A reduced number of mtSNPs saturates mitochondrial DNA haplotype diversity of worldwide population groups

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Salas, Antonio ^a   Amigo, Jorge ^a  

^a UNIVERSITY OF SANTIAGO DE COMPOSTELA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AFRICA; AFRICAN AMERICAN; ALGORITHM; ARTICLE; ASIA; CONTROLLED STUDY; EUROPE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; HAPLOTYPE; HISPANIC; HUMAN; MITOCHONDRION; POPULATION GENETICS; POPULATION RESEARCH; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; COMPUTER SIMULATION; ETHNIC AND RACIAL GROUPS; GENETICS; INTERNATIONAL COOPERATION; MOLECULAR EVOLUTION;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; HUMANS; INTERNATIONALITY; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROUPS;

EID: 77956296353     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010218     Document Type: Article

References (53)

1. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, et al. (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308: 1034-1036.
2. Macaulay V, Richards M, Hickey E, Vega E, Cruciani F, et al. (1999) The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. Am J Hum Genet 64: 232-249.
3. Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M, et al. (2009) Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Curr Biol 19: 1-8.
4. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, et al. (2002) Reduced-median-network analysis of complete mitochondrial DNA codingregion sequences from the major African, Asian, and European haplogroups. Am J Hum Genet 70: 1152-1171.
5. Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, et al. (2008) The dawn of human matrilineal diversity. Am J Hum Genet 82: 1130-1140.
6. Torroni A, Achilli A, Macaulay V, Richards M, Bandelt H-J (2006) Harvesting the fruit of the human mtDNA tree. Trends Genet 22: 339-345.
7. Salas A, Richards M, De la Fé T, Lareu MV, Sobrino B, et al. (2002) The making of the African mtDNA landscape. Am J Hum Genet 71: 1082-1111.
8. Richards M, Macaulay V, Hickey E, Vega E, Sykes B, et al. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67: 1251-1276.
9. Baudouin SV, Saunders D, Tiangyou W, Elson JL, Poynter J, et al. (2005) Mitochondrial DNA and survival after sepsis: a prospective study. Lancet 366: 2118-2121.
10. Achilli A, Perego UA, Bravi CM, Coble MD, Kong Q-P, et al. (2008) The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies. PLoS ONE 3: e1764.
11. Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, et al. (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet 75: 752-770.
12. Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, et al. (2003) The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72: 313-332.
13. Torroni A, Bandelt H-J, D'Urbano L, Lahermo P, Moral P, et al. (1998) mtDNA analysis reveals a major late Paleolithic population expansion from southwestern to northeastern Europe. Am J Hum Genet 62: 1137-1152.
14. Torroni A, Bandelt H-J, Macaulay V, Richards M, Cruciani F, et al. (2001) A signal, from human mtDNA, of postglacial recolonization in Europe. Am J Hum Genet 69: 844-852.
15. Chinnery PF, Howell N, Andrews RM, Turnbull DM (1999) Clinical mitochondrial genetics. J Med Genet 36: 425-436.
16. Chinnery PF, Howell N, Andrews RM, Turnbull DM (1999) Mitochondrial DNA analysis: polymorphisms and pathogenicity. J Med Genet 36: 505-510.
17. Chinnery PF, Johnson MA, Wardell TM, Singh-Kler R, Hayes C, et al. (2000) The epidemiology of pathogenic mitochondrial DNA mutations. Ann Neurol 48: 188-193.
18. Carelli V, Giordano C, d'Amati G (2003) Pathogenic expression of homoplasmic mtDNA mutations needs a complex nuclear-mitochondrial interaction. Trends Genet 19: 257-262.
19. Salas A, Bandelt H-J, Macaulay V, Richards MB (2007) Phylogeographic investigations: the role of trees in forensic genetics. Forensic Sci Int 168: 1-13.
20. Barros F, Lareu MV, Salas A, Carracedo A (1997) Rapid and enhanced detection of mitochondrial DNA variation using single-strand conformation analysis of superposed restriction enzyme fragments from polymerase chain reaction-amplified products. Electrophoresis 18: 52-54.
21. Salas A, Rasmussen EM, Lareu MV, Morling N, Carracedo Á (2001) Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation. Forensic Sci Int 124: 97-103.
22. Álvarez-Iglesias V, Barros F, Carracedo Á, Salas A (2008) Minisequencing mitochondrial DNA pathogenic mutations. BMC Med Genet 9: 26.
23. Quintáns B, Álvarez-Iglesias V, Salas A, Phillips C, Lareu MV, et al. (2004) Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci Int 140: 251-257.
24. Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, et al. (2004) Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Legal Med 118: 137-146.
25. Brandstätter A, Salas A, Niederstätter H, Gassner C, Carracedo Á, et al. (2006) Dissection of mitochondrial superhaplogroup H using coding region SNPs. Electrophoresis 27: 2541-2550.
26. Mosquera-Miguel A, Álvarez-Iglesias V, Lareu MV, Carracedo Á, Salas A (2009) Testing the performance of mtSNP minisequencing in forensic samples. Forensic Sci Int Genet 3: 261-264.
27. Cerezo M, Černý V, Carracedo Á, Salas A (2009) Applications of MALDI-TOF MS to large-scale human mtDNA population-based studies. Electrophoresis 30: 3665-3673.
28. Bandelt H-J, Kong Q-P, Richards M, Macaulay V (2006) Estimation of mutation rates and coalescence times: some caveats. In: Bandelt H-J, Richards M, Macaulay V, eds. Human mitochondrial DNA and the evolution of Homo sapiens. Berlin: Springer-Verlag. pp 47-90.
29. Soares P, Ermini L, Thomson N, Mormina M, Rito T, et al. (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84: 740-759.
30. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, et al. (2008) Climate change and postglacial human dispersals in southeast Asia. Mol Biol Evol 25: 1209-1218.
31. Achilli A, Rengo C, Battaglia V, Pala M, Olivieri A, et al. (2005) Saami and Berbers-an unexpected mitochondrial DNA link. Am J Hum Genet 76: 883-886.
32. Olivieri A, Achilli A, Pala M, Battaglia V, Fornarino S, et al. (2006) The mtDNA legacy of the Levantine early Upper Palaeolithic in Africa. Science 314: 1767-1770.
33. Kivisild T, Tolk H-V, Parik J, Wang Y, Papiha SS, et al. (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19: 1737-1751.
34. Brisighelli F, Capelli C, Álvarez-Iglesias V, Onofri V, Paoli G, et al. (2009) The Etruscan timeline: a recent Anatolian connection. Eur J Hum Genet 17: 693-696.
35. Álvarez-Iglesias V, Mosquera-Miguel A, Cerezo M, Quintáns B, Zarrabeitia MT, et al. (2009) New population and phylogenetic features of the internal variation within mitochondrial DNA macro-haplogroup R0. PLoS ONE 4: e5112.
36. Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, et al. (2008) Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci U S A 105: 1596-1601.
37. Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V (2002) The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71: 1150-1160.
38. Tanaka M, Cabrera VM, González AM, Larruga JM, Takeyasu T, et al. (2004) Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res 14: 1832-1850.
39. FinniläS, Lehtonen MS, Majamaa K (2001) Phylogenetic network for European mtDNA. Am J Hum Genet 68: 1475-1484.
40. Just RS, Diegoli TM, Saunier JL, Irwin JA, Parsons TJ (2008) Complete mitochondrial genome sequences for 265 African American and U.S. "Hispanic" individuals. Forensic Sci Int Genet 2: e45-48.
41. Yao Y-G, Salas A, Logan I, Bandelt H-J (2009) mtDNA data-mining in GenBank needs surveying. Am J Hum Genet in press.
42. Kong Q-P, Salas A, Sun C, Fuku N, Tanaka M, et al. (2008) Distilling artificial recombinants from large sets of complete mtDNA genomes. PLoS ONE 3: e3016.
43. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23: 147.
44. Ewens WJ (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology 3: 87-112.
45. Egeland T, Salas A (2008) Statistical evaluation of haploid genetic evidence. TOForensicSJ 1: 4-11.
46. Egeland T, Salas A (2008) Estimating haplotype frequency and coverage of databases. PLoS ONE 3: e3988.
47. Álvarez-Iglesias V, Jaime JC, Carracedo Á, Salas A (2007) Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Sci Int Genet 1: 44-55.
48. Salas A, Yao Y-G, Macaulay V, Vega A, Carracedo Á, et al. (2005) A critical reassessment of the role of mitochondria in tumorigenesis. PLoS Med 2: e296.
49. Vega A, Salas A, Gamborino E, Sobrido MJ, Macaulay V, et al. (2004) mtDNA mutations in tumors of the central nervous system reflect the neutral evolution of mtDNA in populations. Oncogene 23: 1314-1320.
50. Cerezo M, Bandelt H-J, Martin-Guerrero I, Ardanaz M, Vega A, et al. (2009) High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia. PLoS One 4: e7902.
51. Salas A, Carracedo Á, Macaulay V, Richards M, Bandelt H-J (2005) A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun 335: 891-899.
52. Yao Y-G, Bravi CM, Bandelt H-J (2004) A call for mtDNA data quality control in forensic science. Forensic Sci Int 141: 1-6.
53. Bandelt H-J, Olivieri A, Bravi C, Yao Y-G, Torroni A, et al. (2007) 'Distorted' mitochondrial DNA sequences in schizophrenic patients. Eur J Hum Genet 15: 400-402; author reply 402-404.