Next-generation primate genomics: New genome assemblies unlock new questions

Nonhuman primates provide unique evolutionary and comparative insight into the human phenotype. Genome assemblies are now available for nearly half of the species in the primate order, expanding our understanding of genetic variation within and between species and making important contributions to evolutionary biology, evolutionary anthropology, and human genetics. Nonhuman primates provide unique evolutionary and comparative insight into the human phenotype. Genome assemblies are now available for nearly half of the species in the primate order, expanding our understanding of genetic variation within and between species and making important contributions to evolutionary biology, evolutionary anthropology, and human genetics. Research in nonhuman primates is wide ranging. It extends from comparative work highlighting the origins of human uniqueness to experimental, laboratory-based studies of immunity, neural connectivity, and cognition to field studies of ecology and behavior in natural populations. A unifying theme of these efforts involves understanding trait variation within and among primate taxa, including its emergence across time and space. Starting in the early 2000s, genomic approaches have become foundational to this effort. Indeed, in recognition of the importance of nonhuman primates for understanding the human phenotype, one of the first mammalian genome assemblies to be published after the draft assembly of the human genome was that of the chimpanzee, our closest living relative. Until recently, however, most primate diversity—a widely distributed order that includes over 500 species—has remained uncharacterized. In June 2023, a collection of papers in Science and Science Advances substantially closed this gap. The collection reports the results of a massive effort to sequence previously unrepresented species: in combination with existing assemblies, 233 primate species are represented in the accompanying datasets (211 with newly generated assemblies), including representatives from all 16 extant families (Figure 1). From the perspective of genome assembly, this contribution makes primates one of the most extensively described taxa in the tree of life. The collection therefore lays a scientific foundation that will support work in evolutionary genomics, human genetics, and primatology for many years to come. Although its greatest impact is likely to lie in the resources it provides for future work, the analyses already completed provide a glimpse into what dense phylogenetic sampling, combined with targeted analyses of individual taxa, can reveal. For example, a strong motivation for studying other primates comes from our desire to understand our own species. What similarities do we share with our primate cousins? In what ways are we distinct? What evolutionary mechanisms have shaped these differences, and when and why did they emerge? Bringing comparative genomics to bear on these questions is not a new approach, but it has historically been limited by the small number of primates with available genomes. Key papers in the collection therefore revisit these long-standing themes,1Kuderna L.F.K. Gao H. Janiak M.C. Kuhlwilm M. Orkin J.D. Bataillon T. Manu S. Valenzuela A. Bergman J. Rousselle M. et al.A global catalog of whole-genome diversity from 233 primate species.Science. 2023; 380: 906-913https://doi.org/10.1126/science.abn7829Crossref PubMed Scopus (10) Google Scholar,2Shao Y. Zhou L. Li F. Zhao L. Zhang B.-L. Shao F. Chen J.-W. Chen C.-Y. Bi X. Zhuang X.-L. et al.Phylogenomic analyses provide insights into primate evolution.Science. 2023; 380: 913-924https://doi.org/10.1126/science.abn6919Crossref PubMed Scopus (8) Google Scholar,3Bi X. Zhou L. Zhang J.-J. Feng S. Hu M. Cooper D.N. Lin J. Li J. Wu D.-D. Zhang G. Lineage-specific accelerated sequences underlying primate evolution.Sci. Adv. 2023; 9eadc9507https://doi.org/10.1126/sciadv.adc9507Crossref Scopus (5) Google Scholar drawing on the power of a much-expanded dataset. In some cases, they refine earlier findings. For instance, consistent with previous surveys, Kuderna et al. confirm that humans are among the least genetically diverse primates—closer to endangered golden snub-nosed monkeys, a high-altitude specialist, than to other widely distributed generalists, like rhesus macaques, baboons, or guenons.1Kuderna L.F.K. Gao H. Janiak M.C. Kuhlwilm M. Orkin J.D. Bataillon T. Manu S. Valenzuela A. Bergman J. Rousselle M. et al.A global catalog of whole-genome diversity from 233 primate species.Science. 