Table S1: Geographic Distribution of the Samples Analysed in This Study and Summary Of

Table S1: Geographic distribution of the samples analysed in this study and summary of genetic diversity measures. AR: allelic richness; Ho: observed heterozygosity; Heu: unbiased expected heterozygosity; hD: haplotype diversity; hR: haplotype richness. All sampling locations correspond to the 30 pre-defined populations used in the BAPS analysis

Country / Region within country / Sample size / Microsatellite diversity / Mitochondrial diversity
Microsatellites / Mitochondrial DNA / AR / Ho / Heu / hD / hR
Austria / - / 30 / 21 / 3.88 / 0.58 / 0.66 / 0.61 / 2.29
Belgium / - / 37 / 20 / 3.81 / 0.57 / 0.62 / 0.70 / 1.91
Bulgaria / - / 17 / 1 / 4.61 / 0.59 / 0.65 / - / -
Croatia / - / 23 / 16 / 4.85 / 0.67 / 0.69 / 0.81 / 3.11
Denmark / - / 29 / 21 / 3.07 / 0.47 / 0.47 / 0.26 / 0.73
Estonia / - / 9 / 10 / - / - / - / 0.84 / 3.73
Finland / - / 5 / 3 / - / - / - / - / -
France / Alsace / 15 / 1 / 4.45 / 0.55 / 0.64 / - / -
France / Brittany / 21 / 18 / 3.63 / 0.54 / 0.55 / 0.82 / 3.20
France / Southern France / 5 / 3 / - / - / - / - / -
Germany / - / 27 / 17 / 4.23 / 0.61 / 0.64 / 0.574 / 2.01
Great Britain / Essex / 25 / 0 / 3.55 / 0.55 / 0.55 / - / -
Great Britain / Scotland / 36 / 19 / 3.06 / 0.47 / 0.52 / 0.46 / 1.56
Great Britain / Wales / 30 / 9 / 3.18 / 0.52 / 0.51 / 0 / 0
Hungary / - / 8 / 0 / - / - / - / - / -
Ireland / - / 15 / 0 / 2.81 / 0.38 / 0.42 / - / -
North. Ireland / 25 / 16 / 2.97 / 0.42 / 0.52 / 0.44 / 1.58
Italy / Northern Italy / 31 / 21 / 4.23 / 0.54 / 0.64 / 0.70 / 2.53
Italy / Central Italy / 5 / 1 / - / - / - / - / -
Luxembourg / - / 30 / 18 / 4.27 / 0.57 / 0.63 / 0.84 / 3.40
Norway / - / 20 / 9 / 2.73 / 0.46 / 0.48 / 0.22 / 0.78
Poland / Eastern Poland / 29 / 20 / 4.32 / 0.62 / 0.66 / 0.73 / 2.42
Poland / Western Poland / 19 / 12 / 4.58 / 0.68 / 0.69 / 0.71 / 1.94
Portugal / - / 10 / 10 / 3.52 / 0.54 / 0.53 / 0.87 / 3.78
Serbia / - / 25 / 11 / 5.01 / 0.68 / 0.69 / 0.71 / 2.27
Spain / Barcelona / 30 / 16 / 3.45 / 0.51 / 0.55 / 0.78 / 2.80
Spain / Basque Country / 34 / 7 / 3.62 / 0.54 / 0.55 / 0.81 / 3.00
Sweden / - / 31 / 22 / 2.96 / 0.46 / 0.52 / 0.65 / 1.82
Switzerland / Jura / 36 / 14 / 4.16 / 0.69 / 0.62 / 0.82 / 3.30
Switzerland / Zurich / 18 / 0 / 4.15 / 0.58 / 0.60 / - / -

Table S2: Parameters of the Markov chain Monte Carlo (MCMC) runs of program msvar 1.3 (Storz & Beaumont 2002). For each data set, 12 independent runs were performed initially using parameters Run 1 – 12. In case of non-convergence of independent chains, two additional longer runs (Run 13 & 14) were performed. For further information, see Materials and Methods section.

