How genome divergence eventually leads to speciation is a topic of prime evolutionary interest. Genomic islands of elevated divergence are frequently reported between diverging lineages, and their size is expected to increase with time and gene flow under the speciation-with-gene-flow model. However, such islands can also result from divergent sorting of ancient polymorphisms, recent ecological selection regardless of gene flow, and/or recurrent background selection and selective sweeps in low-recombination regions. It is challenging to disentangle these nonexclusive alternatives, but here we attempt to do this in an analysis of what drove genomic divergence between four lineages comprising a species complex of desert poplar trees. Within this complex we found that two morphologically delimited species, Populus euphratica and Populus pruinosa, were paraphyletic while the four lineages exhibited contrasting levels of gene flow and divergence times, providing a good system for testing hypotheses on the origin of divergence islands. We show that the size and number of genomic islands that distinguish lineages are not associated with either rate of recent gene flow or time of divergence. Instead, they are most likely derived from divergent sorting of ancient polymorphisms and divergence hitchhiking. We found that highly diverged genes under lineage-specific selection and putatively involved in ecological and morphological divergence occur both within and outside these islands. Our results highlight the need to incorporate demography, absolute divergence measurement, and gene flow rate to explain the formation of genomic islands and to identify potential genomic regions involved in speciation.

中文翻译：

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古代多态性和发散搭便促成白杨种复合体内部的基因组发散岛

基因组差异如何最终导致物种形成是主要进化兴趣的话题。在不同谱系之间经常报道差异性升高的基因组岛，并且在“物种与基因一起流动”模型下，它们的大小预计会随着时间和基因流量的增加而增加。但是，这样的岛屿也可能是由于古老多态性的分选，不考虑基因流而进行的近期生态选择，和/或低背景区域的反复背景选择和选择性扫描造成的。弄清这些非排他性的替代方案非常具有挑战性，但是在此，我们尝试分析是什么因素导致了构成沙漠杨树树种复合体的四个谱系之间的基因组差异。在这个复合体中，我们发现了两个在形态上界定的物种，胡杨和胡杨，是共生的，而四个谱系表现出不同水平的基因流动和发散时间，为检验关于发散岛的起源的假设提供了一个良好的系统。我们表明，区分谱系的基因岛的大小和数量与最近的基因流量或发散时间均不相关。取而代之的是，它们最有可能源自古代多态性的发散分类和发散搭便车。我们发现在这些岛的内部和外部都发生了高度分化的基因，这些基因在谱系特异性选择下并可能参与了生态学和形态学的分化。我们的结果强调了需要结合人口统计学，绝对散度测量，