Data from: Population structure and historical demography of Dipteronia dyeriana (Sapindaceae), an extremely narrow palaeoendemic plant from China: implications for conservation in a biodiversity hot spot

Inferring past demography is a central question in evolutionary and conservation biology. It is, however, sometimes challenging to disentangle their roles of contemporary versus historical processes in shaping the current patterns of genetic variation in endangered species. In this study, we used both chloroplast microsatellite (cpSSR) loci and nuclear microsatellite (nSSR) loci to assess the levels of genetic differentiation, genetic effective population size, contemporary/historical levels of gene flow and demographic history for five populations sampled across the range of Dipteronia dyeriana, an endangered palaeoendemism from Southwestern China. We found that D. dyeriana had a mixed pattern of moderate genetic diversity and high inbreeding. Bayesian clustering divided D. dyeriana populations into two nSSR genetic clusters. Coalescent-based approximate Bayesian computation analyses suggest the western and eastern groups of D. dyeriana likely persisted in a long-term refuge in Southern China since the beginning of the last glacial period, whereas increasingly colder and arid climates at the onset of the last glacial maximum might have fostered the fragmentation of D. dyeriana within refugia. Following their divergence, the western group kept relatively stable effective population size, whereas the eastern group had experienced 500-fold population expansion during the Holocene. Although clear loss of genetic diversity by human activities was not suggested, recent habitat fragmentation has led to a reduction of population connectivity and increased genetic differentiation by ongoing genetic drift in isolated populations, possibly owing to decreased population size in recent dozen years. Finally, we discussed the implications of these results on conservation policies.推断过往种群动态是进化生物学与保护生物学领域的核心议题。然而，在濒危物种类群中，厘清当代与历史演化过程对当前遗传变异格局的塑造作用，往往颇具挑战。本研究针对分布于中国西南地区的濒危古特有种云南金钱槭（*Dipteronia dyeriana*），对其跨分布区采样得到的5个种群，同时利用叶绿体微卫星（chloroplast microsatellite, cpSSR）位点与核微卫星（nuclear microsatellite, nSSR）位点，评估其遗传分化水平、有效种群大小、当代与历史基因流水平以及种群历史动态。研究结果显示，云南金钱槭兼具中等水平的遗传多样性与高度近交的特征。基于贝叶斯聚类分析，云南金钱槭种群可被划分为2个核微卫星遗传聚类群。基于溯祖理论的近似贝叶斯计算分析表明，云南金钱槭的东、西两个种群群自末次冰期起始以来，便长期存续于中国南方的一处避难所中；而末次冰盛期伊始逐渐变冷变干的气候，或推动了避难所内云南金钱槭种群的分化与片段化。种群分化之后，西部种群群的有效种群大小保持相对稳定，而东部种群群在全新世时期经历了500倍的种群扩张。尽管研究未发现人类活动导致遗传多样性显著丧失的证据，但近期的生境片段化已造成种群连通性下降，孤立种群中的持续遗传漂变进一步加剧了遗传分化，这一现象或与近十余年种群规模缩减有关。最后，本研究探讨了上述研究结果对保护政策制定的启示意义。