Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations

PLoS ONE

Volumn 1, Issue 1, 2006, Pages

  Endicott, Phillip ^a   Metspalu, Mait ^b   Stringer, Chris ^c   Macaulay, Vincent ^d   Cooper, Alan ^e   Sanchez, Juan J ^f  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF TARTU   (Estonia)

^c DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^d UNIVERSITY OF GLASGOW   (United Kingdom)

^e UNIVERSITY OF ADELAIDE   (Australia)

^f Biology Section Apdo 863 E 41080   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AFRICA; ARTICLE; DNA FINGERPRINTING; ETHNIC GROUP; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; INDIAN; MIGRATION; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH ASIA; UPPER PLEISTOCENE; ASIAN; GENETICS; HISTORY; INDIA; PHYLOGENY; POLYMERASE CHAIN REACTION;

ASIAN CONTINENTAL ANCESTRY GROUP; DNA, MITOCHONDRIAL; GENETICS, POPULATION; HISTORY, 19TH CENTURY; HISTORY, ANCIENT; HUMANS; INDIA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 54949151060     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000081     Document Type: Article

References (55)

1. Torroni A, Achilli A, Macaulay V, Richards M, Bandelt HJ (2006) Harvesting the fruit of the human mtDNA tree. Trends in Genetics in press.
2. Bandelt HJ, Salas A, Bravi C (2004) Problems in FBI mtDNA database. Science 305: 1402-1404.
3. Bandelt HJ, Salas A, Lutz-Bonengel S (2004) Artificial recombination in forensic mtDNA population databases. Int J Legal Med 118: 267-273.
4. Bandelt HJ, Kong QP, Parson W, Salas A (2005) More evidence for nonmaternal inheritance of mitochondrial DNA? J Med Genet 42: 957-960.
5. Bandelt HJ, Hermstadt C, Yao YG, Kong QP, Kivisild T, et al. (2003) Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann Hum Genet 67: 512-524.
6. Bandelt HJ (2004) Etruscan artifacts. Am J Hum Genet 75: 919-920; author reply 923-917.
7. Brandsättter A, Parson W (2003) Mitochondrial DNA heteroplasmy or artefacts-a matter of the amplification strategy? Int J Legal Med 117: 180-184.
8. Yao YG, Macauley V, Kivisild T, Zhang YP, Bandelt HJ (2003) To trust or not to trust an idiosyncratic mitochondrial data set. Am J Hum Genet 72: 1341-1346; author reply 1346-1349.
9. Poropanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6: 847-859.
10. Bandelt HJ, Kivisild T (2006) Quality assessment of DNA sequence data: autopsy of a mis-sequenced mtDNA population sample. Ann Hum Genet 70: 314-326.
11. Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6: 165-183.
12. Behar DM, Metspalu E, Kivisild T, Achilli A, Hadid Y, et al. (2006) The matrilincal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am J Hum Genet 78: 487-497.
13. Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, et al. (2005) Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310: 1016-1018.
14. Cordaux R, Stoneking M (2003) South Asia, the Andamanese, and the genetic evidence for an "early" human dispersal out of Africa. Am J Hum Genet 72: 1586-1590; author reply 1590-1583.
15. Field JS, Lahr MM (2005) Assessment of the southern dispersal: GIS-based analyses of potential routes at oxygen isotopic stage. Journal of World Prehistory 19: 1-45.
16. Forster P, Matsumura S (2005) Evolution. Did early humans go north or south? Science 308: 965-966.
17. Mellars P (2006) Why did modern human populations disperse from Africa ca. 60,000 years ago? A new model. Proc Natl Acad Sci U S A 103: 9381-9386.
18. Endicott P, Gilbert MT, Stringer C, Lalueza-Fox C, Willerslev E, et al. (2003) The genetic origins of the Andaman Islanders. Am J Hum Genet 72: 178-184.
19. Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC, et al. (2003) Genetic affinities of the Andaman Islanders, a vanishing human population. Curr Biol 13: 86-93.
20. Thangaraj K, Chaubey G, Reddy AG, Singh VK, Singh L (2006) Autosomal STR data on the enigmatic Andaman Islanders. Forensic Sci Int.
21. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, et al. (2004) Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet 5: 26.
22. Sun C, Kong QP, Palanichamy MG, Agrawal S, Bandelt HJ, et al. (2006) The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol Biol Evol 23: 683-690.
23. Thangaraj K, Chaubey G, Kivisild T, Reddy AC, Singh VK, et al. (2005) Reconstructing the origin of Andaman Islanders. Science 308: 996.
