Supplemental Material For

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:

Appendix 1. Hardy-Weinberg equilibrium results (population-level test). Statistical significance at α < 0.0147 after B-Y correction is indicated by bold face.
Locus / Colusa NWR / Yolo / Gray Lodge / Gilsizer Slough / Sutter East / Sutter West / American Basin West / Natomas West
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
Locus / Natomas East / Natomas South / Conaway Ranch / Yolo Wildlife Area / Badger Creek / White Slough / Los Banos / Volta Wild Life 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
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 / − / − / −

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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.
Colusa Basin / Butte Basin / Sutter Basin / American Basin / Yolo Basin / Delta Basin / San Joaquin Basin
Colusa NWR / North Yolo / Gray Lodge / Gilsizer Slough / Sutter East Bypass / Sutter West Bypass / American West / Natomas West / Natomas East / Natomas South / Conaway Ranch / Yolo Wildlife Area / Badger Creek / White Slough / Los Banos Creek / Volta Wildlife Area
Colusa NWR / -- / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
North Yolo / 0.042 / -- / 0.001 / 0.000 / 0.002 / 0.000 / 0.000 / 0.001 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Gray Lodge / 0.079 / 0.039 / -- / 0.027 / 0.017 / 0.004 / 0.006 / 0.372 / 0.067 / 0.021 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Gilsizer Slough / 0.089 / 0.046 / 0.013 / -- / 0.009 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Sutter East Bypass / 0.091 / 0.042 / 0.022 / 0.021 / -- / 0.008 / 0.005 / 0.049 / 0.001 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Sutter West Bypass / 0.063 / 0.040 / 0.020 / 0.019 / 0.021 / -- / 0.000 / 0.020 / 0.001 / 0.001 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
American Basin / 0.085 / 0.040 / 0.019 / 0.047 / 0.026 / 0.041 / -- / 0.004 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Natomas West / 0.058 / 0.026 / 0.001 / 0.021 / 0.014 / 0.011 / 0.016 / -- / 0.646 / 0.059 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Natomas East / 0.061 / 0.038 / 0.011 / 0.029 / 0.040 / 0.022 / 0.033 / 0.000 / -- / 0.183 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Natomas South / 0.123 / 0.080 / 0.032 / 0.066 / 0.094 / 0.056 / 0.070 / 0.021 / 0.011 / -- / 0.000 / 0.000 / 0.000 / 0.011 / 0.000 / 0.000
Conaway Ranch / 0.152 / 0.131 / 0.063 / 0.085 / 0.103 / 0.083 / 0.083 / 0.087 / 0.087 / 0.098 / -- / 0.000 / 0.000 / 0.000 / 0.000 / 0.000
Yolo Wildlife Area / 0.132 / 0.118 / 0.068 / 0.070 / 0.099 / 0.057 / 0.084 / 0.080 / 0.082 / 0.097 / 0.034 / -- / 0.000 / 0.000 / 0.000 / 0.000
Badger Creek / 0.131 / 0.096 / 0.082 / 0.060 / 0.096 / 0.076 / 0.101 / 0.064 / 0.068 / 0.078 / 0.166 / 0.121 / -- / 0.000 / 0.000 / 0.000
White Slough / 0.152 / 0.135 / 0.064 / 0.069 / 0.108 / 0.077 / 0.110 / 0.057 / 0.050 / 0.047 / 0.145 / 0.105 / 0.061 / -- / 0.000 / 0.000
Los Banos Creek / 0.268 / 0.242 / 0.202 / 0.189 / 0.256 / 0.224 / 0.250 / 0.192 / 0.202 / 0.228 / 0.332 / 0.278 / 0.123 / 0.185 / -- / 0.000
Volta Wildlife Area / 0.262 / 0.228 / 0.188 / 0.204 / 0.230 / 0.231 / 0.225 / 0.185 / 0.196 / 0.205 / 0.308 / 0.280 / 0.191 / 0.191 / 0.110 / --

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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.
Colusa Basin / Butte Basin / Sutter Basin / American Basin / Yolo Basin / Delta Basin / San Joaquin 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

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).

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