Department of Biology, University of Rochester, Rochester, New York 14627, USA.
Genome Res. 2012 Aug;22(8):1499-511. doi: 10.1101/gr.130922.111. Epub 2012 Apr 13.
The three species of the Drosophila simulans clade--the cosmopolitan species, D. simulans, and the two island endemic species, D. mauritiana and D. sechellia--are important models in speciation genetics, but some details of their phylogenetic and speciation history remain unresolved. The order and timing of speciation are disputed, and the existence, magnitude, and timing of gene flow among the three species remain unclear. Here we report on the analysis of a whole-genome four-species sequence alignment that includes all three D. simulans clade species as well as the D. melanogaster reference sequence. The alignment comprises novel, paired short-read sequence data from a single highly inbred line each from D. simulans, D. mauritiana, and D. sechellia. We are unable to reject a species phylogeny with a basal polytomy; the estimated age of the polytomy is 242,000 yr before the present. However, we also find that up to 4.6% of autosomal and 2.2% of X-linked regions have evolutionary histories consistent with recent gene flow between the mainland species (D. simulans) and the two island endemic species (D. mauritiana and D. sechellia). Our findings thus show that gene flow has occurred throughout the genomes of the D. simulans clade species despite considerable geographic, ecological, and intrinsic reproductive isolation. Last, our analysis of lineage-specific changes confirms that the D. sechellia genome has experienced a significant excess of slightly deleterious changes and a dearth of presumed favorable changes. The relatively reduced efficacy of natural selection in D. sechellia is consistent with its derived, persistently reduced historical effective population size.
模拟果蝇种系的三个物种——世界性物种 D. simulans、两个岛屿特有物种 D. mauritiana 和 D. sechellia——是物种遗传学的重要模型，但它们的系统发育和物种形成历史的一些细节仍未解决。物种形成的顺序和时间存在争议，这三个物种之间基因流的存在、程度和时间尚不清楚。在这里，我们报告了对全基因组四物种序列比对的分析，该比对包括所有三个模拟果蝇种系物种以及 D. melanogaster 参考序列。该比对包括来自 D. simulans、D. mauritiana 和 D. sechellia 的每个高度近交系的新型配对短读序列数据。我们无法拒绝具有基础并系群的物种系统发育；并系群的估计年龄是目前之前的 242000 年。然而，我们还发现，多达 4.6%的常染色体和 2.2%的 X 连锁区的进化历史与大陆物种（D. simulans）和两个岛屿特有物种（D. mauritiana 和 D. sechellia）之间最近的基因流一致。因此，我们的发现表明，尽管存在相当大的地理、生态和内在生殖隔离，基因流已经发生在模拟果蝇种系物种的整个基因组中。最后，我们对谱系特异性变化的分析证实，D. sechellia 基因组经历了大量轻微有害变化的过剩和假定有利变化的缺乏。D. sechellia 中自然选择的相对效率降低与它衍生的、持续降低的历史有效种群大小一致。
