Data from: Population genomic signatures of divergent adaptation, gene flow, and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes

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 hybridisation among the young species. The role of such hybridisation events in the evolutionary history of a group can be assessed by comparing the phylogenetic relationships inferred from different subsets of loci. 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 among genera or male colour types. We then create SNP subsets, which we expect to be characterised to different extents by selection history and neutral processes, and find contrasting population genomic and phylogenomic signals among these datasets. In an attempt to resolve the observed conflicts, we propose at least two intergeneric hybridisation 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.

适应辐射（adaptive radiation）是生物多样性的重要来源，其典型特征是在极短时间内发生大量物种形成事件。已有研究提出，这类辐射事件中极高的物种形成速率，可能由年轻物种间杂交事件产生的全新遗传组合所驱动。要评估这类杂交事件在类群演化历史中的作用，可通过比较不同基因座子集推导的系统发育关系来实现。本研究利用限制性酶切位点相关DNA（restriction site associated DNA, RAD）标签内鉴定出的全基因组范围单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，对东非维多利亚湖大规模慈鲷适应辐射中的两个属——朴丽鱼属（Pundamilia）和姆比皮亚属（Mbipia）的5个同域分布慈鲷物种的共有祖先与适应性分化模式的基因组一致性进行探究。这些物种种对在多个维度存在差异：雄性婚色、摄食生态、栖息深度分布，以及区分两个属的形态性状，还有更细微的形态差异。通过异常位点扫描方法，我们在所有物种种对之间检测到了趋异选择的信号，且多个基因座在属间或雄性色型的重复对比中呈现出平行演化模式。随后我们构建了SNP子集，预期这些子集会在不同程度上受到选择历史与中性演化过程的影响，并发现这些数据集之间呈现出截然不同的群体基因组与系统发育基因组信号。为解决观测到的冲突，我们提出在这5个物种的演化历史中至少发生过两次属间杂交事件（姆比皮亚属与朴丽鱼属之间），该事件或推动了全新性状组合的演化与新物种的形成。