Data from: Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow

The metaphor of “genomic islands of speciation” was first used to describe heterogeneous differentiation among loci between the genomes of closely related species. The biological model proposed to explain these differences was that the regions showing high levels of differentiation were resistant to gene flow between species, while the remainder of the genome was being homogenized by gene flow and consequently showed lower levels of differentiation. However, the conditions under which such differentiation can occur at multiple unlinked loci are restrictive; additionally, essentially all previous analyses have been carried out using relative measures of divergence, which can be misleading when regions with different levels of recombination are compared. Here we test the model of differential gene flow by asking whether absolute divergence is also higher in the previously identified “islands.” Using five species-pairs for which full sequence data is available, we find that absolute measures of divergence are not higher in genomic islands. Instead, in all cases examined we find reduced diversity in these regions, a consequence of which is that relative measures of divergence are abnormally high. These data therefore do not support a model of differential gene flow among loci, though islands of relative divergence may represent loci involved in local adaptation. Simulations using the program IMa2 further suggest that inferences of any gene flow may be incorrect in many comparisons. We instead present an alternative explanation for heterogeneous patterns of differentiation, one in which post-speciation selection generates patterns consistent with multiple aspects of the data.

“物种形成基因组岛（genomic islands of speciation）”这一隐喻最初被用于描述近缘物种基因组间各基因座的异质性分化。此前用以解释这类分化差异的生物学模型提出：分化水平较高的区域可抵御物种间的基因流，而基因组其余区域则会因基因流发生同质化，进而呈现出更低的分化水平。然而，能够在多个非连锁基因座上出现此类分化的条件十分严苛；此外，几乎所有过往分析均采用分化相对度量开展研究，当对比不同重组水平的区域时，这类度量可能会产生误导。本研究通过检验此前所识别的“基因组岛”中是否也存在更高的绝对分化水平，来验证差异基因流模型。我们利用五组具备全序列数据的物种类对开展分析，结果显示，基因组岛中的绝对分化水平并未升高。与之相反，在所考察的全部案例中，我们发现这些区域的遗传多样性有所降低，这一后果会导致分化相对度量出现异常偏高的情况。因此，本研究数据并不支持基因座间存在差异基因流的模型，尽管相对分化岛或许可代表参与局部适应的基因座。借助程序IMa2开展的模拟实验进一步表明，在诸多对比分析中，对基因流的推断可能存在错误。我们就此提出了一种针对异质性分化模式的替代性解释：该模型认为，物种形成后选择所产生的模式与本数据集的多项特征相符。