Supplementary Table 1. Logistic Regression Correlating Presence of a Hybrid Or Riffle Sculpin

Supplementary Table 1. Logistic regression correlating presence of a hybrid or riffle sculpin with specific measured variables related to the dams (see Table 1). Variables include: type of dam (dam2), elevation of dam (ele_d), elevation of site (ele_s), distance of dam from site (d_dam), average release temperature (x_temp), highest release temperature (h_temp), and lowest release temperature (l_temp).

Estimate / Std. Error / t-value / p-value
Hybrid
(Intercept) / -14.0534 / 44.12859 / -0.318 / 0.771
dam2 / -0.75967 / 3.873558 / -0.196 / 0.857
ele_d / -0.00427 / 0.019408 / -0.220 / 0.840
ele_s / 0.00879 / 0.008351 / 1.053 / 0.370
d_dam / -0.00346 / 0.030048 / -0.115 / 0.916
x_temp / 0.135134 / 0.604566 / 0.224 / 0.837
h_temp / 0.253241 / 0.610457 / 0.415 / 0.706
l_temp / 1.016642 / 3.842312 / 0.265 / 0.808
Riffle
(Intercept) / 24.53558 / 46.77865 / 0.525 / 0.636
dam2 / 3.115227 / 4.106177 / 0.759 / 0.503
ele_d / 0.025578 / 0.020573 / 1.243 / 0.302
ele_s / -0.0155 / 0.008853 / -1.751 / 0.178
d_dam / -0.01899 / 0.031853 / -0.596 / 0.593
x_temp / 0.179036 / 0.640872 / 0.279 / 0.798
h_temp / -0.30161 / 0.647117 / -0.466 / 0.673
l_temp / -2.90492 / 4.073055 / -0.713 / 0.527

Supplementary Table 2. Allele frequencies for every locus, across all sampled riffle sculpin (Cottus gulosus) populations. Population numbers are the same as those found in Table 2.

Locus / Allele / 1-Lower American / 2- NMF American / 3- SF American / 5- Upper Mokelumne / 7- Upper Stanislaus / 8- Lower Tuolumne / 9- Upper Tuolumne / 11- Upper Merced / 13- Upper San Joaquin / 14- 180 Bridge Kings / 15- Greenbelt Kings / 16- Avocado Kings / 18- Upper Kings / 19- Kaweah / All_W / All_UW
316 / N / 16 / 25 / 23 / 25 / 22 / 28 / 22 / 30 / 21 / 48 / 19 / 22 / 30 / 16
p: 242 / 0 / 0 / 0 / 0 / 0 / 0 / 0.114 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.007 / 0.008
p: 272 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.021 / 0 / 0 / 0 / 0 / 0.003 / 0.001
p: 275 / 0 / 0 / 0 / 0 / 0.091 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.006 / 0.006
p: 281 / 0.063 / 0.08 / 0 / 0 / 0.318 / 0 / 0 / 0.35 / 0 / 0 / 0 / 0 / 0 / 0 / 0.059 / 0.058
p: 284 / 0 / 0 / 0 / 0 / 0.545 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.035 / 0.039
p: 287 / 0.813 / 0.8 / 1 / 0.6 / 0 / 0.911 / 0 / 0.65 / 1 / 0.635 / 0.474 / 0.614 / 0.383 / 1 / 0.627 / 0.634
p: 290 / 0.094 / 0 / 0 / 0 / 0.045 / 0.089 / 0.773 / 0 / 0 / 0.344 / 0.526 / 0.386 / 0.617 / 0 / 0.218 / 0.205
p: 299 / 0 / 0.12 / 0 / 0.4 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.037 / 0.037
p: 305 / 0.031 / 0 / 0 / 0 / 0 / 0 / 0.068 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.006 / 0.007
p: 308 / 0 / 0 / 0 / 0 / 0 / 0 / 0.045 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.003
318 / N / 16 / 10 / 8 / 18 / 14 / 22 / 15 / 0 / 20 / 50 / 19 / 25 / 30 / 15
p: 239 / 0 / 0 / 0 / 0 / 1 / 0 / 0 / NA / 0 / 0 / 0 / 0 / 0 / 0 / 0.053 / 0.077
p: 243 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / NA / 0 / 0 / 0 / 0 / 0.033 / 0 / 0.004 / 0.003
p: 246 / 0.156 / 0 / 1 / 0 / 0 / 0.5 / 0.967 / NA / 1 / 0.02 / 0 / 0 / 0 / 0.667 / 0.256 / 0.332
