The literature

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

How to read an entry

Direction is assigned by what the source shows, not by its author's beliefs:  supports (the young-earth or design reading), undercuts (it), complicates, or background.  Verified is full when the text was read directly, abstract when only the abstract or a supplement was read, and citation when only the record was seen.  Use says whether the article cites the source or considered it and left it out, and why.  The research trail for each source, with routes and locators, is in the article's research/ dossiers.

Gene order and inversions between humans and apes

Yoo et al. 2025, "Complete sequencing of ape genomes"

Nature 641:401-418.  doi:10.1038/s41586-025-08816-3.  camp: mainstream method: measurement direction: undercuts verified: full use: cited Telomere-to-telomere genomes of six apes.  1,175 inversion calls over 10 kb (171 in chimpanzee);  63.5 percent with duplications at an end, 4.1-fold enrichment;  64-90 percent of homozygous inversions fit the tree, the rest called recurrent;  branch counts track branch length (R² = 0.77);  human branch fivefold short.  Its supplementary Table XII.67 is the data for this article's own tree test and inverted-share computation.

Kronenberg et al. 2018, "High-resolution comparative analysis of great ape genomes"

Science 360:eaar6343.  camp: mainstream method: measurement direction: undercuts verified: full use: cited Ape genomes assembled without human guidance, with two human genomes as controls.  Inversion counts 74 and 55 between humans, 446 chimpanzee.  93 percent of 29 validated large inversions flanked by duplications;  28 percent also polymorphic in humans;  some near genes expressed differently in brain organoids.  Admits earlier assemblies were "humanized".

Chimpanzee Sequencing and Analysis Consortium 2005, "Initial sequence of the chimpanzee genome"

Nature 437:69-87.  camp: mainstream method: measurement direction: background verified: full use: cited About 35 million substitutions, 5 million indels (about 90 Mb), one fusion, at least nine pericentric inversions;  no faster protein evolution on rearranged chromosomes.

Yunis and Prakash 1982, "The origin of man: a chromosomal pictorial legacy"

Science 215:1525-1530.  camp: mainstream method: measurement direction: undercuts verified: abstract use: cited High-resolution banding of four great apes and humans;  most chromosomes like the inferred ancestor;  three rearrangements shared by chimpanzee and human.  Body closed;  cited from its PubMed abstract only.

Feuk et al. 2005, "Discovery of human inversion polymorphisms…"

PLoS Genetics 1:e56.  camp: mainstream method: measurement direction: complicates verified: full use: cited 1,576 candidate inverted regions from the draft alignment, 23 of 27 tested confirmed, but only 11 of 60 supported by BAC sequence;  a human polymorphic inversion at 7p22 shares a break point with an ape pericentric inversion.  Cited both for the reuse example and as a warning against treating 1,576 as a count.

Newman et al. 2005, "A genome-wide survey of structural variation between human and chimpanzee"

Genome Research 15:1344-1356.  camp: mainstream method: measurement direction: complicates verified: full use: considered, not used 651 structural sites from fosmid ends, 174 inversion-like, 78 percent overlapping duplications.  Not used because its own authors say the method cannot separate inversions from duplicative transpositions, and the T2T data supersede its counts.

Kehrer-Sawatzki et al. 2002, chimpanzee 19 / human 17 pericentric inversion

American Journal of Human Genetics 71:375-388.  camp: mainstream method: measurement direction: complicates verified: full use: cited Both break points sequenced;  single-copy, repeat-rich, intergenic, no duplication, no gene disrupted.  Cited as the main exception to the duplication pattern.

Porubsky et al. 2020, "Recurrent inversion toggling and great ape genome evolution"

Nature Genetics 52:849-858.  camp: mainstream method: measurement direction: complicates verified: full use: cited Strand-seq inversions in four apes;  27 homoplastic loci, 85 percent duplication-flanked;  23 toggling hot spots;  a third of 150 human polymorphic inversions overlap an ape inversion.  The source for recurrence, which is both a mechanism the mainstream relies on and a limit on inversions as clean markers.

Catacchio et al. 2018, "Inversion variants in human and primate genomes"

Genome Research 28:910-920.  camp: mainstream method: measurement direction: complicates verified: full use: cited 82 percent of great ape inversions in duplicated regions against 41 percent in macaque;  two African-ape inversions back in the original orientation in chimpanzee, read as flip-back or lineage sorting.

Maggiolini et al. 2020, macaque nested inversions and break-point reuse

Genome Research 30:1680-1693.  camp: mainstream method: measurement direction: complicates verified: full use: considered, not used Human-macaque, not human-chimpanzee;  its reuse finding duplicates Porubsky's for a more distant pair.

