Data from: Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa

Ecological diversification through divergent selection is thought to be a major force during the process of adaptive radiations. However, the large sizes and complexity of most radiations such as those of the cichlids in the African Great Lakes make it impossible to infer the exact evolutionary history of any population divergence event. The genus Alcolapia, a small cichlid lineage endemic to Lakes Magadi and Natron in East Africa, exhibits phenotypes similar to some of those found in cichlids of the radiations of the African Great Lakes. The simplicity within Alcolapia makes it an excellent model system to investigate ecological diversification and speciation. We used an integrated approach including population genomics based on RAD-seq data, geometric morphometrics, and stable isotope analyses to investigate the eco-morphological diversification of tilapia in Lake Magadi and its satellite lake Little Magadi. Additionally, we reconstructed the demographic history of the species using coalescent simulations based on the joint site frequency spectrum. The population in Little Magadi has a characteristically upturned mouth - possibly an adaptation to feeding on prey from the water surface. Eco-morphological differences between populations within Lake Magadi are more subtle, but are consistent with known ecological differences between its lagoons such as high concentrations of nitrogen attributable to extensive guano deposits in Rest of Magadi relative to Fish Springs Lagoon. All populations diverged simultaneously only about 1,100 generations ago. Differences in levels of gene flow between populations and the effective population sizes have likely resulted in the inferred heterogeneous patterns of genome-wide differentiation.

学界普遍认为，通过趋异选择实现的生态分化是适应辐射过程中的核心驱动力。然而，多数适应辐射类群（如非洲大湖慈鲷）的种群规模庞大且演化历程复杂，致使无法精准推断任一种群分化事件的确切演化历史。阿科拉皮亚慈鲷属（Alcolapia）是东非马加迪湖与纳特龙湖特有的小型慈鲷支系，其部分表型与非洲大湖慈鲷适应辐射类群的表型高度相似。该属类群的演化体系相对简洁，因此成为探究生态分化与物种形成的理想模型系统。本研究采用整合分析方法，包括基于限制性位点相关DNA测序（RAD-seq）数据的种群基因组学分析、几何形态测量学分析以及稳定同位素分析，对马加迪湖及其附属湖泊小马加迪湖内的罗非鱼生态形态分化展开探究。此外，本研究基于联合位点频率谱开展溯祖模拟，重构了该类群的种群历史动态。小马加迪湖内的种群具有典型的上翘口部形态，这可能是适应表层水域捕食的演化特征。马加迪湖内部各种群间的生态形态差异相对细微，但与其泻湖间已知的生态差异相吻合：相较于鱼泉泻湖，马加迪其余区域存在大量鸟粪沉积，致使氮浓度显著偏高。所有种群的分化时间均集中在约1100代之前。种群间基因流水平与有效种群大小的差异，大概率是导致全基因组分化呈现异质性模式的原因。