Conserved numts mask a highly divergent mitochondrial- gene in a species complex of Australian stingless bees (Hymenoptera: Apidae).

, and comprise a species complex of Australian stingless bee species known as the 'Carbonaria' group. The species are difficult to distinguish morphologically and the major species-defining characters relate to comb architecture and nest entrance ornamentation. The taxonomy of the group is further complicated by likely nuclear mitochondrial pseudogenes (numts) and inter-specific hybrids. Here we demonstrate the existence of numts and isolate and characterize the 'true' mt- gene in and . Numts were isolated from enriched-nuclear DNA extraction followed by PCR amplification and Sanger sequencing, and were recognized by the presence of deletions and/or premature stop codons in the translated sequences. The mt- sequences were obtained from NGS sequencing using purified mtDNA. In two numts (numt1 and numt2) were identified and a third (numt3) was identified in . Numt2 and numt3 are similar (1.2% sequence divergence), indicating a recent common origin. The genetic distance between the mt- of the two species was higher than might be expected for closely related species, 16.5%, corroborating previous studies in which and were regarded as separate species. The three numts are more similar to the of other stingless bee species, including Australian and South American (81.7-83.9%) than to the mt- of their own species (70-71.4%). This is because the mt- of and differ greatly from other Meliponinae. Our findings explain some formerly puzzling aspects of Carbonaria biogeography, and misinterpreted amplifications.