Data from: Population genomics and morphometric assignment of western honey bees (Apis mellifera L.) in the Republic of South Africa

Backgrounds: Apis mellifera scutellata and A.m. capensis (the Cape honey
bee) are western honey bee subspecies indigenous to the Republic of South
Africa (RSA). Both bees are important for biological and economic reasons.
First, A.m. scutellata is the invasive "African honey bee" of
the Americas and exhibits a number of traits that beekeepers consider
undesirable. They swarm excessively, are prone to absconding (vacating the
nest entirely), usurp other honey bee colonies, and exhibit heightened
defensiveness. Second, Cape honey bees are socially parasitic bees; the
workers can reproduce thelytokously. Both bees are indistinguishable
visually. Therefore, we employed Genotyping-by-Sequencing (GBS), wing
geometry and standard morphometric approaches to assess the genetic
diversity and population structure of these bees to search for diagnostic
markers that can be employed to distinguish between the two subspecies.
Results: Apis mellifera scutellata possessed the highest mean number of
polymorphic SNPs (among 2,449 informative SNPs) with minor allele
frequencies >0.05 (Np = 88%). The RSA honey bees generated a high
level of expected heterozygosity (Hexp = 0.24). The mean genetic
differentiation (FST; 6.5%) among the RSA honey bees revealed that
approximately 93% of the genetic variation was accounted for within
individuals of these subspecies. Two genetically distinct clusters (K = 2)
corresponding to both subspecies were detected by Model-based Bayesian
clustering and supported by Principal Coordinates Analysis (PCoA)
inferences. Selected highly divergent loci (n = 83) further reinforced a
distinctive clustering of two subspecies across geographical origins,
accounting for approximately 83% of the total variation in the PCoA plot.
The significant correlation of allele frequencies at divergent loci with
environmental variables suggested that these populations are adapted to
local conditions. Only 17 of 48 wing geometry and standard morphometric
parameters were useful for clustering A.m. capensis, A.m. scutellata, and
hybrid individuals. Conclusions: We produced a minimal set of 83 SNP loci
and 17 wing geometry and standard morphometric parameters useful for
identifying the two RSA honey bee subspecies by genotype and phenotype. We
found that genes involved in neurology/behavior and development/growth are
the most prominent heritable traits evolved in the functional evolution of
honey bee populations in RSA.