ddRAD statistical analysis
A genotype file was created containing the SNPs genotypes, called from
the ddRAD data, for 87 individuals and 8,236 SNPs. All the SNPs were
checked and were biallelic, and we proceeded with the filtering of the
dataset. The PLINK toolbox (Purcell et al. , 2007) was used to
remove loci that were not genotyped in ≥80% of the individuals.
Additionally, a dataset containing three full-sib families (parents and
two offsprings) was used to check the mendelian inheritance of the
alleles.
The genetic diversity indices as well as a Principal Component Analysis
(PCA), based on Nei’s genetic distance (Nei, Tajima and Tateno, 1983)
were calculated using GENEALEX 6.502 software (Peakall and Smouse,
2006). Population pairwise FST was calculated using Arlequin 3.5
(Excoffier and Lischer, 2010). The genetic structure of grey partridge
was investigated using STRUCTURE 2.3 (Pritchard, Stephens and Donnelly,
2000). The log likelihoods of our data set [ln Pr(X|K)] were
estimated for different numbers of genetic clusters using an admixture
ancestry model based on 100,000 burn-in steps followed by 1,000,000
Markov chain Monte Carlo (MCMC) replicates. We utilized a method
developed by (Evanno, Regnaut and Goudet, 2005) to determine the number
of populations present, based on the second-order rate of change in the
log probability of the data (ΔK) among 20 runs of each assumed K using
the web-based utility “Harvest”
(http://taylor0.biology.ucla.edu/struct_harvest). We then evaluated the
membership coefficient value (q) for each individual.
Analysis for the identification of an informative SNP marker panel for
allowing population assignment and identification of non-native stocks
for captive rearing was performed based on the ”Informativeness of
assignment” method, as implemented in TRES software (Kavakiotis et
al. , 2015). Furthermore, assignment tests were performed according to
Rannala and Mountain method (Rannala and Mountain, 1997) in GENECLASS2
software (Piry et al. , 2004).