Goidts et al. 2004; Kehrer-Sawatzki and Cooper 2007 and 2008; Stanyon et al. 2008

Human Genetics, Chromosome Research.  camp: mainstream verified: citation use: not obtained Reviews and single-inversion studies behind the standard list of nine pericentric inversions.  Springer pages returned bot challenges;  YAML records only.  The T2T data cover the same ground.

Cheng et al. 2005, "A genome-wide comparison of recent chimpanzee and human segmental duplications"

Nature 437:88-93.  camp: mainstream method: measurement direction: background verified: abstract use: considered, not used Says duplications altered 2.7 percent of the genomes against 1.2 percent for substitutions.  Not used because Yoo 2025 gives the same comparison with complete genomes.

Marques-Bonet et al. 2009, "A burst of segmental duplications in the genome of the African great ape ancestor"

Nature 457:877-881.  camp: mainstream method: measurement direction: background verified: full use: considered, not used Duplications are clustered in time and place;  new ones arise beside old ones.  Not used because Yoo 2025 revises its timing (the burst is in the great-ape ancestor) and the article needs only the break-point association.

Where breaks fall, and whether gene order is functional

Bailey et al. 2004, "Hotspots of mammalian chromosomal evolution"

Genome Biology 5:R23.  camp: mainstream method: measurement direction: complicates verified: full use: cited 25 percent of 461 human-mouse breaks contain primate duplications, never matched in 10,000 random placements;  the authors decline to call duplications the cause.

Pevzner and Tesler 2003, "Human and mouse genomic sequences reveal extensive breakpoint reuse"

PNAS 100:7672-7677.  camp: mainstream method: model direction: complicates verified: full use: cited Fragile and solid regions;  at least 190 reuses inferred.  The hidden-block inference is a model result.

Lemaitre et al. 2009, "Analysis of fine-scale mammalian evolutionary breakpoints…"

BMC Genomics 10:335.  camp: mainstream method: measurement direction: complicates verified: full use: cited Breaks avoid genes but are ten times denser between close genes than in gene deserts;  model combines selection and an open-chromatin mutational bias.

Larkin et al. 2009, "Breakpoint regions and homologous synteny blocks…"

Genome Research 19:770-777.  camp: mainstream method: measurement direction: complicates verified: full use: cited Ten amniotes;  conserved blocks enriched for developmental genes, break regions for duplications and adaptive genes.  Evidence for both function and mechanism.

Kikuta et al. 2007, "Genomic regulatory blocks…"

Genome Research 17:545-555.  camp: mainstream method: experiment direction: supports verified: full use: cited Enhancers inside neighbouring genes hold developmental gene blocks together across vertebrates.  The clearest mainstream support for the design side's premise that some gene order is functional.

Lazar et al. 2018, "Epigenetic maintenance of topological domains in the highly rearranged gibbon genome"

Genome Research 28:983-997.  camp: mainstream method: measurement direction: complicates verified: full use: cited 55 of 67 gibbon-human breaks on domain boundaries;  domains moved intact;  fragility and selection both proposed.

Fudenberg and Pollard 2019, "Chromatin features constrain structural variation across evolutionary timescales"

PNAS 116:2175-2180.  camp: mainstream method: measurement direction: supports verified: full use: cited 2,565 fixed ape deletions avoid active chromatin and domain boundaries;  read as purifying selection.  Deletions only.

Gierman et al. 2007, "Domain-wide regulation of gene expression in the human genome"

Genome Research 17:1286-1295.  camp: mainstream method: experiment direction: complicates verified: full use: cited One reporter at 90 sites;  up to eightfold domain effect;  weak, non-significant effect of immediate neighbours.

Wilson et al. 2008, "Species-specific transcription in mice carrying human chromosome 21"

Science 322:434-438.  camp: mainstream method: experiment direction: background verified: full use: cited A whole human chromosome 21 in mouse keeps human-like binding and expression;  sequence over environment.  Cited because Jeanson 2013 uses it for gene order, which it did not test.  Read from the author manuscript and the PubMed abstract.

Hurst, Pál and Lercher 2004; Lercher, Urrutia and Hurst 2002

Nature Reviews Genetics 5:299-310;  Nature Genetics 31:180-183.  camp: mainstream method: review direction: complicates verified: full / abstract use: considered, not used The reviews that set out gene clustering by expression.  Not used because the article's functional point is carried by the experimental papers above;  Lercher 2002 was read in abstract only.

