Rates of DNA duplication and mitochondrial DNA insertion in the human genome

Journal of Molecular Evolution

Volumn 57, Issue 3, 2003, Pages 343-354

  Bensasson, Douda ^a,b   Feldman, Marcus W ^a   Petrov, Dmitri A ^a  

^a STANFORD UNIVERSITY   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Human population genetic markers; Numt; NumtDNA; Segmental duplication

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DNA SEQUENCE; GENE DUPLICATION; GENE INSERTION; GENETIC MARKER; HUMAN; HUMAN GENOME; NUCLEOTIDE SEQUENCE; PHYLOGENY; PSEUDOGENE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ANIMALS; DNA TRANSPOSABLE ELEMENTS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOME, HUMAN; HUMANS; MUTATION; PHYLOGENY; PSEUDOGENES;

INSERTION SEQUENCES; MAMMALIA; PRIMATES;

EID: 0043197403     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-003-2485-7     Document Type: Article

References (35)

1. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwatz S, Adams MD, Myers EW, Li PW, Eichler EE (2002a) Recent segmental duplications in the human genome. Science 297:1003-1007
2. Baíley JA, Yavor AM, Viggiano L, Misceo D, Horvath JE, Archidiacono N, Shchwartz S, Rocchi M, Eichler EE (2002b) Human-specific duplication and mosaic transcripts: The recent paralogous structure of chromosome 22. Am J Hum Gene 70:83-100
3. Bensasson D, Zhang D-X, Hewitt GM (2000) Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes. Mol Biol Evol 17:406-415
4. Bensasson D, Zhang D-X, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: Evolution's misplaced witnesses. Trends Ecol Evol 16:314-321
5. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J Mol Evol 18:225-239
6. Fukuda M, Wakasugi S, Tsuzuki T, Nomiyama H, Shimada K, Miyata T (1985) Mitochondrial DNA-like sequences in the human nuclear genome. J Mol Biol 186:257-266
7. Gellissen G, Michaelis G (1987) Gene transfer: Mitochondria to nucleus. Ann NY Acad Sci 503:391-401
8. Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J, Gunnell G, Groves CP (1998) Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol Phylogenet Evol 9:585-598
9. Graur D, Shuali Y, Li W-H (1989) Deletions in processed pseudogenes accumulate faster in rodents than in humans. J Mol Evol 28:279-285
10. Gu Z, Cavalcanti A, Chen F-C, Li W-H (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19:256-262
11. Hall TA (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis (program for windows 95/98/NT). Nucleic Acids Symp Ser 41:95-98
12. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160-174
13. Hazkani-Covo E, Sorek R, Graur D (2003) Evolutionary dynamics of large numts in the human genome: Rarity of independent insertions and abundance of postinsertion duplications. J Mol Evol 56:169-174
14. Hu G, Thilly WG (1994) Evolutionary trail of the mitchondrial genome as based on human 16S rDNA pseudogenes. Gene 147:197-204
15. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860-921
16. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
17. Long M, Thornton K (2001) Gene duplication and evolution. Science 293:1551a
18. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155
19. Lynch M, Conery JS (2001) Gene duplication and evolution. Science 293:1551a
20. Mourier T, Hansen AJ, Willerslev E, Arctander P (2001) The human genome project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol Biol Evol 18:1833-1837
21. Mundy NI, Pissinatti A, Woodruff DS (2000) Multiple nuclear insertions of mitochondrial cytochrome b sequences in callitrichine primates. Mol Biol Evol 17:1075-1080
22. Ogurtsov AY, Roytberg MA, Shabalina SA, Kondrashov AS (2002) OWEN: Aligning long colinear regions of genomes. Bioinformatics 18:1703-1704
23. Ophir R, Graur D (1997) Patterns and rates of indel evolution in processed pseudogenes from humans and murids. Gene 205:191-202
24. Perna NT, Kocher TD (1996) Mitochondrial DNA: Molecular fossils in the nucleus. Curr Biol 6:128-129
25. Przeworski M, Hudson RR, Di Rienzo A (2000) Adjusting the focus on human variation. Trends Genet 16:296-302
26. Samonte RV, Eichler EE (2002) Segmental duplications and the evolution of the primate genome. Nature Rev Genet 3:65-72
27. Schmitz J, Ohme M, Zischler H (2001) SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157:777-784
28. Schmitz J, Ohme M, Zischler H (2002) The complete mitochondrial sequence of Tarsius bancanus: Evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA. Mol Biol Evol 19:544-553
29. Swofford DL (2002) PAUP*: Phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Sunderland, MA
30. Thomas R, Zischler H, Paabo S, Stoneking M (1996) Novel mitochondrial DNA insertion polymorphism and its usefulness for human population studies. Hum Biol 68:847-854
31. Tourmen Y, Baris O, Dessen P, Jacques C, Malthiėry Y, Reynier P (2002) Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics 80:71-77
32. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276
33. Woischnik M, Moraes CT (2002) Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res 12:885-893
34. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. CABIOS 13
35. Yuan JD, Shi JX, Meng GX, An LG, Hu GX (1999) Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome. Cell Res 9:281-290