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

Strains of the Italian honey bee Apis mellifera ligustica Spinola, 1806 are selectively bred for desirable apiculture traits. Ma et al. (2022) examined SNP differences in mtDNA genomes between a strain bred for enhanced royal jelly production (RJB) with an unselected strain (ITB). Kim et al. (2019) compared SNP and intergenic repeats differences between a Varroa mite resistant strain bred for high-hygienic behavior (HHB) with an unselected low-hygienic strain (LHB). Phylogenetic comparison of 23 complete A. m. ligustica mtDNA sequences, including the two HHB and LHB strains and 15 RJB and ITB haplotypes and those of other subspecies (Carr 2023), shows significant clade structure for SNP differences and amino acid substitutions, however this structure is not diagnostic of the strains under selection. Numbers of repeats show little or no phylogenetic signal: similarities are symplesiomorphic and differences convergent. Differences between the HHB and LHB strains arise from coincidental fixation of alternative SNPs in different clades. Lineages within the RJB and ITB strains are not reciprocally monophyletic, and are often identical or near identical to those in the other strain or to other variant strains. Evaluation of the diagnostic and (or) adaptive significance of mtDNA markers requires broad knowledge of within-subspecies polymorphism.