Genetic differentiation
Piscivorous lake trout groups displayed little genetic differentiation, except for the Giant sub-set, which differed slightly from other groups that were defined by fatty acids. MICROCHECKER identified two loci (OtsG253b and Sco102) that contained null alleles. These loci, along with non-variable loci Sco218 and SSOSL456, were removed, leaving 19 informative loci for subsequent analyses. Descriptive statistics of genetic variation were similar among groups. The number of alleles per locus ranged from four (Smm21) to 41 (SnaMSU10) and averaged 28.75 across all loci. Averaged observed heterozygosity ranged from 0.78 (Giant) to 0.83 (Group 1) while expected heterozygosity was 0.84 for all groups except Group 1 (0.85; Table 2). Allelic richness ranged from 9.57 (Group 2 and 4) to 9.87 (Group 1), while expected private allelic richness ranged from 0.87 (Group 3) to 1.08 (Group 2; Table 2). Only five of 95 tests (all of which involved different loci) showed significant departures from Hardy-Weinberg equilibrium after adjustment for False Discovery Rate (adjusted α = 0.01). Of those five, all were heterozygote deficits and three involved the Giant sub-set. Only nine of 885 tests revealed significant linkage disequilibrium after adjusting for False Discovery Rate (adjusted α = 0.0068). No locus-pair linkage disequilibrium combinations were consistently significant, but seven of nine departures were in the Giant sub-set.
Using our microsatellite data set, the POWSIM analysis indicated a 100% power of detecting FST values as low of 0.01 and 0.005. However, power was reduced to 77% when assessing genetic differentiation at a FST of 0.001. Overall, our microsatellite data set (including the number of loci, alleles per locus, and sample sizes) had sufficient power to detect relatively low levels of genetic differentiation.
Global genetic differentiation was extremely low (θ = 0.001, 95% c.i. = −0.002−0.005) among the groups of piscivorous lake trout. Pairwise FST ranged from -0.004 to 0.016 (Table 3); comparisons that included Giants always differed the most from the other fatty acid groups, and they were involved in the only significant pairwise comparisons (P < 0.05, Table 3). The FSTvalues for the Giant vs. Groups 1 and 4 were generally similar to genetic differentiation among the four original lake trout ecotypes in Great Bear Lake, except for Ecotype 1 vs Ecotype 2 (Table 3). Bayesian clustering implemented in STRUCTURE provided evidence for two genetic clusters when evaluating both lnP(D) or ΔK (Table A2). The admixture plot based on K=2 showed no clear genetic structure between groups defined by fatty acid analysis; however, some differentiation of the Giant sub-set from the fatty acid groups was observed (Fig. 4).
Finally, the Bayesian information criterion in the DAPC analysis (BIC = 185.42, Table A3, Fig. A5 A) suggested that two clusters best explained genetic structure in our study (30 PCs retained as suggested by the cross-validation procedure; Fig. A5 B). A compoplot (barplot showing the probabilities of assignment of individuals to the different clusters) for K=2 revealed no clear genetic structure between two groups identified by the DAPC analysis except for the Giant group, which appeared to have more individuals assigned to cluster two (Fig. 4). Density plots of the discriminant function, however, suggested that the two clusters identified through the DAPC analysis are mostly non-overlapping (Fig. A5 C).