Murphy et al. 2005; Berthelot et al. 2015

Science 309:613-617;  Cell Reports 10:1913-1924.  camp: mainstream verified: citation use: not obtained The 20 percent reuse figure and the main test of three-dimensional chromatin at break points.  Routes tried are in the function dossier.  Not cited in the article.

The Y chromosome

Hughes et al. 2010, "Chimpanzee and human Y chromosomes are remarkably divergent…"

Nature 463:536-539.  camp: mainstream method: measurement direction: complicates verified: full use: cited 98.3 percent identity where aligned;  over 30 percent unalignable;  4 of 16 X-degenerate genes lost in chimpanzee;  two-thirds as many gene families;  four proposed causes.  Quoted from the published Nature text;  the PMC author manuscript differs in wording and is not quoted.

Hughes et al. 2005, "Conservation of Y-linked genes during human evolution…"

Nature 437:100-103.  camp: mainstream method: measurement direction: complicates verified: abstract use: cited Main text not obtained;  abstract and supplementary figures read.  USP9Y splice mutations confirmed in 14 more chimpanzees.

Hughes et al. 2012, "Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes"

Nature 483:82-86.  camp: mainstream method: measurement direction: background verified: full use: cited Human Y gene loss since the rhesus split confined to the youngest stratum.  Quoted from the published abstract.

Makova et al. 2024, "The complete sequence and comparative analysis of ape sex chromosomes"

Nature 630:401-411.  camp: mainstream method: measurement direction: undercuts verified: full use: cited 14-27 percent of the human Y covered by other ape Y chromosomes;  60-87 percent between sister species;  Y divergence 2.68 percent;  per-branch structural variant counts;  sequence-class lengths.  Its Figure 1b, read from the rendered page, supplies the within-kind comparisons.

Cechova et al. 2020, "Dynamic evolution of great ape Y chromosomes"

PNAS 117:26273-26280.  camp: mainstream method: measurement direction: background verified: full use: cited Y-to-autosome substitution ratio 1.76 in chimpanzee, 1.45 in human;  orangutans a case against sperm competition.

Hallast et al. 2023, "Assembly of 43 human Y chromosomes…"

Nature 621:355-364.  camp: mainstream method: measurement direction: undercuts verified: full use: cited Human Y chromosomes 45.2-84.9 Mb;  half the euchromatin in recurrent inversions;  88 structural variants per Y against the reference.  Abstract quoted from the published version;  body numbers from the author manuscript, paraphrased.

Repping et al. 2006, "High mutation rates have driven extensive structural polymorphism among human Y chromosomes"

Nature Genetics 38:463-467.  camp: mainstream method: measurement direction: undercuts verified: abstract use: cited Lower bounds of 2.3-4.4 × 10⁻⁴ large rearrangements per transmission.  Abstract only.

Rhie et al. 2023; Rozen et al. 2003; Hallast et al. 2013; Skaletsky et al. 2003

Nature 621:344-354;  Nature 423:873-876;  PLoS Genetics 9:e1003666;  Nature 423:825-837.  camp: mainstream method: measurement verified: full / abstract use: considered, not used The complete human Y, palindrome gene conversion and the human Y sequence classes.  Not used because Makova 2024 and Hallast 2023 carry the needed numbers;  Rozen's per-nucleotide conversion rate is known only secondhand.

Langergraber et al. 2012, "Generation times in wild chimpanzees and gorillas…"

PNAS 109:15716-15721.  camp: mainstream method: measurement direction: background verified: full use: cited Chimpanzee male generation time 24.1 years;  human 29 years from an earlier survey.

The positions tested

Venema 2010, "Genesis and the genome"

Perspectives on Science and Christian Faith 62:166-178.  camp: theistic-evolution method: review direction: undercuts verified: full use: cited The common-descent synteny prediction in its own words;  the fruit-fly point that many gene orders work.

Venema and Falk 2010, "Signature in the synteny"

BioLogos.  camp: theistic-evolution method: commentary direction: undercuts verified: full use: cited The "no good biological reason" sentence the design side answers.

Venema 2014, "Intelligent design and common ancestry, part 3"; Theobald, 29+ Evidences

BioLogos;  TalkOrigins.  camp: theistic-evolution, mainstream method: commentary verified: full use: considered, not used Restate the synteny argument;  Venema 2010 and Venema and Falk 2010 state it more fully.

