Synteny, Gene Order, and the Y Chromosome

Hughes, Jennifer F. et al.  “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.”  Nature 463:536–539.  Jan 28, 2010.  The finished sequence of the chimpanzee male-specific Y region, from one male, compared with the human one.  The Page laboratory found large differences in structure and gene content and proposed four causes.  The source of most numbers quoted on both sides of this topic.

1. 1a.

   Page 537:  “we found that the degree of similarity between orthologous chimpanzee and human MSY sequences (98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%). Surprisingly, however, >30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa”. ↩ ↩ ↩

2. 1b.

   Page 538:  “we previously discovered that the chimpanzee X-degenerate regions had lost 4 out of 16 genes through inactivating mutations, whereas the human X-degenerate regions had not lost any genes since the time of the last common ancestor”. ↩ ↩ ↩

3. 1c.

   Page 538:  “the chimpanzee MSY contains only two-thirds as many distinct genes or gene families as the human MSY, and only half as many protein-coding transcription units (Table 1).”  “Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation”. ↩ ↩

4. 1d.

   Page 536:  “We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, ‘genetic hitchhiking’ effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour.” ↩

5. 1e.

   Page 539:  “The evolutionary effect of these three MSY features was probably multiplied by sperm competition, especially in the lineage of the modern chimpanzee, in which several males mate with the same female at each oestrus”.  “This heightened sperm competition in the chimpanzee lineage, along with positive selection and hitchhiking effects, may account for greater MSY sequence amplification than in the human MSY, and extensive gene loss compared with little or none in the human MSY.” ↩

Luskin, Casey.  “Bad synteny arguments claim "no functional reason" for genomic arrangements.”  Science and Culture Today.  May 20, 2026.  A Discovery Institute writer replies to the synteny argument in Daniel Kuebler's book Darwin and Doctrine, listing research on three-dimensional genome organization.  The most recent statement of the design reply.

1. 2a.

   Section Very Outdated Science:  “The problem with this argument is it’s based upon very outdated science. In fact, it’s shocking to me that a biologist in the 2020s would claim that there is “no functional reason” for the arrangement of genes on chromosomes.” ↩

2. 2b.

   Section Very Outdated Science:  “Much of what we have learned about genomics shows there are important reasons, core to genome function, for why chromosomes are structured the way they are.” ↩

3. 2c.

   Paragraph 3:  “Given that there seems to be no functional reason the genes found in these synteny blocks should be in a similar order in two distinct species (the likelihood of this happening by chance is vanishingly small), the most parsimonious explanation is that they were inherited in that specific order from a shared common ancestral species.”  Luskin is quoting Kuebler, pages 108–109. ↩

Yoo, DongAhn et al.  “Complete sequencing of ape genomes.”  Nature 641:401–418.  2025.  Telomere-to-telomere genomes of chimpanzee, bonobo, gorilla, two orangutans and siamang, each built from that ape's own long reads and compared with the complete human genome.  Its Supplementary Note XII catalogues 1,175 inversions over 10,000 letters with their break points, duplications and genes, and places them on the ape tree.  The main source for the counts and tests here.

1. 3a.

   Page 401:  “Comparative analyses enabled investigations of the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference genome.” ↩

2. 3b.

   Page 403:  “We inferred ILS for an average of 39.5% of the autosomal genome and 24% of the X chromosome.” ↩

3. 3c.

   Page 406:  “We identified at the sequence level all 26 large-scale chromosomal rearrangements originally described decades ago44 that karyotypically distinguish humans from other great apes”.  Reference 44 is Yunis and Prakash 1982. ↩ ↩ ↩

4. 3d.

   Page 406:  “In total, 416 inversions had an annotated gene mapping to at least 1 of the breakpoints, with 724 apparently devoid of protein-coding genes (Supplementary Table XII.67). Of these inversions, 63.5% (724 out of 1,140) had annotated human SDs at one or both ends of the inversion, a result that represents a significant 4.1-fold enrichment (one-sided, simulation empirical P < 0.001). The strongest signal was for inverted SDs mapping to the breakpoints (6.2-fold; one-sided, simulation empirical P < 0.001), which suggested that non-allelic homologous recombination is driving many of these events.”  The same split, 416 and 724, appears for genes and for duplications.  Supplementary Note XII, page 102, gives both counts separately. ↩ ↩ ↩

5. 3e.

   Page 406:  “We also observed significant enrichment of previously unknown transcripts (Supplementary Table VIII.35) at the breakpoints of the inversions of African great apes (one-sided, simulation empirical P < 0.036).” ↩ ↩

6. 3f.

   Page 406:  “We parsimoniously assigned >64% of homozygous inversions to the ape phylogeny (Supplementary Fig. XII.45), with the remaining inversions predicted to be recurrent. The number of inversions assigned to each branch, based on maximum parsimony, correlated with the length of the branch (linear regression, R2 = 0.77), with the greatest number assigned to the siamang lineage (n = 44). However, the human lineage showed fivefold less than the expected number of inversions based on the branch length, and the trend still held when using the Bornean orangutan as a reference instead of human.” ↩ ↩ ↩ ↩

7. 3g.

   Page 415:  “The African great ape lineage still stands out for having the largest fraction of interspersed SDs—a genomic architectural feature that promotes recurrent rearrangements that facilitate syndromic disease associated with autism and developmental delay in the human species”. ↩

8. 3h.

   Page 413:  “we found the largest number of lineage-specific SDs in the Pongo lineage (100.1 Mb), followed by gorilla-specific and human-specific SDs (69.5 and 41.9 Mb, respectively”.  “In general, the number of SDs assigned to different lineages correlated with branch length (linear regression, R2 = 0.927”. ↩ ↩

9. 3i.