p: 249 / 0.625 / 0.1 / 0 / 1 / 0 / 0.455 / 0 / NA / 0 / 0.98 / 1 / 0.96 / 0.883 / 0.333 / 0.62 / 0.487
p: 252 / 0.219 / 0.9 / 0 / 0 / 0 / 0 / 0 / NA / 0 / 0 / 0 / 0 / 0.05 / 0 / 0.053 / 0.09
p: 255 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / NA / 0 / 0 / 0 / 0 / 0.033 / 0 / 0.004 / 0.003
p: 264 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / NA / 0 / 0 / 0 / 0.02 / 0 / 0 / 0.002 / 0.002
p: 273 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / NA / 0 / 0 / 0 / 0.02 / 0 / 0 / 0.002 / 0.002
p: 276 / 0 / 0 / 0 / 0 / 0 / 0 / 0.033 / NA / 0 / 0 / 0 / 0 / 0 / 0 / 0.002 / 0.003
p: 288 / 0 / 0 / 0 / 0 / 0 / 0.045 / 0 / NA / 0 / 0 / 0 / 0 / 0 / 0 / 0.004 / 0.003
6 / N / 17 / 25 / 23 / 25 / 22 / 32 / 23 / 30 / 22 / 51 / 20 / 25 / 30 / 16
p: 184 / 0.059 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.004
p: 192 / 0.676 / 1 / 1 / 1 / 1 / 1 / 0.935 / 1 / 1 / 0.971 / 1 / 1 / 1 / 0.938 / 0.974 / 0.966
p: 194 / 0.147 / 0 / 0 / 0 / 0 / 0 / 0.065 / 0 / 0 / 0.029 / 0 / 0 / 0 / 0.063 / 0.018 / 0.022
p: 198 / 0.118 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.006 / 0.008
65 / N / 17 / 25 / 23 / 25 / 21 / 32 / 23 / 30 / 22 / 51 / 20 / 25 / 30 / 16
p: 218 / 0.029 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.001 / 0.002
p: 220 / 0.471 / 0.58 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0.01 / 0.025 / 0.02 / 0 / 0 / 0.131 / 0.15
p: 222 / 0.5 / 0.42 / 0 / 1 / 0.548 / 1 / 1 / 0.5 / 0.5 / 0 / 0 / 0 / 0 / 0 / 0.379 / 0.391
p: 223 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.853 / 0.425 / 0.82 / 1 / 0.563 / 0.31 / 0.261
p: 226 / 0 / 0 / 0 / 0 / 0.452 / 0 / 0 / 0.5 / 0.5 / 0.137 / 0.5 / 0.16 / 0 / 0.438 / 0.176 / 0.192
p: 228 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.05 / 0 / 0 / 0 / 0.003 / 0.004
Locus / Allele / pop1 / pop2 / pop3 / pop5 / pop7 / pop8 / pop9 / pop11 / pop13 / pop14 / pop15 / pop16 / pop18 / pop19 / All_W / All_UW
78 / N / 17 / 25 / 23 / 25 / 22 / 32 / 25 / 30 / 22 / 50 / 20 / 25 / 30 / 16
p: 140 / 0 / 0 / 0 / 0 / 0 / 0.031 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
p: 155 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.94 / 0.8 / 0.96 / 1 / 1 / 0.367 / 0.336
p: 158 / 0.206 / 0 / 0 / 0 / 1 / 0.453 / 1 / 0.983 / 0.795 / 0 / 0 / 0 / 0 / 0 / 0.309 / 0.317
p: 159 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.04 / 0.175 / 0 / 0 / 0 / 0.015 / 0.015
p: 163 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.025 / 0.04 / 0 / 0 / 0.004 / 0.005
p: 166 / 0.794 / 1 / 1 / 1 / 0 / 0.484 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.282 / 0.306
p: 171 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.02 / 0 / 0 / 0 / 0 / 0.003 / 0.001
p: 174 / 0 / 0 / 0 / 0 / 0 / 0.031 / 0 / 0 / 0.205 / 0 / 0 / 0 / 0 / 0 / 0.015 / 0.017
p: 186 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.017 / 0 / 0 / 0 / 0 / 0 / 0 / 0.001 / 0.001
8 / N / 17 / 25 / 23 / 25 / 22 / 32 / 25 / 30 / 22 / 50 / 20 / 24 / 30 / 16
p: 241 / 0 / 0 / 0 / 0 / 0 / 0 / 0.06 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.004 / 0.004
p: 243 / 0.882 / 1 / 1 / 1 / 1 / 0.813 / 0.86 / 1 / 1 / 0.98 / 1 / 1 / 1 / 1 / 0.965 / 0.967
p: 245 / 0 / 0 / 0 / 0 / 0 / 0 / 0.06 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.004 / 0.004
