Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex.
Ancient polymorphisms and divergence hitchhiking contribute to genomic islands of divergence within a poplar species complex.
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古老的多态性和分歧搭便车导致杨树物种复合体中的基因组分歧岛
DOI：
10.1073/pnas.1713288114
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发表时间：
2018-01-09
影响因子：
11.1
通讯作者：
Liu J
中科院分区：
文献类型：
--
作者：
Ma T;Wang K;Hu Q;Xi Z;Wan D;Wang Q;Feng J;Jiang D;Ahani H;Abbott RJ;Lascoux M;Nevo E;Liu J
意义理解新物种如何形成的突出问题之一是生殖隔离是如何产生的。特别是，基因流和自然选择在创造两个不同物种方面的相对作用仍然存在争议。在这里，我们表明，在一个杨树的四个连续的物种谱系中，种群的局部基因组分化与最近的基因流动速度或物种分化的时间无关。相比之下，我们发现，这些基因组上的分歧岛很可能是由选择性过程造成的--对古老的遗传多态进行排序，以及附带搭乘连锁变异的便车。这些发现大大加强了我们对物种形成中基因组变化的理解。基因组分化最终如何导致物种形成是一个主要的进化兴趣话题。分化谱系之间的基因组岛经常被报道，在物种形成与基因流模型下，它们的大小预计会随着时间和基因流动而增加。然而，这种孤岛也可能是由于古代多态的不同排序、最近的生态选择而不考虑基因流、和/或重复的背景选择和低重组区域的选择性扫描造成的。要理清这些非排他性的替代方案是具有挑战性的，但在这里，我们试图在分析是什么驱动了四个谱系之间的基因组差异，其中包括沙漠杨树的物种复合体。在这个复合体中，我们发现两个形态上被界定的物种胡杨和黑杨是异源物种，而这四个谱系在基因流动和分歧时间上表现出不同的水平，为检验关于分歧岛起源的假说提供了一个很好的系统。我们表明，区分谱系的基因组岛的大小和数量与最近的基因流动速度或分化时间都不相关。相反，它们很可能来自对古代多态的不同排序和不同的搭便车。我们发现，在谱系特定的选择下，高度分化的基因和可能参与生态和形态差异的基因在这些岛屿内外都存在。我们的结果强调了将人口学、绝对差异测量和基因流动率结合起来解释基因组岛的形成和识别涉及物种形成的潜在基因组区域的必要性。
Significance One of the outstanding questions in understanding how new species form is how reproductive isolation arises. In particular, the relative roles of gene flow and natural selection in creating two separate species remains open for debate. Here we show within the four continuously speciating lineages of a poplar that local genomic differentiation of populations is not associated with either rate of recent gene flow or time of species divergence. By contrast, we found that these genomic islands of divergence most likely came about by selective processes—sorting of ancient genetic polymorphisms and the incidental hitchhiking of linked variations. These findings substantially enhance our understanding of genomic changes in speciation. 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.
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