Ghost mtDNA haplotypes generated by fortuitous NUMTs can deeply disturb infra‐specific genetic diversity and phylogeographic pattern

Nuclear copies of mitochondrial DNA (NUMTs or mitochondrial pseudogenes) are known to impede the detection of interspecific genetic diversity. But the effect of these artifacts on phylogeographic reconstruction remains under evaluated. In this study, we analysed a set of 115 sequences of a fragment of the cytochrome c oxidase subunit I gene (COI) of Monochamus galloprovincialis (Coleoptera, Cerambycidae) for which overlapping signals in sequencing electropherograms were observed. Comparison of full and corrected ‘ambiguities‐free’ data sets reveals the prevalence of numerous supernumerary haplotypes that deeply affect genetic diversity indices and phylogeographic patterns of this species. Slightly divergent pseudogenes were recovered in 49 of the 115 sequences. These results highlight the potential misdetection of NUMTs using current control methods and the consequences on phylogeographic structure. To test the frequency of unintended amplification of NUMTs, a cloning was performed on 15 individuals. An average of 3.72 and a maximum of six paralogous sequences with different levels of divergence were identified among individual cloned. Within individual pairwise distance between paralogs raised 1.4%. This work calls for awareness to the presence of undetected NUMTs within mitochondrial data sets, especially at infra‐specific level.