Genetic diversity of DNA microsatellites and the mtCOI gene
To test for null alleles, large allele dropout, and scoring errors, we
used Microchecker version 2.2.3 (VanOosterhout, Hutchinson, Wills, &
Shipley, 2004). Putative null alleles were detected in five loci (MAT2,
MAT4, MAT10, MAT15, and MAT28) of five populations (DAG, GUA, DOV, QBY,
and YOB; Table 2), which may have biased the estimates of population
structure (Chapuis & Estoup, 2007). We accounted for this bias by
comparing analyses after excluding these loci with those of the entire
data set. Our main results and conclusions remained unchanged, however,
regardless of the loci included in the analyses, and therefore only the
results for the entire data set are presented here. Since A.
cephalotes nests form family units and nestmates are closely related,
only one individual per nest was used to evaluate the Hardy-Weinberg
equilibrium (HWE) and linkage disequilibrium (LD). Tests were performed
for each locus (HWE) and each locus pair (LD) for each population
(Supplementary Table ST2) using GENEPOP (Rousset, 2008). A Bonferroni
correction was applied with a global significance of α=0.05 for multiple
comparisons.
Genetic diversity was characterized for each locus, region, and
population as allele count (Na), allelic richness
(AR), expected (He) and observed
(Ho) heterozygosities, and the inbreeding coefficient
(F IS), using the software GenAlex v. 6.5 (Peakall
and Smouse 2012) and FSTAT v. 2.9.3.2 (Goudet, 1995; 2001) (Table 2,
Supplementary tables ST2, ST3). Tests for significant differences from
zero in the diversity parameters were performed using the ‘aov’function in R (Chambers, Freeny, & Heiberger, 1992). We used the
software Bottleneck (Piry et al. 1999) to estimate recent changes in
population sizes by implementing the IAM and SSM mutation models and a
Wilcoxon signed-rank test to evaluate statistical significances. We also
determined whether the allele frequency distribution differed from the
expected L-shape. Where necessary, significant values were adjusted for
multiple comparisons through Bonferroni correction.
The genetic diversity of mtCOI data was estimated through the
number of haplotypes (h), nucleotide diversity (π), and haplotype
diversity (hd), using DnaSP 5.19 (Librado & Rozas,
2009). Tajima’s D and Fu’s FS neutrality tests were performed to
investigate signatures of recent population expansion (Ramos-Onsins &
Rozas, 2002) when the null hypothesis of neutrality was rejected due to
significant negative values (P < 0.05 for D, P< 0.02 for FS; Supplementary table ST3).