The Occurrence, Detection, and Avoidance of Mitochondrial DNA Translocations in Mammalian Systematics and Phylogeography

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...

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Bibliographic Details
Published in:Journal of mammalogy 2007-08, Vol.88 (4), p.908-920
Main Authors: Triant, Deborah A., DeWoody, J. Andrew
Format: Article
Language:English
Subjects:
Animal ethology
Biological and medical sciences
Biological evolution
Complementary DNA
cytochrome b
Deoxyribonucleic acid
DNA
FEATURE ARTICLES
Fundamental and applied biological sciences. Psychology
Genes
genetic species concept
Genomes
Genomics
Mammalia
Mammalogy
Mammals
Microtus
Microtus ochrogaster
Mitochondrial DNA
numt
Phylogenetics
Polymerase chain reaction
pseudogene
Pseudogenes
Psychology. Psychoanalysis. Psychiatry
Studies
Systematics
Vertebrata
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Summary: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.
ISSN:0022-2372
1545-1542
DOI:10.1644/06-MAMM-A-204R1.1