Collaborative Research: Anthropological Genomics and Phylogeny in New World Monkeys (Primates: Platyrrhini)

Wayne State University, Detroit MI

Investigators

Abstract

Phylogenetic studies of the New World primates are necessary for reconstructing the evolution of their genomes, phenotypes, and behavior. These primates are also the closest living relatives of the catarrhines, the group that includes Old World monkeys, apes, and humans. Thus, New World primate studies represent a necessary comparative perspective for understanding human biology. Despite their important place among primates, the phylogenetic branching order among New World primates has remained controversial, and key questions remain regarding the interrelationships among the individual genera and species. In this study research, platyrrhine phylogeny will be inferred using innovative and efficient genomic and computational techniques. Random genomic libraries, generated from a representative species of each family, will provide up 100 markers of approximately 650 base pairs in length. These unlinked markers, which are estimated to encompass up to 65 kilobases of non-coding, non-genic, non-repetitive nuclear DNA, will be sequenced in at least one representative species of every platyrrhine genus. This large dataset will be combined with and compared to data from traditional molecular markers such as protein coding loci from the nuclear and mitochondrial genomes. Data will be analyzed with a likelihood-based method, taking into account phylogenetic incongruence among markers caused by ancestral polymorphism and rapid divergence in the early stage of diversification of platyrrhine families. Without an accurate New World monkey phylogeny in place, evolutionary reconstructions of anthropoid genomes, phenotypes, and behaviors will be hampered. Key aspects of platyrrhine phylogeny have been difficult to resolve, and studies of DNA substitution rate variation within platyrrhines have been relatively rare compared to catarrhines. Important phenotypic and behavioral features in primates that can be better reconstructed with the proposed phylogeny include twinning, color vision, and encephalization due to an expanded neocortex. This study introduces new approaches to determine the branching order and timing of divergence among all platyrrhine genera. A high-throughput method will be used to generate a large amount of non-coding phylogenetic sequence data for analysis. Moreover, a likelihood-based method that incorporates demographic variables will be used to infer early diversification of New World monkeys. These methods may be further applicable to other phylogenetic groups. Additionally, by uniting molecular and fossil data to estimate times of divergence, variations in the rate of mutation among different platyrrhine groups will be highlighted. Primates are of great public interest, and many of the New World monkeys to be studied are commonly housed at U.S. zoos where they provide educational experiences for the public. Their charismatic behavior and morphology makes them important conservation foci. New World monkeys also are commonly used model organisms for scientific research, and the common marmoset has been targeted for complete genome sequencing. Resolution of the phylogenetic history of these animals will enhance awareness and understanding of these species in the public, conservation, and scientific communities. This project is collaborative, combining the two investigator's complementary strengths in computational genomics and primate evolution and phylogenetics. Students and postdoctoral researchers will be trained and encouraged to seek after collaborative opportunities offered by the two investigator's laboratories. A website devoted to New World monkey biology and diversity will be created. Elucidating the phylogenetic history of these genera will provide a foundation on which future studies can be based. Finally, sequences from all the markers generated by this study will become available in public databases. The sequences obtained during this project will be an important resource for the primate genomics community.