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.