The occurrence, detection, and avoidance of mitochondrial DNA translocations in mammalian systematics and phylogeography

Abstract

The generation and analysis of mitochondrial DNA (mtDNA) sequence data has become routine in mammalogy. Unfortunately, these analyses can be confounded because fragments of the mitochondrial genome are contained in the nucleus of most eukaryotes. Furthermore, these nuclear fragments of mitochondrial genes, or numt pseudogenes, are often represented hundreds of times in mammalian nuclear genomes. Most modern analyses of mtDNA rely on the polymerase chain reaction to generate a population of molecules that can be sequenced. Templates for DNA sequencing reactions should be homogenous, and in the case of mtDNA, cytoplasmic in origin. The unwanted (and often unwitting) amplification of numts results in a heterogenous mixture of nuclear and cytoplasmic amplicons or, if a numt is preferentially amplified, a near-homogenous mixture of the wrong (nuclear) template. These nuclear sequences can cause major - although often cryptic - problems in the analyses of systematic or phylogeographic data. Here, we review the occurrence, detection, and avoidance of numts in mammals. Furthermore, we isolate a cytochrome-b numt and its corresponding mitochondrial sequence in the North American prairie vole (Microtus ochrogaster) to illustrate various methods to detect numts. Finally, we present approaches by which numts, once identified, can be utilized in molecular studies. © 2007 American Society of Mammalogists.