2 Molecular Evidence on Primate Origins and Evolution

Abstract

Over the last decade, research on primate phylogeny has been of increasing interest to the scientific community. From the perspective of molecular evolution, this is mainly due to the fact that the mass generation of molecular sequences has become easy and cost effective. With the generation of complete sequences for several eutherian organisms including humans and the mouse, a well-accepted phylogenetic interpretation for all members of the Euarchontoglires and all major groups of the primate order is feasible and would represent a new starting point for meaningful comparative research. Such a phylogenetic framework would link humans with the mouse, which is generally regarded as the main eutherian model organism. Thus, our knowledge of primate origins and the evolution of primates is a prerequisite for a postgenomic era in which aspects of functional genetics and character evolution will form a focal point of genetic research. Despite the pace at which primate sequences can be generated in whole genome shotgun (WGS)-sequencing projects, primate origins as well as several branching events in primate divergence remain far from settled. First, complete primate genome sequences are currently available for two representatives of the Old World monkeys and hominoids and humans only. Information is lacking on the deeper primate splits and comparative data are restricted to parts of primate genomes (ENCODE project). Second, it is obvious that the peculiar mode of sequence evolution (including gene-, lineage-, and position-specific evolutionary rates), combined with deep splitting events that often occurred during small time intervals may possibly lead to incongruence between gene and species trees. To avoid this, it will be necessary to have enormous amounts of sequence data and the implementation of more realistic assumptions about sequence evolution models in sequence-based phylogenetic tree reconstructions. Moreover, alternative molecular approaches, including both the incorporation of data of so-called “rare genomic changes” (RGCs) and a combination of both neontological and paleontological morphological data in total evidence approaches, are likely to contribute considerably to a firm interpretation on the origin and evolution of primates. Below I summarize and discuss molecular evidence obtained for the origin and evolution of primates, stressing the potential of the inclusion of “RGCs,” mainly retropositions of short interspersed nuclear elements (SINEs) in this context.