p: 247 / 0 / 0 / 0 / 0 / 0 / 0 / 0.02 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.001 / 0.001
p: 253 / 0.118 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.02 / 0 / 0 / 0 / 0 / 0.008 / 0.01
p: 255 / 0 / 0 / 0 / 0 / 0 / 0.188 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.017 / 0.013
Cott582 / N / 17 / 25 / 23 / 25 / 22 / 32 / 25 / 30 / 22 / 50 / 20 / 23 / 30 / 16
p: 200 / 0 / 0 / 0 / 0 / 0.977 / 0 / 0 / 0 / 0 / 0 / 0.025 / 0 / 0 / 0 / 0.061 / 0.072
p: 202 / 0.324 / 0.16 / 0 / 0 / 0 / 0.078 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.033 / 0.04
p: 204 / 0.118 / 0 / 0 / 0 / 0.023 / 0 / 0 / 0 / 0.023 / 0.02 / 0 / 0 / 0 / 0 / 0.011 / 0.013
p: 206 / 0 / 0 / 0 / 0 / 0 / 0.141 / 0.98 / 1 / 0 / 0 / 0 / 0 / 0 / 0 / 0.164 / 0.151
p: 208 / 0.235 / 0.84 / 0.957 / 1 / 0 / 0.734 / 0 / 0 / 0.977 / 0.98 / 0.975 / 1 / 1 / 1 / 0.707 / 0.693
p: 210 / 0 / 0 / 0 / 0 / 0 / 0 / 0.02 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.001 / 0.001
p: 212 / 0 / 0 / 0.043 / 0 / 0 / 0.047 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.007 / 0.006
p: 214 / 0.265 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.013 / 0.019
p: 218 / 0.059 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.004
Cott207 / N / 14 / 0 / 0 / 0 / 0 / 23 / 0 / 0 / 0 / 2 / 0 / 0 / 0 / 0
p: 303 / 0.429 / NA / NA / NA / NA / 0.804 / NA / NA / NA / 0 / NA / NA / NA / NA / 0.628 / 0.411
p: 307 / 0 / NA / NA / NA / NA / 0.109 / NA / NA / NA / 0 / NA / NA / NA / NA / 0.064 / 0.036
p: 309 / 0.071 / NA / NA / NA / NA / 0.043 / NA / NA / NA / 0 / NA / NA / NA / NA / 0.051 / 0.038
p: 311 / 0.036 / NA / NA / NA / NA / 0 / NA / NA / NA / 0.75 / NA / NA / NA / NA / 0.051 / 0.262
p: 313 / 0.036 / NA / NA / NA / NA / 0.043 / NA / NA / NA / 0 / NA / NA / NA / NA / 0.038 / 0.026
p: 315 / 0.036 / NA / NA / NA / NA / 0 / NA / NA / NA / 0.25 / NA / NA / NA / NA / 0.026 / 0.095
p: 317 / 0.393 / NA / NA / NA / NA / 0 / NA / NA / NA / 0 / NA / NA / NA / NA / 0.141 / 0.131
Lce219 / N / 17 / 0 / 0 / 0 / 0 / 32 / 0 / 0 / 0 / 50 / 20 / 24 / 30 / 16
p: 221 / 0 / NA / NA / NA / NA / 0 / NA / NA / NA / 0.95 / 1 / 0.958 / 1 / 1 / 0.722 / 0.701
p: 223 / 1 / NA / NA / NA / NA / 0.984 / NA / NA / NA / 0 / 0 / 0 / 0 / 0 / 0.257 / 0.283
p: 225 / 0 / NA / NA / NA / NA / 0 / NA / NA / NA / 0.01 / 0 / 0.042 / 0 / 0 / 0.008 / 0.007
p: 226 / 0 / NA / NA / NA / NA / 0.016 / NA / NA / NA / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
p: 229 / 0 / NA / NA / NA / NA / 0 / NA / NA / NA / 0.04 / 0 / 0 / 0 / 0 / 0.011 / 0.006
Lce275 / N / 17 / 0 / 0 / 0 / 0 / 32 / 0 / 0 / 0 / 50 / 20 / 24 / 30 / 16
p: 307 / 0.824 / NA / NA / NA / NA / 1 / NA / NA / NA / 1 / 1 / 1 / 1 / 1 / 0.984 / 0.975
p: 309 / 0.176 / NA / NA / NA / NA / 0 / NA / NA / NA / 0 / 0 / 0 / 0 / 0 / 0.016 / 0.025

Supplementary Table 3. Inbreeding coefficient (FIS) calculations by locus and riffle sculpin population. Second section values are p-values for each FIS calculation, indicative ofrandomizations which gave larger FISvalues than observed. Third section values are p-values for each FIS calculation, indicative of randomizations which gave smaller FISvalues than observed. P-values are over 1960 randomizations, indicative of an adjusted nominal level (5%) of 0.00051 and when significant are bolded.