   Section Supplementary Note XII, SI page 101:  “We identified a total of 1,175 inversion variants larger than 10 kbp as well as one large-scale chromosome fusion and one translocation (Supplementary Fig. XII.43) across six species; the breakdown of identified inversions is as follows: 188 in bonobo, 171 in chimpanzee, 199 in gorilla, 180 in Bornean orangutan, 180 in Sumatran orangutan, and 257 in siamang.”  Section Supplementary Note XII, SI page 102:  “Filtering out the false inversion calls of 1,175 inversions larger than 10 kbp, 1,140 inversion calls remain.” ↩ ↩ ↩

10. 3j.

    Section Supplementary Note XII, SI page 102:  “Out of the 1,140 inversions, 632 are homozygous (found in both haplotypes of the same individual), while 508 are heterozygous and potentially polymorphic in the population.”  Supplementary Table XII.67 marks 96 of the 171 chimpanzee calls as homozygous. ↩

11. 3k.

    Section Supplementary Note XII, SI page 102:  “Of the inversions without SDs, 289 have other types of repeat elements mapping at both breakpoints and 35 have repeats at only one breakpoint, while 92 are completely devoid of any repeats.” ↩ ↩

12. 3l.

    Section Supplementary Note XII, SI page 102:  “Investigating 100 kbp flanking regions of inversions, we find that inversion breakpoints are typically enriched for T2T human SDs (p<0.001) compared to random genomic regions by 4.6-fold (flanking of the randomly shuffled inversions; Supplementary Fig. XII.44).” ↩

13. 3m.

    Section Supplementary Note XII, SI pages 101–102:  “We resolved 40 breakpoints of the Yunis and Prakash large chromosome inversions; all breakpoints differ by a maximum of ~700 kbp from previous cytogenetic mapping”. ↩

Yunis, Jorge J., and Om Prakash.  “The origin of man: a chromosomal pictorial legacy.”  Science 215(4539):1525–1530.  Mar 19, 1982.  A comparison of high-resolution banded chromosomes of orangutan, gorilla, chimpanzee and human.  It inferred the chromosomes of the common ancestor and placed each rearrangement on a branch.  Cited here as the first map of human-ape chromosome differences, made from stained chromosomes with no DNA sequence or genome assembly.

1. 4a.

   Section Abstract:  “A comparative analysis of high-resolution chromosomes from orangutan, gorilla, chimpanzee, and man suggests that 18 or 23 pairs of chromosomes of modern man are virtually identical to those of our "common hominoid ancestor", with the remaining pairs slightly different.” ↩ ↩ ↩

2. 4b.

   Section Abstract:  “three major chromosomal rearrangements presumably occurred in a progenitor of chimpanzee and man”. ↩

Chimpanzee Sequencing and Analysis Consortium.  “Initial sequence of the chimpanzee genome and comparison with the human genome.”  Nature 437:69–87.  Sep 1, 2005.  The first chimpanzee genome, a draft from one male, compared with the human genome.  It counted the single-letter differences, the insertions and deletions, and the known chromosome rearrangements, and tested whether proteins evolve faster on rearranged chromosomes.  The source of the event counts used here.

1. 5a.

   Page 73:  “Of course, the number of indel events is far fewer than the number of substitution events (~5 million compared with ~35 million, respectively).” ↩ ↩ ↩

2. 5b.

   Page 73:  “the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions”. ↩

3. 5c.

   Page 75:  “Cytogenetic studies have shown that human and chimpanzee chromosomes differ by one chromosomal fusion, at least nine pericentric inversions, and in the content of constitutive heterochromatin”. ↩ ↩

4. 5d.

   Page 78:  “With our larger data set, we re-examined this issue and found no evidence of accelerated evolution on chromosomes with major rearrangements, even if we considered each rearrangement separately”. ↩

This article's own computation from Supplementary Table XII.67 of Yoo and colleagues 2025, which lists every inversion over 10,000 letters called against the human T2T-CHM13 genome (script research/inversion-table.ts).  For the chimpanzee:  171 inversions, 96 on both chromosome copies;  the union of the inverted stretches, in human coordinates, is 357.0 million letters, 11.5 percent of 3.1 billion (homozygous only:  337.4 million, 10.9 percent).  Nested inversions restore orientation inside, so the union slightly overstates the inverted share.  Gene neighbourhoods:  171 inversions have at most 342 ends, plus the fusion, about 344 in all, against about 20,000 protein-coding genes, so at most about 1.7 percent of gene-to-neighbour adjacencies can be broken.  Only 53 of the 171 have any gene listed in the table's break-point columns, and a listed gene is not necessarily broken. ↩ ↩ ↩

This article's arithmetic.  Substitutions:  about 35 million events, about 35 million letters (the 2005 consortium's 1.23 percent of about 2.4 billion aligned letters;  the 2025 divergence of 1.5 to 1.6 percent raises this to about 40 to 45 million).  Small insertions and deletions:  about 5 million events, about 67 million letters (32 plus 35 million).  All insertions and deletions:  about 90 million letters.  Inversions:  171 events enclosing about 340 to 360 million letters.  By count, 171 inversions among about 40 million events is one in about 235,000;  the text rounds to one in 200,000.  By letters, 90 million in insertions and deletions plus 41.9 million in human-specific duplications against 35 to 45 million substituted gives two to three times;  357 million inside inversions against about 45 million gives about eight times. ↩ ↩

Kronenberg, Zev N. et al.  “High-resolution comparative analysis of great ape genomes.”  Science 360(6393).  Jun 8, 2018.  The Eichler laboratory built chimpanzee and orangutan genomes from long reads without using the human genome as a guide, and compared them with two human genomes built the same way.  The human pair gives a built-in control for structural differences.  It also validated 29 large inversions with physical maps.  Cited here for the assemblies that answer the scaffold objection and for the inversion counts.