2023; 380: 906-913https://doi.org/10.1126/science.abn7829Crossref PubMed Scopus (10) Google Scholar Similarly, Shao et al.2Shao Y. Zhou L. Li F. Zhao L. Zhang B.-L. Shao F. Chen J.-W. Chen C.-Y. Bi X. Zhuang X.-L. et al.Phylogenomic analyses provide insights into primate evolution.Science. 2023; 380: 913-924https://doi.org/10.1126/science.abn6919Crossref PubMed Scopus (8) Google Scholar revisit evidence for a slowdown of nucleotide substitution rates in hominoids (first proposed in 1985 by Morris Goodman) and point again to testis-expressed and immune defense-related genes as common targets of natural selection. Meanwhile, several papers in the collection reinforce the importance of admixture and hybridization in the evolution of many extant primates.4Wu H. Wang Z. Zhang Y. Frantz L. Roos C. Irwin D.M. Zhang C. Liu X. Wu D. Huang S. et al.Hybrid origin of a primate, the gray snub-nosed monkey.Science. 2023; 380eabl4997https://doi.org/10.1126/science.abl4997Crossref Scopus (5) Google Scholar,5Zhang B.-L. Chen W. Wang Z. Pang W. Luo M.-T. Wang S. Shao Y. He W.-Q. Deng Y. Zhou L. et al.Comparative genomics reveals the hybrid origin of a macaque group.Sci. Adv. 2023; 9eadd3580https://doi.org/10.1126/sciadv.add3580Crossref Scopus (6) Google Scholar,6Sørensen E.F. Harris R.A. Zhang L. Raveendran M. Kuderna L.F.K. Walker J.A. Storer J.M. Kuhlwilm M. Fontsere C. Seshadri L. et al.Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.Science. 2023; 380: eabn8153https://doi.org/10.1126/science.abn8153Crossref Scopus (7) Google Scholar This is consistent with earlier arguments that our own complex reticulate history may not be so uncommon. However, the newly expanded dataset also moves forward our understanding of human evolution. For example, several of the analyses highlight how denser sampling alters earlier interpretations of human-specific genetic change. The new data reveal that at least 63% of missense mutations thought to be human specific are in fact shared with other primates.1Kuderna L.F.K. Gao H. Janiak M.C. Kuhlwilm M. Orkin J.D. Bataillon T. Manu S. Valenzuela A. Bergman J. Rousselle M. et al.A global catalog of whole-genome diversity from 233 primate species.Science. 2023; 380: 906-913https://doi.org/10.1126/science.abn7829Crossref PubMed Scopus (10) Google Scholar Indeed, over half of these previous human-specific candidates can be found in at least two other extant primates. This result winnows the set of changes unique to humans while simultaneously indicating that selection on distinctive human phenotypes often has deeper roots in primate evolution.2Shao Y. Zhou L. Li F. Zhao L. Zhang B.-L. Shao F. Chen J.-W. Chen C.-Y. Bi X. Zhuang X.-L. et al.Phylogenomic analyses provide insights into primate evolution.Science. 2023; 380: 913-924https://doi.org/10.1126/science.abn6919Crossref PubMed Scopus (8) Google Scholar For instance, primate phylogeny-wide tests for positive selection suggest that brain function was already the target of adaptation in the common ancestor of all living primates, and a second burst of positive selection and gene family expansion on brain-related genes occurred ∼40 million years ago in the ancestral branch of apes and monkeys. These results agree with other work suggesting that some of the same genes have been repeatedly modified in mammalian evolution to alter neural phenotypes.7Kliesmete Z. Wange L.E. Vieth B. Esgleas M. Radmer J. Hülsmann M. Geuder J. Richter D. Ohnuki M. Götz M. et al.Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals.Elife. 2023; 12e83593https://doi.org/10.7554/eLife.83593Crossref Google Scholar Studying positively selected changes in other primate lineages may therefore have much to teach us about the evolution of canonically “human” traits. Understanding genetic variation in other primates may also help identify variants important to human disease, which has been an important selective force throughout our evolutionary history. The logic here (extending earlier work by Sundaram and colleagues in 2018 and related analyses by the Zoonomia Project) is that common missense variants in other primates must be tolerated by natural selection and are therefore likely to be benign.8Gao H. Hamp T. Ede J. Schraiber J.G. McRae J. Singer-Berk M. Yang Y. Dietrich A.S.D. Fiziev P.P. Kuderna L.F.K. et al.The landscape of tolerated genetic variation in humans and primates.Science. 