Starting values (mean, variance) for / Hyperpriors (α, σ, β, τ) for / Run lengths
log(N0) / log(N1) / log(μ) / log(T) / log(N0) / log(N1) / log(μ) / Log(T) / steps / thinning
Run 1 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 3.4, 2, 0, 0.5 / 5, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 2, 3, 0, 0.5 / 105 / 104
Run 2 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 3.4, 2, 0, 0.5 / 4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 3, 3, 0, 0.5 / 105 / 104
Run 3 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 4, 3, 0, 0.5 / 105 / 104
Run 4 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 2, 3, 0, 0.5 / 105 / 104
Run 5 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 5, 2, 0, 0.5 / 5, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 2, 3, 0, 0.5 / 105 / 104
Run 6 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 4, 2, 0, 0.5 / 4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 5, 2, 0, 0.5 / 105 / 104
Run 7 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 5, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 5, 2, 0, 0.5 / 105 / 104
Run 8 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 5, 3, 0, 0.5 / 105 / 104
Run 9 / 4, 1 / 4, 1 / -3.5, 1 / 3, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 2, 2, 0, 0.5 / 105 / 104
Run 10 / 6, 1 / 6, 1 / -3.5, 1 / 5, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 5, 3, 0, 0.5 / 105 / 104
Run 11 / 6, 1 / 6, 1 / -3.5, 1 / 5, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 5, 3, 0, 0.5 / 105 / 104
Run 12 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 2, 2, 0, 0.5 / 2, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 3.5, 3, 0, 0.5 / 106 / 104
Run 13 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 3.4, 2, 0, 0.5 / 3.4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 2, 3, 0, 0.5 / 106 / 104
Run 14 / 4, 1 / 4, 1 / -3.5, 1 / 2, 1 / 4, 2, 0, 0.5 / 4, 3, 0, 0.5 / -3.5, 0.25, 0, 0.5 / 5, 2, 0, 0.5 / 106 / 104

Table S3: Significance values of GENEPOP exact test for Hardy-Weinberg deviations. Values in bold are significant before correction for multiple tests, the values marked with an asterisk are significant after this correction.