1. 8a.

   Section Introduction:  “the higher quality human genome assemblies have often been used to guide the final stages of nonhuman genome projects, including the order and orientation of sequence contigs and, perhaps more importantly, the annotation of genes.  This bias has effectively "humanized" other ape genome assemblies”. ↩ ↩

2. 8b.

   Section Results, Genome assembly:  “We next scaffolded the chimpanzee and orangutan genomes without guidance from the human reference genome.” ↩

3. 8c.

   Table 3:  Structural variants over 50 letters called against the GRCh38 human reference.  Inversion counts:  CHM13 human 74, Yoruba human 55, chimpanzee 446, gorilla 533, orangutan 969.  Deletions plus insertions, million letters:  CHM13 4.76 + 6.85, Yoruba 4.85 + 7.17, chimpanzee 41.88 + 40.34. ↩ ↩

4. 8d.

   Section Results, Structural variation analyses:  “More than 93% of inversions are flanked by large complex segmental duplication (SD) blocks, 38% of which show evidence of other structural and copy number variation at the boundaries of the inversion”.  “Interestingly, ~28% (8/29) of these ape–human inversions are also polymorphic among humans”. ↩ ↩ ↩ ↩ ↩

5. 8e.

   Section Results, Structural variation analyses:  “among the 18 chimpanzee–human inversions ( Table S12 ), we identified 18 differentially expressed brain genes between chimpanzee and human (10 radial glia, 11 excitatory neurons, 3 common to both sets), of which 78% resided in SD regions.” ↩ ↩

This article's test of Yoo Supplementary Table XII.67 (script research/inversion-tree-test.ts).  Calls in different apes were merged when they overlap by at least 80 percent each way, Yoo's own rule.  An inversion shared by a set of apes fits the tree (((human, (chimpanzee, bonobo)), gorilla), (Bornean, Sumatran orangutan), siamang) if that set is one side of a branch of the tree:  a single ape, chimpanzee with bonobo, the two orangutans, orangutans with siamang, gorilla with orangutans and siamang, or all six apes, which is an inversion specific to humans.  The chance expectation keeps the number of apes sharing each inversion and assigns which apes at random.  All calls over 10,000 letters:  823 merged inversions, 220 shared by two or more apes, 150 fit (68.2 percent), 29.8 expected by chance (13.5 percent).  Homozygous calls only:  132 shared, 91 fit (68.9 percent), 17.6 expected.  Over 100,000 letters:  128 shared, 83 fit, 17.0 expected.  Over 1 million letters:  46 shared, 30 fit, 6.5 expected.  Commonest conflict:  chimpanzee, bonobo and gorilla sharing an inversion that human and the orangutans lack, 14 cases.  Share of inversions with a human duplication at either end:  single-ape inversions 56 percent, shared inversions that fit 60 percent (90 of 150), shared inversions that conflict 71 percent (50 of 70);  Fisher's exact test p = 0.13, not significant.  The test is unrooted and treats a missed call in one ape as a real absence, so some conflicts will be calling errors. ↩ ↩ ↩ ↩ ↩

Porubsky, David et al.  “Recurrent inversion toggling and great ape genome evolution.”  Nature Genetics 52(8):849–858.  2020.  Inversions in chimpanzee, bonobo, gorilla and orangutan found with Strand-seq, a single-cell method that reads which DNA strand each fragment came from, and compared with 150 inversions that vary among humans.  It identified break-point hot spots where the same region has flipped repeatedly.  The main source for recurrence.

1. 10a.

   Section Results, Phylogenetic reconstruction:  “Interestingly, we identified 27 inverted loci that show evidence of homoplasy ( Fig. 2a , black asterisks) either due to recurrent mutation or incomplete lineage sorting. For instance, 5 inversions shared between human, gorilla, and orangutan were absent in the Pan lineage, 11 out of the 27 likely recurrent loci reside on chromosome X, and 85% (23/27) are flanked by known human SDs.”  Section Discussion:  “Several lines favor recurrent hotspots of mutation—85% (23/27) of these hotspots, for example, are flanked by SDs that would promote recurrent mutation by NAHR.” ↩ ↩ ↩

2. 10b.

   Section Results, Human polymorphism and inversion hotspots:  “Strikingly, we found one-third (49/150) of the human polymorphic inversions overlapped with an inversion detected in an NHP”.  “Inversion breakpoints were not randomly distributed but clustered into 23 discrete genomic regions”. ↩ ↩

3. 10c.

   Section Abstract:  “We construct megabase-pair-scale haplotypes for individual chromosomes and identify 23 genomic regions that have recurrently toggled between a direct and inverted state over 15 million years.” ↩

Lazar, Nathan H. et al.  “Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.”  Genome Research 28(7):983–997.  2018.  Maps of three-dimensional chromatin contacts in the gibbon, whose chromosomes are among the most reshuffled of any ape, compared with 67 breaks in gibbon-human gene order.  Most breaks fall on the boundaries of regulatory domains.  The authors weigh fragile boundaries against selection that removes breaks inside domains, and favour both.

1. 11a.

   Section Results, Large new TADs are rarely generated:  “When looking at boundaries of TADs sized 500 kb–1 Mb, we find that 55 of 67 BOS overlap with TAD boundaries in gibbon; for 31 of these BOS, both sides colocalize with TAD boundaries in the human genome, which represents the ancestral state.” ↩ ↩

Kikuta, Hiroshi et al.  “Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.”  Genome Research 17(5):545–555.  2007.  Reporter insertions in zebrafish and the fate of duplicated gene blocks after the fish genome duplication.  Enhancers for developmental genes sit inside neighbouring, unrelated genes, and the blocks were kept intact.  A mainstream paper showing that some shared gene order is held in place by function.

