Data from: Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in Southeast Asia

Tropical rainforests in Southeast Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag-based simple sequence repeats (EST-SSRs) and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the southwestern part of Borneo genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28 to 0.09 million years before present, and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.东南亚热带雨林在过去的冰期曾受到气候波动的影响。为探究伴随气候波动出现的陆地面积与温度变化对该区域雨林树木遗传特性的影响，我们针对广布的龙脑香科物种薄叶娑罗双（Shorea leprosula）的系统地理格局展开了研究。本研究采用两类DNA分子标记：基于表达序列标签的简单序列重复（EST-SSRs）标记，以及叶绿体DNA（cpDNA）序列变异分析。两类标记均揭示出婆罗洲种群与马来半岛-苏门答腊种群（以下简称马-苏种群）之间存在清晰的遗传分化。但在婆罗洲西南部区域，两类标记均检测到两个谱系的遗传混合现象。基于cpDNA序列变异的溯祖模拟结果表明，两个谱系的分化时间距今0.28至0.09百万年，且分化完成后，马来半岛-苏门答腊向婆罗洲的基因流远高于反向迁移。我们得出结论：薄叶娑罗双的遗传结构主要形成于中更新世，后续借助出露成陆的巽他陆架发生东向基因迁移，进而对原有遗传结构进行了改造。