1-Lower American / 2-NMF
American / 3-SF
American / 5-Upper
Mokelumne / 7-Upper
Stanislaus / 8-Lower
Tuolumne / 9-Upper
Tuolumne / 11-Upper
Merced / 13-Upper San
Joaquin / 14-180
Bridge / 15-Greenbelt / 16-Avocado / 18-Upper
Kings / 19-Kaweah
316 / -0.118 / -0.041 / NA / 0.02 / -0.209 / -0.08 / 0.542 / 0.065 / NA / -0.031 / 0.182 / 0.094 / -0.182 / NA
318 / 0.557 / -0.059 / NA / NA / NA / 0.839 / 0.000 / NA / NA / -0.011 / NA / 1.000 / 0.241 / 0.134
6 / 0.095 / NA / NA / NA / NA / NA / -0.048 / NA / NA / NA / NA / 0.662 / NA / -0.034
65 / 0.138 / 0.603 / NA / NA / -0.818 / NA / NA / -1.000 / -1.000 / 0.872 / 0.747 / 0.924 / NA / 1.000
78 / 0.13 / NA / NA / NA / NA / -0.273 / NA / 0.000 / 0.045 / 1.000 / -0.192 / 1.000 / NA / NA
8 / -0.103 / NA / NA / NA / NA / -0.216 / 0.54 / NA / NA / NA / NA / 1.000 / NA / NA
Cott582 / -0.222 / 0.127 / -0.023 / NA / 0.000 / -0.068 / 0.000 / NA / 0.000 / NA / 0.000 / 1.000 / NA / NA
All / 0.076 / 0.238 / -0.023 / 0.02 / -0.465 / 0.103 / 0.394 / -0.472 / -0.552 / 0.352 / 0.316 / 0.540 / -0.049 / 0.526
316 / 1.0000 / 0.6867 / NA / 0.6102 / 0.9429 / 1.0000 / 0.0031 / 0.5337 / NA / 0.723 / 0.3571 / 0.3051 / 0.9036 / NA
318 / 0.0066 / 1.0000 / NA / NA / NA / 0.0005 / 1.0000 / NA / NA / 1.0000 / NA / 0.0138 / 0.1082 / 0.5153
6 / 0.3898 / NA / NA / NA / NA / NA / 1.0000 / NA / NA / NA / NA / 0.0347 / NA / 1.0000
65 / 0.3423 / 0.0031 / NA / NA / 1.0000 / NA / NA / 1.0000 / 1.0000 / 0.0005 / 0.0005 / 0.0005 / NA / 0.0005
78 / 0.5454 / NA / NA / NA / NA / 0.977 / NA / 1.0000 / 0.6378 / 0.0224 / 1.0000 / 0.0005 / NA / NA
8 / 1.0000 / NA / NA / NA / NA / 1.0000 / 0.0041 / NA / NA / NA / NA / 0.0087 / NA / NA
Cott582 / 0.9837 / 0.4837 / 1.0000 / NA / 1.0000 / 0.8015 / 1.0000 / NA / 1.0000 / NA / 1.0000 / 0.0082 / NA / NA
All / 0.1260 / 0.0184 / 1.0000 / 0.6102 / 1.0000 / 0.098 / 0.0005 / 1.0000 / 1.0000 / 0.0066 / 0.0056 / 0.0005 / 0.7434 / 0.0015
316 / 0.5679 / 0.5597 / NA / 0.6923 / 0.1469 / 0.8214 / 0.9985 / 0.7643 / NA / 0.6071 / 0.8934 / 0.8077 / 0.2801 / NA
318 / 0.9985 / 0.948 / NA / NA / NA / 1.0000 / 1.0000 / NA / NA / 0.9821 / NA / 1.0000 / 0.9913 / 0.8781
6 / 0.8526 / NA / NA / NA / NA / NA / 0.9439 / NA / NA / NA / NA / 1.0000 / NA / 0.9597
65 / 0.8097 / 0.9995 / NA / NA / 0.002 / NA / NA / 0.0005 / 0.0005 / 1.0000 / 1.0000 / 1.0000 / NA / 1.0000
78 / 0.9056 / NA / NA / NA / NA / 0.0505 / NA / 1.0000 / 0.8291 / 1.0000 / 0.4199 / 1.0000 / NA / NA
8 / 0.8158 / NA / NA / NA / NA / 0.3036 / 1.0000 / NA / NA / NA / NA / 1.0000 / NA / NA
Cott582 / 0.0776 / 0.9138 / 0.9796 / NA / 1.0000 / 0.4102 / 1.0000 / NA / 1.0000 / NA / 1.0000 / 1.0000 / NA / NA
All / 0.8765 / 0.9883 / 0.9796 / 0.6923 / 0.0010 / 0.9026 / 1.0000 / 0.0005 / 0.0010 / 0.9939 / 0.9949 / 1.0000 / 0.5051 / 0.999

Supplementary Table 4. Allele frequencies for every locus, across all sampled prickly sculpin (Cottus asper)populations. Population numbers are the same as those found in Table 2.

