State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.
Mol Biol Evol. 2023 Jun 1;40(6). doi: 10.1093/molbev/msad129.
Recent genomic analyses of evolutionary radiations suggest that ancient introgression may facilitate rapid diversification and adaptive radiation. The loach genus Triplophysa, a genus with most species endemic to Tibetan Plateau, shows ecological diversity and rapid evolution and represents a potential example of adaptive radiation linked to the uplift of the Tibetan Plateau. Here, we interrogate the complex evolutionary history of Triplophysa fishes through the analysis of whole-genome sequences. By reconstructing the phylogeny of Triplophysa, quantifying introgression across this clade, and simulating speciation and migration processes, we confirm that extensive gene flow events occurred across disparate Triplophysa species. Our results suggest that introgression plays a more substantial role than incomplete lineage sorting in underpinning phylogenetic discordance in Triplophysa. The results also indicate that genomic regions affected by ancient gene flow exhibit characteristics of lower recombination rates and nucleotide diversity and may associate with selection. Simulation analysis of Triplophysa tibetana suggests that the species may have been affected by the Gonghe Movement in the third uplift of the Tibetan Plateau, resulting in founder effects and a subsequent reduction in Ne.
最近对进化辐射的基因组分析表明，古老的基因渗入可能促进了快速多样化和适应性辐射。泥鳅属 Triplophysa 是一个物种主要分布在青藏高原的属，表现出生态多样性和快速进化，代表了与青藏高原隆起相关的适应性辐射的潜在例子。在这里，我们通过全基因组序列分析来探究 Triplophysa 鱼类的复杂进化历史。通过重建 Triplophysa 的系统发育，量化该进化枝中的基因渗入，并模拟物种形成和迁移过程，我们证实了广泛的基因流事件发生在不同的 Triplophysa 物种之间。我们的结果表明，基因渗入在 Triplophysa 的系统发育分歧中起着比不完全谱系分选更重要的作用。结果还表明，受古老基因流影响的基因组区域表现出较低的重组率和核苷酸多样性的特征，并且可能与选择有关。对西藏高原鳅的模拟分析表明，该物种可能受到青藏高原第三次隆起的共和运动的影响，导致奠基者效应和随后 Ne 的减少。
