Data from: Speciation history of a species complex of Primulina eburnea (Gesneriaceae) from limestone karsts of south China, a biodiversity hotspot

Limestone karsts in southern China are characterized by high edaphic and topographic heterogeneity and host high levels of species richness and endemism. However, the evolutionary mechanisms for generating such biodiversity remain poorly understood. Here, we performed species delimitation, population genetic analyses, simulations of gene flow, and analyses of floral morphological traits to infer the geographic history of speciation in a species complex of Primulina eburnea from limestone karsts of south China. Using Bayesian species delimitation, we determined that there are seven distinct species that correspond well to the putative morphological species. Species-tree reconstruction, Structure and Neighbour-Net analyses all recovered four lineages in agreement with currently species geographic boundaries. High levels of genetic differentiation were observed both within and among species. Isolation–migration coalescent analysis provides evidence for significant but low gene flow among species. Approximate Bayesian computation (ABC) analysis supports a scenario of historical gene flow rather than recent contemporary gene flow for most species divergences. Finally, we found no evidence of divergent selection contributing to population differentiation of a suite of flower traits. These results support the prevalence of allopatric speciation and highlight the role of geographic isolation in the diversification process. At small geographic scales, limited hybridization occurred in the past between proximate populations but did not eliminate species boundaries. We conclude that limited gene flow might have been the predominant evolutionary force in promoting population differentiation and speciation.

中国南方的石灰岩喀斯特地貌以极高的生境与地形异质性为典型特征，孕育了丰富的物种多样性与特有类群。然而，造就这类生物多样性的演化机制仍有待深入解析。本研究针对中国南方喀斯特生境中的白花报春苣苔（Primulina eburnea）物种复合群，开展了物种界定、群体遗传分析、基因流模拟以及花部形态性状分析，以推断该类群的物种形成地理历史过程。经贝叶斯物种界定分析，我们确定了7个独立物种，其划分结果与基于形态学的推定物种高度吻合。物种树重建、Structure群体结构分析以及邻网（Neighbour-Net）分析均成功恢复出4个支系，且与当前各物种的地理分布边界一致。研究在物种内部及物种间均检测到高水平的遗传分化。隔离-迁移溯祖分析结果显示，物种间存在显著但强度较低的基因流。近似贝叶斯计算（Approximate Bayesian Computation, ABC）分析支持多数物种分化事件伴随历史基因流，而非近期当代基因流。最后，我们未发现歧化选择对一系列花部性状的群体分化存在贡献。上述结果支持异域物种形成的普遍性，并强调地理隔离在物种分化过程中的关键作用。在较小地理尺度下，邻近种群间曾发生过有限的历史杂交，但并未打破物种边界。综上，有限的基因流可能是推动群体分化与物种形成的主要演化动力。