Primate Phylogeny and the Ancestral Polymorphism

Abstract

As genomic studies have progressed, it has become easier to get the nucleotide sequences at several nuclear loci from many species. Molecular phylogenetic studies have provided the branching (diverging) order and divergence time of many primates. Recent phylogenetic studies have revealed that the most closely related species to humans is the chimpanzee, not the gorilla or orangutan. However, there remain arguments about the time of divergence of many species, including the hominoids. In fact, estimates of the divergence time show a large variation among different loci and this may be due to a large extent on ancestral polymorphism. In this article we present the method to estimate the effective size of an ancestral population and the divergence time simultaneously. We showed both estimates in the lineage leading to extant humans. We will discuss the biological meaning and problems of estimating effective sizes of an ancestral population and divergence times in primate evolution.