Great ape genetic diversity and population history

Abstract

Despite African great apes and orangutans are human’s closest evolutionary relatives, the assessment of their genetic diversity has been systematically delayed in comparison to similar studies in our species. To overcome this limitation, we sequenced to high coverage a total of 79 great ape individuals representing all species and seven subspe- cies across the African continent and South East Asia. We discover ~86.5 million single nucleotide polymorphisms and report a three-fold range in nucleotide diversity among different ape populations. We find extensive inbreeding in almost all wild populations with Eastern gorillas being the most extreme population. 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. Using these data, we develop a framework to understand the recent evolutionary history of hominidae. This resource provides the first catalog of great-ape genome diversity to assist in better understanding our species and more effectively managing wild and captive great ape populations.