Genomics of complex speciation between Drosophila simulans and D. mauritiana

描述（由申请人提供）：这里提出的工作将整合分化种群基因组学和高分辨率遗传学，以剖析毛里求斯果蝇及其姊妹物种D. simulans之间复杂物种形成的历史和功能方面。自25万年前分裂以来，这两个物种在杂交的两个方向上都进化出了完全的杂交雄性不育，但有明确的证据表明，最近与基因流的二次接触（杂交雌性是有生育能力的）。该项目的目标是获得这些部分生殖隔离物种之间的自然选择和基因流动的全面全基因组分析，这是由杂交不相容因素的精细全基因组图谱提供的信息。该项目预计目前正在开发一个庞大的数据集：高覆盖率的全基因组下一代重测序数据，来自毛里求斯果蝇的10个系和模拟果蝇的20个系。该项目有两个互补的组成部分。首先，将开发新的计算和统计推断方法，用于物种分化的全基因组进化分析。其次，将利用新开发的功能遗传资源，构建高分辨率的毛利亚纳毛利亚纳基因组背景中导致杂交不相容的毛利亚纳毛利亚纳遗传因子全基因组图谱；其中2-4个因子将作为分子鉴定和功能表征的目标。这两个组成部分将被整合到：(1)测试基因组的不相容区域是否富集了正选择的特征和/或显示出种间基因流动的减少倾向；(2)确定X染色体在动物物种形成中扮演看似特殊的角色的原因和物理基因组程度。

DESCRIPTION (provided by applicant): The work proposed here will integrate divergence population genomics and high-resolution genetics to dissect the historical and functional aspects of complex speciation between Drosophila mauritiana and its sister species, D. simulans. Since splitting ~250,000 years ago the two species have evolved complete hybrid male sterility in both directions of the cross and yet show clear evidence for recent secondary contact with gene flow (hybrid females are fertile). The goal of this project is to obtain a comprehensive genome-wide analysis of natural selection and gene flow between these partially reproductively isolated species that is informed by a fine-scale genome-wide map of hybrid incompatibility factors. The project anticipates a massive dataset currently in development: high-coverage whole-genome next-generation resequence data from 10 lines of Drosophila mauritiana and 20 lines of D. simulans. The project has two complementary components. First, novel computational and statistical inference methods will be developed for whole-genome evolutionary analysis of species divergence. Second, newly developed functional genetic resources will be used to construct a high-resolution genome-wide map of D. simulans genetic factors that cause hybrid incompatibilities in an otherwise D. mauritiana genomic background; 2-4 of these factors will be targeted for molecular identification and functional characterization. The two components will be integrated to: (1) test if incompatible regions of the genome are enriched for signatures of positive selection and/or show reduced propensity for interspecific gene flow; and (2) determine why, and the physical genomic extent to which, the X chromosome plays a seemingly special role in animal speciation.