; Millar, Craig D.; Holland, Barbara; Drummond, Alexei J.; and Baroni, Carlo. "Rates of Evolution in Ancient DNA from Adélie Penguins." *Science* 295(5563):2270-2273 (2002). doi:10.1126/science.1068105 Paywalled at the publisher; abstract verified via PubMed… No URL was recorded in the original definition. - [^millar-2008] — **retained source note; source identity or source-level note.** **Local key:** `millar-2008`; **file:** `papers/millar-2008_adelie-penguin-mutation-evolutionary-rates.pdf`. **Original-note summary:** Millar, Craig D.; Dodd, Andrew; Anderson, Jennifer; et al. "Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic." *PLoS Genetics* 4(10):e1000209 (2008). The best-controlled test of this question in any species: a pedigree mutation rate and a radiocarbon-calibrated ancient-DNA… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC2546446/. - [^subramanian-2009] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Subramanian, Sankar, et al. "High mitogenomic evolutionary rates and time dependency." *Trends in Genetics* 25(11):482-486 (2009). doi:10.1016/j.tig.2009.09.005 In ancient Adélie penguin mitochondrial genomes up to 44,000 years old, the rate at functionally constrained sites varies more than… No URL was recorded in the original definition. - [^shapiro-2004] — **verification/access flag; source identity or source-level note.** **Local key:** `shapiro-2004`; **file:** `papers/shapiro-2004_beringian-steppe-bison.pdf`. **Original-note summary:** Shapiro, Beth, et al. "Rise and Fall of the Beringian Steppe Bison." *Science* 306(5701):1561-1565 (2004). doi:10.1126/science.1101074 Publisher paywalled; working copy at the Simon Fraser University repository, The bison control-region rate calibrated directly on 220 radiocarbon-dated fossils… Links: https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/15088/11A.pdf. - [^molak-ho] — **retained source note; source identity or source-level note.** **Local key:** `molak-2015`; **file:** `data/molak-2015_prolonged-decay-metazoan-mtdna/`. **Original-note summary:** Molak, Martyna, and Ho, Simon Y. W. "Prolonged decay of molecular rate estimates for metazoan mitochondrial DNA." *PeerJ* 3:e821 (2015). doi:10.7717/peerj.821 Meta-analysis of 239 metazoan mitochondrial rate estimates, finding a significant negative slope of rate against calibration age in every… No URL was recorded in the original definition. - [^wang-2023] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Wang, Richard J.; Al-Saffar, Samer I.; Rogers, Jeffrey; and Hahn, Matthew W. "Human generation times across the past 250,000 years." *Science Advances* 9(1):eabm7047 (2023). Open PDF at CC BY-NC. Generation intervals inferred from the de novo mutation spectrum: overall 26.9 ± 3.4 years, males… Links: https://par.nsf.gov/servlets/purl/10400417. - [^rohde-2004] — **retained source note; source identity or source-level note.** **Local key:** `rohde-2004`; **file:** `papers/rohde-2004_modelling-recent-common-ancestry.pdf`. **Locator recorded:** 31:56. **Original-note summary:** Rohde, Douglas L. T.; Olson, Steve; and Chang, Joseph T. "Modelling the recent common ancestry of all living humans." *Nature* 431:562-566 (30 September 2004). doi:10.1038/nature02842 Full PDF at Their conservative simulation gives a mean genealogical most recent common ancestor at 1415 BC and a… Links: http://www.stat.yale.edu/~jtc5/papers/CommonAncestors/NatureCommonAncestors-Article.pdf. - [^hein-2004] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** 31:51. **Original-note summary:** Hein, Jotun. "Human evolution: Pedigrees for all humanity." *Nature* 431:518-519 (2004). PDF at The News & Views accompanying Rohde et al., and the shortest correct statement of why that result does not bear on mitochondrial Eve: universal genealogical ancestry "does not imply that an individual… Links: http://www.stat.yale.edu/~jtc5/papers/CommonAncestors/Nature_NewsAndViews.pdf. - [^arbeithuber-2025] — **verification/access flag; source identity or source-level note.