A broad-scale survey of nuclear mitochondrial pseudogenes from Orthoptera (Insecta)

Nuclear mitochondrial pseudogenes (numts) are copies of mitochondrial genes that have been inserted into the nuclear genome. Numts are not known to have any function, are prone to mutate frequently, and can be very problematic for researchers using mitochondrial genes. Even when quality control measures are in place, numts can be inadvertently coamplified and sequenced instead of the orthologous mitochondrial DNA. It is important for researchers to understand the extent to which numts are present within and across species and their evolutionary patterns in order to enhance quality control measures and prevent inadvertent numt coamplification. Using Orthoptera as a model system, which is known to have a large number of nutms, we determine how frequently numts from three mitochondrial genes, Cytochrome c Oxidase Subunit I (COI), Cytochrome c Oxidase Subunit II (COII), and NADH Dehydrogease Subunit V (ND5), have occurred in 13 species and characterize them in a phylogenetic framework. We find that numts of all three genes can be coamplified from all species tested to varying degrees using standard insect primers. We also show that fragments of different regions of mitochondrial genome have been continuously incorporated into the nuclear genome many times throughout the evolutionary history of these taxa. Our study calls for more rigorous data exploration when using mitochondrial markers in molecular systematics.