Candidate loci for selection in Iberian honey bees: a genome-wide scan using SNP genotyping

Over the last 20 years Iberian honey bees (IHB) have been scrutinized with a variety of genetic markers including morphology, allozymes, mtDNA, and microsatellites. The complex patterns and processes revealed have yet to be fully understood. While mtDNA is useful to reveal the maternal component, biparental markers capture genome-wide effects (admixture, expansions, and contractions) and locus-specific effects (selection). Accordingly, we expect to dissect out, through genome-wide scans, neutral and selection effects. In this study, the Illumina GoldenGate Assay was used to genotype SNPs across the complete genome of IHBs. The SNP data set was analyzed for evidence of selection using a frequentist, FDIST, and a Bayesian method, BayeScan. Additionally, a spatial analysis method (MatSAM) was used to test for associations between SNPs and climatic variables. With these approaches we detected 8 loci with a strong signal of directional selection. The genome positions and putative gene functions, given in the HB genomic resources, suggest that these putatively selected loci are strong candidates for selection. The spatial representation of these same loci reveals a clinal pattern of variation, further supporting selection. Our approach allows for a rigorous consideration of selection as the underlying cause of observed patterns of diversity and contrast with previous studies where evocation of selection was merely speculative. Fundação para a Ciência e Tecnologia