show Abstracthide AbstractPygmy rabbits (Brachylagus idahoensis) were sequenced throughout the southern Great Basin (California, Nevada, and Oregon) using the 3RAD protocol, as described in Bayona-Vasquez et al. (2019). Sequence data were then used to: a) characterize population genetic differentiation throughout the sampling extent, b) evaluate alternative models of demographic history since the late Pleistocene, and c) identify outlier loci that may be under divergent selection.