Locus / Allele / 1- Lower American / 4- Lower Mokelumne / 6- Lower Stanislaus / 10- Lower Merced / 12- Lower San Joaquin / 14- 180 Bridge Kings / 15- Greenbelt Kings / 16- Avocado Kings / 17- Dam Kings / All_W / All_UW
316 / N / 12 / 28 / 20 / 28 / 28 / 18 / 7 / 29 / 6
p: 248 / 0 / 0 / 0 / 0 / 0.036 / 0 / 0 / 0 / 0 / 0.006 / 0.004
p: 252 / 0 / 0 / 0 / 0 / 0.036 / 0 / 0 / 0 / 0 / 0.006 / 0.004
p: 263 / 0 / 0.071 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.011 / 0.008
p: 269 / 0 / 0.071 / 0.075 / 0 / 0.018 / 0 / 0 / 0 / 0 / 0.023 / 0.018
p: 272 / 1 / 0.857 / 0.9 / 0.946 / 0.911 / 0.917 / 1 / 0.966 / 0.833 / 0.923 / 0.926
p: 275 / 0 / 0 / 0 / 0.018 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
p: 287 / 0 / 0 / 0 / 0.018 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
p: 290 / 0 / 0 / 0 / 0.018 / 0 / 0.083 / 0 / 0.034 / 0.167 / 0.023 / 0.034
p: 302 / 0 / 0 / 0.025 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.003
318 / N / 7 / 23 / 20 / 23 / 23 / 18 / 7 / 31 / 6
p: 243 / 0 / 0.043 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.006 / 0.005
p: 246 / 0.286 / 0.043 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.019 / 0.037
p: 249 / 0.071 / 0.109 / 0 / 0 / 0 / 0.083 / 0 / 0.161 / 0.167 / 0.066 / 0.066
p: 252 / 0.143 / 0.065 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.016 / 0.023
p: 258 / 0 / 0.022 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
p: 261 / 0 / 0.043 / 0 / 0.174 / 0 / 0.028 / 0 / 0 / 0.083 / 0.038 / 0.037
p: 264 / 0 / 0.087 / 0 / 0 / 0.087 / 0 / 0.071 / 0.048 / 0 / 0.038 / 0.033
p: 267 / 0 / 0 / 0.025 / 0.087 / 0.065 / 0.028 / 0.143 / 0.032 / 0.083 / 0.044 / 0.051
p: 270 / 0 / 0.109 / 0.375 / 0.065 / 0.109 / 0.556 / 0.357 / 0.516 / 0.25 / 0.278 / 0.26
p: 273 / 0 / 0.065 / 0 / 0.109 / 0.022 / 0 / 0 / 0.016 / 0 / 0.032 / 0.024
p: 276 / 0 / 0 / 0 / 0.283 / 0.022 / 0.028 / 0 / 0 / 0 / 0.047 / 0.037
p: 279 / 0.5 / 0.152 / 0.4 / 0.13 / 0.674 / 0.278 / 0.357 / 0.226 / 0.333 / 0.316 / 0.339
p: 282 / 0 / 0.065 / 0.2 / 0.109 / 0.022 / 0 / 0.071 / 0 / 0.083 / 0.06 / 0.061
p: 285 / 0 / 0.152 / 0 / 0.043 / 0 / 0 / 0 / 0 / 0 / 0.028 / 0.022
p: 291 / 0 / 0.022 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
p: 303 / 0 / 0.022 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.003 / 0.002
6 / N / 13 / 29 / 22 / 30 / 31 / 18 / 7 / 31 / 8
p: 190 / 1 / 0.983 / 0.977 / 0.817 / 0.79 / 0.944 / 1 / 0.935 / 0.75 / 0.905 / 0.911
p: 192 / 0 / 0.017 / 0.023 / 0.183 / 0.21 / 0.056 / 0 / 0.065 / 0.25 / 0.095 / 0.089
65 / N / 13 / 29 / 22 / 30 / 31 / 18 / 7 / 31 / 8
p: 220 / 0.231 / 0.172 / 0.227 / 0.15 / 0.339 / 0.556 / 0.071 / 0.29 / 0.125 / 0.257 / 0.24
p: 222 / 0.769 / 0.828 / 0.773 / 0.85 / 0.5 / 0 / 0 / 0 / 0 / 0.487 / 0.413
