RUI: Partial lizard genomes and new analytical tools provide a novel conceptual framework for understanding biogeographic patterns throughout the deserts of western North America

RUI：部分蜥蜴基因组和新的分析工具为理解北美西部沙漠的生物地理模式提供了一个新颖的概念框架

• 批准号: 1929679
• 负责人: Christopher Blair
• 金额: $ 41.25万
• 依托单位: CUNY New York City College of Technology
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1929679&HistoricalAwards=false
• 关键词: RUI; Partial; lizard; genomes; new

The goal of many evolutionary biologists is to better understand the processes that lead to the formation of new species. In addition to providing valuable data regarding how Earth's history has shaped diversity, results can directly inform conservation and help address biodiversity loss. This study uses genetic data from lizards distributed throughout the arid regions of western North America to better understand how and why new species arise. This study also investigates the prevalence of species unknown to science, and provides formal descriptions of new species discovered. Results of this project directly inform conservation while simultaneously providing a more thorough understanding of the historical processes that led to the evolution of desert species throughout North America. Importantly, this project introduces evolutionary thinking and data analysis to historically underrepresented students enrolled in an undergraduate bioinformatics curriculum. Undergraduates are involved in all aspects of the project from study design and field work to data analysis and writing. Additional broader impacts include working with local institutions to teach genetic concepts to high school students and teachers, facilitation of an institution-wide bootcamp to enhance networking opportunities, graduate student supervision, and local research talks given to the public and to the greater academic community. Decades of research focused on the phylogeography of taxa inhabiting the arid regions of western North America has provided invaluable information regarding the propensity for cryptic lineages, while simultaneously constructing a comprehensive model describing broad biogeographic patterns observed in co-distributed taxa. However, the majority of our current knowledge comes from limited genetic information (e.g. mtDNA only) coupled with the assumption of gene tree/species tree congruence and strictly bifurcating evolutionary histories. Recent advances in genomic sequencing (e.g. RADseq, GBS) can now be combined with the multispecies coalescent (MSC) model to explicitly accommodate gene tree/species tree discordance due to incomplete lineage sorting (ILS), potentially leading to new insight regarding evolutionary relationships and biogeographic patterns. Although powerful, the MSC assumes no gene flow/introgression once species begin to diverge; an assumption that appears to be violated in a growing number of systems. To date, few empirical studies have used genomic data to explicitly quantifiy bias in parameter estimation when ignoring gene flow. This study uses multiple species of phrynosomatid lizards as models to better understand the role of gene flow during diversification throughout the North American deserts. In instances where introgression is suspected, the project quantifies the impact of ignoring gene flow on parameter estimates such as the species tree topology, divergence times and effective population sizes. This study also combines genomic data with morphological and ecological data to reassess species limits, describe new taxa, and inform conservation. The overarching goal of this study is to use newly generated genomic data from multiple species to formulate a new conceptual framework regarding the diversification and historical biogeography of taxa inhabiting the major deserts of western North America.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.

许多进化生物学家的目标是更好地理解导致新物种形成的过程。除了提供有关地球历史如何塑造多样性的宝贵数据外，研究结果还可以直接为保护提供信息，并帮助解决生物多样性丧失问题。这项研究使用了分布在北美西部干旱地区的蜥蜴的遗传数据，以更好地了解新物种是如何以及为什么会出现的。这项研究还调查了科学未知物种的流行情况，并对发现的新物种进行了正式描述。该项目的结果直接告知保护，同时提供了一个更深入的了解导致整个北美沙漠物种进化的历史过程。重要的是，该项目引入了进化思维和数据分析，历史上代表性不足的学生就读于本科生物信息学课程。本科生参与项目的各个方面，从研究设计和实地工作到数据分析和写作。其他更广泛的影响包括与当地机构合作，向高中学生和教师教授遗传学概念，促进全机构范围的训练营，以加强网络机会，研究生监督，以及向公众和更大的学术界提供当地研究讲座。几十年的研究集中在栖息在北美西部干旱地区的类群的地理分布提供了宝贵的信息，关于神秘的血统的倾向，同时构建一个全面的模型，描述广泛的地理分布模式中观察到的共同分布的类群。然而，我们目前的大部分知识来自有限的遗传信息（例如mtDNA），加上基因树/物种树一致性和严格分叉的进化历史的假设。基因组测序的最新进展（例如RADseq，GBS）现在可以与多物种结合（MSC）模型相结合，以明确适应基因树/物种树不一致，由于不完整的谱系排序（ILS），可能导致新的见解有关的进化关系和地理模式。尽管功能强大，但MSC假设一旦物种开始分化就没有基因流动/基因渗入;这一假设似乎在越来越多的系统中被违反。迄今为止，很少有实证研究使用基因组数据明确量化参数估计时忽略基因流的偏差。这项研究使用多个物种的phrynosomatid蜥蜴作为模型，以更好地了解整个北美沙漠多样化过程中的基因流的作用。在怀疑基因渗入的情况下，该项目量化了忽略基因流对参数估计的影响，如物种树拓扑结构，发散时间和有效种群大小。这项研究还将基因组数据与形态学和生态学数据相结合，以重新评估物种限制，描述新的分类群，并为保护提供信息。这项研究的首要目标是使用新产生的多个物种的基因组数据，制定一个新的概念框架，关于栖息在北美西部主要沙漠的类群的多样性和历史植物地理学。该奖项反映了NSF的法定使命，并已被认为是值得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的支持。

项目成果

Organellar DNA continues to provide a rich source of information in the genomics era

细胞器 DNA 继续为基因组学时代提供丰富的信息来源

• DOI: 10.1111/mec.16872
• 发表时间: 2023
• 期刊: Molecular Ecology
• 影响因子: 4.9
• 作者: Blair, Christopher

Phylogenomics of alligator lizards elucidate diversification patterns across the Mexican Transition Zone and support the recognition of a new genus

• DOI: 10.1093/biolinnean/blab139
• 发表时间: 2021-11-23
• 期刊: BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
• 影响因子: 1.9
• 作者: Blair, Christopher;Bryson, Robert W., Jr.;Klicka, John
• 通讯作者: Klicka, John