Brown Joshua I, Harrigan Ryan J, Lavretsky Philip
Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA.
Center for Tropical Research, University of California, Los Angeles, Los Angeles, California, USA.
Mol Ecol. 2022 May;31(9):2578-2593. doi: 10.1111/mec.16423. Epub 2022 Mar 18.
Throughout the speciation process, genomic divergence can be differentially impacted by selective pressures, as well as gene flow and genetic drift. Disentangling the effects of these evolutionary mechanisms remains challenging, especially for nonmodel organisms. Accounting for complex evolutionary histories and contemporary population structure often requires sufficient sample sizes, for which the expense of full genomes remains prohibitive. Here, we demonstrate the utility of partial-genome sequence data for range-wide samples to shed light into the divergence process of two closely related ducks, the Mexican duck (Anas diazi) and mallard (A. platyrhynchos). We determine the role of selective and neutral processes during speciation of Mexican ducks by integrating evolutionary and demographic modelling with genotype-environment and genotype-phenotype association testing. First, evolutionary models and demographic analyses support the hypothesis that Mexican ducks originally diverged ~300,000 years ago in climate refugia arising during a glacial period in southwest North America, and that subsequent environmental selective pressures played a key role in divergence. Mexican ducks then showed cyclical demographic patterns that probably reflected repeated range expansions and contractions, along with bouts of gene flow with mallards during glacial cycles. Finally, we provide evidence that sexual selection acted on several phenotypic traits as a co-evolutionary process, facilitating the development of reproductive barriers that initially arose due to strong ecological selection. More broadly, this work reveals that the genomic and phenotypic patterns observed across species complexes are the result of myriad factors that contribute in dynamic ways to the evolutionary trajectories of a lineage.
在整个物种形成过程中，基因组分化可能受到选择压力、基因流和遗传漂变的不同影响。厘清这些进化机制的作用仍然具有挑战性，尤其是对于非模式生物而言。考虑复杂的进化历史和当代种群结构通常需要足够的样本量，而全基因组的成本仍然过高。在这里，我们展示了部分基因组序列数据对于广泛样本的效用，以阐明两种亲缘关系密切的鸭子——墨西哥鸭（Anas diazi）和绿头鸭（A. platyrhynchos）的分化过程。我们通过将进化和种群统计学建模与基因型-环境和基因型-表型关联测试相结合，确定了墨西哥鸭物种形成过程中选择和中性过程的作用。首先，进化模型和种群统计学分析支持以下假设：墨西哥鸭最初在约30万年前北美洲西南部冰川期出现的气候避难所中分化，随后的环境选择压力在分化过程中起了关键作用。墨西哥鸭随后呈现出周期性的种群动态模式，这可能反映了反复的范围扩张和收缩，以及在冰川周期中与绿头鸭的基因交流。最后，我们提供证据表明，性选择作为一种共同进化过程作用于几个表型特征，促进了最初因强烈生态选择而产生的生殖隔离的发展。更广泛地说，这项工作揭示了跨物种复合体观察到的基因组和表型模式是众多因素以动态方式促成一个谱系进化轨迹的结果。