Population / Microsatellite locus
Mel101 / Mel102 / Mel103 / Mel104 / Mel106 / Mel107 / Mel108 / Mel110 / Mel112 / Mel113 / Mel114 / Mel115 / Mel117 / Mel1 / Mel10 / mel12 / Mel14 / Mel15
Austria / 0.101 / 0.696 / 0.241 / 0.377 / 0.267 / 0.543 / 0.046 / 0.754 / 0.231 / 0.346 / 0.410 / 0.242 / 0.147 / 0.082 / - / 0.781 / 0.411 / 0.160
Barcelona / 0.130 / 0.011 / 1.000 / 0.974 / 0.405 / 0.247 / 0.134 / 0.617 / 0.081 / 0.434 / 1.000 / 0.091 / 0.952 / 0.152 / - / 0.241 / 0.145 / 1.000
Basque / 0.705 / 0.968 / 0.112 / 0.215 / 0.444 / 0.493 / 1.000 / 0.929 / 0.748 / 0.627 / 1.000 / 0.947 / 0.199 / 0.074 / - / 0.535 / 0.553 / 0.625
Belgium / 0.185 / 0.196 / 0.556 / 0.146 / 0.065 / 0.005 / 0.598 / 0.186 / 0.738 / 0.040 / 0.057 / 0.110 / 0.285 / 0.196 / 0.530 / 0.396 / 0.013 / 0.240
Brittany / 1.000 / 0.723 / 0.280 / 0.655 / 0.575 / 1.000 / 1.000 / 0.420 / 0.445 / 0.517 / 0.581 / 0.592 / 1.000 / 0.383 / 1.000 / 0.343 / 0.762 / 0.187
Bulgaria / 1.000 / 0.742 / 0.178 / 0.300 / 0.529 / 0.099 / 0.120 / 0.653 / 0.682 / 0.732 / 0.855 / 0.385 / 0.007 / 0.161 / 0.278 / 0.244 / 0.286 / 0.041
Croatia / 0.426 / 0.074 / 0.379 / 0.808 / 0.288 / 0.815 / 0.505 / 0.615 / 0.730 / 0.950 / 0.483 / 0.067 / 0.347 / 0.531 / 1.000 / 0.218 / 0.179 / 0.640
Denmark / - / 0.433 / 0.778 / 0.108 / 0.042 / 0.154 / 0.532 / 0.507 / 0.080 / 1.000 / 0.799 / 0.731 / 1.000 / 0.973 / 1.000 / 1.000 / 1.000 / 0.180
East. Poland / 1.000 / 0.032 / 0.144 / 0.039 / 0.058 / 1.000 / <0.001* / 0.534 / 0.298 / 0.224 / 0.105 / 0.156 / 0.238 / 0.246 / 1.000 / 0.010 / 0.118 / 0.958
Essex / 0.429 / 0.214 / 0.692 / 0.190 / 1.000 / 0.893 / 1.000 / 0.129 / 0.647 / 0.499 / 1.000 / 0.015 / 0.663 / 0.055 / 0.331 / 0.777 / 0.180 / 0.798
Germany / - / 0.213 / 0.640 / 0.914 / 0.244 / 0.832 / 0.106 / 0.857 / 0.157 / 0.567 / 0.087 / 0.900 / 0.660 / 0.208 / 0.264 / 0.499 / 0.848 / 0.523
Luxembourg / 0.129 / 0.016 / 0.363 / 0.340 / 0.064 / 0.138 / 0.734 / 0.889 / 0.102 / 0.981 / 0.631 / 0.043 / 0.362 / 0.526 / 0.017 / 0.884 / 0.914 / 0.106
North. Ireland / 0.157 / 0.044 / 0.023 / 0.007 / 0.439 / 1.000 / 1.000 / 0.279 / 0.404 / 0.073 / 0.901 / 0.019 / 0.200 / 0.113 / 0.584 / 0.020 / 0.005 / 0.894
Northern Italy / 1.000 / 0.521 / 0.298 / 0.014 / 0.002* / 0.149 / 0.015 / 0.104 / 0.102 / 0.304 / 0.646 / 0.008 / 0.098 / 0.009 / 1.000 / 0.293 / 0.339 / 0.964
Norway / 0.156 / 0.773 / 0.893 / 1.000 / 1.000 / 0.370 / 0.069 / 0.847 / - / 0.612 / 0.446 / 0.309 / 1.000 / 0.543 / - / 0.620 / 1.000 / 0.433
Portugal / 1.000 / 0.140 / 0.131 / 0.132 / 0.601 / 0.593 / 0.204 / 1.000 / 1.000 / 0.418 / 0.724 / 0.218 / 1.000 / 0.585 / - / 1.000 / 1.000 / 1.000
Scotland / 0.016 / 0.836 / 0.914 / 0.079 / 0.308 / 1.000 / - / 0.406 / 0.423 / 0.232 / 0.197 / 0.792 / 0.038 / 0.013 / 0.499 / 0.060 / 0.744 / 0.564
Serbia / 0.541 / 0.540 / 0.319 / 0.950 / 0.496 / 0.581 / 1.000 / 0.436 / 0.495 / 0.007 / 0.926 / 0.419 / 0.945 / 0.962 / 0.215 / 0.805 / 0.404 / 0.407
South. Ireland / 0.001* / 1.000 / 0.205 / 0.120 / 0.397 / - / - / 1.000 / 0.591 / 0.540 / 0.349 / 0.219 / 0.210 / 1.000 / - / 1.000 / 1.000 / 0.807
Sweden / 0.552 / 0.174 / 0.018 / 0.801 / 0.341 / 0.068 / 1.000 / 0.031 / - / 0.498 / 0.749 / 0.003* / 0.259 / 0.117 / - / 0.012 / 1.000 / 0.245
Swiss Jura / 1.000 / 0.533 / 0.251 / 0.086 / 0.638 / 0.973 / 0.686 / 0.053 / 0.821 / 0.175 / 0.096 / 0.424 / 0.253 / 0.848 / 0.541 / 0.428 / 0.520 / 0.542
Wales / 0.055 / 0.240 / 0.050 / 0.449 / 0.411 / 0.615 / 1.000 / 0.248 / 0.021 / 1.000 / 0.616 / 0.841 / 0.387 / 1.000 / 1.000 / 0.210 / 0.005 / 0.244
West. France / 1.000 / 0.181 / 0.156 / 0.195 / 0.544 / 0.106 / 1.000 / 0.164 / 0.109 / 0.167 / 1.000 / 0.086 / 0.594 / 0.420 / 0.045 / 0.124 / 0.002* / 0.960
West. Poland / 1.000 / 0.723 / 0.599 / 0.342 / 0.856 / 0.698 / 0.051 / 0.009 / 0.979 / 0.482 / 0.634 / 0.822 / 0.122 / 0.443 / 1.000 / 0.651 / 0.345 / 0.544
Zurich / 1.000 / 0.708 / 0.037 / 0.832 / 1.000 / 0.466 / 0.728 / 0.494 / 0.866 / 0.072 / 0.067 / 0.234 / 0.124 / 0.490 / 0.386 / 0.007 / 0.958 / 0.471

