Demography and phylogenetic utility of numt pseudogenes in the southern red-backed vole (myodes gapperi)

Journal of Mammalogy

Volumn 90, Issue 3, 2009, Pages 561-570

  Triant, Deborah A ^a   Dewoody, J Andrew ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

Arvicolinae; Clethrionomys; Cytochrome b; Mitochondrial transfer; Nuclear integration

Indexed keywords

BIOGEOGRAPHY; CYTOCHROME; DATA SET; DEMOGRAPHY; GENE EXPRESSION; GENOME; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; PHYLOGENETICS; RODENT; TAXONOMY;

ARVICOLINAE; CLETHRIONOMYS; CLETHRIONOMYS GAPPERI; MAMMALIA; MURIDAE;

EID: 67649969585     PISSN: 00222372     EISSN: None     Source Type: Journal    
DOI: 10.1644/08-MAMM-A-149R1.1     Document Type: Article

References (61)

1. ANTHONY, N. M., S. L. CLIFFORD, M. BAWE- JOHNSON, K. A. ABERNATHY, M. W. BRUFORD, AND E. J. WICKINGS. 2007. Distinguishing gorilla mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases. Molecular Phylogenetics and Evolution 43:553-566.
2. AVISE, J. C. 2004. Molecular markers, natural history, and evolution. 2nd
3. ed. Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts. BAKER, R. J., J. L. LONGMIRE, M. MALTBIE, M. J. HAMILTON, AND R. A. VAN DEN bUSSCHE. 1997. DNA synapomorphies for a variety of taxonomic levels from a cosmid library from the new world bat Macrotus waterhousii. Systematic Biology 46:579-589.
4. BENSASSON, D., M. W. FELDMAN, AND D. A. PETROV. 2003. Rates of DNA duplication and mitochondrial DNA insertion in the human genome. Journal of Molecular Evolution 57:343-354.
5. BENSASSON, D., D.-X. ZHANG, D. L. HARTL, AND G. M. HEWITT. 2001. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends in Ecology-spai Evolution 16:314-321.
6. BROWN, W. M., M. GEORGE, Jr., and A. C. WILSON. 1979. Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences 76:1967-1971.
7. CARLETON, M. D., AND G. G. MUSSER. 2005. Order Rodentia. Pp. 745-752 in Mammal species of the world: a taxonomic and geographic reference (D. E. Wilson and D. M. Reeder, eds.). 3rd ed. Johns Hopkins University Press, Baltimore, Maryland.
8. CHALINE, J., P. BRUNET-LECOMTE, S. MONTUIRE, L. VIRIOT, AND F. COURANT. 1999. Anatomy of the arvicoline radiation (Rodentia): palaeogeographical, palaeoecological history and evolutionary data. Annales Zoologici Fennici 36:239-267.
9. CHALINE, J., AND J.-D. GRAF. 1988. Phylogeny of the Arvicolidae (Rodentia): biochemical and paleontological evidence. Journal of Mammalogy 69:22-33.
10. CLINE, J., J. C. BRAMAN, AND H. H. HOGREFE. 1996. PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Research 24:3546-3551.
11. COLLURA, R. V., AND C.-B. STEWART. 1995. Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids. Nature 378:485-489.
12. CONROY, C. J., AND J. A. COOK. 2000. Molecular systematics of a Holarctic rodent (Microtus: Muridae). Journal of Mammalogy 81:344-359.
13. COOK, J. A., A. M. RUNCK, AND C. J. CONROY. 2004. Historical biogeography at the crossroads of the northern continents: molecular phylogenetics of red-backed voles. Molecular Phylogenetics and Evolution 30:767-777.
14. CRACRAFT, J., J. FEINSTEIN, J. VAUGHN, AND K. HELM-BYCHOWSKI. 1998. Sorting out tigers {Panthera tigris): mitochondrial sequences, nuclear inserts, systematics, and conservation genetics. Animal Conservation 1:139-150.
15. DEWOODY, J. A., R. K. CHESSER, AND R. J. BAKER. 1999. A translocated cytochrome b pseudogene in voles (Rodentia: Microtus). Journal of Molecular Evolution 48:380-382.
