Given primates are threatened, in many cases, by factors including climate change, habitat loss, and illegal trading and hunting, the need for a more complete understanding of primate genetic diversity is urgent. Characterizing primate variation not only allows us to better understand and conserve these species in the wild, but it also helps us to better understand ourselves.
In a special issue of Science, including two related studies from Science Advances, ten papers provide new insights into primate genomes, far exceeding past genomic analyses of primate species. In one study – results from which provide the foundation for several additional studies in the special issue – Lukas Kuderna and team present whole genome data from 233 primate species representing 86% of the primate genera and all 16 families. They used this dataset to estimate the human-chimpanzee divergence as between 9.0 and 6.9 Ma – slightly older than other recent analyses. The authors also explored the association between genomic variation and variables including climate and sociality. Kuderna et al. further studied whether genetic diversity estimates are correlated with extinction risk in primates, a subject of previous debate. "Despite our broad sampling," the authors write, "we find no global relationship between numerically coded International Union for Conservation of Nature extinction risk categories and estimated heterozygosity." Finally, the authors used the data to generate a better picture of the mutations that arose in the human lineage and have not emerged elsewhere in primates.
Despite the importance of nonhuman primates, reference genomes have been sequenced in
A study by Iker Rivas-González and team addresses questions around the process of speciation among populations, focusing specifically on the way some regions of the genome will not show evidence of difference for a long time after ecological speciation has occurred. This process is called incomplete lineage sorting. By accounting for incomplete lineage sorting across primates, Rivas-González et al. were able to produce a primate phylogeny that agrees with fossil estimates, unlike past attempts.
A study by Hong Wu and colleagues focuses on hybridization in mammalian evolution, the role for which is rarely examined. The authors studied the genome sequences from a group of monkey species in the Rhinopithecus genus and found clear evidence that the gray snub nosed monkey is derived from hybridization between the golden snub nosed monkey and the ancestor of two extant Rhinopithecus species. Further, they report the unusual coat color seen in the gray snub nose is due to this mixing. One group of species that has been identified as having a history of hybridization is that containing the genus Papio, the baboons. Erik Sørensen and colleagues used whole genome sequencing to reveal the evolutionary history of overlapping baboon species and found evidence of repeated admixture. "We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages," they write. Also focused on hybridization in primates, Bao-Lin Zhang and team, in Science Advances, compared reference genomes of 12 macaque species that together cover all the known macaque groups. Their comparative phylogenomic analysis uncovered an ancient hybrid origin of a macaque lineage. "Our study provides both a strategy and a pipeline of genome analyses to identify hybrid speciation, which should pave the way for the identification and exploration of further such events in the future," write Zhang et al.
