Reconstructing the ancestral phenotypes of great apes and humans (Homininae) using subspecies-level phylogenies

Abstract

Abstract Owing to their close affinity, the African great apes are of interest in the study of human evolution. Although numerous researchers have described the ancestors we share with these species with reference to extant great apes, few have done so with phylogenetic comparative methods. One obstacle to the application of these techniques is the within-species phenotypic variation found in this group. Here, we leverage this variation, modelling common ancestors using ancestral state reconstructions (ASRs) with reference to subspecies-level trait data. A subspecies-level phylogeny of the African great apes and humans was estimated from full-genome mitochondrial DNA sequences and used to implement ASRs for 14 continuous traits known to vary between great ape subspecies. Although the inclusion of within-species phenotypic variation increased the phylogenetic signal for our traits and improved the performance of our ASRs, whether this was done through the inclusion of subspecies phylogeny or through the use of existing methods made little difference. Our ASRs corroborate previous findings that the last common ancestor of humans, chimpanzees and bonobos was a chimp-like animal, but also suggest that the last common ancestor of humans, chimpanzees, bonobos and gorillas was an animal unlike any extant African great ape.