The fingerprint of phantom mutations in mitochondrial DNA data

American Journal of Human Genetics

Volumn 71, Issue 5, 2002, Pages 1150-1160

  Bandelt, Hans Jürgen ^a   Quintana Murci, Lluís ^b,c   Salas, Antonio ^d   Macaulay, Vincent ^e  

^a UNIVERSITY OF HAMBURG   (Germany)

^b INSTITUT PASTEUR   (France)

^c CNRS   (France)

^d UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

^e UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DATA ANALYSIS; DNA DETERMINATION; DNA FINGERPRINTING; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; HUMAN; HUMAN CELL; PHANTOM; PHYLOGENY; PRIORITY JOURNAL; QUALITY CONTROL; RELIABILITY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

EID: 0036842923     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/344397     Document Type: Article

References (39)

1. Alves-Silva J, Santos MDS, Guimarães PEM, Ferreira ACS, Bandelt H-J, Pena SDJ, Prado VF (2000) The ancestry of Brazilian mtDNA lineages. Am J Hum Genet 67:444-461 (erratum 67:775)
2. Avise JC (2000) Phylogeography: The History and Formation of Species. Harvard University Press, Cambridge, MA
3. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48
4. Bandelt H-J, Forster P, Sykes BC, Richards MB (1995) Mitochondrial portraits of human populations using median networks. Genetics 141:743-753
5. Bandelt H-J, Lahermo P, Richards M, Macaulay V (2001) Detecting errors in mtDNA data by phylogenetic analysis. Int J Legal Med 115:64-69
6. Bandelt H-J, Macaulay V, Richards M (2000) Median networks: Speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol Phylogenet Evol 16:8-28
7. Bertranpetit J, Sala J, Calafell F, Underhill PA, Moral P, Comas D (1995) Human mitochondrial DNA variation and the origin of Basques. Ann Hum Genet 59:63-81
8. Dimo-Simonin N, Grange F, Taroni F, Brandt-Casadevall C, Mangin P (2000) Forensic evaluation of mtDNA in a population from south west Switzerland. Int J Legal Med 113:89-97
9. Dress A, Hendy M, Huber K, Moulton V (1997) On the number of vertices and edges in the Buneman graph. Ann Combin 1:329-337
10. Easton RD, Merriwether DA, Crews DE, Ferrell RE (1996) mtDNA variation in the Yanomami: Evidence for additional New World founding lineages. Am J Hum Genet 59:213-225
11. Graham RL, Knuth DE, Patashnik O (1990) Concrete Mathematics: A Foundation for Computer Science. Addison-Wesley, Reading, MA
12. Hasegawa M, Di Rienzo A, Kocher TD, Wilson AC (1993) Toward a more accurate time scale for the human mitochondrial DNA tree. J Mol Evol 37:347-354
13. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, Ghosh SS, Olefsky JM, Beal MF, Davis RE, Howell N (2002) Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences from the major African, Asian, and European haplogroups. Am J Hum Genet 70:1152-1171 (erratum 71:448-449)
14. Horai S, Hayasaka K (1990) Intraspecific nucleotide sequence differences in the major noncoding region of human mitochondrial DNA. Am J Hum Genet 46:828-842
15. Horai S, Murayama K, Hayasaka K, Matsubayashi S, Hattori Y, Fucharoen G, Harihara S, Park KS, Omoto K, Pan I-H (1996) mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan. Am J Hum Genet 59:579-590
16. Imaizumi K, Parsons TJ, Yoshino M, Holland MM (2002) A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals. Int J Legal Med 116:68-73
17. Ingman M, Kaessmann H, Pääbo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708-713
18. Jakobsen IB, Easteal S (1996) A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput Appl Biosci 12:291-295
19. Lee SD, Shin CH, Kim KB, Lee YS, Lee JB (1997) Sequence variation of mitochondrial DNA control region in Koreans. Forensic Sci Int 87:99-116
