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.