Strains of <i>Apis mellifera ligustica</i> honey bees artificially bred for apicultural traits are not consistently differentiated by mitochondrial DNA genome markers

Strains of the Italian honey bee <i>Apis mellifera ligustica</i> Spinola, 1806 are selectively bred for desirable apiculture traits. Ma et al. compared SNP differences in mtDNA genomes between a strain bred for enhanced royal jelly production (RJB) and an unselected strain (ITB). Kim et al. compared SNP and intergenic repeats differences between a <i>Varroa</i> mite resistant strain bred for high-hygienic behavior (HHB) and an unselected low-hygienic strain (LHB). Phylogenetic comparison of 23 complete <i>A. m. ligustica</i> mtDNA sequences, including the HHB and LHB strains and 14 RJB and ITB haplotypes, shows significant intrasubspecific clade structure for SNP differences and amino acid substitutions; however, this structure is not diagnostic of the strains under selection. RJB strains occur in three separate clades, and along with HHB are frequently identical or near-identical to other haplotypes. Differences between the selected and unselected strains appear to arise from coincidental fixation of alternative SNPs in different clades. Numbers of repeats show little or no phylogenetic signal: similarities are symplesiomorphic and differences convergent. Evaluation of the diagnostic and (or) adaptive significance of mtDNA markers requires broad knowledge of within-subspecies polymorphism.