2.6.3 Population genetic analyses
Allelic richness (Ar ), observed (Ho ) and expected heterozygosity (He ), and inbreeding coefficient (Fis ) were calculated with the R package ‘diveRsity’ v.9.90 (Keenan, Mcginnity, Cross, Crozier, & Prodöhl, 2013)⁠ from microsatellite data of 613 individuals from 22 populations (see section 2.3)⁠. Each locus and population was tested for Hardy-Weinberg equilibrium using the R package ‘genepop’ v.1.1.7 (Rousset, 2008).⁠ To assess if Fis is positively correlated with homostyle frequency we used a standard linear model with homostyle frequency as independent variable. Given that population size can influence Fis, we included census size as covariable with no interaction among independent variables.
Population specific and pairwise genetic differentiation measured asFst(Weir & Cockerham, 1984)⁠⁠ and its normalized counterpart G’st(Meirmans & Hedrick, 2011)⁠ were estimated with the R package ‘diveRsity’ v.9.90 (Keenan et al., 2013). To discover whether increasing homostyle frequencies correspond to increased genetic differentiation, we tested whether pairwise differences in homostyle frequencies between populations are positively correlated with pairwise G’st values. To test the significance of association between these two matrices, we used a Mantel test as implemented in the R package ‘adegenet’ v2.1.3 (Jombart, 2008)⁠.