Data from: Population genetic structure of Oryza rufipogon and O. nivara: implications for the origin of O. nivara

Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains unclear. Here, based on sequences of 10 nuclear and two chloroplast loci from 26 wild populations across the entire geographic ranges of the two species, we conducted comprehensive analyses using population genetics, phylogeography and species distribution modelling (SDM) approaches. In addition to supporting the two previously reported major subdivisions, we detected four genetically distinct groups within O. rufipogon and found no correlation between the genetic groups and either species identity or geographical regions. The SDM clearly showed substantial change in the distribution range of O. rufipogon in history, demonstrating that the repeated extinction and colonization of local populations due to multiple glacial–interglacial cycles during the Quaternary was most likely the main factor shaping the confounding population genetic structure of O. rufipogon. Moreover, we found significant differences between the two species in climate preferences, suggestive of an important role for climatic factors in the adaptation, persistence and expansion of O. nivara. Finally, based on the genetic pattern and dynamics of the O. nivara populations, we hypothesize that O. nivara might have independently originated multiple times from different O. rufipogon populations.

生态物种形成在推动物种分化与适应进程中居于核心地位。普通野生稻（Oryza rufipogon）与尼瓦拉野生稻（Oryza nivara）为处于物种形成早期阶段的两个初期物种，二者在形态特征、生活史性状及生境偏好上均存在显著差异，因此为生态物种形成研究提供了独特的模式系统。然而，尽管已有大量研究，作为祖先类群的普通野生稻的种群遗传结构仍存在争议，而衍生类群尼瓦拉野生稻的起源问题也尚未明确。本研究基于覆盖两个物种全地理分布范围的26个野生种群的10个核基因座与2个叶绿体基因座序列，综合运用种群遗传学、系统地理学及物种分布模型（SDM）方法开展了全面分析。研究不仅验证了此前报道的两个主要分化支系，还在普通野生稻中检测到4个遗传分化显著的类群，且未发现这些遗传类群与物种身份或地理区域存在相关性。物种分布模型分析清晰显示，普通野生稻的历史分布范围曾发生显著变化，表明第四纪多次冰期-间冰期旋回引发的局域种群反复灭绝与定居事件，极有可能是塑造普通野生稻难以厘清的种群遗传结构的核心因素。此外，本研究发现两个物种在气候偏好上存在显著差异，提示气候因子在尼瓦拉野生稻的适应、存续与扩张过程中发挥了关键作用。最后，基于尼瓦拉野生稻种群的遗传模式与动态特征，本研究提出假说：尼瓦拉野生稻可能多次独立起源于不同的普通野生稻种群。