Data from: Genomics of parallel ecological speciation in Lake Victoria cichlids
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The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case are blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through “hybrid parallel speciation”. Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new “nyererei-like” and “pundamilia-like” species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.
相似物种平行演化的遗传基础，是演化生物学（evolutionary biology）领域备受关注的研究课题。在维多利亚湖慈鲷（Lake Victoria cichlid fishes）的适应性辐射演化中，雄性分别具有蓝色与红色背部婚体色的姊妹物种曾多次独立演化形成，二者的栖息环境通常分别为浅水区与深水区。其中一个典型案例为朴丽鱼属（Pundamilia）的蓝身与红背物种类群：我们近期的研究表明，一个年轻的物种对可能通过‘杂交平行物种形成（hybrid parallel speciation）’演化而来。溯祖模拟（Coalescent simulations）结果显示，较古老的P. pundamilia（蓝色型）与P. nyererei（红背型）物种曾在姆万扎湾（Mwanza Gulf）发生遗传混合，并从该混合种群中演化出全新的‘类nyererei型’与‘类pundamilia型’物种。本研究通过全基因组扫描（genome scans）解析物种分化的基因组架构，并评估杂交作用对该年轻物种对演化的影响。针对两个物种对，我们均在全基因组范围内发现了超过300个高度分化的基因组区域，且这些区域在基因组中分布广泛。古老物种对中分化程度最高的部分区域，在年轻物种对中同样呈现分化特征。这些共有的分化区域往往表现出平行的等位基因频率差异，与‘混合种群衍生的等位基因在杂交群体中受到了歧化选择’的假说相符。然而，年轻物种对间高度分化的基因组区域中，有三分之二并未在古老物种对中呈现显著分化，这提示二者对选择压力存在独立的演化响应。本研究的分析结果揭示了：针对混合种群衍生的遗传变异的歧化选择，如何能够推动新的物种形成事件。
