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

了解生物体之间的相互关系是生物学研究的核心目标，但生命之树的许多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，在物种彼此杂交（或过去曾杂交过）的情况下，它们的后代会成为遗传背景的马赛克，这种遗传混合使得回溯它们过去的关系变得更加困难。杂交在经历过快速辐射的物种群体中特别常见-大量物种在相对较短的时间内进化的情况-同时这些快速辐射是许多其他类型进化分析的模型。该项目将调查在快速辐射期间物种之间交换的基因组区域的类型。研究人员的一个中心目标是开发一种计算机程序，利用大规模基因组数据更好地了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“关于鸟类生物学的一切”网站上增加关于鸟类遗传学和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两国科学基金会共同资助，其总体目标是测试快速辐射下物种间基因组区域交换的程度和类型，并探索系统发育推断的意义。这些目标是基于进一步开发一种新的生物信息学工具（广义系统发生合并采样器- G-PhoCS），该工具将使研究非模式生物的科学家能够测试有关系统发生关系的假设，并生成详细的人口统计推断（例如，量化基因流、有效种群大小和分歧时间）。作为实证测试案例，研究人员将利用两个鸟类辐射的自然进化实验，其中物种对可以根据外部标准（如生态重叠和同域性/异域性）分类为倾向于基因渗入或抗基因渗入。该研究团队汇集了系统学家和计算机科学家，试图通过开发利用其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之间系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.