Mitochondrial pseudogenes: evolution's misplaced witnesses.

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.

[1]  D. Petrov,et al.  Patterns of nucleotide substitution in Drosophila and mammalian genomes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[2]  C. Stewart,et al.  Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids , 1995, Nature.

[3]  X. Yu,et al.  Patching broken chromosomes with extranuclear cellular DNA. , 1999, Molecular cell.

[4]  M. Bulmer,et al.  Neighboring base effects on substitution rates in pseudogenes. , 1986, Molecular biology and evolution.

[5]  R. Baker,et al.  Reduced Number of Ribosomal Sites in Bats: Evidence for a Mechanism to Contain Genome Size , 1992 .

[6]  M. Stoneking,et al.  Novel mitochondrial DNA insertion polymorphism and its usefulness for human population studies. , 1996, Human biology.

[7]  C. Kurland,et al.  Why mitochondrial genes are most often found in nuclei. , 2000, Molecular biology and evolution.

[8]  A. Pissinatti,et al.  Multiple nuclear insertions of mitochondrial cytochrome b sequences in callitrichine primates. , 2000, Molecular biology and evolution.

[9]  F. Riley,et al.  HYBRIDIZATION BETWEEN THE NUCLEAR AND KINETOPLAST DNA'S OF Leishmania enriettii AND BETWEEN NUCLEAR AND MITOCHONDRIAL DNA'S OF MOUSE LIVER. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[10]  P. Sunnucks,et al.  Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). , 1996, Molecular biology and evolution.

[11]  D. Hartl,et al.  Codon usage bias and base composition of nuclear genes in Drosophila. , 1993, Genetics.

[12]  H. E. Vaughan,et al.  The localization of mitochondrial sequences to chromosomal DNA in orthopterans , 1999 .

[13]  W. Thilly,et al.  Applications of constant denaturant capillary electrophoresis / high‐fidelity polymerase chain reaction to human genetic analysis , 1999, Electrophoresis.

[14]  D. -. Zhang,et al.  Highly conserved nuclear copies of the mitochondrial control region in the desert locust Schistocerca gregaria: some implications for population studies , 1996, Molecular ecology.

[15]  G. Hu,et al.  Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome , 1999, Cell Research.

[16]  J. DeWoody,et al.  A Translocated Mitochondrial Cytochrome b Pseudogene in Voles (Rodentia: Microtus) , 1999, Journal of Molecular Evolution.

[17]  R. Mahalingam,et al.  Selected nuclear LINE elements with mitochondrial‐DNA‐like inserts are more plentiful and mobile in tumor than in normal tissue of mouse and rat , 1998, Journal of cellular biochemistry.

[18]  Yangrae Cho,et al.  Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[19]  S. Pääbo,et al.  A nuclear 'fossil' of the mitochondrial D-loop and the origin of modern humans , 1995, Nature.

[20]  D. -. Zhang,et al.  Nuclear integrations: challenges for mitochondrial DNA markers. , 1996, Trends in ecology & evolution.

[21]  G. Gellissen,et al.  Gene Transfer a , 1987, Annals of the New York Academy of Sciences.

[22]  N. Perna,et al.  Mitochondrial DNA: Molecular fossils in the nucleus , 1996, Current Biology.

[23]  F. Canavez,et al.  Mitochondrial DNA-like sequences in the nuclear genome of the opossum genus Didelphis (Marsupialia: Didelphidae). , 1999, The Journal of heredity.

[24]  D. Petrov,et al.  Genomic gigantism: DNA loss is slow in mountain grasshoppers. , 2001, Molecular biology and evolution.

[25]  W. Doolittle.  You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. , 1998, Trends in genetics : TIG.

[26]  W. Thilly,et al.  Evolutionary trail of the mitochondrial genome as based on human 16S rDNA pseudogenes. , 1994, Gene.

[27]  Marcy R. Auerbach,et al.  A quick, direct method that can differentiate expressed mitochondrial genes from their nuclear pseudogenes , 1996, Current Biology.

[28]  D. Bensasson,et al.  Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. , 2000, Molecular biology and evolution.

[29]  H. Zischler.  Nuclear integrations of mitochondrial DNA in primates: Inference of associated mutational events , 2000, Electrophoresis.

[30]  N. Knowlton,et al.  Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. , 2001, Molecular biology and evolution.

[31]  J. Castresana,et al.  A hominoid-specific nuclear insertion of the mitochondrial D-loop: implications for reconstructing ancestral mitochondrial sequences. , 1998, Molecular biology and evolution.

[32]  J. Blanchard,et al.  Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. , 1996, Molecular biology and evolution.

[33]  S. Pääbo,et al.  Nuclear insertion sequences of mitochondrial DNA predominate in hair but not in blood of elephants , 1999, Molecular ecology.

[34]  A. Kitzis,et al.  DNA sequences homologous to mitochondrial genes in nuclei from normal rat tissues and from rat hepatoma cells. , 1989, Biochemical and biophysical research communications.

[35]  M. Lynch,et al.  Organellar genes: why do they end up in the nucleus? , 2000, Trends in genetics : TIG.

[36]  A. Wilson,et al.  SSCP is not so difficult: the application and utility of single‐stranded conformation polymorphism in evolutionary biology and molecular ecology , 2000, Molecular ecology.

[37]  J. V. López,et al.  Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. , 1997, Molecular biology and evolution.

[38]  Cécile Fairhead,et al.  Mitochondrial DNA repairs double-strand breaks in yeast chromosomes , 1999, Nature.

[39]  T. Miyata,et al.  Mitochondrial DNA-like sequences in the human nuclear genome. Characterization and implications in the evolution of mitochondrial DNA. , 1985, Journal of molecular biology.

[40]  P. Arctander,et al.  Comparison of a mitochondrial gene and a corresponding nuclear pseudogene , 1995, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[41]  M. Sorenson,et al.  Numts : A challenge for avian systematics and population biology , 1998 .

[42]  P. Thorsness,et al.  Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus. , 1996, International review of cytology.

[43]  J. Timmis,et al.  Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants. , 1998, Molecular biology and evolution.

[44]  D. Murdock,et al.  Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[45]  A. von Haeseler,et al.  Detecting dinosaur DNA. , 1995, Science.

[46]  M. Nei,et al.  Pseudogenes as a paradigm of neutral evolution , 1981, Nature.

[47]  T. W. Quinn.  The genetic legacy of Mother Goose– phylogeographic patterns of lesser snow goose Chen caerulescens caerulescens maternal lineages , 1992, Molecular ecology.

[48]  K. H. White,et al.  Mechanisms of mitochondrial DNA escape to the nucleus in the yeast Saccharomyces cerevisiae , 1999, Current Genetics.

[49]  J. Searle,et al.  Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, Rodentia) with either great similarity to or high divergence from the true mitochondrial sequence , 2000, Heredity.