Toward proper nomenclature: reassessing honeybee (Apis mellifera) mtDNA nomenclature using phylogeny

Abstract

The western honey bee (Apis mellifera) is one of natures’ most important pollinators and domesticated species. Through human management, it has spread all around the world becoming a cosmopolitan species, and its genetic diversity has been shaped over millennia by anthropogenic influence. Six main mtDNA lineages (M, C, O, Y, A and S) with a large number of existing sublineages are recognized, usually associated with appropriate subspecies. Current nomenclature is inconsistent and the naming of newly identified haplotypes is not standardized. Here we reassessed the nomenclature of C lineage using sequences of the tRNAleu-cox2 intergenic region and complete mitogenomes. Most of the available honey bees’ mtDNA haplotypes are based on the sequence variability of this region while available complete mitogenomes are still few. The first complete mitogenome of Apis mellifera (NC_001566) was used as the reference genome for haplotype determination. We propose that the naming of the mtDNA haplotypes should be performed based on the differences to the reference mitogenome and according to the phylogenetic relationship between detected haplotypes. Our analyses showed that the current nomenclature of C sublineages is not consistent with the phylogenetic relationships between existing haplotypes and that the reassessment followed by the proper naming of haplotypes is needed. We propose to keep the names of the main lineages but correct the names of sublineages using the same approach as in the identification of human mtDNA lineages. This newly standardized nomenclature will bring more order to the studies of honey bees’ genetic diversity.