Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota.
Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia.
Mol Ecol. 2018 Nov;27(22):4397-4416. doi: 10.1111/mec.14877. Epub 2018 Oct 16.
Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into the evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently between diverging lineages than previously thought. In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our data set. The two lineages likely diverged much more recently than previous mitochondrial estimates of 5-7 mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ~161 and 191 k generations ago. The favoured demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified gene flow among all lineages sampled. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite gene flow with surface populations. The recency of these estimated divergence events suggests that selection may drive the evolution of cave-derived traits, as opposed to disuse and drift. Finally, we show that a key trogolomorphic phenotype QTL is enriched for genomic regions with low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. Our study shows that gene flow must be considered in studies of independent, repeated trait evolution.
了解反复进化的表型的分子基础可以为进化过程提供关键的见解。量化种群之间的基因流动对于解释重复表型进化的机制尤为重要，基因组分析表明，在分化的谱系之间，杂交比以前认为的更为频繁。在这项研究中，我们对来自三个洞穴种群、两个地表种群和外群样本的 47 个墨西哥四齿鱼的全基因组进行了重测序。我们证实洞穴种群是多系的，并且我们的数据集中存在两个 Astyanax mexicanus 谱系。这两个谱系的分化时间很可能比以前线粒体估计的 5-7 百万年前更近。洞穴种群与其亲缘关系最近的地表种群的分化很可能发生在大约 161 到 191 万代前。大多数种群对的首选人口模型解释了分歧与二级接触和整个基因组的异质基因流动，并严格地鉴定了所有取样的谱系之间的基因流动。因此，洞穴相关特征的进化比以前认为的要快，尽管与地表种群有基因流动，但 trogolomorphic 特征仍得以维持。这些估计的分歧事件的近期表明，选择可能驱动了洞穴衍生特征的进化，而不是不使用和漂移。最后，我们表明，一个关键的 trogolomorphic 表型 QTL 富含洞穴之间差异较小的基因组区域，这表明洞穴表型的重要区域可能通过基因流在洞穴之间转移。我们的研究表明，在独立的、反复出现的性状进化研究中，必须考虑基因流。
