Mitochondrial pseudogenes: evolution's misplaced witnesses

doi:10.1016/S0169-5347(01)02151-6

Trends in Ecology & Evolution

Volume 16, Issue 6, 1 June 2001, Pages 314-321

https://doi.org/10.1016/S0169-5347(01)02151-6 Get rights and content

Abstract

Nuclear copies of mitochondrial DNA (mtDNA) have contaminated PCR-based mitochondrial studies of over 64 different animal species. Since the last review of these nuclear mitochondrial pseudogenes (Numts) in animals, Numts have been found in 53 of the species studied. The recent evidence suggests that Numts are not equally abundant in all species, for example they are more common in plants than in animals, and also more numerous in humans than in Drosophila. Methods for avoiding Numts have now been tested, and several recent studies demonstrate the potential utility of Numt DNA sequences in evolutionary studies. As relics of ancient mtDNA, these pseudogenes can be used to infer ancestral states or root mitochondrial phylogenies. Where they are numerous and selectively unconstrained, Numts are ideal for the study of spontaneous mutation in nuclear genomes.

Section snippets

Background

There has been recent speculation on the reasons why Numts exist 14, 15, 16. The transfer of mtDNA to the nucleus could be part of an ongoing transfer of functional mitochondrial genes from mitochondrion to nucleus. One of the underlying causes of this process is thought to be a ‘gene transfer ratchet’ ¹⁴. Because the rate of DNA transfer from mitochondrion to nucleus is thought to be much greater than in the reverse direction ¹⁷, a net movement of genes from mitochondrion to nucleus occurs ¹⁴.

A census of mitochondrial pseudogenes

In 1996, Blanchard and Schmidt ³ proposed that Numts are not equally abundant in all species. They observed that a larger proportion of the plant nuclear sequence in GenBank was of mitochondrial origin compared with the nuclear sequences of yeast or humans, and that no Numts were identified in Plasmodium falciparum, Caenorhabditis elegans or Drosophila melanogaster despite these being well-studied species. There might also be differences in Numt abundance among closely related species. For

Molecular troublemakers

Collura and Stewart ⁹ discovered that, under the same experimental conditions, Numts can be preferentially PCR amplified in the orang-utan, although mtDNA predominates in the PCR products of other hominoids. This discrepancy arose because the authentic orang-utan mtDNA sequence had diverged in such a way that the primers used would no longer amplify it, although they were still able to amplify an ancient mitochondrial pseudogene in the nuclear genome. If the phylogenetic placement of

Numts as molecular fossils

Early studies of human Numt sequences revealed that these resembled ‘ancestral’ mitochondrial sequences ²⁵, or ‘molecular fossils,²¹. Because the human nuclear mutation rate is so much lower than that of mtDNA, Numts usually appear ‘frozen’ in comparison with their functional mitochondrial counterparts ²⁵. This is despite these nuclear sequences having lost their function when they were transferred to the nucleus and, therefore, not being selectively constrained ²¹. Similar observations have

Thorns in the evolutionary tree

The differences between nuclear and mitochondrial molecular evolution complicate phylogenetic analysis when it is applied to both nuclear and mitochondrial paralogs. parsimony analysis, in particular, can underestimate branch-length differences between Numt and mtDNA lineages. Although mammalian, bird and plant nuclear rates of evolution can be an order of magnitude different from the mitochondrial rate, parsimony analysis makes no allowance for differing rates of evolution and will ascribe

The many uses of Numts

Even without knowledge of whether Numts are functional, and irrespective of relative rates of nuclear and mitochondrial evolution, Numts can be used as genetic markers. Where the nonfunctionality of Numts can be established, they can also be used in other ways.

Molecular roots and ancestors

When many paralogous Numt sequences are known, they can be used to trace the ancestral states of mtDNA at particular nucleotide sites, as has been done for mammals ²⁶ and insects 27, 41. Independent knowledge of past ancestral states could help resolve branches of mitochondrial phylogenies where such ambiguities exist.

Numts have been used to root phylogenies for human populations ⁴⁸ and birds ⁴⁹. This is particularly useful in humans, where the lack of a suitable outgroup is often limiting. The

Relative rates of evolution

A 7.9-kb noncoding Numt in cats was used to compare the strength of purifying selection among mitochondrial regions ³⁸. Assuming that nuclear mutations accumulate at an equal rate along a Numt sequence, the regions where the mitochondrial sequence is most diverged from the Numt are the least selectively constrained ³⁸. Numts have also been used to compare the rate of nonfunctional nuclear sequence evolution to that of functional mtDNA (Refs 8,34).

The study of nuclear mutation

A promising application of Numt study is its use in the study of nuclear mutation. Patterns of mutation set the baseline on which other evolutionary factors operate, yet spontaneous mutation is poorly characterized in all but a few species. Spontaneous mutation is too slow, and the generation time of most metazoans too long, for the direct experimental study of spontaneous germline mutations. Patterns of spontaneous mutation can be inferred from substitutions accumulated in evolutionary time,

Conclusions and future research

The census that is emerging from GenBank and the published literature shows that there are large differences among organisms in the numbers of mitochondrial pseudogenes that they harbor in their nuclear genomes. There is a growing literature on the conditions of Numt contamination and its avoidance in evolutionary studies and there are also many different ways in which these pseudogenes can now be used in evolutionary biology.

Improved characterization of the taxonomic distribution of Numts

Acknowledgements

We thank Vicki Friesen, Matthew Hare, Nick Harvey, Michael Jensen-Seaman, Werner E. Meyer, Kirstine Nielsen, Antonis Rokas, Paul Sunnucks and Steve Trewick for information on Numts in their study organisms, and to three reviewers for their comments on this article. Work was supported in part by a Royal Society–Fulbright Postdoctoral Fellowship to DB, and an NIH grant GM58423 to DLH.

Glossary

‘Dead-on-arrival’ pseudogene: a pseudogene that loses its function immediately upon its arrival at a locus, as opposed to a gene that evolved under relaxed selective constraints at its current locus before losing its function.
Codon usage bias: the bias in favor of some three-nucleotide sequences (codons) over others that code for the same amino acids.
Copy number: the number of copies of a DNA sequence per nuclear genome or cell.
Episomal DNA: DNA that can exist freely in the cell or integrated into a

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Trends in Ecology & Evolution

ReviewMitochondrial pseudogenes: evolution's misplaced witnesses

Abstract

Section snippets

Background

A census of mitochondrial pseudogenes

Molecular troublemakers

Numts as molecular fossils

Thorns in the evolutionary tree

The many uses of Numts

Molecular roots and ancestors

Relative rates of evolution

The study of nuclear mutation

Conclusions and future research

Acknowledgements

Glossary

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J. Mol. Evol.

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Mol. Biol. Evol.

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Genetics

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Review
Mitochondrial pseudogenes: evolution's misplaced witnesses