16. FUKUDA, M., S. WAKASUGI, T. TSUZUKI. H. NOMIYAMA, AND K. SHIMADA. 1985. Mitochondrial DNA-like sequences in the human nuclear genome. Characterization and implications in the evolution of mitochondrial DNA. Journal of Molecular Biology 186:257- 266.
17. GALEWSKI, T., M. TILAK, S. SANCHEZ, P. CHEVRET, E. PARADIS, AND E. J. P. DOUZERY. 2006. The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phytogenies. BMC Evolutionary Genomics 6:80.
18. GANNON, W. L., R. S. SIKES, and the Animal Care and Use Committee of the American Society of Mammalogists. 2007. Guidelines of the American Society of Mammalogists for the use of wild mammals in research. Journal of Mammalogy 88:809-823.
19. GOLDIN, E., et al. 2004. Transfer of a mitochondrial DNA fragment to MCOLN1 causes an inherited case of mucolipidosis IV. Human Mutation 24:460-465.
20. GROMOV, I. M., AND I. Y. POLYAKOV. 1992. Voles (Microtinae), fauna of the USSR mammals. Vol. 3. Number 8. Smithsonian Institution Libraries and The National Science Foundation, Washington, D.C.
21. HASEGAWA, M., H. KISHINO, AND T. YANO. 1985. Dating of the human- ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174.
22. HAZKANI-COVO, E., R. SOREK, AND D. GRAUR. 2003. Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications. Journal of Molecular Evolution 56:169-174.
23. HEBERT, P. D. N., E. H. PENTON, J. M. BURNS, D. H. JANZEN, AND W. HALLWACHS. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences 101:14812-14817.
24. HUELSENBECK, J. P., AND F. RONQUIST. 2001. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755.
25. IRWIN, D. M., T. D. KOCHER, AND A. C. WILSON. 1991. Evolution of cytochrome b gene of mammals. Journal of Molecular Evolution 32:128-144.
26. JAAROLA, M., et al. 2004. Molecular phylogeny of the speciose vole genus Microtus (Arvicolinae, Rodentia) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution: 33:647-663.
27. JENSKN-SEAMAN, M. I., E. E. SARMIENTO, A. S. DEINARD, AND K. K. KIDD. 2004. Nuclear integrations of mitochondrial DNA in gorillas. American Journal of Primatology 63:139-147.
28. KISHINO, H., J. L. THORNE, AND W. J. BRUNO. 2001. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution 18:352-361.
29. LEISTER, D. 2005. Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends in Genetics 21:655-663.
30. LIU, Y., AND X. ZHAO. 2007. Distribution of nuclear mitochondrial DNA in cattle nuclear genome. Journal of Animal Breeding Genetics 1214:264-268.
31. LOPEZ, J. V., M. CULVER, J. C. STEPHENS, W. E. JOHNSON, AND S. J. O'BRIEN. 1997. Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals. Molecular Biology and Evolution 14:277-286.
32. LOPEZ, J. V., N. YUKI, R. MASUDA, W. MODI, AND S. J. O'BRIEN. 1994. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. Journal of Molecular Evolution 39:174-190.
33. LI), X.-M., Y.-X. FU, AND Y.-P. ZHANG. 2002. Evolution of mitochondrial cytochrome b pseudogene in genus Nycticebus. Molecular Biology and Evolution 19:2337-2341.
34. MOURIER, T., A. J. HANSEN, E. WILLERSLEV, AND P. ARCTANDER. 2001. The human genome project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Molecular Biology and Evolution 18:1833-1837.
35. NOUTSOS, C, T. KLEINE, U. ARMBRUSTER, G. DALCORSO, AND D. LEISTER. 2007. Nuclear insertions of organellar DNA can create novel patches of functional exon sequences. Trends in Genetics 23:597-601.
36. NYLANDER, J. A. A., J. C. WILGENBUSCH, D. L. WARREN, AND D. L. SWOFFORD. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581-583.
