2.4. Population genetic diversity
We used the populations module in STACKS v.2.61 (Catchen
et al., 2013) to calculate diversity statistics per population,
including the observed heterozygosity (Ho), expected heterozygosity
(He), nucleotide diversity (Pi), inbreeding coefficient (Fis) and number
of private alleles (PAs). Allelic richness (Ar) was calculated with the
‘hierfstat’ package in R (Goudet et al., 2015) using four random
individuals per population, i.e. the minimum number of samples per
population (minimum number of alleles, min.all=8). Significant
associations between genetic diversity indexes (He, Pi, Ar, Fis) and
geographic variables (islet surface area, maximum altitude, and the
shoreline development index, SDI, i.e., a measure of island perimeter
complexity, all log-transformed) were assessed with simple and multiple
linear regression in R.