1 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet2 CSIC-Universitat Pompeu Fabra3 University of Washington4 University of Michigan5 Harvard Medical School6 Stanford University7 University of Arizona8 unknown9 Center for Bioinformatik (BiRC)10 Department of Biology, Faculty of Science, Københavns Universitet11 University of Washington12 University of Michigan13 University of Arizona14 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet15 Department of Biology, Faculty of Science, Københavns Universitet
Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria-Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.