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A global test of differentiation among samples based on haplotype frequencies was performed using the Arlequin program.
Pairwise test of differentiation (θ, upper), and P-values from exact test in TFPGA (lower) between spawning char in PAL (P1 - 3), TUN (T1 - 2) and a mixed summer sample in PAL (X).
The SNPs having minor allele frequencies of over 5%, Exon2+751 (rs5751876) and IVS2+28 (rs34923252), were used for a global test of differentiation among samples based on haplotype frequencies using the Alrequin program.
Possible genetic segregation among lakes and sites and their significance were tested with the FST analogue θ [ 148] and pairwise test of differentiation in FSTAT, and by exact test (Raymond and Rousset 1995) in TFPGA, all with 15.000 permutations.
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In pair-wise tests of differentiation, most population pairs were significantly differentiated (only 13 out of 595 pair-wise comparisons were not significantly differentiated).
Furthermore, European populations were genetically differentiated (FST = 0.065 and most exact tests of differentiation were significant).
No significant divergence was evident between mainland-beach sites 20-Finger Beach and 24-Knutson Beach (all tests of differentiation: p > 0.1; see additional file 1), and both appeared significantly differentiated from tributaries for 'Outlier 2' with exception of 16-Chinkelyes Creek, but less for the other two sets.
Hardy-Weinberg proportions occurred in all groups (p>0.05), there was no evidence of linkage disequilibrium, and all pairwise tests of differentiation were significant (p<0.05) after Bonferroni correction.
Results are congruent to those from exact tests of differentiation (Additional file 6).
Pairwise FST and tests of differentiation were conducted in F stat.
The incorporation of divergences between haplotypes in tests of differentiation with amova and estimates of ΦST adds additional power to tests of geographic structure.
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