Table S4. Mean, median and mode values and four quantiles of the posterior distribution of model parameters under scenario 4 in DIYABC.

Parameter / mean / median / mode / q025 / q050 / q950 / q975
Scandinavian / 2,47E+003 / 2,18E+003 / 1,98E+003 / 6,67E+002 / 8,32E+002 / 5,25E+003 / 6,71E+003
Balkans / 1,65E+004 / 1,68E+004 / 1,69E+004 / 1,21E+004 / 1,31E+004 / 1,91E+004 / 1,95E+004
Iberian / 8,93E+003 / 9,07E+003 / 9,16E+003 / 7,17E+003 / 7,61E+003 / 9,79E+003 / 9,89E+003
t1 / 2,34E+003 / 1,76E+003 / 1,29E+003 / 4,01E+002 / 5,25E+002 / 6,39E+003 / 8,42E+003
t2 / 2,08E+004 / 2,02E+004 / 1,91E+004 / 1,90E+004 / 1,91E+004 / 2,45E+004 / 2,52E+004

Table S5: Linear models testing for the effect of on genetic diversity of European badgers. The calculations were performed on the ‘complete’ data set consisting of 25 pre-defined populations and a ‘partial’ data set consisting of one population per inferred genetic cluster.

Marker type / Diversity
measure / Explanatory variable / Data set / Slope / Intercept / R2 / P-value
Microsatellites / AR / Longitude / Complete / 0.045 / 3.490 / 0.423 / <0.001
AR / Longitude / Partial / 0.042 / 3.448 / 0.379 / 0.019
AR / Latitude / Complete / -0.064 / 6.987 / 0.285 / 0.006
AR / Latitude / Partial / -0.091 / 8.328 / 0.497 / 0.005
HeU / Longitude / Complete / 0.005 / 0.543 / 0.469 / <0.001
HeU / Longitude / Partial / 0.004 / 0.549 / 0.368 / 0.021
HeU / Latitude / Complete / -0.005 / 0.852 / 0.167 / 0.043
HeU / Latitude / Partial / -0.008 / 1.003 / 0.382 / 0.019
Mitochondrial DNA / hD / Longitude / Complete / 0.005 / 0.599 / 0.038 / 0.309
hD / Longitude / Partial / 0.014 / 0.498 / 0.238 / 0.091
hD / Latitude / Complete / -0.022 / 1.718 / 0.308 / 0.009
hD / Latitude / Partial / -0.025 / 1.877 / 0.265 / 0.072
hR / Longitude / Complete / 0.010 / 2.216 / 0.009 / 0.678
hR / Longitude / Partial / 0.046 / 1.768 / 0.169 / 0.163
hR / Latitude / Complete / -0.093 / 6.956 / 0.310 / 0.009
hR / Latitude / Partial / -0.120 / 8.179 / 0.372 / 0.027

AR = allelic richness, HeU = unbiased expected heterozygosity, hD = haplotype diversity, hR = haplotype richness

Table S6: Estimates of the multivariate Gelman Rubin’s diagnostic testing convergence of multiple independent MCMC chains in the MSVAR analysis of European badger populations. Only populations with a sample size of N³20 were included in the analysis. Point estimates of <1.1 indicating good convergence, with a value of <1.2 indicating approximate convergence. The estimates are based on 12 chains that were run using different random seeds, starting values, priors and run lengths, except those indicated by an asterisk. These latter estimates were based on three longer chains of 1010 steps (see Materials and Methods).

