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

合作研究：NSFDEB-BSF：量化非模型辐射中的基因组孔隙度

• 批准号: 1555754
• 负责人: Irby Lovette
• 金额: $ 39.22万
• 依托单位: Cornell University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-03-01 至 2020-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1555754&HistoricalAwards=false
• 关键词: COLLABORATIVE; RESEARCH; NSFDEB; BSF; Quantifying

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.

了解生物体如何相互关联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 序列的比较已被用来为许多生物体群体建立可靠的进化树。然而，在物种相互杂交的情况下（或过去曾经这样做过），它们的后代就会成为遗传背景的马赛克，而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尤其常见，即大量物种在相对较短的时间内进化的情况，而同时这些快速辐射是许多其他类型的进化分析的模型。该项目将研究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。该工具将提供给研究界，以帮助生物学家了解生命树尖端的进化。该项目将为非常成功的 All About Bird Biology 网站添加基于交互式多媒体的系统发育学和系统学模块。 该项目由美国国家科学基金会和以色列两国科学基金会合作资助。该项目的总体目标是测试有关快速辐射下物种之间基因组区域交换的程度和类型的问题，并探索其对系统发育推断的影响。这些目标基于新的生物信息学工具（广义系统发育合并采样器 - G-PhoCS）的进一步开发，该工具将使研究非模型生物的科学家能够使用各种基因组规模的数据集来测试有关系统发育关系的假设，并在整个系统发育中生成详细的人口统计推论（例如，量化基因流、有效群体规模和分歧时间）。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，根据生态重叠和同域/异域等外部标准，可以将物种对分为易渗入或抗渗入。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兴高通量序列数据的全部潜力。这项合作将更广泛地拓宽对基因组区域之间谱系不一致的模式和过程的理解。