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.
New World monkeys (platyrrhines) inhabit subtropical and tropical habitats in the Americas. They are the closest living relatives of Old World monkeys and apes (catarrhines). Due to their position in the primate evolutionary tree New World monkeys (NWM) are a key comparative group of animals that inform the biology of catarrhines, including humans. Despite many molecular and morphological studies the phylogenetic relationships among several platyrrhine families and genera is controversial. An accurate platyrrhine phylogenetic framework is necessary to reconstruct the evolutionary history of their phenotypes and behaviors. Platyrrhines exhibit great variation in their patterns of reproduction, their color vision, and their relative brain size. There is also great variation in features of development, life history, and behavior amongst New World monkeys. As a necessary first step toward accurately reconstructing these traits we have inferred platyrrhine phylogeny using non-coding genomic markers generated specifically for this purpose. We also compared these to traditional molecular markers to identify the most effective markers for phylogenetic analysis within platyrrhines. Using the newly developed phylogeny framework we were able to infer at what time and geographic location major diversification events occurred. Finally, in an effort to enable efficient data dissemination we have constructed a website containing both background information on NWM taxonomy and phylogeny and downloadable datasets. We have also presented our work on this project at national and international scientific meetings. The lack of available platyrrhine genomic data required the generation of a large molecular dataset from which we could obtain non-genic regions for use as phylogenetic marker loci. This was accomplished by sequencing millions of base pairs of DNA from three platyrrhine species, Aotus lemurinus, Cacajao calvus, and Ateles belzebuth. The resulting sequences were then compared with publicly available genomes to estimate genome location, repeat presence, GC content, and the presence of orthologous sequences in the newly sequenced species. A description of this technique and the fully annotated sequences were published in the following manuscript: "Development and annotation of shotgun sequence libraries from New World monkeys" (PMID: 22715851). From this molecular dataset 64 non-genic markers were chosen and sequenced producing a 40 taxa x 40,986 bp matrix. All phylogenetic analysis converged on an identical topology with well-supported relationships among species. When compared with other phylogenetic analyses we found that our non-genic molecular markers out performed other markers in terms of phylogenetic signal. Comparisons with an equally sized coding gene dataset and an non-genic dataset of roughly 25% the size we found that both the size, 40 kb, and type of data, non-genic, were required to achieve the strongly supported phylogeny. We have suggested that due to the lack of evolutionary constraints on non-genic sequences they would be relatively free from selection pressures that constrain the evolution of protein coding sequences. Indeed, in a comparison of our human and chimpanzee data we find that non-genic sequences are in fact under fewer constraints, as they have more sequence variation among them (1.9%) than the genomes do as a whole (1.2%). With the completed phylogenetic framework we were then able to estimate the times of linage divergences as well as reconstruct the ancestral geographic areas of NWMs. The divergence dating analysis estimated the median age of the most recent common ancestor (mrca) of catarrhines and platyrrhines at approximately 38 million years ago and the mrca of extant platyrrhines is estimated to have lived between 25 and 26 millions of years ago. The geographic range of ancestral platyrrhines was inferred though reconstruction of the historical biogeography of each living genus. These analyses identified Amazonia, specifically a region of South America containing parts of the Amazon rainforest, Guiana Shield, and the northern Andes, as the range of the ancestral crown platyrrhines. We were also able to determine that migration and diversification of crown NWMs was not prompted by speciation due to the development of aquatic barriers to dispersal, but rather because the formation of the Amazon rainforest promoting an environment so diverse that it allowed for nearly sympatric speciation among platyrrhines. These data along with the phylogenetic analysis has been submitted for publication as: "The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis". We have developed a website describing NWM taxonomy and phylogeny. This website also contains all published sequence data generated during the life of this grant as well as the multiple sequence alignment files and program control files. We have also made the sequence data publicly available in GenBank. Our hope is that members of the primatology research community will continue to build upon these molecular resources. This information can be used by those with access to a larger variety of platyrrhine species to expand the dataset weâ€™ve begun and create phylogenies of each genus with deep and comprehensive species and population coverage.