Population / Gelman & Rubin diagnostic
N0 / N1 / ta
Austria* / 1.16 / 1.04 / 1.16
Barcelona / 1.11 / 1.05 / 1.09
Basque* / 1.03 / 1.02 / 1.03
Belgium* / 1.04 / 1.01 / 1.05
Brittany / 1.13 / 1.02 / 1.14
Croatia / 1.08 / 1.02 / 1.10
Denmark / 1.18 / 1.01 / 1.15
East. Poland / 1.13 / 1.01 / 1.12
Essex / 1.12 / 1.01 / 1.10
Germany / 1.08 / 1.01 / 1.08
Luxembourg / 1.03 / 1.01 / 1.04
North. Ireland / 1.05 / 1.01 / 1.05
North Italy / 1.09 / 1.01 / 1.08
Norway / 1.05 / 1.01 / 1.05
Scotland* / 1.18 / 1.01 / 1.19
Serbia* / 1.35 / 1.02 / 1.34
Sweden / 1.13 / 1.01 / 1.12
Swiss Jura / 1.11 / 1.01 / 1.08
Wales / 1.05 / 1.01 / 1.06

Table S7: Estimates of the Gelman & Rubin’s diagnostic (GRD) for convergence of multiple MCMC chains in the MSVAR analysis of simulated bottlenecked populations. The data sets differed with regard to the sample size, time since the decline (ta) and current effective population size (N0). MSVAR was run using 12 independent chains, except for the data sets in bold, for which three longer chains were of 1010 steps were run (see Materials and Methods). The two data sets highlighted by an asterisk replace two data sets that did not converge.

Sample size: 20 / Sample size: 50
Simulated / GRD for chains estimating / Simulated / GRD for chains estimating
ta / N0 / log(N0) / log(N1) / log(ta) / ta / N0 / log(N0) / log(N1) / log(ta)
25 / 50 / 1.05 / 1.01 / 1.04 / 25 / 50 / 1.10 / 1.01 / 1.15
25 / 50 / 1.12 / 1.01 / 1.11 / 25 / 50 / 1.20 / 1.01 / 1.12
25 / 50 / 1.11 / 1.00 / 1.10 / 25 / 50 / 1.13 / 1.02 / 1.20
25 / 50 / 1.16 / 1.00 / 1.14 / 25 / 50 / 1.17 / 1.01 / 1.16
25 / 50 / 1.12 / 1.01 / 1.11 / 25 / 50 / 1.14 / 1.01 / 1.14
25 / 150 / 1.19 / 1.05 / 1.15 / 25 / 150 / 1.17 / 1.02 / 1.17
25 / 150 / 1.10 / 1.02 / 1.08 / 25* / 150 / 1.10 / 1.04 / 1.20
25* / 150 / 1.08 / 1.02 / 1.07 / 25 / 150 / 1.11 / 1.05 / 1.10
25 / 150 / 1.10 / 1.01 / 1.07 / 25 / 150 / 1.14 / 1.02 / 1.15
25 / 150 / 1.19 / 1.03 / 1.12 / 25 / 150 / 1.08 / 1.04 / 1.07
25 / 1000 / 1.06 / 1.02 / 1.34 / 25 / 1000 / 1.11 / 1.02 / 1.23
25 / 1000 / 1.04 / 1.02 / 1.13 / 25 / 1000 / 1.09 / 1.02 / 1.22
25 / 1000 / 1.05 / 1.02 / 1.24 / 25 / 1000 / 1.08 / 1.03 / 1.32
25 / 1000 / 1.13 / 1.03 / 1.21 / 25 / 1000 / 1.12 / 1.02 / 1.24
25 / 1000 / 1.07 / 1.02 / 1.34 / 25 / 1000 / 1.08 / 1.02 / 1.28