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Given that substitution rates were calculated from the phylogeny of ortholog families rather than from averages of pairwise comparisons, it is therefore unlikely that the switching of genes between strands could produce the observed variation in substitution rates.
For lakes containing more than one haplotype, averages of pairwise genetic distances were calculated with equal weighting given to haplotypes as sampling bias is likely to have been high due to sites being represented by only a few individuals.
Moving averages of pairwise F ST values between each hatchery line and the P1 founders at mapped markers were calculated using a kernel smoothing sliding window approach (Hohenlohe et al. 2010; Brieuc et al. 2015).
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(a) Average of pairwise geodesic distances.
The M value represents the arithmetic average of pairwise variation.
Then reference expression stability measure (M value) is calculated with the average of pairwise variations.
In other cases, an average of pairwise interactions between the two considered core positions from all other members of the screened fold family is used in this step.
π, nucleotide diversity (average of pairwise differences).
For each clique, average dN/dS ratio was computed as the average of pairwise omega parameters.
Average of pairwise amino acid difference was calculated using MEGA version 4 [ 48].
Phenotypic distance: average of pairwise phenotype hamming distances between all individuals in the population normalized over the number of phenotype genes.
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