Ecological Archives A020-032-A1

Dylan J. Fraser, Aimee Lee S. Houde, Paul V. Debes, Patrick O'Reilly, James D. Eddington, and Jeffrey A. Hutchings. 2010. Consequences of farmed–wild hybridization across divergent wild populations and multiple traits in salmon. Ecological Applications 20:935–953.

Appendix A. Neutral genetic divergence between parental populations.

Population genetic relationships were characterized between TUSK, STEW and the ancestral wild population of FARM (Saint John River) (Fig. 2, main article). Samples consisted of non-lethal fin tissue samples collected from juveniles and preserved in ethanol for DNA analysis. Samples were obtained from multiple sites within each river in 1999 or 2000 (sample size = 60 individuals per population). DNA was extracted as described in Carr et al. (2004). Each individual was then genotyped at seven polymorphic and presumably selectively neutral microsatellite loci: Ssa197 and Ssa202 (O’Reilly et al. 1996); SSsp1605, SSsp2210, SSsp2215, SSsp2216, and SSsp1G7 (Paterson et al. 2004). PCR amplification and electrophoresis conditions were as described in Carr et al. (2004). Resulting amplified fragments were size fractionated and detected using an MJ Basestation Fragment analyzer (MJ Bioworks).

We verified Hardy-Weinberg equilibrium (HWE) expectations of genotypic frequencies across loci in each sample and at each locus, as well as genotypic linkage equilibrium between all loci pairs, using GENEPOP 3.3 (Raymond and Rousset 1995; Rousset 2008). Corrections for multiple tests were made using the sequential Bonferroni approach of Rice (1989). Alpha levels (P = 0.05) for table-wide comparisons were adjusted based on K = 21 and K = 7 tests for analyses of linkage disequilibrium (LD) and HWE, respectively. Following such corrections, HWE was only rejected for one locus in one population (TUSK SSsp1G7, p = 0.002); nevertheless, three loci-pairs in each population still exhibited significant LD. The nine tests exhibiting significant levels of LD involved many different loci, but SSsp1605 was implicated in four of them. Note, however, that whether or not this locus was removed from analyses of genetic distance and genetic differentiation below, the estimates between populations remained very similar (data not shown). Consequently, reported estimates of genetic distance and genetic differentiation between our parental populations included SSsp1605.

Estimates of Nei’s 1972 and Nei's 1978 genetic distances (DS and D, respectively) between parental populations, as well as Weir and Cockerham’s FST (θ), were calculated using the program Genetix 4.05.2 (Belkhir et al. 2000). Tests of significance of pair-wise distance estimates from zero (homogeneity) were made using the permutation procedure implemented in Genetix, where observed values were compared to the distribution of 2000 pair-wise values obtained by randomly re-sampling genotypes across pairs of simulated sample collections. Pair-wise estimates between parental populations are reported in Table 1 of the main article.


Belkhir, K., P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme. 2000. GENETIX 4.02, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UPR 9060, Université de Montpellier II, Montpellier, France.

Carr, J. W., F. Whoriskey, and P. O’Reilly. 2004. Efficacy of releasing captive reared broodstock into an imperilled wild Atlantic salmon population as a recovery strategy. Journal of Fish Biology 65(A):38–54.

Nei, M. 1972. Genetic distance between populations. American Naturalist 106:283–292.

Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590.

O’Reilly, P., L. Hamilton, S. K. McConnell, and J. M. Wright. 1996. Rapid analysis of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of tetranucleotide and dinucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences 53:2292–2298.

Paterson, S., S. B. Piertney, D. Knox, J. Gilbey, and E. Verspoor. 2004. Characterisation and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar) microsatellites. Molecular Ecology Notes 4:160–162.

Raymond, M., and F. Rousset. 1995. Genepop Version.1.2: Population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248–249.

Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223–225.

Rousset, F. 2008. GENEPOP ‘007: a complete reimplementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103–106.

Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370.

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