Collaborative Research: The evolution of the anthropoid genome

这项合作研究的目标是利用基因组数据来解决灵长类动物进化的基本问题。研究人员将对大约36种类人猿（猴子和猿）的基因组进行测序，这些类人猿的基因组数据很少或根本没有。对不同但密切相关的生物体的基因组进行比较，可以对它们的生物学产生许多见解，例如基因组的哪些区域影响生物学上重要的特征，以及灵长类动物生命树上发生重要分支事件的时间。对猴子和猿基因组的研究也为理解人类基因组的独特之处提供了比较数据。这项研究将产生一个免费访问的类人猿灵长类基因组数据库，并将促进研究生、本科生和高中生（包括纽约市公立学校的学生）在最先进的生物信息学和分子实验室技术方面的培训。鉴定DNA替换的变异模式并了解其原因是比较遗传学的中心目标。偏离“基线”中性分子进化速率的基因组区域可能具有生物学功能，因此影响适应性表型。当更多来自生命之树主要分支的物种被包括进来时，许多比较分析的能力就会提高。到目前为止，相对较少的猴子物种已经成为大规模测序工作的目标。研究人员将使用短读和长分子DNA测序相结合的方法来获得大约36个类人猿属的基因组序列，然后将这些序列与已经测序的12个类人猿属结合起来。有了这个庞大的比较数据集，研究人员将1)推断出可能的最佳灵长类树，包括估计主要分支之间分裂的时间；2)确定哪些生活史特征（如世代长度）导致了猴、猿和人类谱系中基因组进化速率的差异；3)扫描类人猿树中可能具有功能意义的主要分支的基因组区域。

The goal of this collaborative research is to use genomic data to address fundamental questions about the evolution of primates. The investigators will sequence the genomes of the roughly 36 anthropoid (monkey and ape) genera for which little or no genomic data are available. Comparisons of the genomes of different but closely related organisms can yield many insights into their biology, such as which areas of the genome affect traits of biological importance, and when important branching events occurred in the primate tree of life. Studies of monkey and ape genomes also provide comparative data for understanding what is unique about the human genome. This research will result in a freely accessible anthropoid primate genomic database and will facilitate the training of graduate, undergraduate, and high school students, including students from New York City public schools, in state-of-the-art bioinformatics as well as molecular laboratory techniques.Identifying patterns of variation in DNA substitutions and understanding their causes is a central goal of comparative genetics. Genomic regions that depart from 'baseline' neutral rates of molecular evolution may have biological function and therefore influence adaptive phenotypes. The power of many comparative analyses improves when more species from major branches of the tree of life are included. Up to now, relatively few monkey species have been the target of large-scale sequencing efforts. The researchers will use a combination of short-read and long-molecule DNA sequencing to obtain genomic sequences of ~36 anthropoid genera and then combine these with the 12 that are already sequenced. With this large comparative dataset, the researchers will 1) infer the best possible primate tree, including estimates of the timing of splits among major branches; 2) determine which life history traits such as generation length cause variations in the rate of genomic evolution among monkey, ape, and human lineages; and 3) scan for areas of the genome of major branches of the anthropoid tree that might be of functional significance.