1. 12a.

   Section Abstract:  “After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact.”  “These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments”. ↩ ↩ ↩ ↩

Venema, Dennis R., and Darrel R. Falk.  “Signature in the synteny.”  The BioLogos Forum.  Apr 19, 2010.  A BioLogos essay presenting shared gene order between humans and chimpanzees as evidence of common ancestry, written in reply to intelligent-design writers.  The source of the "no good biological reason" claim that young-earth writers answer.  Mirror:  Archive.org

1. 13a.

   Paragraph What makes shared synteny:  “What makes shared synteny for humans and chimpanzees challenging from an anti-common descent viewpoint is that there is no good biological reason to find the same genes in the same order in unrelated organisms, and every good reason to expect very different gene orders.”  Paragraph In summary:  “In summary, should God have wished to avoid the appearance of common ancestry between humans and chimpanzees, there seem to have been many gene orders and chromosome structures available to Him to use for either species.” ↩ ↩ ↩

Jeanson, Nathaniel T.  “An update on chromosome 2 'fusion'.”  Acts & Facts 42(9):13.  2013.  A young-earth biologist's short reply to the BioLogos synteny argument, arguing that chimpanzee gene order had not been independently determined and that gene order may be functional.

1. 14a.

   Paragraph Second:  “when the chimpanzee DNA sequence was elucidated, the researchers did not independently determine the gene order along all of the chimpanzee chromosomes, and this led to gross overestimates of the overall genetic similarity between the two species.” ↩ ↩

2. 14b.

   Paragraph Second:  “Conversely, of the two chimpanzee chromosomes for which the gene order has been more precisely determined (e.g., the Y chromosome and chromosome 22), the Y chromosome possesses a gene order dramatically different from humans.” ↩

3. 14c.

   Paragraph Even if the gene order:  “These claims represent premature assumptions stated as fact. No one has comprehensively tested whether gene order along human chromosome 2 has a functional impact on the gene’s function.” ↩

4. 14d.

   Paragraph Even if the gene order:  “when human chromosome 21 was inserted into mouse cells, this experiment revealed that the chromosomal context—and gene order—for a gene does impact its function.”  Jeanson's reference is Wilson and colleagues 2008. ↩

Tomkins, Jeffrey P.  “Debunking the debunkers: a response to criticism and obfuscation regarding refutation of the human chromosome 2 fusion.”  Answers Research Journal 10:45–54.  2017.  A young-earth geneticist's reply to critics of his work on the chromosome 2 fusion site.  Cited for his argument that synteny evidence then rested on a chimpanzee assembly scaffolded on the human genome.

1. 15a.

   Page 50:  “Clearly the assembly of chimpanzee chromosome 2B is full of meaningless data. In other words, proclaiming that gene synteny supports fusion based on a highly suspect assembly using human as a scaffold is an error of logic called begging the question.”  “At this point, the issue of synteny between human and chimpanzee around the cryptic centromere remains to be resolved until an unbiased assembly of the chimpanzee genome is achieved.” ↩ ↩ ↩

Makova, Kateryna D. et al.  “The complete sequence and comparative analysis of ape sex chromosomes.”  Nature 630:401–411.  Jun 13, 2024.  Telomere-to-telomere X and Y chromosomes of five great apes and the siamang, one male each, compared with the complete human X and Y.  It measured alignability, divergence, structural variants per branch, palindromes, satellites and gene copy numbers.  The main source for the Y here, including the within-kind comparisons.

1. 16a.

   Page 402:  “Only 14–27% of the human Y chromosome was covered by alignments to the other ape Y chromosomes, whereas as much as 93–98% of the human X chromosome was covered by alignments to the other ape X chromosomes”.  “the human–chimpanzee divergence was 2.68% on the Y chromosome and 0.97% on the X chromosome.” ↩

2. 16b.

   Page 402:  “The same pattern was observed for closely related species, with only 60–87% of the Y chromosome, but more than 95% of the X chromosome, aligned between them”.  The paper's two pairs of closely related species are chimpanzee with bonobo and Bornean with Sumatran orangutan. ↩ ↩

3. 16c.

   Page 402:  “Ape Y chromosomes ranged in size from 30 Mb in siamang to 68 Mb in S. orangutan and differed by as much as 19 Mb between the two orangutan species and 11 Mb between bonobo and chimpanzee.” ↩

4. 16d.

   Page 402:  “chimpanzee and bonobo, which diverged from each other around 2.5 Ma”. ↩

5. 16e.

   Page 403, figure 1b:  Share of each reference Y covered by alignments to each other ape's Y.  Human Y covered by chimpanzee 26.2 percent;  chimpanzee Y covered by human 45.1 percent;  chimpanzee Y covered by bonobo 65.3 percent;  bonobo Y covered by chimpanzee 59.6 percent;  Bornean orangutan Y covered by chimpanzee 30.8 percent;  chimpanzee Y covered by Bornean orangutan 40.6 percent. ↩ ↩ ↩ ↩

6. 16f.

   Table Supplementary Table S14:  Y chromosome lengths by sequence class, in letters.  Human (CHM13):  total 62,460,029, satellite 37,014,638, ancestral (X-degenerate) 6,945,812, ampliconic 11,744,642, X-transposed 3,387,391.  Chimpanzee:  total 36,445,859, satellite 8,308,921, ancestral 7,391,585, ampliconic 17,202,790. ↩ ↩ ↩

7. 16g.

   Table Supplementary Table S11:  Structural variants on the Y by branch of origin.  Chimpanzee branch:  242 deletions, 747 insertions, 0 inversions, over 16.36 million aligned letters.  Bonobo branch:  240 deletions, 608 insertions, 4 inversions, over 16.61 million. ↩

8. 16h.

