Drainage basins serve as multiple glacial refugia for alpine habitats in the Sierra Nevada Mountains, California

The evolutionary histories of alpine species are often directly associated
with responses to glaciation. Deep divergence among populations and
complex patterns of genetic variation have been inferred as consequences
of persistence within glacier boundaries (i.e. on nunataks), while shallow
divergence and limited genetic variation is assumed to result from
expansion from large refugia at the edge of ice shields (i.e. massifs de
refuge). However, for some species, dependence on specific microhabitats
could profoundly influence their spatial and demographic response to
glaciation, and such a simple dichotomy may obscure the localization of
actual refugia. In this study, we use the Nebria ingens complex
(Coleoptera: Carabidae), a water-affiliated ground beetle lineage, to test
how drainage basins are linked to their observed population structure. By
analyzing mitochondrial COI gene sequences and genome-wide single
nucleotide polymorphisms, we find that the major drainage systems of the
Sierra Nevada Mountains in California best explain the population
structure of the N. ingens complex. In addition, we find that an
intermediate morphotype within the N. ingens complex is the product of
historical hybridization of N. riversi and N. ingens in the San Joaquin
basin during glaciation. This study highlights the importance of
considering ecological preferences in how species respond to climate
fluctuations and provides an explanation for discordances that are often
observed in comparative phylogeographic studies.