Redefinition of hypervariable region I in mitochondrial DNA control region and comparing its diversity among various ethnic groups

Mitochondrion

Volumn 8, Issue 2, 2008, Pages 146-154

  Tzen, Jessica M ^a   Hsu, Hsiu Jun ^b   Wang, Man Ning ^c  

^a Taipei American School   (Taiwan)

^b MACKAY MEMORIAL HOSPITAL   (Taiwan)

^c Prevision Medical Corp   (Taiwan)

Author keywords

Anthropology; Genetic diversity; Hypervariable region I (HVR I); Mitochondrial DNA

Indexed keywords

MITOCHONDRIAL DNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AFRICA; ARTICLE; ASIA; CONTROLLED STUDY; DNA DETERMINATION; DNA EXTRACTION; DNA POLYMORPHISM; DNA SEQUENCE; DNA STRUCTURE; ETHNIC DIFFERENCE; EUROPE; GENETIC CONSERVATION; GENETIC REGULATION; GENETIC VARIABILITY; GEOGRAPHY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; POLYMERASE CHAIN REACTION; POPULATION GENETICS; PRIORITY JOURNAL; WESTERN HEMISPHERE;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; COMPLEMENTARITY DETERMINING REGIONS; DNA, MITOCHONDRIAL; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; FORENSIC ANTHROPOLOGY; FORENSIC SCIENCES; HUMANS; POLYMORPHISM, GENETIC; VARIATION (GENETICS);

EID: 40149110485     PISSN: 15677249     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mito.2007.11.002     Document Type: Article

References (65)

