EAGER: The Genomic Landscape of Species Divergence in an Extraordinary Avian Radiation

物种形成，即一个祖先种群产生两个或两个以上具有不同特征的后代物种，是产生地球上生命多样性的基本进化过程。该项目将利用DNA测序技术的最新进展，以前所未有的细节来研究历史、地理和自然选择结合产生新物种进化的基因变化的方式。这是一项基础研究，旨在推进物种形成基因组学的新领域，增加对自然界的基础知识，同时验证对少数基因的自然选择足以产生新物种的假设。该项目还将为确定保护优先事项提供重要数据，为研究生提供分子和计算生物学方面的高级培训，并为学生和公众提供参与现代基因组学研究的机会，并提供一个涉及鸟类的可访问示例。本研究的重点是12种雀属（Lonchura属），它们代表了鸟类最近和快速多样化的最不寻常的案例之一。由于羽毛图案的多样性和生活在同一地理区域的近亲物种的复制例子，这个群体非常适合解决关于物种形成的基因组学的基本问题。利用全基因组测序与定向重测序相结合的方法，研究Lonchura地区物种和种群的遗传多样性和分化模式，目的是：1)评估物种形成早期分化的基因组区域（即基因）的数量、大小和位置；2)测试这些地区遗传变异（即等位基因）的起源和历史的替代模型。一般假设认为，每个物种的表型都是通过少数基因的遗传变异固定而进化的，这些基因的系统发育历史在很大程度上与全基因组的遗传变异模式脱钩，这一假设将得到检验。特别令人感兴趣的是，新的遗传变异可能通过杂交在物种之间转移，从而通过一小部分基因组位点上的等位基因的独特组合产生新的表型。

Speciation, in which one ancestral population gives rise to two or more descendant species with distinct characteristics, is the fundamental evolutionary process generating the diversity of life on earth. This project will harness recent advances in DNA sequencing technology to examine in unprecedented detail the ways in which history, geography and natural selection combine to produce the genetic changes responsible for the evolution of new species. This is basic research that aims to advance the new field of speciation genomics and increase fundamental knowledge of the natural world, while testing the hypothesis that natural selection on a small number of genes is sufficient to generate new species. The project will also generate important data for setting conservation priorities, provide advanced training in molecular and computational biology for a graduate student, and create opportunities for engaging students and the general public in modern genomics research with an accessible example involving birds.This research focuses on twelve finch species (genus Lonchura) that represent one of the most extraordinary cases of recent and rapid diversification in birds. With a diversity of plumage patterns and replicate examples of closely related species living in the same geographic regions, this group is ideally suited for addressing fundamental questions about the genomics of speciation. Whole genome sequencing combined with targeted re-sequencing will be used to characterize patterns of genetic diversity and divergence among species and populations in the Lonchura radiation and to: 1) assess the number, size and location of genomic regions (i.e., genes) diverging early in the speciation process; and 2) test alternative models for the origin and history of genetic variants (i.e., alleles) in these regions. The general hypothesis that each species' phenotype has evolved through the fixation of genetic variants at a small number of genes and that the phylogenetic history of these genes is largely decoupled from genome-wide patterns of genetic variation will be tested. Of particular interest is the possibility that novel genetic variants have been transferred between species via hybridization, resulting in novel phenotypes generated by unique combinations of alleles across a small subset of genomic loci.