Nuclear Sequences of Mitochondrial Origin as Phylogenetic Markers

Abstract

Numts (nuclear sequence of mitochondrial origin) are fragments of mitochondrial DNA present in the nuclear genomes of most eukaryotes. Numts have unique characteristics that make them useful as nuclear and mitochondrial phylogenetic markers. Numts utilities include analysis of nuclear mutational spectra and the relative rates of the mitochondria and the nucleus. Additionally, because numt appearance in the same position in multiple species indicates its ancestry, numts are valuable for phylogentic tree reconstruction. Numts are also beneficial to study mitochondrial evolution as it can uncover extinct mtDNA variations. Despite the potential for confusion with bona fide mtDNA, the increasing number of genomes sequenced will make it easier to identify numts from mitochondrial DNA and to use them for taxonomy and phylogeny.

Key Concepts:

  • Numts have unique characteristics that make them suitable as phylogenetic markers.

  • Verified numts are useful both for the study of mitochondrial evolution and for the study of nuclear evolution.

Keywords: Numts; taxonomy; molecular evolution; mitochondrial pseudogenes; phylogenetic marker

Figure 1.

The placement of numt in the nuclear genome can be used as a nuclear taxonomic marker. First, the existence of multiple numts (thick line) is tested in each of the five species of phylogenic interest using polymerase chain reaction (left). Polymerase chain reaction primers are used both within and outside the numt. Dollo parsimony, where each numt is inferred to have arisen only once during evolution of these species, is then used to build a phylogenetic tree. One possible tree is shown with the common form of numt relations among the species shown below branches.

Figure 2.

Numts can be used to fill gaps in mitochondrial evolution. In metazoans where the evolutionary rate is lower in the nuclear than in the mitochondria, numts appear as frozen mitochondrial sequences. Therefore, their placement and dating on a mitochondrial tree can inform us about mitochondria evolution. numt i shows an example of recent insertion in species A, numt ii is a common insertion in AB and numt iii is an ancient insertion that can be used to root a mitochondrial tree.

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Further Reading

Hazkani‐Covo E and Covo S (2008) Numt‐mediated double‐strand break repair mitigates deletions during primate genome evolution. PLoS Genetics 4: e1000237.

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Triant DA and DeWoody JA (2009) Demography and phylogenetic utility of numt pseudogenes in the southern red‐backed vole (Myodes gapperi). Journal of Mammalogy 90: 561–570.

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Hazkani‐Covo, Einat(Oct 2010) Nuclear Sequences of Mitochondrial Origin as Phylogenetic Markers. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022877]