Data from: Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae)

The present study investigated the genetic diversity, population structure, FST outliers, and extent and pattern of linkage disequilibrium in five populations of Keteleeria davidiana var. formosana, which is listed as a critically endangered species by the Council of Agriculture, Taiwan. Twelve amplified fragment length polymorphism primer pairs generated a total of 465 markers, of which 83.74% on average were polymorphic across populations, with a mean Nei’s genetic diversity of 0.233 and a low level of genetic differentiation (approximately 6%) based on the total dataset. Linkage disequilibrium and HICKORY analyses suggested recent population bottlenecks and inbreeding in K. davidiana var. formosana. Both STRUCTURE and BAPS observed extensive admixture of individual genotypes among populations based on the total dataset in various clustering scenarios, which probably resulted from incomplete lineage sorting of ancestral variation rather than a high rate of recent gene flow. Our results based on outlier analysis revealed generally high levels of genetic differentiation and suggest that divergent selection arising from environmental variation has been driven by differences in temperature, precipitation, and humidity. Identification of ecologically associated outliers among environmentally disparate populations further support divergent selection and potential local adaptation.

本研究针对被中国台湾地区农业委员会列为极危物种的台湾油杉（Keteleeria davidiana var. formosana）的5个种群，分析了其遗传多样性、种群结构、FST异常位点（FST outlier）以及连锁不平衡的程度与模式。本研究使用12对扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）引物组合，共获得465个分子标记；种群间平均多态性比率达83.74%，基于全数据集计算的Nei氏平均遗传多样性为0.233，整体遗传分化水平较低（约6%）。连锁不平衡（Linkage Disequilibrium, LD）分析与HICKORY软件分析结果显示，台湾油杉近期经历了种群瓶颈事件并存在近交现象。STRUCTURE与BAPS两种聚类分析工具在多种聚类场景下，基于全数据集均发现种群间个体基因型存在广泛的遗传混合现象，该现象更可能源于祖先变异的不完全谱系分选，而非近期高水平的基因流。基于异常位点分析的结果表明，整体遗传分化水平较高，提示环境异质性引发的歧化选择受温度、降水与湿度差异驱动。对不同环境梯度种群间与生态相关的异常位点的鉴定，进一步支持了歧化选择与潜在的本地适应过程。