Supplemental Material For

Table 1. Supplemental Material for:

Defining population structure and genetic signatures of decline in the giant gartersnake

(Thamnophis gigas): Implications for conserving threatened species within highly altered landscapes

Dustin A. Wooda, Brian J. Halstead, Michael L. Casazza, Eric Hansen, Glenn D. Wylie, and Amy G.

Vandergast

aCorresponding author: E-mail: [email protected]

1 Appendix 1. Hardy-Weinberg equilibrium results (population-level test). Statistical significance at α < 0.0147 after B-Y correction is indicated by bold face.

Gilsize Colus America Gray r Sutter Sutter Natoma a Yolo n Basin Lodge Sloug East West s West NWR West h Locus TRI_58P 0.438 0.051 0.323 0.247 0.281 0.962 0.363 0.484 DI_907 0.732 0.197 0.051 0.729 0.578 0.598 1.000 0.053 TRI_TSC 0.076 0.264 0.062 0.001 0.760 0.140 0.130 0.320 DI_2229 0.357 0.063 0.027 0.190 0.304 0.910 0.520 0.141 TRI_TOA 0.911 0.155 0.297 0.686 0.199 1.000 0.679 0.145 TRI_ISV 0.239 0.232 0.488 0.389 0.102 0.217 0.830 0.018 PEN_5ZB 0.961 0.605 0.515 0.978 0.702 0.273 0.378 0.118 TET969 0.944 0.434 0.448 0.491 1.000 1.000 0.940 0.021 PEN1170 0.016 1.000 0.035 0.000 0.034 0.162 0.000 0.000 TRI_ONY 0.136 0.028 0.279 0.392 0.598 0.317 0.642 0.078 TRI_AOC 0.925 0.070 0.101 0.752 0.710 0.952 0.505 0.061 TET_790 0.357 0.288 0.310 0.266 0.043 0.366 1.000 0.933 TET_567 0.001 0.088 0.076 0.017 0.269 0.010 0.001 0.001 PEN_61U 0.219 0.357 0.024 0.094 0.113 0.033 0.798 0.455 TRI_3VL 0.203 0.229 0.320 0.471 0.665 0.705 0.457 0.157

Yolo Volta Nato Badge White Natoma Conawa Wildli Los Wild mas r Sloug s South y Ranch fe Banos Life East Creek h Locus Area Area TRI_58P 0.913 0.261 0.983 0.294 0.567 0.273 1.000 0.470 DI_907 0.091 no info 1.000 1.000 0.426 0.032 1.000 0.458 TRI_TSC 0.208 1.000 0.221 0.000 0.053 0.249 1.000 0.424 DI_2229 0.750 1.000 0.099 0.086 0.941 0.584 0.811 0.615 TRI_TOA 0.411 0.198 0.522 0.471 0.547 1.000 1.000 0.028 TRI_ISV 0.600 1.000 1.000 1.000 0.066 1.000 no info 0.199 PEN_5ZB 0.206 0.582 0.227 0.793 0.278 0.625 1.000 0.543 TET969 0.742 0.554 0.621 0.003 0.389 0.766 0.736 0.369 PEN1170 0.003 no info no info 0.027 0.000 0.247 0.018 0.000 TRI_ONY 1.000 1.000 0.392 0.282 0.340 0.167 no info 0.849 TRI_AOC 0.747 0.560 0.125 0.027 0.341 0.298 0.794 0.045 TET_790 0.646 0.435 0.894 0.043 0.860 0.124 0.776 0.090 TET_567 0.000 0.027 0.056 0.022 0.000 0.441 0.002 0.000 PEN_61U 0.019 0.022 0.594 0.548 0.838 0.396 1.000 0.454 TRI_3VL 0.076 0.483 0.490 0.770 0.666 1.000 no info no info

2 Appendix 2. Hardy-Weinberg equilibrium results (global tests) with p-values and standard errors (S.E.). Population (multi-locus) Locus (multi-populations)

Population p- value S.E. Locus p- value S.E. Colusa NWR 0.969 0.003 TRI_58P 0.905 0.007 North Yolo 0.996 0.001 DI_907 0.968 0.002 Gray lodge 0.926 0.005 TRI_TSC 1.000 0.000 Gilsizer Slough 1.000 0.000 DI_2229 0.743 0.012 Sutter East of Bypass 0.953 0.003 TRI_TOA 0.026 0.002 Sutter West of Bypass 0.982 0.002 TRI_ISV 0.846 0.004 American West 0.654 0.009 PEN_5ZB 0.406 0.011 Natomas West 1.000 0.000 TET969 0.708 0.009 Natomas East 1.000 0.000 PEN1170 1.000 0.000 Natomas South 0.916 0.003 TRI_ONY 0.981 0.001 Conaway Ranch 0.972 0.003 TRI_AOC 0.189 0.010 Yolo Wildlife Area 1.000 0.000 TET_790 0.892 0.008 Badger Creek 1.000 0.000 TET_567 1.000 0.000 White Slough 0.947 0.003 PEN_61U 0.996 0.001 Los Banos Creek 0.879 0.005 TRI_3VL 0.747 0.005 Volta Wildlife Area 0.973 0.002 − − −