   Page 409:  “In contrast to the X chromosome, the Y chromosome has undergone rapid evolution in all ape species. It has accumulated repetitive elements and experienced elevated rates of nucleotide substitutions, intrachromosomal rearrangements and segmental duplications, probably owing to the loss of recombination over most of its length.” ↩

Wood, Todd Charles.  “Baraminological analysis places Homo habilis, Homo rudolfensis, and Australopithecus sediba in the human holobaramin.”  Answers Research Journal 3:71–90.  2010.  A young-earth statistical baraminology study of published skull and tooth measurements of fossil hominins and living apes, proposing which taxa share a created kind with humans.  Cited for its proposed grouping of both chimpanzee species and its conclusion that humans and apes are separate kinds.

1. 17a.

   Page 86, table Summary of proposed holobaramins:  The row "Australopith #2" lists Pan troglodytes, Pan paniscus, Gorilla gorilla, Au. afarensis, Au. garhi and S. tchadensis, with Pongo pygmaeus among possible additional taxa.  “The discontinuity here demonstrated between Homo sensu lato (including “Au.” sediba) and nonhuman primates confirms the creationist prediction that humans and apes are separate created kinds.” ↩ ↩

Lightner, Jean K.  “Mammalian Ark kinds.”  Answers Research Journal 5:151–204.  2012.  A survey, published by Answers in Genesis, assigning living mammals to the kinds that would have been on the Ark, usually at the level of the family, with hybrid records as the main evidence.  Cited for its single great ape kind.

1. 18a.

   Page 171:  “Pongidae (Great ape kind) Wilson and Reeder (2005) place the great apes in Hominidae with humans, but given the significant differences between us and apes compared to some of the differences between other families, this seems ludicrous. Therefore, the older designation Pongidae is used here. There are three genera and six species in this family, which includes the gorilla, chimpanzee, and orangutan.” ↩ ↩

Hallast, Pille et al.  “Assembly of 43 human Y chromosomes reveals extensive complexity and variation.”  Nature 621:355–364.  2023.  Near-complete assemblies of 43 Y chromosomes from men of 21 Y lineages, most of them African, compared with each other.  The first direct view of how much human Y chromosomes differ in size and structure.  The within-species control for the chimpanzee-human comparison.

1. 19a.

   Page 355:  “Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes.” ↩ ↩ ↩ ↩

2. 19b.

   Section Results, Size variation of the assembled Y chromosomes:  Assembled Y chromosomes range from 45.2 to 84.9 million letters, with the heterochromatic Yq12 region alone ranging from 17.6 to 37.2 million. ↩ ↩

3. 19c.

   Section Results, Y-chromosomal inversions:  About one recurrent inversion per 603 father-to-son transmissions, with a 95 percent interval of 533 to 684. ↩ ↩

4. 19d.

   Section Results, Distribution and frequency of genetic variants:  On average 88 insertions and deletions over 50 letters, three large inversions, 2,168 small insertions and deletions and 3,228 single-letter differences per Y assembly, compared with the GRCh38 reference Y. ↩

Tomkins, Jeffrey P., and Jerry Bergman.  “Genomic monkey business: estimates of nearly identical human-chimp DNA similarity re-evaluated using omitted data.”  Journal of Creation 26(1):94–100.  2012.  Two young-earth writers survey published human-chimp comparisons and argue that similarity was overstated by leaving out unaligned sequence.  Its section on the Y is the strongest creationist statement that the Y difference refutes common ancestry.

1. 20a.

   Paragraph Several recent research reports:  “the extreme dissimilarity discovered is an insurmountable paradox for common ancestry in primate evolution because it is by far the least variable chromosome in the human genome.”  Section The Y-chromosome bombshell:  “Instead, it appears to be very static and stable, with very few structural differences and little sequence diversity among human males worldwide.” ↩ ↩

This article's arithmetic, offered as a rough comparison.  Pan:  Makova 2024, Supplementary Table S11, assigns to the Y 242 deletions and 747 insertions to the chimpanzee branch over 16.36 million aligned letters, and 240 deletions, 608 insertions and 4 inversions to the bonobo branch over 16.61 million;  1,841 in all, about 112 per million letters.  Human:  Hallast 2023 report an average of 88 insertions and deletions over 50 letters per Y assembly against the GRCh38 reference Y, across male-specific euchromatin of about 23 million letters (22.80 million in Hughes 2010, Supplementary Table 2), about 3.8 per million.  Ratio:  about 21 by count, about 29 per million letters.  On the young-earth timeline both sets accumulated since the Flood from a single Y, so the ratio is the required ratio of rates;  generation times, 24.1 years for chimpanzee fathers⁴⁶ against about 29 for humans, change it by under 20 percent.  The two studies used different callers and references, and Makova counted only alignable sequence, so the factor could be off by about two either way. ↩ ↩

Feuk, Lars et al.  “Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.”  PLoS Genetics 1(4):e56.  2005.  A computer scan of the 2005 human-chimpanzee alignments for stretches in opposite orientation, with laboratory checks of 27 of them.  It found that many such stretches are flanked by duplications and that some still vary among humans.  Its raw list of 1,576 candidates is cited here with the authors' own warning that it holds many false positives.

1. 22a.

   Page 0489:  “we identified a total of 1,576 putative regions of inverted orientation, covering more than 154 mega-bases of DNA. … Using PCR and fluorescence in situ hybridization we experimentally validated 23 of 27 (85%) semi-randomly chosen regions”. ↩ ↩

2. 22b.

