A statistical approach to identify ancient template DNA

Journal of Molecular Evolution

Volumn 65, Issue 1, 2007, Pages 92-102

  Helgason, Agnar ^a   Pálsson, Snæbjörn ^a,b   Lalueza Fox, Carles ^c   Ghosh, Shyamali ^a   Siguroardóttir, Sigrún ^a   Baker, Adam ^a   Hrafnkelsson, Birgir ^b   Árnadóttir, Lilja ^d   Porsteinsdóttir, Unnur ^a   Stefánsson, Kári ^a  

^a DECODE GENETICS   (Iceland)

^b UNIVERSITY OF ICELAND   (Iceland)

^c UNIVERSITY OF BARCELONA   (Spain)

^d Pjoominjasafn Islands   (Iceland)

Author keywords

Ancient DNA; Authentication; Postmortem damage; Statistical method

Indexed keywords

CYTOSINE DEAMINASE; DNA; NUCLEOTIDE;

AMINO ACID COMPOSITION; ARTICLE; AUTOPSY; DNA DETERMINATION; DNA SEQUENCE; GENE AMPLIFICATION; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; PROTEIN MOTIF; STATISTICAL ANALYSIS;

DATA INTERPRETATION, STATISTICAL; DNA; DNA DAMAGE; HUMANS; MITOCHONDRIA; MODELS, STATISTICAL; POSTMORTEM CHANGES;

EID: 34547656210     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-006-0259-8     Document Type: Article

References (30)

1. Abbott A (2003) Anthropologists cast doubt on human DNA evidence. Nature 423:468
2. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48
3. Binladen J, Wiuf C, Gilbert MT, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SY, Hansen AJ, Willerslev E (2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172:733-741
4. 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
5. Caramelli D, Lalueza-Fox C, Condemi S, Longo L, Milani L, Manfredini A, de Saint Pierre M, Adoni F, Lari M, Giunti P, Ricci S, Casoli A, Calafell F, Mallegni F, Bertranpetit J, Stanyon R, Bertorelle G, Barbujani G (2006) A highly divergent mtDNA sequence in a Neandertal individual from Italy. Curr Biol 16:R630-R632
6. Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res 35:1-10
7. Gilbert MT, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, Lynnerup N, Cooper A (2003) Characterization of genetic miscoding lesions caused by postmortem damage. Am J Hum Genet 72:48-61
8. Gilbert MTP, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541-544
9. Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, Simons JF, Du L, Egholm M, Rothberg JM, Paunovic M, Paabo S (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444:330-336
10. Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tanzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, Burger J (2005) Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310:1016-1018
11. Handt O, Krings M, Ward RH, Pääbo S (1996) The retrieval of ancient human DNA sequences. Am J Hum Genet 59:368-376
12. Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P (2001) Statistical evidence for miscoding lesions in ancient DNA templates. Mol Biol Evol 18:262-265
13. Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, Gilichinsky DA, Ronn R, Willerslev E (2006) Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics 173:1175-1179
14. Hebsgaard MB, Phillips MJ, Willerslev E (2005) Geologically ancient DNA: Fact or artefact? Trends Microbiol 13:212-220
15. Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Pääbo S (2001a) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29:4793-4799
16. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S (2001b) Ancient DNA. Nat Rev Genet 2:353-359
17. Krings M, Stone A, Schmitz RW, Krainitzki H, Stoneking M, Pääbo S (1997) Neandertal DNA sequences and the origin of modern humans. Cell 90:19-30
18. Mitchell D, Willerslev E, Hansen A (2005) Damage and repair of ancient DNA. Mutat Res 571:265-276
19. Pääbo S (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 86:1939-1943
20. Pääbo S, Irwin DM, Wilson AC (1990) DNA damage promotes jumping between templates during enzymatic amplification. J Biol Chem 265:4718-4721
21. Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M (2004) Genetic analyses from ancient DNA. Annu Rev Genet 38:645-679
22. Rollo F, Ermini L, Luciani S, Marota I, Olivieri C, Luiselli D (2006) Fine characterization of the Iceman's mtDNA haplogroup. Am J Phys Anthropol 130:557-564
23. Rudbeck L, Gilbert MT, Willerslev E, Hansen AJ, Lynnerup N, Christensen T, Dissing J (2005) mtDNA analysis of human remains from an early Danish Christian cemetery. Am J Phys Anthropol 128:424-429
24. Sampietro ML, Gilbert MT, Lao O, Caramelli D, Lari M, Bertranpetit J, Lalueza-Fox C (2006) Tracking down human contamination in ancient human teeth. Mol Biol Evol 23:1801-1807
25. Schmitz RW, Serre D, Bonani G, Feine S, Hillgruber F, Krainitzki H, Pääbo S, Smith FH (2002) The Neandertal type site revisited: interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc Natl Acad Sci USA 99:13342-13347
26. Serre D, Langaney A, Chech M, Teschler-Nicola M, Paunovic M, Mennecier P, Hofreiter M, Possnert GG, Pääbo S (2004) No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol 2:E57
27. Smith CI, Chamberlain AT, Riley MS, Cooper A, Stringer CB, Collins MJ (2001) Neanderthal DNA. Not just old but old and cold? Nature 410:771-772
28. Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keats SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, Wuenschell GE, Termini J, Hofreiter M, Jaenicke-Despres V, Pääbo S (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci USA 103:13578-13584
29. Topf AL, Gilbert MT, Dumbacher JP, Hoelzel AR (2006) Tracing the phylogeography of human populations in Britain based on 4th-11th century mtDNA genotypes. Mol Biol Evol 23:152-161
30. Willerslev E, Cooper A (2005) Ancient DNA. Proc Biol Sci 272:3-16