24. Palanichamy MG, Agrawal S, Yao YC, Kong QP, Sun C, et al. (2006) Comment on "Reconstructing the origin of Andaman islanders". Science 311: 470; author reply 470.
25. Salas A, Carracedo A, Macaulay V, Richards M, Bandelt HJ (2005) A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun 335: 891-899.
26. Bandelt HJ, Quintana-Murci L, Salas A, Macaulay V (2002) The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71: 1150-1160.
27. Bandelt HJ, Lahermo P, Richards M, Macaulay V (2001) Detecting errors in mtDNA data by phylogenetic analysis. Int J Legal Med 115: 64-69.
28. Bandelt HJ, Achilli A, Kong QP, Salas A, Lutz-Bonengel S, et al. (2005) Low "penetrance" of phylogenetic knowledge in mitochondrial disease studies. Biochem Biophys Res Common 333: 122-130.
29. Yao YG, Salas A, Bravi CM, Bandelt HJ (2006) A reappraisal of complete mtDNA variation in East Asian families with hearing impairment. Hum Genet 119: 505-515.
30. Cooper A, Poinar HN (2000) Ancient DNA. do it right or not at all. Science 289: 1139.
31. Bandelt HJ (2005) Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity. Eur J Hum Genet 13: 1106-1112.
32. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, et al. (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38: 645-679.
33. Sanchez JJ, Borsting C, Morling N (2005) Typing of Y chromosome SNPs with multiplex PCR methods. Methods Mol Biol 297: 209-228.
34. Syävnen AC (1999) From gels to chips: "minisequencing" primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 13: 1-10.
35. Vallone PM, Buder JM (2004) Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension. J Forensic Sci 49: 723-732.
36. Syvänen AC, Sajantila A, Lukka M (1993) Forensic DNA typing by the solid-phase minisequencing method. Exs 67: 275-282.
37. 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.
38. Umetsu K, Tanaka M, Yuasa I, Adachi N, Miyoshi A, et al. (2005) Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations. Electrophoresis 26: 91-98.
39. Brandstätter A, Salas A, Niederstatter H, Gassner C, Carracedo A, et al. (2006) Dissection of mitochondrial superhaplogroup H using coding region SNPs. Electrophoresis.
40. Quintans B, Alvarez-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.
41. Krause J, Dear PH, Pollack JL, Slatkin M, Spriggs H, et al. (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439: 724-727.
42. Sanchez JJ, Endicott P (2006) Developing high-definition multiplexed SNP assays wth special reference to degraded DNA templates. Nature Protocols: in press.
43. 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.
44. Bower MA, Spencer M, Matsumura S, Nisbet RE, Howe CJ (2005) How many clones need to be sequenced from a single forensic or ancient DNA sample in order to determine a reliable consensus sequence? Nucleic Acids Res 33: 2549-2556.
45. Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, et al. (2003) Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences. Am J Hum Genet 73: 671-676.
46. Portman MV (1990 [1899]) A history of our relations with the Andamanese. New Delhi: Asian Educational Services.
47. Man EH (1932 [1884]) On the aboriginal inhabitants of the Andaman Islands. London: Royal Anthropological Insitutue of Great Britain and Ireland.
48. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, et al. (2003) Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci U S A 100: 171-176.
49. Sampietro ML, Gilbert MT, Lao O, Caramelli D, Lari M, et al. (2006) Tracking down human contamination in ancient human teeth. Mol Biol Evol 23: 1801-1807.
50. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning. A Laboratory Manual. Cold Spring HarborNY: Cold Spring Harbor Laboratory.
51. 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.
52. Barnard R, Futo V, Pecheniuk N, Slattery M, Walsh T (1998) PCR bias toward the wild-type k-ras and p53 sequences: implications for PCR detection of mutations and cancer diagnosis. Biotechniques 25: 684-691.
53. Haff LA, Smirnov IP (1997) Multiplex genotyping of PCR products with Mass Tag-labeled primers. Nucleic Acids Res 25: 3749-3750.
54. Norton N, Williams NM, Williams HJ, Spurlock G, Kirov G, et al. (2002) Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum Genet 110: 471-478.
55. Gilbert MT, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20: 541-544.