Figure Legends
Figure 1 . Sample sites of the Nebria ingens complex in
the Sierra Nevada, California. Collecting sites of N. riversi ,
the intermediate morphotype, and N. ingens are depicted with
solid triangles, squares, and circles, respectively. The survey sites
where no populations were located (despite survey efforts) are denoted
by x marks. The extent of last glacial maximum is shown as a grey line
(Rood, Burbank, & Finkel, 2011). Geographical names for each site can
be found in Table 2 .
Figure 2 . The Bayesian mitochondrial COI gene tree of theNebria ingens complex with posterior probabilities listed above
the nodes and divergence time listed beneath the nodes. Divergence time
is estimated using a strict molecular clock (0.0113 substitutions per
lineage per million years) and is denoted by the mean and 95%
confidence interval. The two major clades correspond to a northern clade
consisting of N. riversi , intermediate morphotypes, and someN. ingens samples, and a southern clade consisting solely of the
intermediate morphotype and N. ingens .
Figure 3. The SNAPP species tree of individuals from eight
sites using the fully-filtered SNP dataset. The thick black line
shows the consensus tree, and the numbers at each node denote the
posterior probability.
Figure 4 . Population structure of the N. ingens complex
based on sNMF clustering analysis for K=6 (left) and K=10 (right). The
concatenated ML tree is shown on the K=6 map with bootstrap support for
major nodes. The colors of population clusters and clades reflect the
major drainage basins of the Sierra Nevada, and the drainage is roughly
circled by the dashed lines.
Figure 5. The model accuracies estimated using conSturct. For
the K=3 to K=8, spatial models are significantly more accurate than
non-spatial models (p <0.05).
Figure 6. Stairway plots of eight selected sites including site
1 (A), site 3 (B), site 9 (C), site 10 (D), site 12 (E), site 17 (F),
site 24 (G), and site 27 (H). The solid lines, dashed lines, and dotted
lines represent the median, 12.5% and 87.5%, and 2.5% and 97.5%
confidence intervals, respectively. All sites show dramatic population
declines in past 30 thousand years.
Figure 7. Measurements of TMRCA (A) andF ST (B) for paired populations from the same
(solid circle) and different (empty circle) drainages, plotted against
geographical distance. For TMRCA (A), there is a significant difference
between same and different drainage population pairs, with no
significant correlation between TMRCA and geographical distance. The
TMRCA across different drainages mostly predates the last glacial
maximum (LGM), which is denoted by the grey box. ForF ST (B), there is no significant difference
between population pairs within and among drainages, but the correlation
between F ST and geographic distance is
significant.