The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing
The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing
复制标题
DOI：
10.1371/journal.pgen.1000550
复制
发表时间：
2009-07-01
期刊：
影响因子：
4.5
通讯作者：
Noor, Mohamed A. F.
中科院分区：
文献类型：
--
作者：
Kulathinal, Rob J.;Stevison, Laurie S.;Noor, Mohamed A. F.
在自然界中，密切相关的物种可以杂交，同时仍然保留其独特的身份。在杂交中经历减少重组的染色体区域，例如倒位，已经被假设有助于维持物种的完整性。在这里，我们研究基因组序列密切相关的果蝇类群的果蝇pseudobscura亚组重建其进化历史和过去的基因交换模式。从拟暗果蝇（Drosophila pseudobscura）的两个亚种（D. ps.）和外群种D.米兰达这些新的组件进行了比较，可用组件的D。PS. Pseudobscura和D. Persimilis，北美洲西部有重叠分布区的两个种。在反向区域内，三个物种之间的核苷酸分歧是可比的，而D。PS. Pseudobscura和D.在非倒置区域中，Persimilis的变异水平要低得多，并且更接近种内变异水平。使用分子标记侧翼的每个主要的染色体倒位，我们确定了强大的交换抑制F（1）杂交超过2兆碱基对（Mbp）超出倒位断点。这些交叉抑制区域也表现出与反向区域相关的高核苷酸差异。最后，通过与地理上孤立的亚种比较，D. PS. bogotana之间的常染色体基因交换，我们的研究结果表明，北美物种，D。PS. Pseudobscura和D. persimilis，自亚种分裂以来发生，可能在过去20万年内。我们的结论是，染色体重排一直是至关重要的持续存在的这些物种，尽管最近的杂交。我们的研究作为一个证明的原则，如何全基因组测序可以应用于制定和测试假设的物种形成在鲜为人知的非模型系统。
In nature, closely related species may hybridize while still retaining their distinctive identities. Chromosomal regions that experience reduced recombination in hybrids, such as within inversions, have been hypothesized to contribute to the maintenance of species integrity. Here, we examine genomic sequences from closely related fruit fly taxa of the Drosophila pseudoobscura subgroup to reconstruct their evolutionary histories and past patterns of genic exchange. Partial genomic assemblies were generated from two subspecies of Drosophila pseudoobscura (D. ps.) and an outgroup species, D. miranda. These new assemblies were compared to available assemblies of D. ps. pseudoobscura and D. persimilis, two species with overlapping ranges in western North America. Within inverted regions, nucleotide divergence among each pair of the three species is comparable, whereas divergence between D. ps. pseudoobscura and D. persimilis in non-inverted regions is much lower and closer to levels of intraspecific variation. Using molecular markers flanking each of the major chromosomal inversions, we identify strong crossover suppression in F(1) hybrids extending over 2 megabase pairs (Mbp) beyond the inversion breakpoints. These regions of crossover suppression also exhibit the high nucleotide divergence associated with inverted regions. Finally, by comparison to a geographically isolated subspecies, D. ps. bogotana, our results suggest that autosomal gene exchange between the North American species, D. ps. pseudoobscura and D. persimilis, occurred since the split of the subspecies, likely within the last 200,000 years. We conclude that chromosomal rearrangements have been vital to the ongoing persistence of these species despite recent hybridization. Our study serves as a proof-of-principle on how whole genome sequencing can be applied to formulate and test hypotheses about species formation in lesser-known non-model systems.