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.

人们普遍认为，趋异选择驱动的生态分化是适应性辐射过程中的核心演化动力。然而，多数辐射类群（如非洲大湖慈鲷（cichlids））种群规模庞大且演化背景复杂，致使研究者无法精准推断任意种群分化事件的完整演化历史。阿尔科拉普丽鱼属（Alcolapia）是东非马加迪湖与纳特龙湖特有的小型慈鲷支系，其表型特征与非洲大湖辐射类慈鲷的部分类群高度相似。该属类群的演化背景相对简洁，使其成为探究生态分化与物种形成的理想模式系统。本研究采用整合研究策略，结合基于RAD-seq数据的群体基因组学分析、几何形态测量学（geometric morphometrics）与稳定同位素分析，对马加迪湖及其附属湖泊小马加迪湖内罗非鱼的生态形态分化模式展开了系统探究。此外，本研究基于联合位点频率谱（joint site frequency spectrum）开展溯祖模拟，重构了该类群的种群历史动态。小马加迪湖的种群具有典型的上位口形态——这一特征大概率是其适应取食水面猎物的演化结果。马加迪湖内部各群体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一致：例如，相较于鱼泉泻湖，马加迪湖其余区域因大量鸟粪沉积而呈现更高的氮浓度水平。所有种群的分化事件均发生于约1100代之前，且为同步分化。种群间基因流水平与有效种群大小的差异，极有可能是导致全基因组分化呈现异质性模式的核心成因。