Systematics, introgression, and adaptation in Western Rattlesnakes: a model system for studying gene flow, selection, and speciation

西部响尾蛇的系统学、基因渗入和适应：研究基因流、选择和物种形成的模型系统

• 批准号: 1655571
• 负责人: Todd Castoe
• 金额: $ 86.74万
• 依托单位: University of Texas at Arlington
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-06-01 至 2023-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1655571&HistoricalAwards=false
• 关键词: Systematics; introgression; adaptation; Western; Rattlesnakes

Despite substantial research, the roles of natural selection in the formation of species and in preventing hybridization between species remain poorly understood. In a rapidly changing world, there is an urgent need to understand the importance of these processes in species formation and the impact of these processes on how scientists identify and name species. This research program will study genetic, venom protein, and anatomical data to test how natural selection shapes and maintains species, and it will use these results to test several approaches for appropriately identifying species in nature. The researchers will focus on a widespread and medically important group of rattlesnake species (Western Rattlesnakes and their close relatives) as a model system to study species formation. Many previous studies have disagreed about how many species should be recognized within this group of snakes, and different populations can produce diverse symptoms from snake bite due to differences in venom biochemistry. This study will resolve these issues by developing a new system for naming species, provide new insight into the process of species formation, develop new methods for identifying species, and refine the appropriate medical treatment of snakebite in North America. The proposed research includes methodological and theoretical scientific innovation, undergraduate and graduate student training, establishment of collaborative networks, and public outreach. Public outreach will be conducted at the Dallas and Denver Zoos, thereby reaching millions of public visitors per year.The overarching goals of this research program are to understand the interaction of admixture and selection in speciation, and to leverage an empirical system to test how these processes may influence coalescent-based species delimitation methods. This research program will focus on the Western Rattlesnake species group (Crotalus viridis species complex and its sister taxon, C. scutulatus; collectively Cvos hereafter) as a study system. This recently diverged species complex has offered major challenges for systematics, yet provides an ideal model system for studying speciation and species delimitation. This integrated study will combine genomic and phenotypic data to delimit species, inform species delimitation approaches, and provide new genome-scale insight into the process of speciation. This research program will also test hypotheses about the repeatability of patterns selection in the processes of speciation and resistance to gene flow and hybridization. The specific aims of this proposal are to: (1) integrate genome-wide sampling and ecological niche modeling to infer population structure and test hypotheses of gene flow among lineages of Cvos; (2) analyze selection in contact zones between putative taxa by integrating niche modeling, genotypic, and phenotypic data to test hypotheses regarding divergence and selection in the speciation process; and (3) develop and test new approaches for delimiting species that more appropriately handle admixture and selection, and apply these methods to test taxonomic hypotheses for the Cvos complex. Successful completion of the project will provide important data to understanding the role of admixture and selection in speciation and vastly improve our analytical methods for delimiting species in the presence of interbreeding across organismal groups. Additionally, an added benefit of the project is the information that will be obtained regarding venom complexity and evolution, which could contribute to better treatment of envenomation from snake bites.

