Predicted Continuity, Observed Discontinuity: Ape Y Chromosome Architecture as a Test of Bounded Diversity

• D. Budinsky

  Author

• M. Nailor

  Author

The male-specific region of the Y chromosome provides an unusually stringent test of competing models of primate origins because it is inherited as a single paternal unit while preserving both a constrained functional core and rapidly changing chromosome-scale architecture. We conducted a prediction-based comparison of common descent and bounded diversity using complete telomere-to-telomere sex-chromosome assemblies from humans and six nonhuman apes, together with earlier finished primate Y sequences and population-level analyses. Common descent permits accelerated Y evolution but still predicts graded phylogenetic continuity, whereas bounded diversity predicts conservation of indispensable functions accompanied by substantially greater architectural continuity within independently specified biological groups than across their boundaries. Only 14–27% of the human Y chromosome aligns with other ape Y chromosomes, compared with 93–98% of the human X. Among bases in sequences exhibiting interspecies variation, approximately 99% of affected Y sequence occurs within large structural variants; Y inversions average approximately eight times the length of X inversions, and Y insertions approximately three times longer. By contrast, Y alignability increases to 60–87% between the closest sampled species pairs, with recognizable ampliconic homology concentrated within those pairs despite continuing internal rearrangement. The most decisive result is prospective rather than merely surprising. Because palindromes facilitate gene conversion and counteract Y degeneration, Makova et al. (2024) explicitly expected Y palindromes to be conserved. Instead, homologous palindrome clusters declined from 21, 12 and 9 on the X to only two, one and zero on the Y across African great apes, all great apes and all species analyzed, respectively. Most Y palindromes proved species-specific or restricted to the closest relatives. This failed expectation is reinforced by a broader pattern of revisions to simple Y-evolution models. Gene loss in the older human Y strata evidently ceased more than 25 million evolutionary years ago, and the rhesus Y lost no older ancestral genes during that interval, contradicting continuing-decay and Y-extinction extrapolations; yet the chimpanzee Y underwent wholesale structural renovation and extensive lineage-specific gene loss rather than approaching architectural stasis. Approximately 99.97% identity between human palindrome arms was once interpreted through molecular-clock reasoning as evidence of recent duplication, but at least six palindromes were subsequently shown to predate the proposed human–chimpanzee divergence, requiring recurrent Y–Y gene conversion to explain their maintained identity. Human Y nucleotide diversity is approximately an order of magnitude below the simple neutral expectation of one-quarter autosomal diversity, and sex-biased demography alone cannot reproduce the observed genomic pattern. Surviving ancestral Y genes are likewise nonrandom, being disproportionately enriched for broadly expressed, dosage-sensitive regulators, while overall human Y gene content is more similar to gorilla than to chimpanzee despite the accepted species relationship. Each discordance can be individually accommodated through linked selection, gene conversion, differential loss, drift or lineage-specific turnover, but accommodation after discovery is not equivalent to prospective success. We also confront the strongest evidence for descent: the conserved single-copy core recovers the accepted species topology, and structural-variant abundance increases with inferred phylogenetic branch length. We argue that these observations are compatible with genuine descent within created kinds and hierarchical template reuse between them, whereas the concentration of shared function in a small conserved core surrounded by sharply lineage-specific architecture is predicted more directly by bounded diversity. We conclude that the present chromosome-wide pattern favors bounded diversity and establish prospective tests requiring future assemblies to distinguish boundary-associated discontinuity from variation explained solely by elapsed time, demography, selection and reproductive biology.

1. D. Budinsky

   Donny worked as a Registered Practical Nurse for many years. During his time working as an RPN, he converted to Christianity and became a Young Earth Creationist. This was after being confronted with evidence that contradicted his belief in evolution. 

2. M. Nailor

   Sindonologist and gerontologist specializing in the biology of aging and disease, Matt Nailor holds a Doctor of Divinity. His research focuses on the evolutionary theory of aging, which accounts for senescence through mutation accumulation, antagonistic pleiotropy, and disposable soma theory. This work engages origins science, with particular attention to molecular aging, mutation rates and accumulation, biological evolution, genetic variation, and historical linguistics.

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