3 Appendix 3. Pairwise genetic differentiation estimates (FST) among populations using 12 loci (TRI_AOC, DI_2229, and PEN_61U were removed from the dataset) below the diagonal, and p-values above the diagonal. Statistical significance at α < 0.009 after B-Y method correction is indicated by bold face. Butte Colusa Basin Basin Sutter Basin American Basin Yolo Basin Delta Basin Y o l o

W i Sutte Gilsiz Sutte l r Amer Nato Nato Badge Colusa North Gray er r East Conaway d West ican mas mas r NWR Yolo Lodge Sloug Bypa Ranch l Bypa West West South Creek h ss i ss f e

A r e a 0 . 0 0 Colusa NWR -- 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0 0.000 0 . 0 0 North Yolo 0.042 -- 0.001 0.000 0.002 0.000 0.000 0.001 0.000 0.000 0 0.000 0 . 0 0 Gray Lodge 0.079 0.039 -- 0.027 0.017 0.004 0.006 0.372 0.021 0.000 0 0.000 0 . 0 0 Gilsizer Slough 0.089 0.046 0.013 -- 0.009 0.000 0.000 0.000 0.000 0.000 0 0.000 0 . 0 0 Sutter East Bypass 0.091 0.042 0.022 0.021 -- 0.008 0.005 0.049 0.000 0.000 0 0.000 Sutter West 0.063 0.040 0.020 0.019 0.021 -- 0.000 0.020 0.001 0.000 0 0.000 Bypass . 0

4 0 0 0 . 0 0 American Basin 0.085 0.040 0.019 0.047 0.026 0.041 -- 0.004 0.000 0.000 0 0.000 0 . 0 0.01 0 Natomas West 0.058 0.026 0.001 0.021 0.014 0.011 6 -- 0.059 0.000 0 0.000 0 . 0 0.03 0 Natomas East 0.061 0.038 0.011 0.029 0.040 0.022 3 0.000 0.183 0.000 0 0.000 0 . 0 0.07 0 Natomas South 0.123 0.080 0.032 0.066 0.094 0.056 0 0.021 -- 0.000 0 0.000 0 . 0 0.08 0 Conaway Ranch 0.152 0.131 0.063 0.085 0.103 0.083 3 0.087 0.098 -- 0 0.000 0.08 - Yolo Wildlife Area 0.132 0.118 0.068 0.070 0.099 0.057 4 0.080 0.097 0.034 - 0.000 0 . 1 0.10 2 Badger Creek 0.131 0.096 0.082 0.060 0.096 0.076 1 0.064 0.078 0.166 1 -- 0 . 1 0.11 0 White Slough 0.152 0.135 0.064 0.069 0.108 0.077 0 0.057 0.047 0.145 5 0.061 -- 0 . 2 0.25 7 Los Banos Creek 0.268 0.242 0.202 0.189 0.256 0.224 0 0.192 0.228 0.332 8 0.123 0 . 2 0.22 8 Volta Wildlife Area 0.262 0.228 0.188 0.204 0.230 0.231 5 0.185 0.205 0.308 0 0.191

5 Appendix 4. Pairwise genetic differentiation (FST) among regional drainage basins (below diagonal) using 12 loci (TRI_AOC, DI_2229, and PEN_61U were removed from the dataset) and p-values (above diagonal). Statistical significance at α < 0.0137 after B-Y correction (Narum, 2006) is indicated by bold face.

San Butte Sutter America Yolo Delta Colusa Basin Joaquin Basin Basin n Basin Basin Basin Basin

Colusa Basin − 0.000 0.000 0.000 0.000 0.000 0.000 Butte Basin 0.053 − 0.009 0.080 0.000 0.000 0.000 Sutter Basin 0.050 0.012 − 0.000 0.000 0.000 0.000 American Basin 0.047 0.006 0.019 − 0.000 0.000 0.000 Yolo Basin 0.111 0.055 0.059 0.065 − 0.000 0.000 Sacramento Delta 0.095 0.057 0.052 0.062 0.103 − 0.000 San Joaquin Basin 0.220 0.166 0.181 0.181 0.263 0.148 −

Appendix 5. Analysis of molecular variance (AMOVA) with 12 loci (TRI_AOC, DI_2229, and PEN_61U were removed from the dataset). Source of genetic variation Percent Variance P-value Among Drainage basins 9% 0.000 Among populations with basins 3% 0.000 Among individuals within populations 7% 0.000 Within individuals 81% 0.000

6 Appendix 6. Genetic structure of populations on the basis of 12 loci and a correlated allele frequencies model. A. Each individual sampled is represented by a single column with group membership probabilities for each cluster (K) indicated as the relative proportion of each color. B. Maximum number of clusters to which individuals could be assigned on the basis of 15 loci where the LnP(K|D) plateaus. C. Maximum number of clusters to which individuals could be assigned on the basis of 12 loci where the LnP(K|D) plateaus. In B and C, data points are the means and standard deviations for 10 MCMC simulations at each K (range = 1 - 16).