Data from: Speciation of two desert poplar species triggered by Pleistocene climatic oscillations

Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two species to estimate the divergence time between them and to test whether gene flow occurred after species separation. Divergence time between the two species was estimated to be 0.66–1.37 million years ago (Ma), a time at which glaciation was at its maximum in China and deserts developed widely in central Asia. Isolation-with-Migration model also indicated that the two species had diverged in the presence of gene flow. We also detected evidence of selection at GO in P. euphratica and to a lesser extent at PhyB2. Together, these results underscore the importance of Pleistocene climate oscillations in triggering plant speciation as a result of habitats divergence.尽管已有研究证实更新世（Pleistocene）气候波动对种内多样性的分布格局产生了强烈影响，但学界对其在种间分化过程中的影响仍知之甚少。本研究旨在验证一项假说：两种荒漠杨属物种——胡杨（*Populus euphratica* Oliv.）与灰胡杨（*P. pruinosa* Schrenk.）的物种分化事件发生于更新世时期。我们对源自两个物种的共60个个体的11个核基因座（nuclear loci）进行了测序，以此估算二者的物种分化时间，并检验物种分化后是否存在基因流（gene flow）。经估算，两个物种的分化时间约为66万至137万年前（Ma），该时期正值中国境内冰川作用的鼎盛阶段，同时中亚地区荒漠广泛发育。隔离与基因流模型（Isolation-with-Migration model）分析结果同样表明，两个物种在分化过程中伴随有基因交流。我们还检测到胡杨中GO基因座存在选择信号，而在光敏素B2（PhyB2）中该信号相对较弱。综上，上述研究结果凸显了更新世气候波动通过驱动生境分化进而触发植物物种形成的重要作用。