A Molecular Phylogeny of Living Primates

TLDR

Comparative genomic analyses of primates hold promise for elucidating the processes that shape the human genome, yet primate taxonomy remains complex and controversial with little consensus on the evolutionary hierarchy of extant species. We generated ~8 Mb of genomic sequence from 186 primates representing 61 genera (≈90 % of described genera) and included outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resulting phylogeny is exceptionally robust, resolves numerous taxonomic controversies, illuminates human evolutionary history, and reveals ongoing speciation, reticulate evolution, ancient relic lineages, unequal evolutionary rates, and disparate indel distributions, providing a framework for studies of human adaptation, zoonotic disease emergence, comparative genomics, taxonomy, and conservation.

Abstract

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.