Jensen Evelyn L, Gaughran Stephen J, Garrick Ryan C, Russello Michael A, Caccone Adalgisa
Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
Department of Biology, University of Mississippi, Oxford, Mississippi, USA.
Mol Ecol. 2021 Dec;30(23):6325-6339. doi: 10.1111/mec.16176. Epub 2021 Sep 25.
Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of diversity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three individuals of the 12 extant lineages of Galapagos giant tortoise and estimate diversity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within individuals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in-depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.
全基因组测序能深入洞察一个物种的进化历史，包括多样性模式、选择信号和历史种群统计学。当应用于具有丰富背景知识的近缘分类群时，群体基因组学为解释群体遗传汇总统计数据以及将实证结果与群体遗传理论预期进行比较提供了一个比较背景。加拉帕戈斯象龟（Chelonoidis spp.），一种标志性的快速且近期辐射演化的物种，提供了这样一个机会。在这里，我们对加拉帕戈斯象龟现存12个谱系中的三个个体进行了全基因组测序，并估计了多样性指标，重建了随着时间推移合并率的变化。我们还比较了每个谱系中衍生等位基因的数量，以推断同义突变和非同义突变积累率如何与种群大小和生活史特征相关联。值得注意的是，我们发现同一谱系内个体的分子进化模式相似，但不同谱系之间可能存在显著差异，这强化了加拉帕戈斯象龟物种的进化独特性。值得注意的是，谱系间突变积累的差异与简单的群体遗传预测不一致，这表明纯化选择的驱动因素比目前所认识的更为复杂。通过将早期群体遗传和系统地理学研究的结果与全基因组分析的新发现相结合，我们提供了迄今为止关于加拉帕戈斯象龟进化的最深入见解，并确定了群体遗传理论预期与实证数据之间需要进一步审视的差异。
