Fig 1.
Map of kangaroo rat samples used in this study.
Filled stars indicate contemporary Dipodomys elator samples whereas circles with an ‘x’ are historical D. elator samples. Twenty-eight historical samples in Hardeman are represented by one filled circle with an ‘x’. Filled squares represent D. ordii samples used in the study. Note the contemporary sampling gap located in Foard County, most of Hardman County, and in south Wilbarger County. Trapping restrictions and topography prevented collections in those regions. D. elator is thought to be extirpated in all counties except Cottle, Childress, Hardeman, Wilbarger, and Wichita counties. Map was constructed using ArcMap v10.8.1 and the 1:1,000,000-Scale National Boundaries of the United States data from the USGS EROS (Earth Resources Observatory and Science) Center).
Fig 2.
Extended Bayesian Skyline Plot for Dipodomys elator (top) from 34 individuals and 47 loci and for D. ordii (bottom) from 15 individuals and 49 loci. X-axis is thousands of years ago. Y-axis is effective population size (Ne) in thousands. The y-axis is on a log scale. The dark line on each plot is the mean effective population size, while the shaded gray portions represent the upper highest posterior density (HPD) estimate and the lower highest posterior density (LHD).
Fig 3.
STRUCTURE plot of 60 D. elator samples across three time periods (see text for time breakdown).
The “sampling gap” individuals, those that were found in the areas of Wilbarger and Baylor counties prior to 1980, are completely divergent from later samples;. These results show greater admixture among contemporary subpopulations, though there appears to be some structure in the contemporary east and west samples.
Fig 4.
Principal components analysis on the genotypes for 55 D. elator samples (historical and contemporary) using the dudi.pca function in R package ‘adegenet’.
While there are no clear clusters emerging on PC1, geographic location seems to correspond with PC2.