Data from: Genome-wide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River

The lower Congo River (LCR) is a freshwater biodiversity hotspot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome we analyzed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.

下刚果河（Lower Congo River, LCR）是非洲境内的淡水生物多样性热点区域，拥有全球规模最大的急流之一。然而，对于塑造这一区域生物多样性的演化驱动力，目前仍知之甚少——该区域栖息有大量特有鱼类。本研究结合区域地理与水文背景，对梯丽鲷属（Teleogramma）——一类小型喜流性慈鲷的系统地理学关联展开了探究。此前的研究因候选物种间核基因变异匮乏、离散形态性状区分度不足，无法厘清梯丽鲷属内的系统发育关系。为了在全基因组范围内更广泛地采样，本研究针对该属所有已描述物种的53个个体，分析了双酶切限制性位点相关DNA测序（double-digest restriction-associated sequencing, ddRAD）数据。本研究还评估了各分类群内部及类群间的体型形态与线粒体基因组变异情况。系统发育分析揭示了此前未被发现的演化支，以及仅间隔约1.5公里就出现的微异域分化案例。各物种的分布范围似乎与被主要水文与地形屏障分隔的地理区域高度契合，这表明这些屏障可能是物种分化的重要驱动力。核质冲突现象表明该类群曾发生过一次或多次渐渗杂交事件，但核基因组中并未发现明确的基因混合证据，提示这些事件发生年代较为久远。对雌性个体鳍部斑纹的调查显示，此前未被发现的演化支特异性斑纹模式，可能在强化物种生殖统一性方面发挥作用。本研究的分析结果凸显了水文复杂性在特定淡水系统中推动生物多样性形成的重要性，同时也证实了ddRAD测序数据在解析物种水平上下的分化过程方面的应用价值。