** **Local key:** `arbeithuber-2025`; **file:** `papers/arbeithuber-2025_human-oocyte-mtdna-no-age-increase.html`. **Original-note summary:** Arbeithuber, Barbara; Ebner, Thomas; Makova, Kateryna D.; 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 CC BY-NC. Duplex sequencing, whose error rate is below… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC12327460/. - [^arbeithuber-2025:a] — **retained source note; quote/data note; parent [^arbeithuber-2025].** **Local key:** `arbeithuber-2025`; **file:** `papers/arbeithuber-2025_human-oocyte-mtdna-no-age-increase.html`. **Original-note summary:** The same laboratory's earlier results in other mammals, which is why the human null should be quoted with its limits rather than as a settled fact. Mouse: Arbeithuber et al., "Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues," *PLoS Biology*… Links: https://pmc.ncbi.nlm.nih.gov/articles/PMC7363077/; https://pmc.ncbi.nlm.nih.gov/articles/PMC9169796/. - [^henn-2009] — **retained source note; source identity or source-level note.** **Local key:** `henn-2009`; **file:** `papers/henn-2009_time-dependency-mtdna-rate.pdf`. **Original-note summary:** Henn, Brenna M.; Gignoux, Christopher R.; Feldman, Marcus W.; and Mountain, Joanna L. "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 The live Oxford Academic page returns a… Links: https://web.archive.org/web/2017/http://mbe.oxfordjournals.org/content/26/1/217.full.pdf. - [^henn-2009:a] — **retained source note; quote/data note; parent [^henn-2009].** **Local key:** `henn-2009`; **file:** `papers/henn-2009_time-dependency-mtdna-rate.pdf`. **Original-note summary:** The magnitudes, verbatim from the Discussion: "based estimates decline by about 5-fold, whereas the coding region rates decline only about 2-fold in comparison to pedigree-based estimates." Their fourteen hypervariable-region rates run from 1.10 × 10^-7^ per site per year (Japan, calibrated at… No URL was recorded in the original definition. - [^clade-rate-test] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Original-note summary:** Original to this article, and it corrects a claim an earlier draft made too strongly. The 229 radiocarbon-dated haplogroup U genomes described under the branch-shortening regression[^branch-shortening] were refitted twice: once with one slope shared across the four subclades and a separate… No URL was recorded in the original definition. - [^neanderthal-requirement] — **retained source note; source identity or source-level note.** **Local key:** —; **file:** —. **Locator recorded:** table above, and the shortfall column is 0. **Original-note summary:** Original to this article. The symmetric restatement uses the pairwise root-to-tip figures from the relative-rate alignment:[^rate-test] across all 1,890 human-by-Neanderthal pairs the Neanderthal branch averages 93.6 substitutions from the common ancestor and the human branch 102.9, a mean of 98.3… No URL was recorded in the original definition. - ## New draft footnote outside the original 173-ID namespace - [^gupta-2026] — **retained source; added for the new draft.** **Local key/file:** `gupta-2026` at `/home/projects/bereanarchive/sources/papers/gupta-2026_age-related-mtdna-blood.pdf` (text extraction alongside it). Gupta, Rahul, et al. “Mechanism of age-related accumulation of mtDNA mutations in human blood.” *Nature* 656:140–148 (6 August 2026; online 27 May 2026). DOI: [10.1038/s41586-026-10569-6](https://doi.org/10.1038/s41586-026-10569-6); [Nature article page](https://www.nature.com/articles/s41586-026-10569-6). CC BY 4.0. Whole-genome data from 736,038 people, with 620,385 retained after quality control, support age-related detection of low-level somatic blood mtSNVs through clonal expansion. This is not a maternal germline mutation-rate or mitochondrial-Eve clock measurement.