Understanding the Co-Evolution of Phylogenomic Signal, Gene Linkage, and Recombination Rate Through Comparative Genomics

通过比较基因组学了解系统发育信号、基因连锁和重组率的共同进化

• 批准号: 2150664
• 负责人: William Murphy
• 金额: $ 120万
• 依托单位: Texas A&M University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2150664&HistoricalAwards=false
• 关键词: Understanding; Co; Evolution; Phylogenomic; Signal

One of the major themes that have emerged from the genetics literature from the past decade is that each species’ genome is a mosaic of many different genetic histories. A daunting challenge facing biologists is how to accurately interpret this large and complex collection of genetic histories to identify which of these most likely represent the true relationships among living and extinct species. The rate at which chromosomes exchange information (i.e., recombine) has been shown to be one of the most reliable predictors of which DNA sequences within chromosomes can best reconstruct ancient relationships of living species. Our goal is to retrace the evolution of mammalian chromosomes and their recombination rates across time, from the genomes of living species back to their inferred 100-million-year-old ancestor. We will identify those shared chromosome regions that have recombined at the slowest rates and provide the greatest fidelity to reconstructing mammalian evolutionary history. We will also determine whether specific genes preferentially evolve within regions of historically high or low rates of chromosomal change. Our findings will greatly benefit researchers seeking to resolve other parts of the Tree of Life, by leading to more efficient approaches for determining evolutionary history at both shallow and deep evolutionary timescales. We will create a new public web-database for mammalian genetic maps that allows researchers to browse chromosomes, genes, and recombination rates across the mammalian Tree of Life. This project will train a diverse cohort of scientists across multiple academic levels. Our proposal is predicated upon pairing new high-quality, chromosome-level mammalian genome assemblies with a recombination map. An explicit goal of this project is to generate a detailed history of mammalian genes and chromosomes annotated with their local recombination rates. We will create a novel, publicly accessible resource of recombination maps allowing researchers to trace the evolution of recombination rate and chromosome evolution across the mammalian tree of life, from the inferred ancestor to each living species. We will also generate the first mammalian phylogeny based on Y chromosome data, the only chromosome that contains regions that have historically lacked meiotic recombination. Our findings will contribute to the goal of resolving the mammalian tree of life and inform ongoing controversies surrounding the mode and tempo of early placental mammal evolution, while improving our understanding of the relationship between chromosome architecture, recombination, and local gene content.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在过去的十年里，遗传学文献中出现的一个主要主题是，每个物种的基因组都是许多不同遗传历史的马赛克。生物学家面临的一个艰巨挑战是如何准确地解释这个庞大而复杂的遗传历史集合，以确定哪些最有可能代表现存物种和灭绝物种之间的真实关系。染色体交换信息的速率（即，重组）已被证明是最可靠的预测之一，其中染色体内的DNA序列可以最好地重建活物种的古老关系。我们的目标是追溯哺乳动物染色体的进化及其重组率，从现存物种的基因组追溯到它们推断的一亿年前的祖先。我们将确定那些以最慢速率重组的共享染色体区域，并为重建哺乳动物进化史提供最大的保真度。我们还将确定特定基因是否优先在历史上染色体变化率高或低的区域内进化。我们的发现将极大地有利于研究人员寻求解决生命之树的其他部分，通过导致更有效的方法来确定在浅层和深层进化时间尺度的进化历史。我们将创建一个新的哺乳动物遗传图谱的公共网络数据库，使研究人员能够浏览哺乳动物生命之树的染色体，基因和重组率。该项目将培养跨多个学术层次的多元化科学家群体。我们的建议是基于配对新的高质量，染色体水平的哺乳动物基因组组装与重组图谱。该项目的一个明确目标是生成一个详细的哺乳动物基因和染色体的历史，并注明其局部重组率。我们将创建一个新的，可公开访问的重组图谱资源，使研究人员能够跟踪整个哺乳动物生命树的重组率和染色体进化的演变，从推断的祖先到每个活的物种。我们还将根据Y染色体数据生成第一个哺乳动物的染色体发生，Y染色体是唯一一个包含历史上缺乏减数分裂重组的区域的染色体。我们的发现将有助于解决哺乳动物生命树的目标，并为围绕早期胎盘哺乳动物进化的模式和克里思的持续争议提供信息，同时提高我们对染色体结构，重组，该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响进行评估，被认为值得支持审查标准。

项目成果

Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation

• DOI: 10.1016/j.xgen.2023.100482
• 发表时间: 2024-02-14
• 期刊: CELL GENOMICS
• 作者: Foley，Nicole M.;Harris，Andrew J.;Murphy，William J.
• 通讯作者: Murphy，William J.

Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution

• DOI: 10.1038/s41588-023-01548-y
• 发表时间: 2023-11-02
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Bredemeyer, Kevin R.;Hillier, LaDeana;Murphy, William J.
• 通讯作者: Murphy, William J.