Genomics of complex speciation between Drosophila simulans and D. mauritiana

描述(申请人提供)：这里提出的工作将结合发散种群基因组学和高分辨率遗传学来剖析毛果蝇及其姊妹种拟果蝇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，但显示出最近与基因流的二次接触的明显证据(杂交雌性是可育的)。该项目的目标是获得对自然选择和这些部分繁殖隔离物种之间的基因流动的全面基因组分析，这是由杂交不亲和因素的精细全基因组图谱提供信息的。该项目预计目前正在开发的大规模数据集：来自10个毛果果蝇品系和20个拟果蝇品系的高覆盖率全基因组下一代重测序数据。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理方法，用于物种分化的全基因组进化分析。第二，新开发的功能性遗传资源将被用于构建高分辨率的仿生石杉遗传因素的全基因组图谱，这些遗传因素在其他情况下导致毛叶石杉基因组背景下的杂交不亲和性；其中2-4个因素将被用于分子鉴定和功能表征。这两个部分将被整合到：(1)测试基因组的不相容区域是否丰富了正选择的签名和/或显示了物种间基因流动的减少倾向；以及(2)确定X染色体在动物物种形成中发挥似乎特殊作用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.