2023; 380: eabn8197https://doi.org/10.1126/science.abn8197Crossref Scopus (12) Google Scholar In contrast, sites that are intolerant of variation across primates are more likely to be pathogenic when found (typically as rare variants) in humans. In support of this idea, using the frequency of common genetic variants in other primates to weight a rare-variant polygenic risk score (PRS) increases the power of the PRS to predict clinically relevant phenotypes in the UK Biobank.8Gao H. Hamp T. Ede J. Schraiber J.G. McRae J. Singer-Berk M. Yang Y. Dietrich A.S.D. Fiziev P.P. Kuderna L.F.K. et al.The landscape of tolerated genetic variation in humans and primates.Science. 2023; 380: eabn8197https://doi.org/10.1126/science.abn8197Crossref Scopus (12) Google Scholar,9Fiziev P.P. McRae J. Ulirsch J.C. Dron J.S. Hamp T. Yang Y. Wainschtein P. Ni Z. Schraiber J.G. Gao H. et al.Rare penetrant mutations confer severe risk of common diseases.Science. 2023; 380: eabo1131https://doi.org/10.1126/science.abo1131Crossref Scopus (6) Google Scholar Similar machine learning-based methods are now being extended to proteome-wide predictions of pathogenic variants as well. Together, these results nicely illustrate the synergy between evolutionary thinking and biomedical applications. They also suggest that capturing additional genetic diversity in nonhuman primates—especially within-species variation—may further improve genetic prediction. Consistent with a principal motivation for studying primates, most of the collection focuses on primate evolution per se and its implications for understanding humans. However, such a densely sampled radiation (i.e., a group of species recently derived from a common ancestor) also provides an opportunity to study the evolutionary process more generally. For instance, Rivas-González and colleagues take advantage of a set of high-quality genomes from 50 species (27 newly generated) to investigate patterns of incomplete lineage sorting (ILS, where gene trees do not match the species tree).10Rivas-González I. Rousselle M. Li F. Zhou L. Dutheil J.Y. Munch K. Shao Y. Wu D. Schierup M.H. Zhang G. Pervasive incomplete lineage sorting illuminates speciation and selection in primates.Science. 2023; 380eabn4409https://doi.org/10.1126/science.abn4409Crossref Scopus (6) Google Scholar They provide convincing evidence that, because the amount of ILS depends on the timing of serial speciation events rather than sequence divergence (which varies across the genome and also depends on effective population size), it can be leveraged to infer speciation times independently of fossil calibration. The authors also show that variation in ILS across the genome is explained, in part, by variation in the strength of natural selection: regions of the genome strongly affected by selection tend to have smaller effective population sizes, which in turn locally reduces ILS. Such results illustrate the potential for primates to serve as a model for the evolutionary process as a whole and not only the piece of it that concerns humans. The analyses presented in this collection also generate new hypotheses. For example, several of the papers identify putative targets of lineage-specific selection and suggest that these signatures may be responsible for distinctive lineage-specific phenotypes. In particular, Bi et al. and Shao et al. identify regions that carry a signature of selection specific to gibbons—small-bodied arboreal apes found in southern and southeastern Asia—that are associated with genes involved in limb development and limb bone morphology.2Shao Y. Zhou L. Li F. Zhao L. Zhang B.-L. Shao F. Chen J.-W. Chen C.-Y. Bi X. Zhuang X.-L. et al.Phylogenomic analyses provide insights into primate evolution.Science. 2023; 380: 913-924https://doi.org/10.1126/science.abn6919Crossref PubMed Scopus (8) Google Scholar,3Bi X. Zhou L. Zhang J.-J. Feng S. Hu M. Cooper D.N. Lin J. Li J. Wu D.