Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

Although population genomic studies using next generation sequencing (NGS) data are becoming increasingly common, studies focusing on phylogenetic inference using these data are in their infancy. Here, we use NGS data generated from reduced representation genomic libraries of restriction-site-associated DNA (RAD) markers to infer phylogenetic relationships among 16 species of cichlid fishes from a single rocky island community within Lake Victoria's cichlid adaptive radiation. Previous attempts at sequence-based phylogenetic analyses in Victoria cichlids have shown extensive sharing of genetic variation among species and no resolution of species or higher-level relationships. These patterns have generally been attributed to the very recent origin (<15 000 years) of the radiation, and ongoing hybridization between species. We show that as we increase the amount of sequence data used in phylogenetic analyses, we produce phylogenetic trees with unprecedented resolution for this group. In trees derived from our largest data supermatrices (3 to >5.8 million base pairs in width), species are reciprocally monophyletic with high bootstrap support, and the majority of internal branches on the tree have high support. Given the difficulty of the phylogenetic problem that the Lake Victoria cichlid adaptive radiation represents, these results are striking. The strict interpretation of the topologies we present here warrants caution because many questions remain about phylogenetic inference with very large genomic data set and because we can with the current analysis not distinguish between effects of shared ancestry and post-speciation gene flow. However, these results provide the first conclusive evidence for the monophyly of species in the Lake Victoria cichlid radiation and demonstrate the power that NGS data sets hold to resolve even the most difficult of phylogenetic challenges.

尽管基于下一代测序（next generation sequencing, NGS）数据的群体基因组学研究日益普及，但利用此类数据开展系统发育推断的相关研究仍处于起步阶段。本研究利用基于限制性酶切位点相关DNA（restriction-site-associated DNA, RAD）标记的简化基因组文库所产生的NGS数据，对维多利亚湖慈鲷适应性辐射中单一岩岛群落内的16种慈鲷鱼类的系统发育关系进行推断。此前针对维多利亚湖慈鲷开展的基于序列的系统发育分析研究显示，物种间广泛存在遗传变异共享，且无法解析物种乃至更高分类阶元的系统发育关系。这些现象通常被归因于该辐射事件距今不足1.5万年的极晚起源，以及物种间持续存在的杂交现象。我们的研究表明，随着系统发育分析中所用序列数据量的增加，能够为该类群构建出分辨率前所未有的系统发育树。在基于最大规模数据超级矩阵（跨度达300万至超580万个碱基对）构建的系统发育树中，各物种均呈现互为单系群的特征，且具有较高的自举支持值（bootstrap support），树内绝大多数内部分支也获得了较高的支持度。鉴于维多利亚湖慈鲷适应性辐射所代表的系统发育问题极具挑战性，该研究结果尤为引人注目。对本文所呈现的拓扑结构进行严格解读需谨慎，因为利用超大型基因组数据集开展系统发育推断仍存在诸多待解问题，且本次分析无法区分共同祖先效应与物种形成后的基因流影响。然而，本研究结果首次为维多利亚湖慈鲷辐射类群的物种单系性提供了确凿证据，并证明了NGS数据集即便在解决最具挑战性的系统发育问题时也具备强大效力。