From the popular tRNA^leu-COX2 intergenic region to the mitogenome: insights from diverse honey bee populations of Europe and North Africa

The tRNA -COX2 intergenic region of the mitochondrial DNA has been used for assessing diversity in honey bee (Apis mellifera L.) populations worldwide. However, differential mutation rates in different partitions of the mitogenome may produce incongruent results. In this study, we sequenced 123 mitogenomes of 7 subspecies from lineages A, M, and C. This allowed generating a comprehensive dataset to investigate the phylogenetic and phylogeographic congruence among the mitogenome, individual genes, and the tRNA -COX2 region. We showed that the diversity patterns inferred from the tRNA -COX2 marker are not fully paralleled by those obtained with the mitogenome and the individual genes; while the three lineages are supported by these, the African sub-lineages and the haplotypes are not. Thus, conclusions drawn from the tRNA -COX2 region need to be taken with caution and this marker may not be appropriate to infer phylogenetic relationships between honey bee colonies. leu leu leu leuWe are deeply indebted to John C. Patton, Phillip San Miguel, Paul Parker, and Rick Westerman, Univer sity of Purdue, for resequencing the whole genomes, and to Pilar de la Rúa and to Carlo Amodeo for providing A. m. sahariensis and A. m. siciliana samples, respectively. Analyses were performed using computational resources at the Polytechnic Institute of Bragança. DH was supported by a PhD scholarship (SFRH/BD/84195/2012) from the Portuguese Science Foundation (FCT). This work was supported by FCT through the programs COMPETE/QREN/EU (PTDC/BIA-BEC/099640/2008) and the 2013-2014 BiodivERsA/ FACCE-JPI joint call for research proposals, with the national funders FCT (Portugal), CNRS (France), and MEC (Spain)