Dimensions: Landscape Genomics of an Adaptive Radiation using Ultra-High Resolution Genetic, Morphometric, and Spatial Analysis

在适应性辐射期间，一组生物体多样化，形成适合不同环境或生态角色的各种形式。加勒比大安的列斯群岛上的Anolis蜥蜴(Anoles)经历了反复的适应性进化，导致不同岛屿上形成了不同的物种，这些物种进化出了相似的特征，占据了森林栖息地的相似部分。这是一个值得注意的收敛进化和生态分化的例子，前者是不同物种独立进化出相似的特征，后者是物种对环境的反应多样化。因此，无性系提供了回答几个重要问题的机会，包括什么因素在物种的重要生态特征中产生多样性？这些特征的遗传基础是什么？相同的基因是否参与了不同物种特定特征的重复进化？产生变异的过程什么时候会导致物种形成，即一个物种多样化成多个不同的物种？该项目将研究环境中的空间差异如何导致适应性生理特征的差异，以及物种内部和物种之间的基因组差异。研究人员将使用遗传学、形态学和空间统计学中的先进方法，从不同环境中收集的十几种变态动物中分析个体动物。通过研究多个物种和每个物种中的许多个体，研究人员将能够识别在适应进化的不同阶段产生不同水平生物多样性的因素。该项目还将培训两名博士后研究人员和众多研究生和本科生，包括来自传统代表性不足背景的学生。研究人员还计划将该项目的结果整合到针对K-12学生的适应性辐射的生态学和进化的课堂学习模块中。适应性辐射，如大安的列斯群岛上的Anolis蜥蜴通过新特征的进化复制多样化为生态形态课堂，为研究生态分歧和平行进化提供了极好的系统。拟议研究的首要目标将是研究空间环境变化如何在Anolis蜥蜴的复制适应性辐射中产生适应性表型多样性(功能维度)、种群基因组多样性(遗传维度)和生态形态物种多样性(系统发育维度)。具体地说，该项目将测试遗传和表型变异的模式是否取决于环境的空间结构或物种的生态；平行表型分化是否涉及平行的遗传分化；环境变异是否在物种内和物种之间产生异质基因组差异；以及基因组的相同区域是否重复地参与产生生态形态多样性。这些问题将通过使用尖端数据收集方法收集来自大安的列斯群岛的12种Anolis物种的超高分辨率环境、形态和遗传数据集来回答。该项目将使用陆地激光雷达扫描结构生境和在地理信息系统中对生物气候层进行地理空间分析来生成环境数据，使用外显子捕获和整个外显子测序来生成遗传数据，并使用微型CT扫描来为形态数据生成实地收集的标本的三维重建。然后将使用创新的分析方法来整合这些不同的数据集，以了解不同阶段适应性辐射多样化的基础过程。

During adaptive radiation, a group of organisms diversifies into a variety of forms specialized for different environments or ecological roles. Anolis lizards (anoles) on the Greater Antillean islands in the Caribbean have undergone repeated adaptive evolution, resulting in the formation of different species on different islands that have evolved similar traits for occupying similar parts of the forest habitat. This is a remarkable case of convergent evolution, in which separate species independently evolve similar traits, and ecological divergence, in which species diversify in response to the environment. Thus, anoles present opportunities to answer several important questions, including what are the factors that produce diversity in the important ecological traits of a species? What is the genetic basis for these traits, and are the same genes involved in the repeated evolution of particular traits in different species? When do the processes generating variation lead to speciation, in which one species diversifies into multiple, distinct species? This project will examine how spatial variation in the environment leads to variation in adaptive physical traits and variation across the genome both within and between species. The researchers will use advanced methods in genetic, morphology, and spatial statistics to analyze individual animals from a dozen species of anoles collected across different environments. By examining multiple species and many individual from each species, the researchers will be able to identify the factors that generate different levels of biodiversity during different stages of adaptive evolution. This project will also result in the training of two postdoctoral researchers and numerous graduate and undergraduate students, including students from traditionally underrepresented backgrounds. The researchers also plan to integrate the results of the project into classroom learning modules on the ecology and evolution of adaptive radiations for K-12 students.Adaptive radiations, like the replicated diversification of Anolis lizards on the Greater Antilles into ecomorph classes through the evolution of novel traits, present excellent systems in which to study ecological divergence and parallel evolution. The overarching goal of the proposed research will be to examine how spatial environmental variation generates adaptive phenotypic diversity (Functional dimension), population genomic diversity (Genetic dimension), and ecomorphological species diversity (Phylogenetic dimension) in replicated adaptive radiations of Anolis lizards. Specifically, this project will test whether patterns of genetic and phenotypic variation depend upon the spatial structure of the environment or the ecology of the species; whether parallel phenotypic divergence involves parallel genetic divergence; whether environmental variation generates heterogeneous genomic divergence both within and between species; and whether the same regions of the genome are repeatedly involved in generating ecomorphological diversity. These questions will be answered by assembling ultra-high resolution environmental, morphological, and genetic datasets for 12 Anolis species from the Greater Antilles using cutting-edge data collection methods. This project will use terrestrial-LiDAR scans of structural habitats and geospatial analysis of bioclimatic layers in a GIS (Geographical Information System) to generate the environmental data, exon capture and whole exome sequencing to produce the genetic data, and micro-CT scanning to generate 3D reconstructions of field-collected specimens for the morphological data. Innovative analytical approaches will then be used to integrate these diverse datasets to understand the processes underlying diversification across different stages of adaptive radiation.