Data from: Phylogeography and species biogeography of montane Great Basin stoneflies

Sky islands are ideal systems for determining the effects of climatic oscillations on species distributions and genetic structure. Our study focused on montane stonefly populations in the Great Basin of western North America. We used niche-based distribution modelling, phylogeography and traditional species-based biogeography to test several hypotheses as follows: (i) genetic differentiation among Doroneuria baumanni populations will be independent of hydrologic connectivity (headwater model); (ii) Sky islands were colonized when habitat was more continuous and populations likely experienced multiple expansions and contractions; (iii) Colonization events were coincident with the late Pleistocene and Holocene; and (iv) Shared topography and climate history will result in concordant patterns of genetic differentiation in D. baumanni and occurrences of 32 stonefly species across the region. Overall, ΦST’s and coalescent-based estimates of migration were consistent with the headwater model. Maximum likelihood and Bayesian gene trees identified three major nonoverlapping east-west clades. Distribution modelling indicated more suitable habitat in the Great Basin during the Last Glacial Maximum than at present, but none during the last interglacial period. Demographic analyses showed evidence of population expansion in one of the three major east–west clades. Intra-clade divergence times (60 000–183 000 ybp) were well within the late Pleistocene while among-clade divergence times (499 000–719 000 ybp) were deeper. Genetic differentiation in D. baumanni and distributions of stonefly species were significantly concordant. These results imply that climatic oscillations have played major roles in shaping the genetic structure and distributions of Great Basin stoneflies, but that divergence among clades occurred much earlier than our late Pleistocence/early Holocene predictions.天空岛（Sky islands）是探究气候震荡对物种分布及遗传结构影响的理想研究系统。本研究聚焦于北美西部大盆地的山地石蝇种群。我们采用基于生态位的分布模型、系统地理学以及传统物种生物地理学方法，对以下多项假说进行了验证：（i）鲍氏裸石蝇（Doroneuria baumanni）种群间的遗传分化与水文连通性无关（源头水系模型，headwater model）；（ii）当地表生境更为连续时，天空岛便会被定殖，且种群大概率经历过多次扩张与收缩事件；（iii）定殖事件与晚更新世及全新世时期相吻合；（iv）共同的地形与气候历史，将使鲍氏裸石蝇的遗传分化模式，与该区域32种石蝇的分布格局呈现一致性。整体而言，ΦST值以及基于溯祖理论的迁移速率估计结果均与源头水系模型相符。最大似然法与贝叶斯基因树分析共识别出3个主要的、互不重叠的东西向支系。分布模型结果显示，末次盛冰期时大盆地的适宜生境面积大于当前，但末次间冰期时期该区域并无适宜生境。种群历史动态分析表明，3个东西支系中的其中一支存在种群扩张的信号。支系内的分化时间为60000–183000年前（years before present, ybp），完全处于晚更新世范围内；而支系间的分化时间则为499000–719000年前，分化时间更为古老。鲍氏裸石蝇的遗传分化与石蝇物种的分布格局存在显著的一致性。本研究结果暗示，气候震荡在塑造大盆地石蝇的遗传结构与分布格局中发挥了核心作用，但支系间的分化时间远早于我们基于晚更新世/全新世早期做出的预测。