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

在适应性辐射过程中，一组生物体分化成各种形式，专门用于不同的环境或生态作用。 在加勒比海的大安的列斯群岛上的阿诺利斯蜥蜴（anoles）经历了反复的适应性进化，导致在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。 这是趋同进化和生态分化的一个显著例子，在趋同进化中，不同的物种独立地进化出相似的特征，在生态分化中，物种根据环境的变化而多样化。 因此，变色龙提供了回答几个重要问题的机会，包括什么因素产生了物种重要生态特征的多样性？ 这些特征的遗传基础是什么？不同物种中特定特征的重复进化是否涉及相同的基因？ 什么时候产生变异的过程导致物种形成，即一个物种分化成多个不同的物种？ 该项目将研究环境中的空间变化如何导致适应性物理性状的变化以及物种内和物种间基因组的变化。 研究人员将使用遗传学，形态学和空间统计学的先进方法来分析在不同环境中收集的十几种变色龙的个体动物。 通过研究多个物种和每个物种的许多个体，研究人员将能够确定在适应性进化的不同阶段产生不同生物多样性水平的因素。 该项目还将培训两名博士后研究人员和许多研究生和本科生，包括来自传统上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K-12学生的适应性辐射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ecomorph类，提供了研究生态分歧和平行进化的优秀系统。拟议的研究的总体目标将是研究空间环境变化如何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），和生态形态学物种多样性（系统发育维度）在复制的适应性辐射的阿诺利斯蜥蜴。具体而言，该项目将测试遗传和表型变异的模式是否取决于环境或物种生态的空间结构;平行表型差异是否涉及平行遗传差异;环境变化是否在物种内和物种间产生异质基因组差异;以及基因组的相同区域是否重复参与产生生态形态多样性。这些问题将通过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栖息地和地理空间分析地理信息系统（GIS）中的生物气候层，以生成环境数据，外显子捕获和整个外显子组测序以生成遗传数据，微CT扫描以生成实地收集的标本的3D重建形态数据。创新的分析方法，然后将被用来整合这些不同的数据集，以了解适应性辐射的不同阶段的多样化背后的过程。

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.