Phylogenomics and the roles of chromosome architecture, recombination and hybridization on phylogenetic accuracy in the cat family (Felidae)

系统发育学以及染色体结构、重组和杂交对猫科（猫科）系统发育准确性的作用

• 批准号: 1753760
• 负责人: William Murphy
• 金额: $ 93.91万
• 依托单位: Texas A&M AgriLife Research
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1753760&HistoricalAwards=false
• 关键词: Phylogenomics; roles; chromosome; architecture; recombination

Accurately determining the pattern and timing of the evolutionary history of Earth's species is essential to understand how geologic and environmental forces drive the origin, diversification, and extinction of species. The advent of low-cost genome sequencing has revolutionized the field of systematics and the use of genetic data to infer the evolutionary relationships of organisms. But the ability to generate data on genome structure and variation has outpaced understanding on how to use it to infer evolutionary history and species relationships. This project will analyze the impact of genomic features on evolutionary inference in the cat family. Because cat species relationships are well understood, genomic data are available for several species, and genetic tools are available that allow detailed analyses, cats are an excellent system to investigate how chromosome characteristics and structural variation in the genome affect evolution and the inference of evolutionary history. This study promises to have a large impact on the field of systematics and evolutionary biology. This study also has broader impacts on society. Cats are consistently ranked as the most charismatic and recognizable symbols of wildlife and animal conservation, and provide a gateway to engagement and learning about biology and evolution across diverse socioeconomic backgrounds. One of the most important project outcomes will be the development of a website by student recruits and researchers, describing and integrating research outcomes with information on the members of the cat family, and connecting these to the public.Using the remarkable radiation of the cat family Felidae as a model system, this project will generate high quality genome sequence assemblies from all living species to identify the impact of chromosomal characteristics on the accuracy of species tree inference. Novel computational algorithms will be developed to search, sort, and characterize genome-wide variation in topology, tree shape and divergence time, and connect this variation to genomic features predictive of the species tree. The ultimate goal is to understand which chromosomal features have positive and negative influences on accurate species tree estimation, to guide future principles and applications of phylogenomics. Felids are an excellent model system because of the high rate of recombination within the family and the existence of established genomic tools and information.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.

准确确定地球物种进化历史的模式和时间对于了解地质和环境力量如何驱动物种的起源，多样化和灭绝至关重要。低成本基因组测序的出现彻底改变了系统学领域，并利用遗传数据来推断生物体的进化关系。但是，产生基因组结构和变异数据的能力已经超过了如何利用它来推断进化历史和物种关系的理解。这个项目将分析基因组特征对猫科动物进化推理的影响。由于猫物种关系很好地理解，基因组数据可用于几个物种，遗传工具可用于详细分析，猫是一个很好的系统，以研究染色体特征和基因组结构变异如何影响进化和进化历史的推断。这项研究有望对系统学和进化生物学领域产生重大影响。这项研究也对社会产生了更广泛的影响。猫一直被列为野生动物和动物保护的最具魅力和可识别的象征，并提供了一个参与和学习生物学和进化的门户，跨越不同的社会经济背景。最重要的项目成果之一将是由学生招募和研究人员开发一个网站，描述和整合研究成果与猫科成员的信息，并将这些与公众联系起来。使用猫科动物的显着辐射作为模型系统，该项目将从所有现存物种中产生高质量的基因组序列组合，以确定染色体特征对物种树推断准确性的影响。将开发新的计算算法来搜索，排序和表征拓扑结构，树形和发散时间的全基因组变化，并将这种变化与预测物种树的基因组特征联系起来。最终的目标是了解哪些染色体特征对物种树的准确估计有积极和消极的影响，以指导未来的染色体组学的原则和应用。Felids是一个优秀的模型系统，因为家族内重组率高，并且存在已建立的基因组工具和信息。该奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.

Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species

• DOI: 10.1093/molbev/msz139
• 发表时间: 2019-10-01
• 期刊: MOLECULAR BIOLOGY AND EVOLUTION
• 影响因子: 10.7
• 作者: Li, Gang;Figueiro, Henrique;Murphy, William J.
• 通讯作者: Murphy, William J.

A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids

• DOI: 10.1098/rspb.2020.0690
• 发表时间: 2020-06-10
• 期刊: PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
• 影响因子: 4.7
• 作者: Allen, Richard;Ryan, Hannah;Larson, Greger
• 通讯作者: Larson, Greger

Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast

美国墨西哥湾沿岸神秘濒临灭绝的红狼基因组祖先的持续存在和扩张

• DOI: 10.1111/mec.16200
• 发表时间: 2021
• 期刊: Molecular Ecology
• 影响因子: 4.9
• 作者: vonHoldt, Bridgett M.;Brzeski, Kristin E.;Aardema, Matthew L.;Schell, Christopher J.;Rutledge, Linda Y.;Fain, Steven R.;Shutt, Amy C.;Linderholm, Anna;Murphy, William J.
• 通讯作者: Murphy, William J.

Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

• DOI: 10.1146/annurev-animal-061220-023149
• 发表时间: 2021-01-01
• 期刊: ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 9, 2021
• 作者: Murphy, William J.;Foley, Nicole M.;Springer, Mark S.
• 通讯作者: Springer, Mark S.