Data from: Genomic islands of divergence are not affected by geography of speciation in sunflowers.

Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.物种形成的基因组学研究通常会报道：在由弱分化位点构成的基因组背景中，散布着高度分化的基因组区域。这类物种形成岛（speciation islands）的形成机制，一般被归因于经受歧化选择（divergent selection）的位点附近种群间基因流减弱，但目前鲜有研究对这一假说开展严谨的验证。本研究针对四对物种形成地理背景存在差异的新近分化向日葵属（Helianthus）物种对，开展了转录组扫描（transcriptome scans）分析。我们发现，同域（sympatric）与邻域（parapatric）物种对的遗传分化水平更低，这与基因流可侵蚀中性遗传差异的理论推论相符。不过，所有比较组中，分化基因组岛的数量均较多且尺度较小；且与理论预期相悖的是，基因组岛的数量与大小并未受到种间基因流水平的显著影响。与之相反，基因组岛的形成与重组率降低存在极强的关联。整体而言，本研究结果表明，基因组的功能架构对基因组分化的塑造作用，较物种形成的地理格局更为显著。