Multiple mitogenomes indicate Things Fall Apart with Out of Africa or Asia hypotheses for the phylogeographic evolution of Honey Bees (Apis mellifera)

Previous morpho-molecular studies of evolutionary relationships within the economically important genus of honey bees (Apis), including the Western Honey Bee (A. mellifera L.), have suggested Out of Africa or Asia origins and subsequent spread to Europe. I test these hypotheses by a meta-analysis of complete mitochondrial DNA coding regions (11.0 kbp) from 22 nominal subspecies represented by 78 individual sequences in A. mellifera. Parsimony, distance, and likelihood analyses identify six nested clades: Things Fall Apart with Out of Africa or Asia hypotheses. Molecular clock-calibrated phylogeographic analysis shows instead a basal origin of A. m. mellifera in Europe similar to 780 Kya, and expansion to Southeast Europe and Asia Minor similar to 720 Kya. Eurasian bees spread southward via a Levantine/Nilotic/Arabian corridor into Africa similar to 540 Kya. An African clade re-established in Iberia similar to 100 Kya spread thereafter to westerly Mediterranean islands and back into North Africa. Nominal subspecies within the Asia Minor and Mediterranean clades are less differentiated than are individuals within other subspecies. Names matter: paraphyletic anomalies are artefacts of mis-referral in GenBank of sequences to the wrong subspecies, or use of faulty sequences, which are clarified by inclusion of multiple sequences from available subspecies.

Automated summary

Previous studies have suggested African or Asian origins for honey bees, including the Western Honey Bee (A. mellifera L.). However, a meta-analysis of mitochondrial DNA coding regions reveals a basal origin in Europe around 780,000 years ago, with subsequent expansion to Southeast Europe, Asia Minor, and Africa. The inclusion of multiple sequences from available subspecies clarifies mis-referral and faulty sequences in GenBank.