-D. Zhang G. Lineage-specific accelerated sequences underlying primate evolution.Sci. Adv. 2023; 9eadc9507https://doi.org/10.1126/sciadv.adc9507Crossref Scopus (5) Google Scholar This result is potentially linked to the unique features of the gibbon skeleton that enable brachiation (the suspensory swinging pattern made famous by the fictional story character Tarzan), which is their dominant form of locomotion. Similarly, analysis of the baboon radiation highlights changes potentially involved in aridity tolerance and pelage color evolution,6Sørensen E.F. Harris R.A. Zhang L. Raveendran M. Kuderna L.F.K. Walker J.A. Storer J.M. Kuhlwilm M. Fontsere C. Seshadri L. et al.Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.Science. 2023; 380: eabn8153https://doi.org/10.1126/science.abn8153Crossref Scopus (7) Google Scholar and sequence comparisons in snub-nosed monkeys point to pigmentation-related genes that might explain the black color of some species but the striking bright gold and blue colors of others.4Wu H. Wang Z. Zhang Y. Frantz L. Roos C. Irwin D.M. Zhang C. Liu X. Wu D. Huang S. et al.Hybrid origin of a primate, the gray snub-nosed monkey.Science. 2023; 380eabl4997https://doi.org/10.1126/science.abl4997Crossref Scopus (5) Google Scholar Many more candidates are proposed with potential links to an array of different tissues and phenotypes (Table 1). Together, they represent a possible treasure trove for understanding both traits of long-standing interest to evolutionary biologists (such as brain size and diet adaptation) and traits of biomedical relevance (such as fat metabolism, immune function, and lifespan).Table 1Functional associations with primate genomic variation and in vitro experimental systemsTissue systemAssociated biological processesRelevant established primate in vitro systemsConnective•bone/skeletal development•chondrocyte morphogenesis•limb bone morphology•caudal vertebrae number•adipocyte differentiation•cornification/keratinization•pigmentation/melanogenesis•osteogenic cells (PMID 35263340)•fibroblasts (PMID 12840040)Immune•immune response•lymphoid cell lines (PMID 21321133)Metabolic•nutrient digestion•metabolite detoxification•non-shivering thermogenesis•endodermal cells (PMID 30322406)Nervous•brain development•dendrite morphogenesis•sensory perception (visual, taste, olfaction)•neurohormonal signaling•social behavior•brain organoids (PMID 30735633)Renal•sodium reabsorption•kidney cells (PMID 37146034)Reproductive•male gamete generation•sexual reproduction•endometrial organoids (PMID 32937244)Whole body•body size•cilia-related functions•neural crest cells (PMID 26365491)•cardiomyocytes (PMID 30333510) Open table in a new tab Getting to that point, though, will require integrating experimental tests of mechanism. In particular, although phylogenomics, population genomics, and predictive machine learning play key roles in these papers, functional genomic analyses are noticeably missing. Therefore, inferences about the phenotypic consequences of selected sites are predominantly based on Gene Ontology and pathway enrichment analysis (although a few studies explore function via single-locus techniques, such as luciferase reporter and LacZ reporter assays3Bi X. Zhou L. Zhang J.-J. Feng S. Hu M. Cooper D.N. Lin J. Li J. Wu D.-D. Zhang G. Lineage-specific accelerated sequences underlying primate evolution.Sci. Adv. 2023; 9eadc9507https://doi.org/10.1126/sciadv.adc9507Crossref Scopus (5) Google Scholar,4Wu H. Wang Z. Zhang Y. Frantz L. Roos C. Irwin D.M. Zhang C. Liu X. Wu D. Huang S. et al.Hybrid origin of a primate, the gray snub-nosed monkey.Science. 2023; 380eabl4997https://doi.org/10.1126/science.abl4997Crossref Scopus (5) Google Scholar,11Qi X.-G. Wu J. Zhao L. Wang L. Guang X. Garber P.A. Opie C. Yuan Y. Diao R. Li G. et al.Adaptations to a cold climate promoted social evolution in Asian colobine primates.Science. 