Data from: Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.跨物种基因流在生命之树中普遍存在。尽管新的分析方法推动了种群间基因流的检测，但确定杂交的时间与地理模式仍颇具挑战，针对历史基因流的研究更是如此。要推断祖先种群的分布重叠范围，需采用具备地理显性特征的系统发育研究方法。本研究针对棘蜥属（Sceloporus）spinosus类群的蜥蜴开展了种群遗传分析、物种界定、模拟实验，以及新近提出的物种树扩散（species tree diffusion）方法，以推断该类群的系统地理学历史、基因流发生时间与地理分布范围。该类群包含两个物种：S. spinosus与S. horridus，分别分布于墨西哥东部与西部，但二者的种群在墨西哥南部高地存在同域分布现象。我们分别为148与68个个体构建了包含3个线粒体基因与8个核基因座的数据集。本研究界定出该类群的6个演化支，但在S. spinosus与S. horridus的同域种群中，因线粒体基因渐渗（mitochondrial introgression）现象，发现了显著的核质不一致（mito-nuclear discordance）证据。我们采用溯合模拟（coalescent simulations）区分祖先基因流与次生接触两种模型，但两种模型均获得了部分支持证据。贝叶斯系统地理学（Bayesian phylogeography）分析显示，自物种分化以来，S. spinosus与S. horridus的祖先种群的分布区重叠率超过60%。然而，隔离-迁移（isolation-migration）分析显示，这些祖先种群间的基因流水平近乎为零。综合模拟与实证数据的分析结果表明：尽管这两个物种有着长期的同域分布历史，但该类群的基因流仅在近期才得以发生。