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).