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

合作研究：新大陆猴（扁鼻猴）的人类学基因组学和系统发育学

• 批准号: 0751481
• 负责人: Soojin Yi
• 金额: $ 18.53万
• 依托单位: Georgia Tech Research Corporation
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-06-01 至 2012-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0751481&HistoricalAwards=false
• 关键词: Collaborative; Research; Anthropological; Genomics; Phylogeny

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 biologybiology. Despite their important place among primates, the phylogenetic branching order among New World primates has remained controversial despite many molecular and morphological studies, 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.

新世界灵长类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动物的近亲，包括旧大陆的猴子，猿和人类。因此，新世界灵长类动物的研究代表了理解人类生物学的一个必要的比较视角.尽管它们在灵长类动物中占有重要地位，但尽管进行了许多分子和形态学研究，新世界灵长类动物之间的系统发育分支顺序仍然存在争议，并且有关各个属和种之间相互关系的关键问题仍然存在。在这项研究中，将使用创新和有效的基因组和计算技术推断阔鼻鱼的生殖。从每个家族的代表性物种产生的随机基因组文库将提供长达约650个碱基对的100个标记。这些未连锁的标记，估计包括多达65个非编码，非基因，非重复的核DNA的内切酶，将在每个阔鼻属的至少一个代表性物种中进行测序。这一大型数据集将与来自传统分子标记的数据相结合并进行比较，例如来自核和线粒体基因组的蛋白质编码位点。数据将采用基于似然性的方法进行分析，考虑到由祖先多态性和阔鼻猴家族多样化早期阶段的快速分化引起的标记之间的系统发育不一致性。如果没有准确的新世界猴系统发育，将阻碍对阔鼻猴基因组、表型和行为的进化重建。与卡他鼻类相比，阔鼻类的DNA置换率变异的研究相对较少。灵长类动物中重要的表型和行为特征，可以更好地重建与拟议的遗传学，包括孪生，色觉，脑化由于扩大的新皮层。这项研究介绍了新的方法来确定分支顺序和时间的分歧之间的所有宽鼻属。将使用高通量方法生成大量非编码系统发育序列数据以供分析。此外，一个基于可能性的方法，结合人口统计变量将被用来推断新世界猴的早期多样化。这些方法可能进一步适用于其他系统发育组。此外，通过结合分子和化石数据来估计分歧的时间，将突出不同阔鼻类群体之间突变率的变化。灵长类动物引起了公众的极大兴趣，许多被研究的新世界猴子通常被安置在美国动物园，在那里他们为公众提供教育经验。它们的魅力行为和形态使它们成为重要的保护焦点。新世界猴也是科学研究中常用的模式生物，普通的绒猴已经成为全基因组测序的目标。解决这些动物的系统发育史将提高公众，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，结合了两位研究者在计算基因组学、灵长类进化和遗传学方面的互补优势。学生和博士后研究人员将接受培训，并鼓励他们寻求两个研究人员实验室提供的合作机会。将建立一个专门介绍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史将为今后的研究提供基础。最后，本研究产生的所有标记的序列将在公共数据库中提供。在这个项目中获得的序列将是灵长类基因组学社区的重要资源。