Data from: Contrasting patterns of population history and seed-mediated gene flow in two endemic Costa Rican oak species

Lower Central America is an important area to study recent population history and diversification of Neotropical species due to its complex and dynamic geology and climate. Phylogeographic studies in this region are few in comparison with other regions and even less for tree species. The aim of the present study was to characterize the phylogeographic structure in two partially co-distributed endemic oak species (Quercus costaricensis and Q. bumelioides) of the Costa Rican mountains using chloroplast short sequence repeats (cpSSRs), and to test for the effect of geological and palaeoclimatic processes on their population history. Genetic diversity and structure, haplotype networks, patterns of seed-mediated gene flow and historical demography were estimated for both species. Results suggested contrasting patterns. Quercus costaricensis exhibited high values of genetic diversity, a marked phylogeographic structure, a north-to-south genetic diversity gradient and evidence of a demographic expansion during the Quaternary. Quercus bumelioides did not show significant genetic structure and the haplotype network and historical demography estimates suggested a recent population expansion probably during the Pleistocene-Holocene transition. Phylogeographic structure of Q. costaricensis seems to be related to Pleistocene altitudinal migration due to its higher altitudinal distribution. Meanwhile, historical seed-mediated gene flow through the lower altitudinal distribution of Q. bumelioides may have promoted the homogenization of genetic variation. Population expansion and stable availability of suitable climatic areas in both species probably indicate that palaeoclimatic changes promoted downwards altitudinal migration and formation of continuous forests allowing oak species to expand their distribution into the Panamanian mountains during glacial stages.中美洲南部因其复杂多变的地质与气候环境，是研究新热带区物种近期种群历史与分化过程的关键区域。相较于其他区域，该区域的系统地理学研究本就匮乏，针对树木类群的相关研究更是少之又少。本研究借助叶绿体简单序列重复（chloroplast short sequence repeats，cpSSRs）标记，对哥斯达黎加山地两种部分同域分布的特有栎属物种——哥斯达黎加栎（Quercus costaricensis）与扁叶栎（Quercus bumelioides）的系统地理结构进行表征，并检验地质与古气候过程对其种群历史的影响。研究分别估算了两个物种的遗传多样性与群体结构、单倍型网络、种子介导的基因流模式以及历史种群动态。结果显示二者呈现出截然相反的演化模式：哥斯达黎加栎具有较高的遗传多样性、显著的系统地理结构、由北至南的遗传多样性梯度，且存在第四纪时期种群扩张的证据；而扁叶栎未表现出显著的遗传结构，其单倍型网络与历史种群动态估算结果表明，其种群可能在更新世-全新世过渡阶段发生了近期扩张。哥斯达黎加栎的系统地理结构似乎与其较高的海拔分布带来的更新世垂直迁移活动相关。与此同时，扁叶栎依托较低的海拔分布范围，其历史上的种子介导基因流可能促进了群体遗传变异的均质化。两个物种的种群扩张与适宜气候区域的持续存在，或许表明古气候变化推动了种群向下的垂直迁移，形成了连续的森林群落，使得栎属物种能够在冰期阶段将分布范围扩展至巴拿马山地。