Nuclear mitochondrial DNA: an Achilles’ heel of molecular systematics, phylogenetics, and phylogeographic studies of stingless bees

Mitochondrial-like DNA (numt) has been found in a variety of insect species. In this work, our objective was to create a phylogeographic hypothesis of Melipona capixaba based on the complete COI sequence. However, several inconsistencies were found, such as 1–2-bp-long indels and a stop codon within the putative amino acid sequences. This led us to infer that M. capixaba has numts. A phylogenetic analysis which included COI sequences of several species of Melipona Illiger, 1806 revealed that numts are also common among other species of the genus. Based on our results, we have proposed a checklist to help to identify the most conspicuous numts; however, it does not ensure that all numts will be identified, since not all numts present explicit signals. Therefore, we recommend taking the maximum care in phylogeographic and phylogenetic analysis within Melipona as well as Hymenoptera, since several evidences of numts were found within this order.