p: 223 / 0 / 0 / 0 / 0 / 0.161 / 0.361 / 0.643 / 0.661 / 0.688 / 0.222 / 0.279
p: 226 / 0 / 0 / 0 / 0 / 0 / 0.083 / 0.214 / 0.048 / 0.125 / 0.029 / 0.052
p: 228 / 0 / 0 / 0 / 0 / 0 / 0 / 0.071 / 0 / 0.063 / 0.005 / 0.015
78 / N / 13 / 29 / 22 / 30 / 31 / 18 / 7 / 31 / 8
p: 155 / 0 / 0 / 0 / 0 / 0 / 0.083 / 0 / 0.081 / 0.125 / 0.026 / 0.032
p: 158 / 0 / 0 / 0.023 / 0.017 / 0 / 0 / 0 / 0 / 0 / 0.005 / 0.004
p: 163 / 0 / 0 / 0 / 0 / 0.016 / 0.028 / 0.143 / 0 / 0.125 / 0.016 / 0.035
p: 166 / 0 / 0.034 / 0 / 0 / 0.065 / 0 / 0 / 0 / 0 / 0.016 / 0.011
p: 171 / 0 / 0 / 0 / 0 / 0.177 / 0.889 / 0.571 / 0.919 / 0.75 / 0.317 / 0.367
p: 174 / 0.692 / 0.707 / 0.932 / 0.983 / 0.726 / 0 / 0 / 0 / 0 / 0.54 / 0.449
p: 175 / 0 / 0 / 0 / 0 / 0 / 0 / 0.214 / 0 / 0 / 0.008 / 0.024
p: 179 / 0 / 0 / 0 / 0 / 0 / 0 / 0.071 / 0 / 0 / 0.003 / 0.008
p: 182 / 0.077 / 0.241 / 0.045 / 0 / 0.016 / 0 / 0 / 0 / 0 / 0.05 / 0.042
p: 190 / 0.231 / 0.017 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.019 / 0.028
8 / N / 13 / 29 / 22 / 29 / 31 / 18 / 7 / 31 / 8
p: 243 / 0 / 0.034 / 0 / 0.017 / 0 / 0.028 / 0 / 0.032 / 0.125 / 0.021 / 0.026
p: 253 / 0.5 / 0.345 / 0.045 / 0.552 / 0.371 / 0.833 / 0.643 / 0.823 / 0.438 / 0.497 / 0.505
p: 255 / 0.154 / 0.586 / 0.955 / 0.345 / 0.629 / 0.139 / 0.357 / 0.145 / 0.438 / 0.439 / 0.416
p: 257 / 0.346 / 0.034 / 0 / 0.086 / 0 / 0 / 0 / 0 / 0 / 0.043 / 0.052
Cott582 / N / 13 / 29 / 22 / 30 / 31 / 17 / 7 / 31 / 7
p: 194 / 0 / 0.052 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.008 / 0.006
p: 200 / 0.385 / 0.724 / 0.227 / 0.783 / 0.403 / 0.588 / 0.5 / 0.468 / 0.429 / 0.524 / 0.501
p: 202 / 0.462 / 0.017 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.035 / 0.053
p: 204 / 0.154 / 0.207 / 0.773 / 0.183 / 0.581 / 0.353 / 0.5 / 0.435 / 0.429 / 0.398 / 0.402
p: 206 / 0 / 0 / 0 / 0.033 / 0 / 0 / 0 / 0 / 0 / 0.005 / 0.004
p: 208 / 0 / 0 / 0 / 0 / 0 / 0.059 / 0 / 0.097 / 0.143 / 0.027 / 0.033
p: 212 / 0 / 0 / 0 / 0 / 0.016 / 0 / 0 / 0 / 0 / 0.003 / 0.002
Locus / Allele / pop1 / pop4 / pop6 / pop10 / pop12 / pop14 / pop15 / pop16 / pop17 / All_W / All_UW
Cott207 / N / 13 / 29 / 22 / 30 / 31 / 16 / 7 / 30 / 6
p: 309 / 0.346 / 0.172 / 0.205 / 0.217 / 0.258 / 0.094 / 0.071 / 0 / 0.083 / 0.168 / 0.161
p: 311 / 0 / 0 / 0.023 / 0.183 / 0.145 / 0.594 / 0.429 / 0.767 / 0.083 / 0.253 / 0.247
p: 313 / 0.115 / 0.224 / 0 / 0 / 0.032 / 0.281 / 0.071 / 0.183 / 0.083 / 0.109 / 0.11
p: 315 / 0.462 / 0.259 / 0.182 / 0.15 / 0.371 / 0.031 / 0.214 / 0.05 / 0.417 / 0.215 / 0.237
p: 317 / 0.077 / 0.241 / 0.182 / 0.067 / 0.065 / 0 / 0.214 / 0 / 0.167 / 0.101 / 0.112
p: 319 / 0 / 0.103 / 0.386 / 0.383 / 0.065 / 0 / 0 / 0 / 0 / 0.136 / 0.104
p: 321 / 0 / 0 / 0.023 / 0 / 0.065 / 0 / 0 / 0 / 0.167 / 0.019 / 0.028