20. Malyarchuk BA, Rogozin IB, Berikov VB, Derenko MV (2002) Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region. Hum Genet 111:46-53
21. Merriwether DA, Kemp BM, Crews DE, Neel JV (2000) Gene flow and genetic variation in the Yanomama as revealed by mitochondrial DNA. In: Renfrew C (ed) America Past, America Present: Genes and Languages in the Americas and Beyond. McDonald Institute for Archaeological Research, Cambridge, pp 89-124
22. Meyer S, Weiss G, von Haeseler A (1999) Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152:1103-1110
23. Parson W, Parsons TJ, Scheithauer R, Holland MM (1998) Population data for 101 Austrian Caucasian mitochondrial DNA D-loop sequences: Application of mtDNA sequence analysis to a forensic case. Int J Legal Med 111:124-132
24. Quintana-Murci L, Semino O, Bandelt H-J, Passarino G, McElreavey K, Santachiara-Benerecetti AS (1999) Genetic evidence for an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat Genet 23:437-441
25. Rando JC, Pinto F, González AM, Hernández M, Larruga JM, Cabrera VM, Bandelt H-J (1998) Mitochondrial DNA analysis of Northwest African populations reveals genetic exchanges with European, Near-Eastern, and sub-Saharan populations. Ann Hum Genet 62:531-550
26. Richards M, Macaulay V, Hickey E, Vega E, Sykes B, Guida V, Rengo C, et al (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67:1251-1276
27. Röhl A, Brinkmann B, Forster L, Forster P (2001) An annotated mtDNA database. Int J Legal Med 115:29-39
28. Sajantila A, Lahermo P, Anttinen T, Lukka M, Sistonen P, Savontaus M-L, Aula P, Beckman L, Tranebjaerg L, Gedde-Dahl T, Issel-Tarver L, Di Rienzo A, Pääbo S (1995) Genes and languages in Europe: An analysis of mitochondrial lineages. Genome Res 5:42-52
29. Salas A, Comas D, Lareu MV, Bertranpetit J, Carracedo A (1998) mtDNA analysis of the Galician population: A genetic edge of European variation. Eur J Hum Genet 6:365-375
30. Santos SEB, Ribeiro-dos-Santos AKC, Meyer D, Zago MA (1996) Multiple founder haplotypes of mitochondrial DNA in Amerindians revealed by RFLP and sequencing. Ann Hum Genet 60:305-319
31. Seo Y, Stradmann-Bellinghausen B, Rittner C, Takahama K, Schneider PM (1998) Sequence polymorphism of mitochondrial DNA control region in Japanese. Forensic Sci Int 97:155-164
32. Škrekovski R (2001) Two relations for median graphs. Discrete Math 226:351-353
33. Soltan PS, Chepoi VD (1987) The solution of the Weber problem for discrete median spaces. Trudy Tbilisscogo Mat Inst 85:52-76 (in Russian)
34. Stenico M, Nigro L, Bertorelle G, Calafell F, Capitanio M, Corrain C, Barbujani G (1996) High mitochondrial sequence diversity in linguistic isolates of the Alps. Am J Hum Genet 59:1363-1375
35. Tsai LC, Lin CY, Lee JCI, Chang JG, Linacre A, Goodwin W (2001) Sequence polymorphism of mitochondrial D-loop DNA in the Taiwanese Han population. Forensic Sci Int 119:239-247
36. Vernesi C, Di Benedetto G, Caramelli D, Secchieri E, Simoni L, Katti E, Malaspina P, Novelletto A, Marin VTW, Barbujani G (2001) Genetic characterization of the body attributed to the evangelist Luke. Proc Natl Acad Sci USA 98:13460-13463
37. Vernesi C, Fuselli S, Castrì L, Bertorelle G, Barbujani G. Mitochondrial diversity in linguistic isolates of the Alps: A reappraisal. Hum Biol (in press)
38. Yang Z, Kumar S (1996) Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol Biol Evol 13:650-659
39. Yao Y-G, Kong Q-P, Bandelt H-J, Kivisild T, Zhang Y-P (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70:635-651