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

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，结果还可以直接为保护提供信息，并帮助解决生物多样性的丧失问题。这项研究使用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出现的。这项研究还调查了科学上未知物种的流行情况，并对新发现的物种进行了正式描述。该项目的结果直接为保护提供了信息，同时提供了对导致整个北美沙漠物种进化的历史过程的更彻底的了解。重要的是，这个项目向本科生物信息学课程中历史上代表性不足的学生介绍了进化思维和数据分析。本科生参与该项目的方方面面，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生和教师教授遗传学概念，促进机构范围内的训练营以加强联网机会，研究生监督，以及向公众和更广泛的学术界举办地方研究讲座。几十年来对生活在北美西部干旱地区的分类群系统地理的研究提供了关于神秘谱系倾向的宝贵信息，同时建立了一个全面的模型，描述在共同分布的分类群中观察到的广泛的生物地理模式。然而，我们目前的大部分知识来自有限的遗传信息(例如，只有线粒体DNA)，再加上基因树/物种树同余的假设和严格分叉的进化史。基因组测序的最新进展(如RADseq、GBS)现在可以与多物种结合(MSC)模型相结合，以明确地解释由于不完全谱系排序(ILS)导致的基因树/物种树不一致，这可能导致对进化关系和生物地理模式的新见解。尽管功能强大，但一旦物种开始分化，MSC就假设没有基因流动/导入；这一假设似乎在越来越多的系统中被违反。到目前为止，很少有实证研究使用基因组数据来明确量化参数估计中的偏差，而忽略了基因流动。这项研究使用了多个物种的硬体蜥蜴作为模型，以更好地了解基因流动在北美沙漠多样化过程中的作用。在被怀疑为渐渗的情况下，该项目量化了忽略基因流动对参数估计的影响，如物种树拓扑结构、分歧时间和有效种群规模。这项研究还将基因组数据与形态和生态数据相结合，以重新评估物种限制，描述新的分类群，并为保护提供信息。这项研究的总体目标是使用新产生的来自多个物种的基因组数据来制定一个关于北美西部主要沙漠中栖息的类群的多样性和历史生物地理的新概念框架。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.