Population Genetic Statistics
After loci filtering using the population program, 18,182 loci were kept, composed of 1,696,358 sites with 16,796 variant sites (SNPs). The final matrix used in all downstream analyses was then composed of 135 individuals of A. mantiqueira and 6 individuals of A. alalia . Most sequenced SNPs (10,884, 64.8%) were in Hardy-Weinberg equilibrium (p < 0.05), while three of the populations have more than 1,000 SNPs out of HWE. The population with the highest mean nucleotide diversity and inbreeding coefficient (FIS) is Delfim Moreira (‘mDM’).
The Slatkin pairwise FST values ranged from 0 to 0.45 (‘aBJ’, A. alalia x ‘mMV’, A. mantiqueira ) (Table 2). The mean FST within populations of A. mantiqueira was 0.0122 ± 0.0136. Interspecific FST varied from 0.30 (‘aFL’ x ‘mBoc’) to 0.45 (‘aBJ’ x ‘mMV’), with a much higher average (0.3685 ± 0.035) than the FST between A. mantiqueira populations.
Table 2. Slatkin pairwise FST values calculated from the SNPs for A. alalia (a localities) and A. mantiqueira (m localities). The codes correspond to the GBS-sampling locations in Table 1. Bold numbers are significant values under α = 0.05.