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

对新大陆灵长类动物的系统发育研究对于重建它们的基因组、表型和行为的进化是必要的。这些灵长类动物也是卡他类的近亲，卡他类包括东半球的猴子、猿和人类。因此，新世界灵长类动物研究为理解人类生物学提供了一个必要的比较视角。尽管它们在灵长类中占有重要地位，但新大陆灵长类之间的系统发育分支顺序仍然存在争议，关键问题仍然是关于个别属和物种之间的相互关系。在这项研究中，将使用创新和高效的基因组和计算技术来推断鸭嘴兽的系统发育。随机基因组文库由每个科的代表性物种产生，将提供多达100个标记，长度约为650个碱基对。这些非连锁标记估计包含多达65千碱基的非编码、非基因、非重复的核DNA，将在每个鸭嘴兽属的至少一个代表性物种中进行测序。这个庞大的数据集将与来自传统分子标记的数据相结合，并与之进行比较，例如来自核和线粒体基因组的蛋白质编码基因座。数据将使用基于似然的方法进行分析，考虑到祖先的多态和鸭嘴兽家族多样性早期阶段快速分化导致的标记之间的系统发育不一致。如果没有准确的新大陆猴子系统发育，类人基因组、表型和行为的进化重建将受到阻碍。鸭嘴兽系统发育的关键方面一直很难解决，与卡他类相比，关于鸭嘴兽内DNA替换率变异的研究相对较少。灵长类动物的重要表型和行为特征可以通过所提出的系统发育更好地重建，包括双胞胎、色觉和由于新皮质扩大而形成的脑化。这项研究介绍了一种新的方法来确定所有鸭嘴兽属之间的分枝顺序和分化的时间。将使用高通量方法生成大量用于分析的非编码系统发育序列数据。此外，一种结合了人口统计变量的基于可能性的方法将被用来推断新大陆猴子的早期多样化。这些方法可能进一步适用于其他系统发育类群。此外，通过联合分子和化石数据来估计分歧的时间，将突出不同白颈鹿群体之间突变率的差异。灵长类动物非常受公众关注，许多将被研究的新大陆猴子通常被安置在美国动物园，在那里它们为公众提供教育体验。它们极具魅力的行为和形态使它们成为重要的保护焦点。新大陆猴也是科学研究常用的模式生物，常见的绒猴已被确定为完成基因组测序的目标。解决这些动物的系统发育历史将提高公众、自然保护和科学界对这些物种的认识和理解。这个项目是合作的，结合了两位研究人员在计算基因组学、灵长类进化和系统发育方面的互补优势。学生和博士后研究人员将接受培训，并鼓励他们寻找两个研究人员实验室提供的合作机会。将创建一个致力于新世界猴子生物学和多样性的网站。阐明这些属的系统发育历史将为未来的研究提供基础。最后，这项研究产生的所有标记的序列将在公共数据库中可用。在这个项目中获得的序列将成为灵长类基因组学社区的重要资源。

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.