COLLABORATIVE RESEARCH: NSFDEB-BSF: Quantifying genomic porosity in non-model radiations

了解生物体是如何相互联系的是生物学研究的中心目标，然而生命之树的分支结构仍然不完全清楚。DNA序列的比较已经被用来为许多生物群体建立可靠的进化树。然而，在物种相互杂交的情况下（或者过去曾经这样做过），它们的后代变成了遗传背景的马赛克，这种基因混合使得回溯计算它们过去的关系变得更加困难。杂交在经历快速辐射的物种群体中尤其常见——大量物种在相对较短的时间内进化的情况——同时，这些快速辐射为许多其他种类的进化分析提供了模型。该项目将研究在快速辐射期间物种间交换的基因组区域类型。研究人员的一个中心目标是开发一个计算机程序，利用大规模的基因组数据来更好地理解物种之间的系统发育关系，提高整合过去杂交事件影响的能力。这个工具将提供给研究界，以帮助生物学家了解生命之树顶端的进化。该项目将在非常成功的All About Bird Biology网站上添加基于系统发育和系统分类学的交互式多媒体模块。该项目由美国国家科学基金会和以色列国家科学基金会共同资助。该项目的总体目标是测试有关物种之间在快速辐射中交换的基因组区域的程度和类型的问题，并探索系统发育推断的含义。这些目标是基于一种新的生物信息学工具（广义系统发育聚结取样器- G-PhoCS）的进一步发展，该工具将允许科学家研究非模式生物来测试关于系统发育关系的假设，并产生详细的人口统计学推断（例如，量化基因流，有效种群大小和分化时间），跨越系统发育，使用各种基因组规模的数据集。作为实证测试案例，研究人员将利用两种鸟类辐射的自然进化实验，在这些实验中，基于生态重叠和同域/异域性等外部标准，一对对物种可以被分类为易渗入或耐渗入。该研究团队汇集了系统学家和计算机科学家，试图通过开发利用他们提供的丰富信息的推理方法来实现新出现的高通量序列数据的全部潜力。这种合作将更广泛地拓宽对基因组区域间家谱不一致的模式和过程的理解。

Understanding how organisms are related to each other is a central goal of biological research, yet much of the branching structure of the tree of life remains imperfectly known. Comparisons of DNA sequences have been used to build reliable evolutionary trees for many groups of organisms. Yet in cases where species hybridize with one another (or have done so in the past), their descendants become a mosaic of genetic backgrounds, and this genetic mixing makes it more difficult to back-calculate their past relationships. Hybridization is particularly common in groups of species that have undergone rapid radiations - situations when large numbers of species evolve over a relatively short period of time - while at the same time these rapid radiations are models for many other kinds of evolutionary analysis. This project will investigate the type of genomic regions that are exchanged among species during rapid radiations. A central goal of the researchers is to develop a computer program that leverages large-scale genomic data to better understand the phylogenetic relationships among species, improving the ability to incorporate the effects of past hybridization events. This tool will be made available to the research community to help biologists understand evolution at the tips of the tree of life. The project will add interactive multimedia-based modules on phylogenetics and systematics to the highly successful All About Bird Biology website. The project is a funded collaboratively by the NSF and the Binational Science Foundation of Israel.The overarching goals of this project are to test questions about the degree and type of genomic regions exchanged among species in rapid radiations, and to explore the implications for phylogenetic inference. These objectives are based on the further development of a new bioinformatics tool (Generalized Phylogenetic Coalescent Sampler - G-PhoCS) that will allow scientists studying non-model organisms to test hypotheses about phylogenetic relationships and generate detailed demographic inferences (e.g., quantifying gene flow, effective population sizes and divergence times) across a phylogeny, using a variety of genomic-scale datasets. As empirical test cases, the researchers will leverage natural evolutionary experiments in two avian radiations in which pairs of species can be classified as either introgression-prone or introgression-resistant based on external criteria such as ecological overlap and sympatry/allopatry. The research team brings together systematists and computer scientists attempting to realize the full potential of newly emerging high throughput sequence data by developing inference methods that make use of the rich information they provide. This collaboration will more generally broaden the understanding of the patterns and processes underlying genealogical discordance among regions of the genome.