We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.
This content will become publicly available on June 13, 2025
- PAR ID:
- 10519789
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Springer Nature
- Date Published:
- Journal Name:
- Nature
- Volume:
- 630
- Issue:
- 8016
- ISSN:
- 0028-0836
- Page Range / eLocation ID:
- 401 to 411
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Objectives Great apes provide a point of reference for understanding the evolution of locomotion in hominoids and early hominins. We assessed (1) the extent to which great apes use diagonal sequence, diagonal couplet gaits, like other primates, (2) the extent to which gait and posture vary across great apes, and (3) the role of body mass and limb proportions on ape quadrupedal kinematics.
Methods High‐speed digital video of zoo‐housed bonobos (
Pan paniscus, N = 8), chimpanzees (Pan troglodytes, N = 13), lowland gorillas (Gorilla gorilla, N = 13), and orangutans (Pongo spp. N = 6) walking over‐ground at self‐selected speeds were used to determine the timing of limb touch‐down, take‐off, and to measure joint and segment angles at touch‐down, midstance, and take‐off.Results The great apes in our study showed broad kinematic and spatiotemporal similarity in quadrupedal walking. Size‐adjusted walking speed was the strongest predictor of gait variables. Body mass had a negligible effect on variation in joint and segment angles, but stride frequency did trend higher among larger apes in analyses including size‐adjusted speed. In contrast to most other primates, great apes did not favor diagonal sequence footfall patterns, but exhibited variable gait patterns that frequently shifted between diagonal and lateral sequences.
Conclusion Similarities in the terrestrial walking kinematics of extant great apes likely reflect their similar post‐cranial anatomy and proportions. Our results suggest that the walking kinematics of orthograde, suspensory Miocene ape species were likely similar to living great apes, and highlight the utility of videographic and behavioral data in interpreting primate skeletal morphology.
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Multicopy ampliconic gene families on the Y chromosome play an important role in spermatogenesis. Thus, studying their genetic variation in endangered great ape species is critical. We estimated the sizes (copy number) of nine Y ampliconic gene families in population samples of chimpanzee, bonobo, and orangutan with droplet digital polymerase chain reaction, combined these estimates with published data for human and gorilla, and produced genome-wide testis gene expression data for great apes. Analyzing this comprehensive data set within an evolutionary framework, we, first, found high inter- and intraspecific variation in gene family size, with larger families exhibiting higher variation as compared with smaller families, a pattern consistent with random genetic drift. Second, for four gene families, we observed significant interspecific size differences, sometimes even between sister species—chimpanzee and bonobo. Third, despite substantial variation in copy number, Y ampliconic gene families’ expression levels did not differ significantly among species, suggesting dosage regulation. Fourth, for three gene families, size was positively correlated with gene expression levels across species, suggesting that, given sufficient evolutionary time, copy number influences gene expression. Our results indicate high variability in size but conservation in gene expression levels in Y ampliconic gene families, significantly advancing our understanding of Y-chromosome evolution in great apes.more » « less
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Abstract Sex determination, the developmental process by which sexually dimorphic phenotypes are established, evolves fast. Evolutionary turnover in a sex determination pathway may occur via selection on alleles that are genetically linked to a new master sex determining locus on a newly formed proto‐sex chromosome. Species with polygenic sex determination, in which master regulatory genes are found on multiple different proto‐sex chromosomes, are informative models to study the evolution of sex determination and sex chromosomes. House flies are such a model system, with male determining loci possible on all six chromosomes and a female‐determiner on one of the chromosomes as well. The two most common male‐determining proto‐Y chromosomes form latitudinal clines on multiple continents, suggesting that temperature variation is an important selection pressure responsible for maintaining polygenic sex determination in this species. Temperature‐dependent fitness effects could be manifested through temperature‐dependent gene expression differences across proto‐Y chromosome genotypes. These gene expression differences may be the result of
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