2023; 380eabl8621https://doi.org/10.1126/science.abl8621Crossref Scopus (4) Google Scholar). An important next step for primate genomics will be to integrate the increasingly comprehensive assembly and sequence datasets with a better understanding of function. This synthesis will make it possible to test both trait-specific hypotheses and questions of general evolutionary or biomedical relevance. For example, are putative targets of natural selection more likely to perturb gene regulation than the genome-wide background? Is gene flow restricted for functionally important variants or regulatory elements, as suggested for human admixture with archaic hominins? To what degree do functional annotations further improve conservation score-based prediction of traits in humans? And what are the molecular and cellular consequences of variants hypothesized to drive the evolution of specific traits—and do those effects support the predicted genotype-phenotype link? Functional and experimental work in primates is far more difficult than in classical model systems like Drosophila and mouse. However, technologies to address this challenge are now being developed. For example, several groups have made a concerted effort to generate primate induced pluripotent stem cell (iPSC) lines for general research use, adding to the set of previously published primary and immortalized nonhuman primate cell lines (Figure 1). The ability to subject these lines to many different cell differentiation schemes opens the door to studying a much wider array of cell types and tissue types than are otherwise accessible. For example, by fusing human and chimpanzee iPSCs to form allotetraploid composite cell lines, followed by differentiation, researchers have been able to study the evolution of gene regulation during neural development12Agoglia R.M. Sun D. Birey F. Yoon S.-J. Miura Y. Sabatini K. Pașca S.P. Fraser H.B. Primate cell fusion disentangles gene regulatory divergence in neurodevelopment.Nature. 2021; 592: 421-427https://doi.org/10.1038/s41586-021-03343-3Crossref PubMed Scopus (34) Google Scholar—overcoming the difficulties of invasively sampling early developmental time points. Gene-editing technologies can also be combined with these new models. In a recent study, genome-wide CRISPR editing screens in human and chimpanzee iPSCs were used to identify genes that are essential for cell cycle and cellular proliferation, but in a species-specific manner.13She R. Fair T. Schaefer N.K. Saunders R.A. Pavlovic B.J. Weissman J.S. Pollen A.A. Comparative landscape of genetic dependencies in human and chimpanzee stem cells.Cell. 2023; 186: 2977-2994.e23https://doi.org/10.1016/j.cell.2023.05.043Abstract Full Text Full Text PDF PubMed Scopus (2) Google Scholar Seventy-five such genes were identified, each of which provides a direct link between sequence divergence in recent human evolution and a fundamental component of cell biology. These types of approaches make it an opportune time to put the hypotheses emerging from the special collection to the test. For instance, several selection scans point to strong, selectively mediated change in skeletal tissue and suggest responsible genes or variants.2Shao Y. Zhou L. Li F. Zhao L. Zhang B.-L. Shao F. Chen J.-W. Chen C.-Y. Bi X. Zhuang X.-L. et al.Phylogenomic analyses provide insights into primate evolution.Science. 2023; 380: 913-924https://doi.org/10.1126/science.abn6919Crossref PubMed Scopus (8) Google Scholar,3Bi X. Zhou L. Zhang J.-J. Feng S. Hu M. Cooper D.N. Lin J. Li J. Wu D.-D. Zhang G. Lineage-specific accelerated sequences underlying primate evolution.Sci. Adv. 2023; 9eadc9507https://doi.org/10.1126/sciadv.adc9507Crossref Scopus (5) Google Scholar,6Sørensen E.F. Harris R.A. Zhang L. Raveendran M. Kuderna L.F.K. Walker J.A. Storer J.M. Kuhlwilm M. Fontsere C. Seshadri L. et al.Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.Science. 2023; 380: eabn8153https://doi.org/10.1126/science.abn8153Crossref Scopus (7) Google Scholar By pairing cell-fusion and/or editing techniques with primate skeletal cell culture systems, it should now be possible to investigate the molecular consequences of these candidate loci. Functional genomic approaches therefore provide one means for moving from the initial identification of interesting variants toward the difficult, but important, task of understanding what they actually do. Simultaneously, sequence-based analyses can provide evolutionary context for the results of functional genomic screens. To support these efforts, primate genome assemblies will need to be improved. The current collection is remarkable in its phylogenetic scope. However, several papers already limit their analyses to the 50 or so species (less than a quarter of the full set) with the most complete assemblies,2Shao Y. Zhou L. Li F. Zhao L. Zhang B.-L. Shao F. Chen J.-W. Chen C.-Y. Bi X. Zhuang X.