Luskin 2026, "Bad synteny arguments…"; Luskin 2026c on Kuebler's book

Science and Culture Today.  camp: intelligent-design method: commentary direction: supports verified: full use: cited (2026b); considered (2026c, used only for Kuebler's name and post) Gene order is functional, so "no functional reason" is outdated.  Quotes Kuebler, Darwin and Doctrine, pp. 108-109;  the book itself was not obtained.

Carter 2010, "Chimpanzee Y chromosome is radically different from human"

creation.com.  camp: creationist method: commentary direction: supports verified: full use: cited Mostly accurate report of Hughes 2010;  one slip, treating "under 10 percent lacks a counterpart" as a 10 percent divergence.

Carter 2016, "The four dimensional human genome…"

creation.com.  camp: creationist method: commentary direction: supports verified: full use: cited Genes used together sit together in three-dimensional space.

Carter 2021, "Species were designed to change, part 3"

creation.com.  camp: creationist verified: full use: considered, not used Mentions lack of shared synteny as a species barrier in general terms;  no human-ape claim.

Tomkins and Bergman 2012, "Genomic monkey business"

Journal of Creation 26(1):94-100.  camp: creationist method: review direction: supports verified: full use: cited The Y as an "insurmountable paradox" because it is the "least variable chromosome";  says human Ys show "very few structural differences", which Repping 2006 had already contradicted.

Tomkins 2017, "Debunking the debunkers"

Answers Research Journal 10:45-54.  camp: creationist method: commentary direction: supports verified: full use: cited Synteny evidence rested on a human-scaffolded assembly;  asks for an unbiased assembly, which now exists.

Tomkins 2024, "New DNA sequences of the Y chromosome refute human-ape evolution"

ICR.  camp: creationist method: commentary direction: supports verified: full use: cited Reports Makova's 26.2 percent coverage as "26% similar";  calls chimpanzees, gorillas and orangutans each a kind;  transcribes one figure as 40.1 where the figure reads 41.1.

Tomkins and Thomas 2010; Tomkins 2013 (ARJ 6:63-69); Bergman and Tomkins 2011; Tomkins and Bergman 2011

ICR, Answers Research Journal, Journal of Creation.  camp: creationist verified: full use: considered, not used Earlier statements of the same Y and scaffold arguments.  Not used because Tomkins and Bergman 2012 and Tomkins 2024 state them more fully;  the 53 and 33 percent gene figures in the 2010 piece come from Hughes's Table 1.

Jeanson 2013, "An update on chromosome 2 'fusion'"

Acts & Facts 42(9):13.  camp: creationist method: commentary direction: supports verified: full use: cited Gene order not independently determined;  no one has tested its function;  cites Wilson 2008 for gene order, which that study did not test.

Jeanson 2017, Replacing Darwin

Master Books.  camp: creationist verified: full (search inside) use: considered, not used No synteny or chimpanzee-Y passage;  orangutans discussed as two species with no kind statement.

Wood 2006, "The chimpanzee genome and the problem of biological similarity"

Occasional Papers of the BSG 7:1-18.  camp: creationist method: review direction: complicates verified: full use: cited Accepts near-identity of gene sequences;  calls the effect of gene arrangement on expression a "foundational assumption".

Wood 2010, "Chimp and human Y chromosomes radically different?"

Todd's Blog.  camp: creationist method: commentary direction: undercuts verified: full use: cited Accepts Hughes 2010 and expects a variable region like the Y to differ;  disagrees in substance with Tomkins and Bergman.

Wood 2010, "Baraminological analysis places Homo habilis… in the human holobaramin"

Answers Research Journal 3:71-90.  camp: creationist method: model direction: complicates verified: full use: cited Proposed holobaramin with both chimpanzee species and gorilla;  humans and apes separate kinds.

Lightner 2012, "Mammalian Ark kinds"

Answers Research Journal 5:151-204.  camp: creationist method: review direction: complicates verified: full use: cited One great ape kind for gorilla, chimpanzee and orangutan.

O'Micks 2016, reply on taxon sample in hominin baraminology

Answers Research Journal 9:373-375.  camp: creationist verified: full use: considered, not used Humans and chimpanzees in separate baramins "intuitively";  adds nothing on ape kinds.

Sherwin 2023, "Dubious views on octopus evolution"

ICR.  camp: creationist method: commentary direction: supports verified: full use: cited Creationists accept observed synteny and question the inference of divergence.

Hardy and Carter 2014, "The biblical minimum and maximum age of the earth"

Journal of Creation 28(2):89-96.  camp: creationist method: model direction: background verified: full use: cited Flood certainly between 3386 and 2256 BC;  used for the time window in the Y pricing.