   Page 0496:  “With a starting set of more than 6,000 regions from the raw alignment, only 1,576 regions remained after filtering.”  “Analyses of the overlap between our computationally predicted regions and the BAC sequences supported 11 out of 60 regions that could be unambiguously mapped.” ↩

3. 22c.

   Page 0496:  “We also observe that the breakpoint of the 730-kb inversion on 7p22, which was found to be polymorphic in the human population, maps to exactly the same region as the breakpoint for the pericentric inversion that occurred after the divergence of higher primates from the orangutan”. ↩

Catacchio, Claudia Rita et al.  “Inversion variants in human and primate genomes.”  Genome Research 28(6):910–920.  2018.  Inversions over 100,000 letters between human, chimpanzee, gorilla, orangutan and macaque, checked by cloned DNA and by fluorescent probes on chromosomes, and placed on the primate tree.  Its own checks found many alignment calls to be assembly errors, so it is a conservative count.

1. 23a.

   Section Results:  “Of the great ape inversions, 82% (32 of 39) map to segmentally duplicated regions of the genome, compared to the inversion events identified in macaque that overlap with segmental duplications at their breakpoints in only 41% of the cases (seven out of 17)”. ↩

2. 23b.

   Section Results, Evolutionary analyses:  “Here, either the region flipped back to the ancestral orientation in the chimpanzee lineage or the chimpanzee configuration may represent a case of incomplete lineage sorting”. ↩

Kehrer-Sawatzki, Hildegard et al.  “Molecular characterization of the pericentric inversion that causes differences between chimpanzee chromosome 19 and human chromosome 17.”  American Journal of Human Genetics 71(2):375–388.  2002.  The first human-chimpanzee pericentric inversion sequenced across both break points.  Both lie in single-copy, repeat-rich DNA between genes, with no duplication at either end, so it is the clearest exception to the duplication pattern.

1. 24a.

   Section Abstract:  “By sequencing the junction fragments, we localized breakpoints in intergenic regions rich in repetitive elements.  Our findings suggest that repeat-mediated nonhomologous recombination has facilitated inversion formation.” ↩

2. 24b.

   Section Abstract:  “The inversion affects neither the genomic structure nor the gene-activity state with regard to replication timing of these genes.” ↩

Bailey, Jeffrey A. et al.  “Hotspots of mammalian chromosomal evolution.”  Genome Biology 5(4):R23.  2004.  A comparison of the 461 breaks in shared gene order between human and mouse with primate segmental duplications, tested against 10,000 random placements of the breaks.  The authors are careful to say the duplications mark fragile regions rather than cause the breaks.

1. 25a.

   Section Abstract, Results:  “Using conservative criteria, we find that 25% (122/461) of all breakpoints contain ≥ 10 kb of duplicated sequence. This association is highly significant (p < 0.0001) when compared to a simulated random-breakage model.”  Section Results:  “On the basis of 10,000 replicates, the simulated count (maximum 50) never exceeded the observed count of 122”. ↩

2. 25b.

   Section Abstract, Conclusion:  “However, segmental duplications are not necessarily the cause of the rearrangements. Rather, our analysis supports a nonrandom model of chromosomal evolution that implicates specific regions within the mammalian genome as having been predisposed to both recurrent small-scale duplication and large-scale evolutionary rearrangements.” ↩

Pevzner, Pavel, and Glenn Tesler.  “Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution.”  Proceedings of the National Academy of Sciences 100(13):7672–7677.  2003.  A computational reconstruction of the rearrangements between the human and mouse genomes from 281 large blocks of shared order.  It inferred many short hidden blocks and concluded that breaks are reused at fragile regions, against the older random-breakage model.  The inference of hidden blocks is a model result.

1. 26a.

   Page 7672:  “Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements.” ↩

Lemaitre, Claire et al.  “Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation.”  BMC Genomics 10:335.  2009.  Breaks in gene order between human and five other mammals, located to within about 27,000 letters, compared with gene density and GC content.  Breaks avoid genes but crowd into gene-rich, open chromatin.  The authors combine selection and mutational bias.

1. 27a.

   Section Abstract:  “In agreement with the Intergenic Breakage Model, we observed that breakpoints are under-represented in genes.”  “Surprisingly however, the density of breakpoints in small intergenes (1 per Mb) appears significantly higher than in gene deserts (0.1 per Mb).”  “We propose a model to describe the heterogeneous distribution of evolutionary breakpoints along human chromosomes that combines natural selection and a mutational bias linked to local open chromatin state.” ↩

Hughes and colleagues 2010, Table 1, give 6 copies of the TSPY family in chimpanzee and about 35 in human, and list TMSB4Y among the four X-degenerate genes lost in chimpanzee.  Makova and colleagues 2024, Supplementary Table S36, give 24 TSPY copies in chimpanzee and 44 in the human Y they assembled, and their Supplementary Table S39 calls chimpanzee TMSB4Y present.  Makova's paper reports that ampliconic regions were "shorter (by 2.5-25 Mb) in previous Y assemblies than in our T2T-Y assemblies, suggesting their collapse in the earlier assemblies" (page 404).  Hughes 2005, Supplementary Figure 8, shows a splice-site mutation in chimpanzee TMSB4Y.  Both counts come from one male per species. ↩ ↩

Cechova, Monika et al.  “Dynamic evolution of great ape Y chromosomes.”  Proceedings of the National Academy of Sciences 117(42):26273–26280.  2020.  Draft Y assemblies of bonobo and orangutan compared with human, chimpanzee and gorilla, measuring substitution rates and gene loss on each branch.  The authors test sperm competition as an explanation and report the orangutan as a case against it.

1. 29a.

