The maternally inherited mitochondrial DNA has been the marker of choice for assessing Iberian honey bee variation, particularly the intergenic tRNA leu -cox2 region. The data generated by massive sampling of this region confirmed early findings of coexistence of African (A) and western European (M) lineages, forming a southwestern–northeastern cline, and revealed unparalleled levels of haplotype diversity and complexity. Accordingly, it has been suggested that Iberia served as a glacial refuge, and as a place of secondary contact between European and African lineages. While we have learned a great deal with this region, due to its high levels of variation and repetitive structure, there are evolutionary questions that an only be properly addressed using other mitochondrial regions. In this study, we used NGS technology to sequence the mitogenomes of 92 individuals and analyzed the data using two phylogenetic methods.We are deeply grateful to numerous people that collaborated in this
study. Beekeepers from Spain and Portugal helped obtaining Iberian
samples. Antonio Pajuelo provided the contacts of Spanish beekeepers.
Margarida Neto, Andreia Brandão and Irene Muñoz collaborated in the
sampling. Pilar de la Rúa, Wahida Loucif, Per Kryger, Bjorn Dahle, Lionel
Garnery, Raffaele Dall’ Olio, and Romée van der Zee provided the
reference samples. Phillip San Miguel and Paul Parker sequenced the
whole genomes and Rick Westerman performed the mapping (Purdue
University). Dora Henriques and Julio Chávez-Galarza are supported by
Fundação para a Ciência e Tecnologia through the scholarships
SFRH/BD/84195/2012 and SFRH/BD/68682/2010, respectively. This
research was funded by Fundação para a Ciência e Tecnologia and
COMPETE/QREN/EU through the project PTDC/BIA-BEC/099640/2008.info:eu-repo/semantics/publishedVersio