-L. et al.Phylogenomic analyses provide insights into primate evolution.Science. 2023; 380: 913-924https://doi.org/10.1126/science.abn6919Crossref PubMed Scopus (8) Google Scholar,5Zhang B.-L. Chen W. Wang Z. Pang W. Luo M.-T. Wang S. Shao Y. He W.-Q. Deng Y. Zhou L. et al.Comparative genomics reveals the hybrid origin of a macaque group.Sci. Adv. 2023; 9eadd3580https://doi.org/10.1126/sciadv.add3580Crossref Scopus (6) Google Scholar,10Rivas-González I. Rousselle M. Li F. Zhou L. Dutheil J.Y. Munch K. Shao Y. Wu D. Schierup M.H. Zhang G. Pervasive incomplete lineage sorting illuminates speciation and selection in primates.Science. 2023; 380eabn4409https://doi.org/10.1126/science.abn4409Crossref Scopus (6) Google Scholar typically built with long-read technologies. Because many analyses require long stretches of contiguous sequence, the genomes that will be the most useful for the research community going forward will likely be this set. Indeed, as the recent human telomere-to-telomere (T2T) project demonstrates, full characterization of both sequence and structural variation will demand even better reference genomes. Efforts are already underway to fill these gaps, ranging from the Hi-C-based pseudochromosomal assemblies from DNAZoo, which has released several dozen primate genome sequences to date, to the high-quality reference genomes generated by the Vertebrate Genomes Project to the recently initiated T2T-Primates project, which has already generated draft assemblies, including the X and Y chromosomes, for five of the great apes plus siamangs (one of the so-called “lesser apes”). Finally, these resources will also support investigation of intraspecific genetic variation and focused analyses of individual radiations. Several publications already foreshadow the potential for such work—characterizing, for example, the social and genetic predictors of gene expression in baboon populations14Lea A.J. Akinyi M.Y. Nyakundi R. Mareri P. Nyundo F. Kariuki T. Alberts S.C. Archie E.A. Tung J. Dominance rank-associated gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons.Proc. Natl. Acad. Sci. USA. 2018; 115: E12163-E12171https://doi.org/10.1073/pnas.1811967115Crossref PubMed Scopus (37) Google Scholar or demonstrating the complexity of gene flow in recent ape and monkey radiations.6Sørensen E.F. Harris R.A. Zhang L. Raveendran M. Kuderna L.F.K. Walker J.A. Storer J.M. Kuhlwilm M. Fontsere C. Seshadri L. et al.Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons.Science. 2023; 380: eabn8153https://doi.org/10.1126/science.abn8153Crossref Scopus (7) Google Scholar,15Pawar H. Rymbekova A. Cuadros-Espinoza S. Huang X. de Manuel M. van der Valk T. Lobon I. Alvarez-Estape M. Haber M. Dolgova O. et al.Ghost admixture in eastern gorillas.Nat. Ecol. Evol. 2023; 7: 1503-1514https://doi.org/10.1038/s41559-023-02145-2Crossref Scopus (1) Google Scholar Expanding the taxonomic breadth of such work, especially to the relatively underrepresented strepsirrhine (lemurs, lorises, and galagos) and platyrrhine (the monkeys of Central and South America) lineages, will be one exciting next step. More attention to within-species variation should also provide opportunities to link genetic data to trait variation beyond the broad classes emphasized in the current collection (e.g., nervous, immune, skeletal, or digestive phenotypes; Table 1). Here, measurable, well-characterized traits of known selective importance (e.g., as revealed through the long tradition of primate field studies) would be of particular interest. In sum, the recent collection of primate genomics papers represents a massive undertaking to increase the phylogenetic breadth of available genome assemblies and illustrates their value for both evolutionary and biomedical research. Together, they contribute the most expansive description of genetic variation across the primate order to date. There is clearly more work to be done to characterize primate genomic variation, clarify its relationship to humans, and understand its evolutionary history and implications for trait variation. Nevertheless, this effort provides a valuable resource that lays a foundation for years of primate genomics research to come. J.T. is grateful for support from the United States National Institutes of Health awards R24 AG065172, R01 AG057235, and R01 AG075914. The authors have no interests to declare.