   Section Results, Substitution Rates on the Y:  “the Y-to-autosomal substitution rate ratio was higher in the Pan lineage, including the chimpanzee (1.76) and bonobo (1.64) lineages and the lineage of their common ancestor (1.78), than in the human lineage (1.45).” ↩

2. 29b.

   Section Discussion, Substitution Rates:  “Contradicting this expectation, orangutans have limited sperm competition … but exhibit strong male mutation bias”. ↩

Carter, Robert W.  “Chimpanzee Y chromosome is radically different from human.”  Creation Ministries International.  Aug 15, 2010.  A young-earth geneticist's summary of Hughes 2010 for general readers, arguing that the Y data weaken the case for common ancestry and that the earlier chimpanzee assembly leaned on the human genome.

1. 30a.

   Paragraph 1:  “The chimp Y chromosome is radically different”.  Paragraph What are the differences?:  “The idea that the Y chromosome is evolving at a high rate is based on the assumption of common ancestry.”  Paragraph last:  “The new data on the chimp Y chromosome makes the case for common ancestry that much worse.” ↩

2. 30b.

   Paragraph What are the differences?:  “The X-degenerate regions of chimp and man differ by a full 10%.”  Hughes and colleagues wrote that under 10 percent of X-degenerate sequence has no alignable counterpart (page 537), which is a measure of missing sequence, not of divergence. ↩

Tomkins, Jeffrey P.  “New DNA sequences of the Y chromosome refute human-ape evolution.”  Institute for Creation Research.  Jan 4, 2024.  A young-earth geneticist's report on the 2023 preprint of Makova and colleagues' complete ape Y chromosomes.  It quotes their coverage figures as similarities and argues that each great ape is its own kind.

1. 31a.

   Paragraph 2:  “Shockingly, when the new chimp Y chromosome was compared to the human Y chromosome, it was only 26% similar!” ↩

2. 31b.

   Paragraph From a Genesis-based interpretation:  “In other words, chimpanzees, gorillas, and orangutans are each a unique ape kind, which makes perfect sense since none of them can interbreed with each other, and each has its own set of unique biological and anatomical features.” ↩

3. 31c.

   Paragraph Another very interesting angle:  “each great ape Y chromosome was unique from that of other ape kinds.”  Tomkins gives the orangutan Y covered by chimpanzee alignments as 40.6 and 40.1 percent;  Makova's Figure 1b gives 40.6 and 41.1. ↩

Wood, Todd Charles.  “Chimp and human Y chromosomes radically different?”  Todd's Blog.  Jan 27, 2010.  A young-earth baraminologist's same-month response to Hughes 2010.  He accepts the data, notes that the chimpanzee male-specific Y is under 1 percent of the genome, and argues that the Y is a region of high variation, so a large difference is expected.

1. 32a.

   Paragraph 7:  “The Y chromosome certainly fits that bill. Variations in the human Y chromosome are known to be much higher than in the human autosomes, and there are lots of segmental duplications on the human Y chromosome. It's not terribly surprising that such variable regions of human DNA would also be quite different from their chimpanzee counterparts.”  Wood is quoting his own 2006 chimpanzee genome paper. ↩

This article's arithmetic from Makova 2024.  Figure 1b gives 26.2 percent of the human Y covered by chimpanzee alignments.  Supplementary Table S14 gives the human (CHM13) Y as 62.46 million letters, of which 37.01 million are satellite and 3.39 million are the X-transposed region, a block copied from the X onto the human Y after the human-chimpanzee split.  26.2 percent of 62.46 million is 16.4 million letters, which is 64 percent of the 25.45 million non-satellite letters and 74 percent of the 22.06 million left after also setting aside the X-transposed block.  This assumes the covered sequence is almost all non-satellite, which is approximately but not exactly true. ↩

Repping, Sjoerd et al.  “High mutation rates have driven extensive structural polymorphism among human Y chromosomes.”  Nature Genetics 38:463–467.  2006.  One Y chromosome from each of 47 branches of the human Y family tree, searched for large rearrangements in four regions.  Counting changes on the tree gave lower bounds on how often each kind of rearrangement happens per generation.

1. 34a.

   Section Abstract:  Lower bounds of 2.3, 4.4, 2.3 and 3.8 in 10,000 large-scale mutations per father-to-son Y transmission, for changes in the length of the distal heterochromatin, in the length of the TSPY gene array, in the orientation of the 3.6-million-letter IR3 region, and in the AZFc region. ↩ ↩

Hardy, Chris, and Robert Carter.  “The biblical minimum and maximum age of the earth.”  Journal of Creation 28(2):89–96.  2014.  Two young-earth writers work through the Masoretic, Samaritan and Septuagint numbers in the Genesis genealogies to bound the date of the Flood and of creation.  Cited here for the widest Flood window a biblical chronology allows.

1. 35a.

   Page 96:  “The Flood probably occurred between 2600 bc and 2300 bc, but certainly between 3386 bc and 2256 bc (table 5).” ↩

Hughes, Jennifer F. et al.  “Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee.”  Nature 437:100–103.  2005.  A gene-by-gene comparison of the single-copy Y genes of chimpanzee and human, with RNA tests in several tissues and checks in 14 more chimpanzees.  All were intact in humans;  several were disabled in the chimpanzee.  The Page laboratory, which sequenced the human Y.

1. 36a.

   Figure Supplementary Figure 7:  “We identified three splice-site mutations in the genomic sequence: a 4 bp deletion at the donor site of exon 8 and two GT -> AT substitutions at the donor sites of exons 34 and 39.”  “Fourteen additional chimpanzee samples were sequenced to confirm that these mutations were not unique to the particular chimpanzee whose genome was sequenced in the present analysis.” ↩ ↩

Hughes, Jennifer F. et al.  “Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.”  Nature 483:82–86.  2012.  The rhesus macaque male-specific Y region sequenced and compared with the human one, gene by gene and layer by layer.  Old Y genes turned out to be strictly conserved;  loss was confined to the youngest layer.

