Data_Sheet_2_Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae).zip

Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure and the phylogeographic history of Lycium ruthenicum, a plant species adapted to the climate in northwestern China. We identified 20 chloroplast haplotypes of which two were dominant and widely distributed in almost all populations. The species has high haplotype diversity and low nucleotide diversity based on the cpDNA data. The EST-SSR results showed a high percentage of total genetic variation within populations. Both the cpDNA and EST-SSR results indicated no significant differentiation among populations. By combining the evidence from ENM and demographic analysis, we confirmed that both the last interglacial (LIG) and late-glacial maximum (LGM) climatic fluctuations, aridification might have substantially narrowed the distribution range of this desert species, the southern parts of the Junggar Basin, the Tarim Basin, and the eastern Pamir Plateau were the potential glacial refugia for L. ruthenicum during the late middle Pleistocene to late Pleistocene Period. During the early Holocene, the warm, and humid climate promoted its demographic expansion in northwestern China. This work may provide new insights into the mechanism of formation of plant diversity in this arid region.

在更新世期间，气候振荡对西北中国众多植物物种的遗传多样性和历史种群结构的形成起到了重要作用。本研究中，我们利用从表达序列标签（EST-SSR）衍生的11个简单序列重复、两个叶绿体DNA（cpDNA）片段以及生态位模型（ENM）来研究适应于西北中国气候的植物物种 Lycium ruthenicum 的种群结构和系统地理历史。我们鉴定出20个叶绿体单倍型，其中两个在几乎所有种群中占主导地位并广泛分布。基于cpDNA数据，该物种具有高单倍型多样性和低核苷酸多样性。EST-SSR结果显示，种群内遗传变异的总比例较高。cpDNA和EST-SSR结果均表明，在种群间没有显著差异。通过结合ENM和种群动态分析的证据，我们证实了末次间冰期（LIG）和晚冰期最大值（LGM）的气候波动和干旱化可能极大地缩小了这种沙漠物种的分布范围，准噶尔盆地的南部、塔里木盆地以及帕米尔高原的东部在晚中新世至晚更新世期间可能是L. ruthenicum 的潜在冰川避难所。在早全新世，温暖湿润的气候促进了其在西北中国的种群扩张。这项研究可能为探讨这一干旱地区植物多样性形成的机制提供新的见解。