Open AccessGhost mt DNA haplotypes generated by fortuitous NUMT s can deeply disturb infra‐specific genetic diversity and phylogeographic pattern
Author(s) -
Haran Julien,
Koutroumpa Fotini,
Magnoux Emmanuelle,
Roques Alain,
Roux Géraldine
Publication year - 2015
Publication title -
journal of zoological systematics and evolutionary research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.769
H-Index - 50
eISSN - 1439-0469
pISSN - 0947-5745
DOI - 10.1111/jzs.12095
Subject(s) - biology , pseudogene , mitochondrial dna , evolutionary biology , coalescent theory , nucleotide diversity , phylogeography , genetics , haplotype , genetic diversity , phylogenetic tree , gene , population , genotype , genome , demography , sociology
Nuclear copies of mitochondrial DNA ( NUMT s 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 M onochamus galloprovincialis ( C oleoptera, C erambycidae) 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 NUMT s using current control methods and the consequences on phylogeographic structure. To test the frequency of unintended amplification of NUMT s, 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 NUMT s within mitochondrial data sets, especially at infra‐specific level.