1. 37a.

   Page 82:  “We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY.” ↩

Venema, Dennis R.  “Genesis and the genome: genomics evidence for human-ape common ancestry and ancestral hominid population sizes.”  Perspectives on Science and Christian Faith 62(3):166–178.  Sep 2010.  A biologist who accepts evolution sets out the genomic evidence for human-ape common ancestry for Christian readers, including synteny, and answers intelligent-design objections.  The common-descent argument in its own words.

1. 38a.

   Page 167:  “Put more simply, the hypothesis of common ancestry predicts that not only will related species have similar genes, but that they will also have these genes in a very similar spatial pattern.” ↩

2. 38b.

   Page 172:  “The results of these analyses demonstrate that the Drosophilid body plan and biochemistry are well served by a wide array of synteny arrangements, with chromosomal rearrangements greatly more diverse in this group than that observed between humans and chimpanzees.” ↩

Carter, Robert W.  “The four dimensional human genome defies naturalistic explanations.”  Creation Ministries International.  Oct 6, 2016.  A young-earth geneticist's popular essay on the layers of genome organization, from the letter sequence to three-dimensional folding.  Cited for its claim that genes used together are placed together.

1. 39a.

   Section The Third Dimension: 3-D DNA architecture:  “genes that are used together are generally found next to each other in 3D space, even when they are found on different chromosomes!” ↩

Wood, Todd Charles.  “The chimpanzee genome and the problem of biological similarity.”  Occasional Papers of the Baraminology Study Group 7:1–18.  Feb 20, 2006.  A young-earth baraminologist's review of the 2005 chimpanzee genome, accepting its near-identity of gene sequences and arguing that the meaningful differences lie in arrangement and repeats.  The fullest creationist treatment of human-chimp similarity by a working geneticist.

1. 40a.

   Page 13:  “Even though chimpanzees and humans belong to different baramins, the chimpanzee genome reinforces the foundational assumption of genomic modularity: that the arrangement of genes influences their expression.” ↩

Sherwin, Frank.  “Dubious views on octopus evolution.”  Institute for Creation Research.  Feb 2, 2023.  An Institute for Creation Research article on an octopus genome paper.  Cited only for its statement of how creationists treat shared gene order.

1. 41a.

   Paragraph The authors use the term synteny:  “Creationists would agree with the definition of the term (which is observed), but openly question the appeal to evolutionary divergence (supposedly occurring mainly in the distant past).” ↩

Larkin, Denis M. et al.  “Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories.”  Genome Research 19(5):770–777.  2009.  Gene-order maps of ten amniote genomes, divided into 2,233 conserved blocks and 1,064 break regions.  Break regions are rich in duplications and copy-number variants;  blocks conserved in all ten hold developmental genes.  Evidence for both mechanism and function in one dataset.

1. 42a.

   Page 770:  “msHSBs are significantly enriched for genes involved in development of the central nervous and other organ systems, whereas EBRs are enriched for genes associated with adaptive functions.”  “natural selection acts on the genome to maintain combinations of genes and their regulatory elements that are essential to fundamental processes of amniote development and biological organization.” ↩

Fudenberg, Geoff, and Katherine S. Pollard.  “Chromatin features constrain structural variation across evolutionary timescales.”  Proceedings of the National Academy of Sciences 116(6):2175–2180.  2019.  A comparison of 2,565 deletions fixed in great apes, and deletions that vary among healthy humans, with human chromatin features.  Both avoid active chromatin and domain boundaries;  deletions found in patients with developmental disorders do not.  Read by the authors as purifying selection.

1. 43a.

   Page 2177:  “Collectively these findings argue that purifying selection acts to remove deleterious variants that would perturb functionally important chromatin features, including TAD boundaries, at the timescale of great ape evolution.” ↩ ↩

Gierman, Hinco J. et al.  “Domain-wide regulation of gene expression in the human genome.”  Genome Research 17(9):1286–1295.  2007.  One identical reporter gene placed at 90 sites in a human cell line.  Its activity followed the activity of the surrounding stretch of tens of genes, up to eightfold, while the immediate neighbours had a weak effect.  Direct evidence that position matters, at the scale of domains.

1. 44a.

   Page 1286:  “These domains are up to 80 genes long and can exert an eightfold effect on the expression levels of integrated genes.” ↩

2. 44b.

   Page 1291:  “Immediate neighboring genes also influence GFP expression, but this effect is more limited.” ↩

Wilson, Michael D. et al.  “Species-specific transcription in mice carrying human chromosome 21.”  Science 322(5900):434–438.  2008.  Liver cells of a mouse strain that carries a whole human chromosome 21, compared with human and mouse liver.  Transcription-factor binding and expression on the human chromosome stayed human-like in the mouse nucleus.  No gene was moved, so the study tests DNA sequence against cellular environment, not gene order.

1. 45a.

   Page 434:  “Thus, in homologous tissues, genetic sequence is largely responsible for directing transcriptional programs; interspecies differences in epigenetic machinery, cellular environment, and transcription factors themselves play secondary roles.” ↩

Langergraber, Kevin E. et al.  “Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution.”  Proceedings of the National Academy of Sciences 109(39):15716–15721.  2012.  Parentage of 226 wild chimpanzees from eight communities and of wild gorillas, used to measure the average age of parents.  Cited here only for the chimpanzee generation time.

1. 46a.

   Page 15717:  “the average generation time for males and females is essentially the same (24.1 and 25.2 y, respectively).”  “inferred an average human generation time of 29 y”.  The 29-year human figure is the authors' summary of an earlier survey. ↩