Electronic supplementary material

Population genetic structure of protected allis shad (Alosa alosa) and twaite shad (Alosa fallax)

Marc T. Jolly, Miran W. Aprahamian, Stephen J. Hawkins, Peter A. Henderson,

Rob Hillman, Niall Ó Maoiléidigh, Peter S. Maitland, Rayner Piper and Martin J. Genner

Table S1. Inbreeding periods (FIS) and tests of significant departures from Hardy-Weinberg Equilibrium proportions (HWE). Significant departures are highlighted in bold.

Species / Location code / N / Collection year(s) / Locus FIS / Multilocus FIS
AA14 / ASA9 / ASAC051 / ASAD021 / ASAD055
A. alosa / Aa-SOL / 13 / 1989-90 / 0.236 / 0.657* / 0.259 / 0.559* / 0.686*** / 0.469***
21 / 1991-92 / 0.369* / -0.013 / 0.517*** / 0.310* / 0.455* / 0.411***
13 / 1993-94 / 0.344 / - / 0.447* / 0.250 / 0.378* / 0.368*
12 / 2004-05 / 0.218 / 0.000 / 0.120 / 0.263 / 0.263 / 0.207
12 / 2006-08 / 0.224 / -0.048 / 0.259 / 0.165 / 0.015 / 0.148
Aa-TAM / 28 / 2000-05 / 0.091* / 0.003 / 0.042 / 0.503*** / 0.353** / 0.202***
31 / 2006-08 / 0.423*** / 0.184 / 0.109 / 0.169 / -0.022 / 0.184***
A. fallax fallax / Af-SOL / 23 / 1989-90 / 0.527*** / 0.036 / 0.280* / 0.509** / 0.379** / 0.319***
23 / 1991-92 / 0.663*** / 0.347*** / 0.512** / 0.224 / 0.272 / 0.392***
31 / 1993-94 / 0.411** / 0.168 / 0.584*** / 0.291 / 0.638*** / 0.422***
14 / 2004-05 / 0.631* / 0.193 / -0.258 / -0.130 / 0.079 / 0.109
25 / 2006-08 / 0.773*** / -0.046 / 0.025 / -0.263 / 0.376** / 0.192***
Af-BAR / 19 / 1986 / -0.044 / 0.164 / 0.294 / 0.220 / 0.489* / 0.271
Af-TYW / 13 / 1990-01 / 0.489* / 0.226* / 0.861*** / 1.000*** / 0.566** / 0.569***
Af-USK / 11 / 1987 / 0.200 / -0.084 / 0.206 / 0.000 / -0.085 / 0.039
23 / 1988 / 0.445** / 0.099 / 0.505*** / 0.784** / 0.314 / 0.382***
15 / 1989-90 / -0.077 / 0.243 / 0.274 / 0.000 / -0.037 / 0.152
13 / 2002 / -0.061 / -0.195 / 0.343 / 0.294 / 0.106 / 0.049
Af-WYE / 17 / 1979 / 0.506* / -0.195 / 0.106 / 0.243 / 0.309 / 0.155*
31 / 2002 / 0.257* / 0.072 / 0.173 / 0.177 / 0.268* / 0.182*
Af-SEV / 14 / 1979 / 0.469 / 0.008 / 0.679*** / - / 0.667** / 0.441***
20 / 2000 / 0.762*** / -0.066 / -0.179 / -0.056 / -0.154 / 0.065
22 / 2002 / -0.129 / 0.231 / 0.062 / -0.053 / 0.128 / 0.093
Af-LOO / 16 / 2000 / 0.669*** / 0.676*** / 0.325 / 0.777*** / 0.497* / 0.606***
Af-HAS / 12 / 2009 / 0.102 / 0.395* / -0.108 / 0.766** / 0.364 / 0.325*
Af-SIZ / 33 / 2009 / 0.294* / 0.250** / 0.374 / 0.225 / 0.241* / 0.269
A fallax killarnensis / Af-KIL / 24 / 1986 / -0.167 / 0.367* / - / 0.369* / -0.024 / 0.229*

*** P< 0.001; ** P< 0.01; * P< 0.001

Fig. S1. Distribution of Q-values (probability of membership to Alosa alosa) for genetic identification of hybrids, performed with STRUCTURE and five microsatellite loci. These results are from the prior population information model using gill raker count to train the genetic clustering. Presented here are results from 147 individuals sampled between 1993 and 2008 at the Solway Firth, which were the only samples for which gill raker count data were available, but all sampled individuals were included in the analysis. Individuals were originally classified as A. alosa (circles), A. f. fallax (triangles) and hybrids (squares) based on gill raker counts (less than 60 for A. f. fallax; over 90 for A. alosa). On the basis of these results we assigned all individuals with Q = 0 to 0.06 as microsatellite-identified A. f. fallax, Q = 0.96 to 1.00 as microsatellite-identified A. alosa, and Q = 0.11–0.89 as microsatellite-identified hybrids.

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