Nuclear copies of mitochondrial genes: another problem for ancient DNA

Springer Science and Business Media LLC - 2010
Robert-Jan den Tex1, Jesus E. Maldonado2,3, Richard Thorington3, Jennifer A. Leonard2,4,1
1Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
2Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, USA
3Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, USA
4Estación Biológica de Doñana, CSIC, Sevilla, Spain

Tóm tắt

The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.

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Tài liệu tham khảo

Arctander P (1995) Comparison of a mitochondrial gene and a corresponding nuclear pseudogene. Proc R Soc Lond B 262:13–19

Behura SK (2007) Analysis of nuclear copies of mitochondrial sequences in honeybee (Apis mellifera) genome. Mol Biol Evol 24:1492–1505

Bensasson D, Zhang D-X, Hewitt GM (2000) Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Mol Biol Evol 17:406–415

den Tex R-J, Thorington R, Maldonado JE, Leonard JA (2010) Speciation dynamics in the SE Asian tropics: putting a time perspective on the phylogeny and biogeography of Sundaland tree squirrels, Sundasciurus. Mol Phylogen Evol 55:711–720

Gonzalez-Ittig RE, Gardenal CN (2008) Co-amplification of mitochondrial pseudogenes in Calomys musculinus (Rodentia, Cricetidae): a source of error in phylogeographic studies. Genome 51:73–78

Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S (2001) Ancient DNA. Nat Rev Genet 2:353–359

Kim J-H, Antunes A, Lou S-J, Menninger J, Nash WG, O’Brien SJ, Johnson WE (2006) Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species. Gene 366:292–302

Kolokotronis S-O, MacPhee RDE, Greenwood A (2007) Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen. BMC Evol Biol 7:67

Leonard JA, Vilà C, Wayne RK (2005) Legacy lost: genetic variability and population size of extirpated US gray wolves (Canis lupus). Mol Ecol 14:9–17

Leonard JA, Shanks O, Hofreiter M, Kreuz E, Hodges L, Ream W, Wayne RK, Fleischer RC (2007) Animal DNA in PCR reagents plagues ancient DNA research. J Archaeo Sci 34:1361–1366

Mirol PM, Mascheretti S, Searle JB (2000) Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, Rodentia) with either great similarity to or high divergence from the true mitochondrial sequence. Heredity 84:538–547

Orlando L, Leonard JA, Laudet V, Guerin C, Hänni C (2003) Ancient DNA analysis reveals wooly rhino evolutionary relationships. Mol Phylo Evol 28:76–90

Pereira SL, Baker AJ (2004) Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evol Biol 4:17. doi:10.1186/1471-2148-4-17

Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081–1084

Sambrook E, Fritsch F, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Press, Cold Spring Harbor

Sorenson MD, Quinn TW (1998) Numts: a challenge for avian systematics and population biology. Auk 115:214–221

Tourmen Y, Baris O, Dessen P, Jacques C, Malthièry Y, Reynier P (2002) Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics 80:71–77

Triant DA, DeWoody JA (2007a) The occurrence, detection, and avoidance of mitochondrial DNA translocations in mammalian systematics and phylogeography. J Mamm 88:908–920

Triant DA, DeWoody JA (2007b) Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications. Gene 401:61–70

Wayne RK, Leonard JA, Cooper A (1999) Full of sound and fury: the recent history of ancient DNA. Annu Rev Ecol Syst 30:457–477

Williams ST, Knowlton N (2001) Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Mol Biol Evol 18:1484–1493

Zhang D-X, Hewitt GM (1996) Nuclear integrations: challenges for mitochondrial DNA markers. Trends Evol Ecol 11:247–251

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