尽管进行了大量的研究，但对自然选择在物种形成和防止物种间杂交中的作用仍然知之甚少。在一个快速变化的世界中，迫切需要了解这些过程在物种形成中的重要性，以及这些过程对科学家如何识别和命名物种的影响。该研究计划将研究遗传，毒液蛋白和解剖数据，以测试自然选择如何塑造和维持物种，并将使用这些结果来测试几种方法，以适当地识别自然界中的物种。研究人员将专注于一个广泛和医学上重要的响尾蛇物种（西部响尾蛇及其近亲），作为研究物种形成的模型系统。许多以前的研究都不同意在这组蛇中应该识别多少种，不同的种群可以产生不同的症状，由于毒液生物化学的差异，蛇咬伤。这项研究将通过开发一个新的物种命名系统来解决这些问题，为物种形成的过程提供新的见解，开发识别物种的新方法，并改进北美蛇咬伤的适当医疗方法。拟议的研究包括方法和理论的科学创新，本科生和研究生的培训，建立合作网络，和公众宣传。公众宣传将在达拉斯和丹佛动物园进行，从而达到每年数百万的公众visitors. This研究计划的总体目标是了解混合物和选择的相互作用，在物种形成，并利用实证系统来测试这些过程可能会影响聚结为基础的物种划界方法。这项研究计划将集中在西部响尾蛇种组（Crotalus viridis物种复合体及其姐妹分类群，C。scutulatus;以下统称Cvos）作为研究系统。这一新近分化的物种复合体为系统学研究带来了重大挑战，同时也为研究物种形成和物种定界提供了理想的模式系统。这项综合研究将结合联合收割机基因组和表型数据来界定物种，为物种界定方法提供信息，并为物种形成过程提供新的基因组尺度的见解。这项研究计划还将测试有关模式选择的可重复性的假设，在物种形成和基因流和杂交的阻力的过程。该方案的具体目标是：（1）整合全基因组取样和生态位模型，以推断群体结构和检验Cvos谱系间基因流的假设;（2）通过整合生态位模型、基因型和表型数据，分析假定分类群之间接触区的选择，以检验物种形成过程中的分歧和选择假设;和（3）开发和测试新的方法来界定物种，更适当地处理混合和选择，并应用这些方法来测试Cvos复合体的分类学假设。该项目的成功完成将提供重要的数据，以了解混合物和选择在物种形成中的作用，并大大提高我们的分析方法，在存在跨生物群的杂交育种的情况下界定物种。此外，该项目的另一个好处是将获得有关毒液复杂性和进化的信息，这可能有助于更好地治疗蛇咬伤的毒液。

项目成果

Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation

• DOI: 10.1093/sysbio/syy034
• 发表时间: 2018-11-01
• 期刊: SYSTEMATIC BIOLOGY
• 影响因子: 6.5
• 作者: Adams, Richard H.;Schield, Drew R.;Castoe, Todd A.
• 通讯作者: Castoe, Todd A.

Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues

• DOI: 10.1093/gbe/evaa068
• 发表时间: 2020-04
• 期刊: Genome Biology and Evolution
• 影响因子: 3.3
• 作者: G. M. Pasquesi;B. W. Perry;Michael W. Vandewege;Robert Ruggiero;Drew R. Schield;T. Castoe

Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation

• DOI: 10.1093/biolinnean/blz077
• 发表时间: 2019-06
• 期刊: Biological Journal of the Linnean Society
• 影响因子: 1.9
• 作者: Drew R. Schield;B. W. Perry;Richard H. Adams;D. Card;Tereza Jezkova;G. M. Pasquesi;Zachary L. Nikolakis;Kristopher W. Row;J. Meik;Cara F. Smith;S. Mackessy;T. Castoe

Population genomic analyses confirm male-biased mutation rates in snakes

群体基因组分析证实蛇的雄性突变率

• DOI: 10.1093/jhered/esab005
• 发表时间: 2021
• 期刊: Journal of Heredity
• 影响因子: 3.1
• 作者: Schield, Drew R;Perry, Blair W;Nikolakis, Zachary L;Mackessy, Stephen P;Castoe, Todd A
• 通讯作者: Castoe, Todd A

Geographic variation in morphology in the Mohave Rattlesnake (Crotalus scutulatus Kennicott 1861) (Serpentes: Viperidae): implications for species boundaries

莫哈维响尾蛇 (Crotalus scutulatus Kennicott 1861)（蛇类：蝰蛇科）形态的地理变异：对物种边界的影响

• DOI: 10.11646/zootaxa.4683.1.7
• 发表时间: 2019
• 期刊: Zootaxa
• 影响因子: 0.9
• 作者: WATSON, JESSICA A.;SPENCER, CAROL L.;SCHIELD, DREW R.;BUTLER, BRETT O.;SMITH, LYDIA L.;FLORES-VILLELA, OSCAR;CAMPBELL, JONATHAN A.;MACKESSY, STEPHEN P.;CASTOE, TODD A.;MEIK, JESSE M.
• 通讯作者: MEIK, JESSE M.