Lce219 / N / 13 / 29 / 22 / 30 / 31 / 17 / 7 / 31 / 7
p: 212 / 0 / 0 / 0 / 0 / 0 / 0.029 / 0 / 0 / 0 / 0.003 / 0.003
p: 221 / 0 / 0 / 0 / 0 / 0 / 0.176 / 0.143 / 0.194 / 0.143 / 0.059 / 0.073
p: 223 / 0 / 0.017 / 0.068 / 0.067 / 0 / 0 / 0 / 0 / 0 / 0.021 / 0.017
p: 229 / 0.615 / 0.672 / 0.841 / 0.883 / 0.935 / 0.794 / 0.714 / 0.806 / 0.786 / 0.805 / 0.783
p: 231 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.071 / 0.003 / 0.008
p: 232 / 0.385 / 0.207 / 0 / 0.033 / 0.016 / 0 / 0 / 0 / 0 / 0.067 / 0.071
p: 238 / 0 / 0 / 0.091 / 0 / 0.048 / 0 / 0 / 0 / 0 / 0.019 / 0.015
p: 246 / 0 / 0 / 0 / 0 / 0 / 0 / 0.143 / 0 / 0 / 0.005 / 0.016
p: 253 / 0 / 0.052 / 0 / 0.017 / 0 / 0 / 0 / 0 / 0 / 0.011 / 0.008
p: 256 / 0 / 0.052 / 0 / 0 / 0 / 0 / 0 / 0 / 0 / 0.008 / 0.006
Lce275 / N / 13 / 29 / 22 / 30 / 31 / 17 / 7 / 31 / 7
p: 307 / 1 / 0.983 / 1 / 0.983 / 1 / 1 / 1 / 1 / 1 / 0.995 / 0.996
p: 309 / 0 / 0.017 / 0 / 0.017 / 0 / 0 / 0 / 0 / 0 / 0.005 / 0.004

Supplementary Table 5. Inbreeding coefficient (FIS) by locus and prickly sculpin population. Second section is p-values for each FIScalculation, indicative ofrandomizations which gave larger FISvalues than observed. Third section is p-values for each FIScalculation, indicative ofrandomizations which gave smaller FISvalues than observed. P-values are over 1800 randomizations, indicative of an adjusted nominal level (5%) of 0.00056 and when significant are bolded.

1-Lower American / 4-Lower
Mokelumne / 6-Lower
Stanislaus / 10-Lower
Merced / 12-Lower
SanJoaquin / 14-180
Bridge / 15-Greenbelt / 16-Avocado / 17-Dam
316 / NA / -0.102 / -0.063 / -0.019 / 0.794 / -0.063 / NA / -0.018 / 1.000
318 / 0.400 / 0.534 / 0.414 / 0.241 / -0.063 / -0.166 / 0.463 / -0.071 / 0.231
6 / NA / 0.000 / 0.000 / 0.457 / -0.054 / -0.03 / NA / -0.053 / 1.000
65 / 0.172 / -0.191 / -0.273 / -0.16 / 0.116 / 0.324 / 0.265 / 0.670 / 0.051
78 / 0.368 / 0.078 / -0.033 / 0.000 / 0.568 / -0.071 / -0.111 / -0.071 / 1.000
8 / -0.361 / 0.115 / -0.024 / -0.073 / 0.255 / 0.056 / -0.500 / -0.162 / 0.432
Cott582 / 0.287 / -0.025 / -0.012 / 0.163 / -0.016 / 0.356 / 0.217 / 0.24 / 0.586
Lce 207 / 0.208 / 0.050 / 0.165 / 0.078 / -0.043 / 0.247 / 0.647 / 0.655 / -0.020
Lce 219 / 0.065 / 0.257 / -0.114 / 0.237 / -0.039 / -0.191 / 0.429 / -0.017 / 0.647
Lce275 / NA / 0.000 / NA / 0.000 / NA / NA / NA / NA / NA
All / 0.165 / 0.157 / 0.088 / 0.123 / 0.122 / 0.100 / 0.246 / 0.195 / 0.460
316 / NA / 1.0000 / 1.0000 / 1.0000 / 0.0006 / 1.0000 / NA / 1.0000 / 0.0928
318 / 0.0922 / 0.0006 / 0.0100 / 0.0094 / 0.8111 / 0.9161 / 0.0372 / 0.8128 / 0.2200
6 / NA / 1.0000 / 1.0000 / 0.0367 / 0.7994 / 1.0000 / NA / 1.0000 / 0.0194
65 / 0.5344 / 1.0000 / 1.0000 / 1.0000 / 0.2461 / 0.0706 / 0.2733 / 0.0006 / 0.5833
