Discussion
The main goal of this study was to test competing hypotheses for the location of glacial refugia in an alpine beetle species, including a hypothesis focusing on the role of drainage basins as refugia. By focusing on analyses of population structure and TMRCA estimates from paired populations of the cold-specialized, riparian beetles in the alpine N. ingenscomplex, we found strong evidence that population structure and patterns of lineage divergence are correlated with drainage basins in the Sierra Nevada Mountains, California. This supports the hypothesis that drainage basins, and by extension microhabitat preferences of a species, allow for persistence in multiple refugia across the mountain range. We also provide evidence that post-glacial gene flow can readily obscure the signature of glacial refugia, if not carefully dissected, and that episodes of glaciation enhanced lineage diversity in this alpine species complex through both isolation and hybridization.