Holocene-era landscape conditions affect genetic connectivity in a sagebrush obligate species, the pygmy rabbit (Brachylagus idahoensis)

Environmental changes produce discontinuities in suitable habitat. However, drawing inference into the effects of these changes on contemporary genetic patterns is often difficult. Recent approaches for evaluating landscape resistance facilitate increased understanding of landscape effects on gene flow. We investigated the effects of pluvial lakes and sagebrush cover on genetic connectivity for the pygmy rabbit (Brachylagus idahoensis), a sagebrush obligate species. We predicted that sagebrush-based surfaces would be more explanatory than pluvial lake surfaces. Furthermore, we predicted that habitat characteristics during the mid-Holocene would explain genetic differentiation better than those during the late-Pleistocene. We leveraged a genetic dataset to evaluate the explanatory power of landscape resistance surfaces. We generated resistance surfaces that represent varying degrees of resistance associated with pluvial lakes and sagebrush cover, then projected sagebrush distribution back to the mid-Holocene and late-Pleistocene. Representations based on sagebrush distribution were more explanatory than those based on pluvial lakes. Projections of sagebrush distribution back in time indicate concordance between genetic connectivity and mid-Holocene sagebrush distribution. Limited numbers of dispersal pathways were apparent among study regions, suggesting spatially restricted corridors of connectivity. We demonstrate that shifts in vegetative cover can shape contemporary patterns of genetic connectivity. By coupling testing of resistance surfaces with estimates of past vegetative change, we provide insights into the time scales over which genetic differentiation may occur. Given projections of future declines in sagebrush, maintaining sagebrush cover will be critical to population persistence of pygmy rabbits.