FIGURE CAPTIONS

Fig 1. Bayesian tree based on 107 unique haplotypes in the combined cytochrome b and control region dataset (1652 bp) calculated in BEAST. Black dots indicate nodes with a posterior probability (BPP) of 1.0. Three lineages (East, Midwest, and Southwest) received high support whereas Central did not (BPP = 0.652). Time since most recent common ancestor (TMRCA) analysis estimated the oldest split as Southwest vs. the other lineages. Each TMRCA estimate is positioned above its corresponding node along with its 95% confidence interval.

Fig 2. Geographic distribution (A), principal coordinates analysis (PCoA, B), and median joining haplotype network (C) for the combined cytochrome b and control region (1652 bp, n = 118). The Central (light blue, squares), East (dark blue, diamonds), Midwest (purple, circles), and Southwest (orange, triangles) showed differentiation in both the PCoA and haplotype network with Central in the middle of the three other lineages. The first axis of the PCoA (variance explained = 25.78%) separated Southwest and Central (negative values) from Midwest and East (positive values) whereas the second axis (variance explained = 21.71%) separated East and Midwest. Correspondingly, the median joining haplotype network exhibited four main groups separated by a minimum of 15 mutational steps. The most divergent groups were Southwest and Midwest (52 total mutational steps).

Fig 3. Results of the reduced control region dataset (636 bp) in 336 white-footed mice. Greater geographic sampling clarified the distribution of each lineage (A) where Central (light blue, squares) occurred in the southern Midwest and parts of the southwest, East (dark blue, diamonds) in most of the eastern United States and Canada, Midwest in the upper Midwest (purple, circles), and Southwest within Texas, Mexico, Oklahoma, and New Mexico (orange, triangles). Despite decreased power in the reduced dataset, all four lineages were apparent in the principal coordinate analysis (PCoA; B), and median joining haplotype network (C). Axis 1 of the PCoA separated Central, Midwest, and Southwest (negative values) from East (positive values; variance explained = 29.67%). The second axis revealed differentiation between Midwest, Central, and Southwest (variance explained = 13.42%). In the haplotype network, all lineages were separated by at least 6 mutational steps, and the most divergent groups were Southwest and East (17 total mutation steps).