Microsatellite statistical analysis
Observed (Ho) and expected (He)
heterozygosity values for each locus were calculated using GENEPOP 4.0
(Rousset, 2008). Deviation from Hardy-Weinberg (HW) equilibrium was
tested using Fisher’s exact tests (Rousset 2008) with the same software.
FSTAT 2.9.3.2 (Goudet, 1995) was used to compute inbreeding coefficient
values (F IS) and allelic richness
(AR ). CERVUS 3.0.3 (Kalinowski, Taper and
Marshall, 2007) was used to evaluate polymorphic information content
(PIC), null allele probability and the mean number of alleles for each
locus. Fst values between pairs of groups were calculated using Fstat
2.9 software (Goudet, 1995).
The genetic structure of grey partridge was investigated using a
Bayesian clustering method. STRUCTURE 2.3 (Pritchard, Stephens and
Donnelly, 2000) was used to infer the number of genetic clusters
(K ). 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 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).