DISSERTATION RESEARCH: Delineation of populations, species, and genomic adaptations across a widely distributed venomous snake species complex

描述生命的多样性和相关性是进化生物学的一个重要目标，我们对这种多样性的理解为解决重要问题提供了一个框架。这些问题中的许多都与适应有关，这些适应是随着时间的推移而进化的，以更好地使生物体适应其环境。特别是，人们很少了解相同的进化力量和过程是否可能以类似的方式在密切相关的谱系中产生局部适应的特征。某些基因或基因组区域是否在占据截然不同的栖息地和气候的物种之间反复成为自然选择的目标？这项研究旨在利用一种独特的北美响尾蛇系统，即Crotalus viridis物种复合体来解决这些问题。这类蛇在颜色、大小和毒液成分上高度多样化，在不同的生态区域茁壮成长。这个研究项目将对这一群体成员之间的进化关系产生一个强有力的理解，这也将为检验自然选择如何推动其多样化的假设提供一个背景框架。然后，该研究项目将使用从这些谱系的整个基因组中收集的信息来寻找基因和基因组的证据，这些基因和基因组是当地适应选择的共同目标。了解物种复合体的系统分类学是具有挑战性的，但是新的和强大的分析方法，以及来自下一代测序技术的大型基因组规模数据集，使这一挑战变得越来越容易处理。尽管研究物种复合体存在固有的困难，但这些系统是将我们对其生物多样性的理解与塑造其进化和多样性的基因组过程联系起来的理想选择。这个项目试图用一个比较系统来建立这些联系，这个系统是Crotalus viridis物种复合体。该研究计划将利用全基因组单核苷酸多态性数据，为该复合体生成第一个强大的物种树，该复合体在历史上一直是系统学家的一个有问题的群体。这个系统发育框架将被用作谱系内和谱系间选择下基因和基因组区域分析的比较平台。这项研究将询问多个种群和物种的基因组，以解决选择机制是否针对这样一个物种复合体中的共同位点，或者基因和基因的功能类别是否被谱系特异性地靶向的问题。总的来说，这项研究将描述一个多样化和医学相关的毒蛇群体的进化史，并将大大增加我们对适应和趋同进化在多个尺度上产生生物多样性中所起作用的认识。

Characterizing the diversity and relatedness of life is an important goal of evolutionary biology, and our understanding of this diversity provides a framework to address important questions. Many of these questions relate to adaptations that are evolved over time to better suit organisms to their environment. In particular, it is little understood whether the same evolutionary forces and processes may act in a similar manner to produce locally adapted traits in closely related lineages. Are certain genes or genomic regions repeatedly targeted by natural selection across species that occupy drastically different habitats and climates? This research aims to address these questions using a unique system of North American rattlesnakes, the Crotalus viridis species complex. Snakes of this group are highly diverse in their coloration, size, and venom composition, and thrive in diverse ecoregions. This research program will generate a robust understanding of the evolutionary relationships among members of this group, which will also provide a contextual framework for testing hypotheses of how natural selection has driven their diversification. This research program will then use information collected from throughout the genomes of these lineages to look for evidence of genes and sets of genes that are common targets of selection for local adaptation.Understanding the systematics of species complexes can be challenging, but new and robust analytical approaches, together with large genome-scale datasets from next-generation sequencing technology are making this challenge increasingly manageable. Despite the difficulties inherent in studying species complexes, these systems are ideal for linking our understanding of their biodiversity with the genomic processes that have shaped their evolution and diversity. This project seeks to make these connections using a comparative phylogenetic system, the Crotalus viridis species complex. The research program will generate the first robust species tree for the complex, which has historically been a problematic group for systematists, using genome-wide single nucleotide polymorphism data. This phylogenetic framework will then be used as a comparative platform for analyses of genes and genomic regions under selection within and among lineages. This research will interrogate the genomes of multiple populations and species to address the question of whether selection regimes target common loci across such a species complex, or if genes and functional categories of genes are idiosyncratically targeted by lineage. Collectively, this research will characterize the evolutionary history of a diverse and medically relevant venomous snake group and will add considerably to our knowledge of the roles that adaptation and convergent evolution play in the generation of biodiversity at multiple scales.