1. Allen M., Engström A.S., Meyers S., Handt O., Saldeen T., von Haeseler A., Pääbo S., and Gyllensten U. Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J. Forensic Sci. 43 (1998) 453-464
2. Árnason E. Genetic heterogeneity of Icelanders. Ann. Hum. Genet. 67 (2003) 5-16
3. Baasner A., Schafer C., Junge A., and Madea B. Polymorphic sites in human mitochondrial DNA control region sequences: population data and maternal inheritance. Forensic Sci. Int. 98 (1998) 169-178
4. Bandelt H.J., Lahermo P., Richards M., and Macaulay V. Detecting errors in mtDNA data by phylogenetic analysis. Int. J. Legal. Med. 115 (2001) 64-69
5. Bandelt H.J., Quintana-Murci L., Salas A., and Macaulay V. The fingerprint of phantom mutations in mitochondrial DNA data. Am. J. Hum. Genet. 71 (2002) 1150-1160
6. Batista O., Kolman C.J., and Bermingham E. Mitochondrial DNA diversity in the Kuna Amerinds of Panama. Hum. Mol. Genet. 4 (1995) 921-929
7. Brakez Z., Bosch E., Izaabel H., Akhayat O., Comas D., Bertranpetit J., and Calafell F. Human mitochondrial DNA sequence variation in the Moroccan population of the Souss area. Ann. Hum. Biol. 28 (2001) 295-307
8. Brandstätter A., Peterson C.T., Irwin J.A., Mpoke S., Koech D.K., Parson W., and Parsons T.J. Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database. Int. J. Legal Med. 118 (2004) 294-306
9. Chen M.H., Lee H.M., and Tzen C.Y. Polymorphism and heteroplasmy of mitochondrial DNA in the D-loop region in Taiwanese. J. Formos. Med. Assoc. 101 (2002) 268-276
10. Comas D., Calafell F., Mateu E., Perez-Lezaun A., and Bertranpetit J. Geographic variation in human mitochondrial DNA control region sequence: the population history of Turkey and its relationship to the European populations. Mol. Biol. Evol. 13 (1996) 1067-1077
11. Cõrte-Real H.B., Macaulay V.A., Richards M.B., Hariti G., Issad M.S., Cambon-Thomsen A., Papiha S., Bertranpetit J., and Sykes B.C. Genetic diversity in the Iberian Peninsula determined from mitochondrial sequence analysis. Ann. Hum. Genet. 60 (1996) 331-350
12. Crespillo M., Luque J.A., Paredes M., Fernandez R., Ramirez E., and Valverde J.L. Mitochondrial DNA sequences for 118 individuals from northeastern Spain. Int. J. Legal Med. 114 (2000) 130-132
13. Delghandi M., Utsi E., and Krauss S. Saami mitochondrial DNA reveals deep maternal lineage clusters. Hum. Hered. 48 (1998) 108-114
14. Dennis C. Error reports threaten to unravel databases of mitochondrial DNA. Nature 421 (2003) 773-774
15. Di Bernardo G., Del Gaudio S., Galderisi U., and Cipollaro M. 2000 Year-old ancient equids: an ancient-DNA lesson from pompeii remains. J. Exp. Zoolog. B. Mol. Dev. Evol. 302 (2004) 550-556
16. Dimo-Simonin N., Grange F., Taroni F., Brandt-Casadevall C., and Mangin P. Forensic evaluation of mtDNA in a population from south west Switzerland. Int. J. Legal Med. 113 (2000) 89-97
17. Doda J.N., Wright C.T., and Clayton D.A. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA 78 (1981) 6116-6120
18. Forster P. To err is human. Ann. Hum. Genet. 67 (2003) 2-4
19. Fucharoen G., Fucharoen S., and Horai S. Mitochondrial DNA polymorphisms in Thailand. J. Hum. Genet. 46 (2001) 115-125
20. Fuselli S., Tarazona-Santos E., Dupanloup I., Soto A., Luiselli D., and Pettener D. Mitochondrial DNA diversity in South America and the genetic history of Andean highlanders. Mol. Biol. Evol. 20 (2003) 1682-1691
21. Graven L., Passarino G., Semino O., Boursot P., Santachiara-Benerecetti S., Langaney A., and Excoffier L. Evolutionary correlation between control region sequence and restriction polymorphisms in the mitochondrial genome of a large Senegalese Mandenka sample. Mol. Biol. Evol. 12 (1995) 334-345
22. Green L.D., Derr J.N., and Knight A. mtDNA affinities of the peoples of North-Central Mexico. Am. J. Hum. Genet. 66 (2000) 989-998
23. Greenberg B.D., Newbold J.E., and Sugino A. Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA. Gene 21 (1983) 33-49
24. Hasegawa M., Di Rienzo A., Kocher T.D., and Wilson A.C. Toward a more accurate time scale for the human mitochondrial DNA tree. J. Mol. Evol. 37 (1993) 347-354
25. Helgason A., Sigureth ardottir S., Gulcher J.R., Ward R., and Stefansson K. mtDNA and the origin of the Icelanders: deciphering signals of recent population history. Am. J. Hum. Genet. 66 (2000) 999-1016
26. Huoponen K., Schurr T.G., Chen Y., and Wallace D.C. Mitochondrial DNA variation in an aboriginal Australian population: evidence for genetic isolation and regional differentiation. Hum. Immunol. 62 (2001) 954-969
27. Kivisild T., Bamshad M.J., Kaldma K., Metspalu M., Metspalu E., Reidla M., Laos S., Parik J., Watkins W.S., Dixon M.E., Papiha S.S., Mastana S.S., Mir M.R., Ferak V., and Villems R. Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages. Curr. Biol. 9 (1999) 1331-1334
28. Kivisild T., Tolk H.V., Parik J., Wang Y., Papiha S.S., Bandelt H.J., and Villems R. The emerging limbs and twigs of the East Asian mtDNA tree. Mol. Biol. Evol. 19 (2002) 1737-1751
29. Kivisild T., Reidla M., Metspalu E., Rosa A., Brehm A., Pennarun E., Parik J., Geberhiwot T., Usanga E., and Villems R. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am. J. Hum. Genet. 75 (2004) 752-770
30. Kolman C.J., Sambuughin N., and Bermingham E. Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics 142 (1996) 1321-1334
31. Krings M., Salem A.E., Bauer K., Geisert H., Malek A.K., Chaix L., Simon C., Welsby D., Di Rienzo A., Utermann G., Sajantila A., Paabo S., and Stoneking M. mtDNA analysis of Nile River Valley populations: a genetic corridor or a barrier to migration?. Am. J. Hum. Genet. 64 (1999) 1166-1176
32. Lee S.D., Shin C.H., Kim K.B., Lee Y.S., and Lee J.B. Sequence variation of mitochondrial DNA control region in Koreans. Forensic Sci. Int. 87 (1997) 99-116
