at nSSR loci
The distribution of genetic diversity in M. fragrans (N =
393 individuals) was characterized at the population level
(N POP = 5) by estimating the following indices
using SPAGeDi v.1.5 : the number of alleles (N A),
observed and expected heterozygosity (H O andH E respectively), rarefied allelic richness
(AR ), and inbreeding coefficient (F IS).
We then calculated the F ST among populations and
among sub-populations within each population using the hierfstatR package (Goudet, 2005) in R (R Core Team, 2013). Moreover, we
characterized genetic structure using a Bayesian clustering approach as
implemented in STRUCTURE v.x.x software with the following parameters:
admixture model, sampling location as prior, independent allele
frequencies. The number of clusters was set from K = 1 to 10, with 10
iterations for each K. We ran the analysis with 20,000 burn-in periods
and 100,000 MCMC replicates. The value of K that best explained the data
was estimated using STRUCTURE HARVESTER . We then summarized STRUCTURE
results using CLUMPP and projected the barplot using CLUMPAK .
Genetic diversity and population structure of M. fragrans