78 / 0.1183 / 0.3511 / 1.0000 / 1.0000 / 0.0006 / 1.0000 / 0.8472 / 1.0000 / 0.0078
8 / 0.9889 / 0.2800 / 1.0000 / 0.7706 / 0.1439 / 0.3844 / 1.0000 / 1.0000 / 0.1122
Cott582 / 0.1372 / 0.6556 / 0.7344 / 0.2344 / 0.6244 / 0.0744 / 0.5756 / 0.0700 / 0.0517
Lce 207 / 0.1922 / 0.365 / 0.1239 / 0.2633 / 0.7711 / 0.1506 / 0.0022 / 0.0006 / 0.7683
Lce 219 / 0.6344 / 0.0461 / 1.0000 / 0.1189 / 1.0000 / 1.0000 / 0.1678 / 0.7294 / 0.0800
Lce275 / NA / 1.0000 / NA / 1.0000 / NA / NA / NA / NA / NA
All / 0.0300 / 0.0006 / 0.0922 / 0.0050 / 0.0122 / 0.0661 / 0.0139 / 0.0006 / 0.0006
316 / NA / 0.5594 / 0.8378 / 0.9456 / 1.0000 / 0.9189 / NA / 0.9806 / 1.0000
318 / 0.9833 / 1.0000 / 0.9989 / 0.9983 / 0.4556 / 0.2272 / 0.9933 / 0.3400 / 0.9700
6 / NA / 1.0000 / 1.0000 / 0.9983 / 0.6289 / 0.9700 / NA / 0.9039 / 1.0000
65 / 0.925 / 0.4178 / 0.2583 / 0.4928 / 0.8572 / 0.9728 / 0.9389 / 1.0000 / 0.8167
78 / 0.9811 / 0.7861 / 0.9306 / 1.0000 / 1.0000 / 0.8294 / 0.5733 / 0.8467 / 1.0000
8 / 0.0689 / 0.8333 / 0.9767 / 0.3744 / 0.9722 / 0.7339 / 0.3256 / 0.3278 / 0.9783
Cott582 / 0.9417 / 0.5556 / 0.7306 / 0.9283 / 0.5694 / 0.9789 / 0.9172 / 0.9656 / 1.0000
Lce 207 / 0.9289 / 0.7894 / 0.9483 / 0.8561 / 0.4056 / 0.9467 / 1.0000 / 1.0000 / 0.7472
Lce 219 / 0.7994 / 0.9867 / 0.5806 / 0.9856 / 0.9067 / 0.4733 / 0.9906 / 0.7089 / 1.0000
Lce275 / NA / 1.0000 / NA / 1.0000 / NA / NA / NA / NA / NA
All / 0.9739 / 1.0000 / 0.9094 / 0.9956 / 0.9883 / 0.9350 / 0.9939 / 1.0000 / 1.0000

Supplementary Table 6. Adjusted population numbers (unique N = groups) when accounting for full siblings according to colony. All sibling “groups” had a probability > 0.600. An asterisk indicates locations which shared at least one “group” with another location in that river system.

Riffle / Prickly
Location / N / N(unique) / N / N(unique)
Lower American / 17 / 5 / 12 / 4
NMF American / 23 / 2* / - / -
SF American / 21 / 1* / - / -
Lower Mokelumne / - / - / 28 / 12
Upper Mokelumne / 24 / 1 / - / -
Lower Stanislaus / - / - / 22 / 16
Upper Stanislaus / 21 / 2 / - / -
Lower Tuolumne / 30 / 3 / - / -
Upper Tuolumne / 23 / 2 / - / -
Lower Merced / - / - / 29 / 10
Upper Merced / 30 / 1 / - / -
Lower San Joaquin / - / - / 30 / 12
Upper San Joaquin / 22 / 1 / - / -
180_Bridge / 24 / 5* / 7 / 6*
Greenbelt / 20 / 5* / 7 / 4*
Avocado / 45 / 8* / 18 / 7*
Dam / - / - / 31 / 10*
Upper Kings / 30 / 2 / - / -
Kaweah / 16 / 1 / - / -

Supplementary Figure 7 Graphical representation of natural log likelihood values versus potential K (number of clusters) produced in structure, as visualized in structure harvester. A = All locations, B = Only prickly sculpin locations, and C = Only riffle sculpin locations.