Adaptive radiations are an important source of biodiversity and are often characterized by many speciation events in very short succession. It has been proposed that the high speciation rates in these radiations may be fuelled by novel genetic combinations produced in episodes of hybridization among the young species. The role of such hybridization events in the evolutionary history of a group can be investigated by comparing the genealogical relationships inferred from different subsets of loci, but such studies have thus far often been hampered by shallow genetic divergences, especially in young adaptive radiations, and the lack of genome-scale molecular data. Here, we use a genome-wide sampling of SNPs identified within restriction site-associated DNA (RAD) tags to investigate the genomic consistency of patterns of shared ancestry and adaptive divergence among five sympatric cichlid species of two genera, Pundamilia and Mbipia, which form part of the massive adaptive radiation of cichlids in the East African Lake Victoria. Species pairs differ along several axes: male nuptial colouration, feeding ecology, depth distribution, as well as the morphological traits that distinguish the two genera and more subtle morphological differences. Using outlier scan approaches, we identify signals of divergent selection between all species pairs with a number of loci showing parallel patterns in replicated contrasts either between genera or between male colour types. We then create SNP subsets that we expect to be characterized to different extents by selection history and neutral processes and describe phylogenetic and population genetic patterns across these subsets. These analyses reveal very different evolutionary histories for different regions of the genome. To explain these results, we propose at least two intergeneric hybridization events (between Mbipia spp. and Pundamilia spp.) in the evolutionary history of these five species that would have lead to the evolution of novel trait combinations and new species.

译文

适应性辐射是生物多样性的重要来源,通常以非常短的连续发生许多物种形成事件为特征。已经提出,这些辐射中的高物种形成率可能是由年轻物种之间杂交过程中产生的新型遗传组合推动的。可以通过比较从不同基因座子集推断出的系谱关系来研究此类杂交事件在群体进化史中的作用,但是到目前为止,此类研究经常受到浅遗传差异的阻碍,尤其是在年轻的适应性辐射中,以及缺乏基因组规模的分子数据。在这里,我们使用在限制性位点相关DNA (RAD) 标签中鉴定的snp的全基因组采样来研究Pundamilia和Mbipia这两个属的五个同族丽鱼科鱼物种之间共享祖先和适应性差异模式的基因组一致性,构成东非维多利亚湖丽鱼科鱼大规模适应性辐射的一部分。物种对沿几个轴不同: 雄性婚育颜色,摄食生态,深度分布以及区分两个属的形态特征和更细微的形态差异。使用异常值扫描方法,我们可以识别所有物种对之间不同选择的信号,其中许多基因座在属之间或雄性颜色类型之间的复制对比中显示平行模式。然后,我们创建了SNP子集,我们希望通过选择历史和中性过程对其进行不同程度的表征,并描述了这些子集的系统发育和种群遗传模式。这些分析揭示了基因组不同区域的进化历史非常不同。为了解释这些结果,我们在这五个物种的进化史中提出了至少两个属间杂交事件 (在Mbipia spp。和Pundamilia spp。之间),这将导致新的性状组合和新物种的进化。

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