33. Lutz S., Weisser H.J., Heizmann J., and Pollak S. Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany. Int. J. Legal Med. 111 (1998) 67-77
34. Mateu E., Comas D., Calafell F., Perez-Lezaun A., Abade A., and Bertranpetit J. A tale of two islands: population history and mitochondrial DNA sequence variation of Bioko and Sao Tome, Gulf of Guinea. Ann. Hum. Genet. 61 (1997) 507-518
35. Meyer S., Weiss G., and von Haeseler A. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152 (1999) 1103-1110
36. Nasidze I., and Stoneking M. Mitochondrial DNA variation and language replacements in the Caucasus. Proc. Biol. Sci. 268 (2001) 1197-1206
37. Ohno K., Tanaka M., Suzuki H., Ohbayashi T., Ikebe S., Ino H., Kumar S., Takahashi A., and Ozawa T. Identification of a possible control element, Mt5, in the major noncoding region of mitochondrial DNA by intraspecific nucleotide conservation. Biochem. Int. 24 (1991) 263-272
38. Orekhov V., Poltoraus A., Zhivotovsky L.A., Spitsyn V., Ivanov P., and Yankovsky N. Mitochondrial DNA sequence diversity in Russians. FEBS Lett. 445 (1999) 197-201
39. Parson W., Parsons T.J., Scheithauer R., and Holland M.M. 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 (1998) 124-132
40. Pfeiffer H., Steighner R., Fisher R., Mornstad H., Yoon C.L., and Holland M.M. Mitochondrial DNA extraction and typing from isolated dentin-experimental evaluation in a Korean population. Int. J. Legal Med. 111 (1998) 309-313
41. Pfeiffer H., Brinkmann B., Huhne J., Rolf B., Morris A.A., Steighner R., Holland M.M., and Forster P. Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography. Int. J. Legal Med. 112 (1999) 291-298
42. Pfeiffer H., Forster P., Ortmann C., and Brinkmann B. The results of an mtDNA study of 1,200 inhabitants of a German village in comparison to other Caucasian databases and its relevance for forensic casework. Int. J. Legal Med. 114 (2001) 169-172
43. Pereira L., Cunha C., and Amorim A. Predicting sampling saturation of mtDNA haplotypes: an application to an enlarged Portuguese database. Int. J. Legal Med. 118 (2004) 132-136
44. Piercy R., Sullivan K.M., Benson N., and Gill P. The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. Int. J. Legal Med. 106 (1993) 85-90
45. Pult I., Sajantila A., Simanainen J., Georgiev O., Schaffner W., and Paabo S. Mitochondrial DNA sequences from Switzerland reveal striking homogeneity of European populations. Biol. Chem. Hoppe. Seyler. 375 (1994) 837-840
46. Qian Y.P., Chu Z.T., Dai Q., Wei C.D., Chu J.Y., Tajima A., and Horai S. Mitochondrial DNA polymorphisms in Yunnan nationalities in China. J. Hum. Genet. 46 (2001) 211-220
47. Rando J.C., Pinto F., Gonzalez A.M., Hernandez M., Larruga J.M., Cabrera V.M., and Bandelt H.J. Mitochondrial DNA analysis of northwest African populations reveals genetic exchanges with European, near-eastern, and sub-Saharan populations. Ann. Hum. Genet. 62 (1998) 531-550
48. Robin E.D., and Wong R. Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J. Cell. Physiol. 136 (1988) 507-513
49. Rousselet F., and Mangin P. Mitochondrial DNA polymorphisms: a study of 50 French Caucasian individuals and application to forensic casework. Int. J. Legal Med. 111 (1998) 292-298
50. Salas A., Comas D., Lareu M.V., Bertranpetit J., and Carracedo A. mtDNA analysis of the Galician population: a genetic edge of European variation. Eur. J. Hum. Genet. 6 (1998) 365-375
51. Santos S.E., Ribeiro-Dos-Santos A.K., Meyer D., and Zago M.A. Multiple founder haplotypes of mitochondrial DNA in Amerindians revealed by RFLP and sequencing. Ann. Hum. Genet. 60 (1996) 305-319
52. Seo Y., Stradmann-Bellinghausen B., Rittner C., Takahama K., and Schneider P.M. Sequence polymorphism of mitochondrial DNA control region in Japanese. Forensic Sci. Int. 97 (1998) 155-164
53. Stoneking M. Hypervariable sites in the mtDNA control region are mutational hotspots. Am. J. Hum. Genet. 67 (2000) 1029-1032
54. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
55. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
56. Tzen C.Y., Wu T.Y., and Liu H.F. Sequence polymorphism in the coding region of mitochondrial genome encompassing position 8389-8865. Forensic Sci. Int. 120 (2001) 204-209
57. Wakeley J. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37 (1993) 613-623
58. Ward R.H., Frazier B.L., Dew-Jager K., and Paabo S. Extensive mitochondrial diversity within a single Amerindian tribe. Proc. Natl. Acad. Sci. USA 88 (1991) 8720-8724
59. Watson E., Bauer K., Aman R., Weiss G., von Haeseler A., and Paabo S. mtDNA sequence diversity in Africa. Am. J. Hum. Genet. 59 (1996) 437-444
60. Wen B., Xie X., Gao S., Li H., Shi H., Song X., Qian T., Xiao C., Jin J., Su B., Lu D., Chakraborty R., and Jin L. Analyses of genetic structure of Tibeto-Burman populations reveals sex-biased admixture in southern Tibeto-Burmans. Am. J. Hum. Genet. 74 (2004) 856-865
61. Yao Y.G., Lü X.M., Luo H.R., Li W.H., and Zhang Y.P. Gene admixture in the silk road region of China: evidence from mtDNA and melanocortin 1 receptor polymorphism. Genes Genet. Syst. 75 (2000) 173-178
62. Yao Y.G., Watkins W.S., and Zhang Y.P. Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia. Hum. Genet. 107 (2000) 504-512
63. Yao Y.G., Kong Q.P., Bandelt H.J., Kivisild T., and Zhang Y.P. Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am. J. Hum. Genet. 70 (2002) 635-651
64. Yao Y.G., Nie L., Harpending H., Fu Y.X., Yuan Z.G., and Zhang Y.P. Genetic relationship of Chinese ethnic populations revealed by mtDNA sequence diversity. Am. J. Phys. Anthropol. 118 (2002) 63-76
65. Yao Y.G., and Zhang Y.P. Phylogeographic analysis of mtDNA variation in four ethnic populations from Yunnan Province: new data and a reappraisal. J. Hum. Genet. 47 (2002) 311-318