37. PARR, R. L., et al. 2006. The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation. BMC Genomics 7:185.
38. PEREIRA, S. L., AND A. J. BAKER. 2004. Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics. BMC Evolutionary Biology 4:17.
39. PONTIUS, J. U., et al. 2007. Initial sequence and comparative analysis of the cat genome. Genome Research 17:1675-1689.
40. PROMISLOW, D. E. L., I. K. JORDAN, AND J. F. M. MCDONALD. 1998. Genomic demography: a life-history analysis of transposable elements. Proceedings of the Royal Society of London, B. Biological Sciences 266:1555-1560.
41. REPENNING, C. A. 2003. Mimomys in North America. Bulletin of the American Museum of Natural History 279:469-512.
42. RICCHETTI, M., F. TEKAIA, AND B. DUJON. 2004. Continued colonization of the human genome by mitochondrial DNA. PLoS Biology 2:e273.
43. ROBINSON-RECHAVI, M., AND D. HUCHON. 2000. RRTree: relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16:296-297.
44. RONQUIST, F., AND J. P. HUELSENBECK. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
45. ROZAS, J., J. C. SANCHEZ-DELBARRIO, X. MESSEGUER, AND R. ROZAS. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497.
46. SAMBROOK, J., AND D. W. RUSSELL. 2001. Molecular cloning: a laboratory manual. 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
47. SCHMITZ, J., O. PISKUREK, AND H. ZISCHELR. 2005. Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates. Journal of Molecular Evolution 61:1-11.
48. SHEDLOCK, A. M., K. TAKAHASHI, AND N. OKADA. 2004. SINES of speciation: tracking lineages with retroposons. Trends in Ecology &Evolution 19:545-553.
49. SWOFFORD, D. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Inc., Publishers, Sunderland, Massachusetts.
50. TAMURA, K., J. DUDLEY, M. NEI, AND S. KUMAR. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599.
51. THORNE, J. L., AND H. KISHINO. 2002. Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology 51:689-702.
52. THORNE, J. L., H. KISHINO, AND I. S. PAINTER. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15:1647-1657.
53. TRIANT, D. A., AND J. A. DEWOODY. 2007a. The occurrence, detection and avoidance of mitochondrial DNA translocations in mammalian systematics and phylogeography. Journal of Mammalogy 88:908-920.
54. TRIANT, D. A., AND J. A. DEWOODY. 2007b. Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications. Gene 401:61- 70.
55. TRIANT, D. A., AND J. A. DEWOODY. 2008. Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvico- line rodents. Genetica 132:21-33.
56. WALLACE, D. C, C. STUGARD, D. MURDOCK, T. SCHURR, AND M. D. BROWN. 1997. Ancient mtDNA sequences in the human genome: a potential source of errors in identifying pathogenic mutations. Proceedings of the National Academy of Sciences 94:14900-14905.
57. YANG, Z. 1997. PAML: a program package for phylogeetic analysis by maximum likelihood. Computer Applications in the Biosciences 13:555-556.
58. YANG, Z., S. KUMAR, AND M. NEI. 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650.
59. ZHANG, D. X., AND G. M. HEWITT. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology &Evolution 11:247-251.
60. ZISCHLER, H., H. GEISERT, AND J. CASTRESANA. 1998. A hominoid- specific nuclear insertion of the mitochondrial D-loop: implications for reconstructing ancestral mitochondrial sequences. Molecular Biology and Evolution 15:463-469.
61. ZISCHLER, H., M. Hoss, O. HANDT, AND A. vON HAESELER. 1995. Detecting dinosaur DNA. Science 268:1192-1193.