Fragmentation of contaminant and endogenous dna in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  García Garcerà, Marc ^a   Gigli, Elena ^a   Sanchez Quinto, Federico ^a   Ramirez, Oscar ^a   Calafell, Francesc ^a   Civit, Sergi ^b   Lalueza Fox, Carles ^a  

^a INSTITUTE OF EVOLUTIONARY BIOLOGY CSIC UNIVERSITAT POMPEU FABRA   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BLEACHING AGENT; DNA;

ANIMAL TISSUE; ARTICLE; BONE; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA CONTAMINATION; DNA DEPURINATION; DNA FRAGMENTATION; DNA SEQUENCE; EXTINCT SPECIES; GENETIC PROCEDURES; GENOMICS; GOAT; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; LYNX; MYOTRAGUS BALEARICUS; NEANDERTAL; NEOLITHIC; NONHUMAN; PALEOGENOMICS; PALEONTOLOGY; PREHISTORIC PERIOD; PYROSEQUENCING; SPAIN; ANIMAL; FOSSIL; GENETICS; METHODOLOGY;

CAPRA HIRCUS; LYNX; MYOTRAGUS BALEARICUS;

ANIMALS; DNA; FOSSILS; GENOMICS; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 80052307945     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024161     Document Type: Article

References (28)

1. Cooper A, Poinar HN, (2000) Ancient DNA: do it right or not at all. Science 289: 1139.
2. 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 (23): 4793-4799.
3. Hofreiter M, Serre D, Poinar HN, Kuch M, Pääbo S, (2001b) Ancient DNA. Nat Rev Genet 2 (5): 353-359.
4. Malmström H, Svensson EM, Gilbert MTP, Willerslev E, Götherström A, et al. (2007) More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA. Mol Biol Evol 24 (4): 998-1004.
5. Fortea J, de la Rasilla M, García-Tabernero A, Gigli E, Rosas A, et al. (2008) Excavation protocol of bone remains for Neandertal DNA analysis in El Sidrón Cave (Asturias, Spain). J Hum Evol 55 (2): 353-357.
6. Sampietro ML, Gilbert MPT, Lao O, Caramelli D, Lari M, et al. (2006) Tracking down Human Contamination in Ancient Human Teeth. Mol Biol Evol 23 (9): 1801-1807.
7. Helgason A, Pálsson S, Lalueza-Fox C, Ghosh S, Sigur{eth}ardóttir S, et al. (2007) A statistical approach to identify ancient template DNA. J Mol Evol 65: 92-102.
8. Vives S, Gilbert MT, Arenas C, Gigli E, Lao O, et al. (2008) Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA. BMC Res Notes 1: 40.
9. Lindahl T, (1993) Recovery of antediluvian DNA. Nature 365: 700.
10. Miller W, Drautz DI, Ratan A, Pusey B, Qi J, et al. (2008) Sequencing the nuclear genome of the extinct wolly mammoth. Nature 456 (7220): 387-90.
11. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463 (7282): 757-762.
12. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722.
13. Reich D, Green RE, Kircher M, Krause J, Patterson N, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468 (7327): 1053-1060.
14. Green RE, Malaspinas AS, Krause J, Briggs A, Johnson PLF, et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134 (3): 416-426.
15. Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, et al. (2009) The Neandertal genome and ancient DNA authenticity. EMBO J 28 (17): 494-502.
16. Wall JD, Kim SK, (2007) Inconsistencies in the Neanderthal genomic DNA sequences. Plos Genet 3 (10): e175.
17. Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA 104 (37): 14616-14621.
18. Ginolhac A, Rasmussen M, Gilbert MTP, Willerslev E, Orlando L, (2011) mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics in press. PMID: 21659319, doi: 10.1093/bioinformatics/btr347.
19. Briggs AW, Good JM, Green RE, Krause J, Maricic T, et al. (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325 (5938): 318-321.
20. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, et al. (2010) A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol 20 (3): 231-237.
21. Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, et al. (in press) True Single-Molecule DNA Sequencing of a Pleistocene Horse bone. Gen Res.
22. Lalueza-Fox C, Castresana J, Sampietro L, Marqués-Bonet T, Alcover JA, et al. (2005) Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, en extinct endemic Balearic mammal. BMC Evol Biol 5: 70.
23. Ramírez O, Gigli E, Bover P, Alcover JA, Bertranpetit J, et al. (2009) Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. PloS One 22;4 (5): e5670.
24. Rodríguez R, Ramírez O, Valdiosera CE, García N, Alda F, et al. (in press) 50,000 years of genetic uniformity in the critically endangered Iberian lynx. Mol Ecol.
25. Sampietro ML, Lao O, Caramelli D, Lari M, Pou R, et al. (2007) Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe. Proc R Soc B 274 (1622): 2161-2167.
26. Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, et al. (2005) Genomic sequencing of Pleistocene cave bears. Science 309 (5734): 597-599.
27. Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, et al. (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311 (5759): 392-394.
28. Blow MJ, Zhang T, Woyke T, Speller CF, Krivoshapkin A, et al. (2008) Identification of the source of ancient remains through genomic sequencing. Gen Res 18 (8): 1347-1353.