Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 39, 2013, Pages 15758-15763

  Dabney, Jesse ^a   Knapp, Michael ^b,c   Glocke, Isabelle ^a   Gansauge, Marie Theres ^a   Weihmann, Antje ^a   Nickel, Birgit ^a   Valdiosera, Cristina ^d,e   García, Nuria ^d,f   Pääbo, Svante ^a   Arsuaga, Juan Luis ^d,f   Meyer, Matthias ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b BANGOR UNIVERSITY   (United Kingdom)

^c UNIVERSITY OF OTAGO   (New Zealand)

^d Centro UCM ISCIII para la Evolución y Comportamiento Humanos   (Spain)

^e LA TROBE UNIVERSITY   (Australia)

^f UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT;

ARTICLE; BEAR; DNA EXTRACTION; DNA LIBRARY; DNA SEQUENCE; GENE SEQUENCE; MIDDLE PLEISTOCENE; MITOCHONDRIAL GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PERMAFROST; PHYLOGENY; PLEISTOCENE; PRIORITY JOURNAL; UPPER PLEISTOCENE;

ANIMALS; BASE SEQUENCE; CAVES; DNA; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; TIME FACTORS; URSIDAE;

EID: 84884624229     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1314445110     Document Type: Article

References (49)

1. Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362(6422):709-715.
2. Briggs AW, et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA 104(37):14616-14621.
3. Allentoft ME, et al. (2012) The half-life of DNA in bone: Measuring decay kinetics in 158 dated fossils. Proc Biol Sci 279(1748):4724-4733.
4. Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S (2012) Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7(3): e34131.
5. Smith CI, Chamberlain AT, Riley MS, Stringer C, Collins MJ (2003) The thermal history of human fossils and the likelihood of successful DNA amplification. J Hum Evol 45(3): 203-217.
6. Willerslev E, et al. (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300(5620):791-795.
7. Willerslev E, et al. (2007) Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science 317(5834):111-114.
8. Orlando L, et al. (2013) Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature 499(7456):74-78.
9. Orlando L, et al. (2006) Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence. Curr Biol 16(11):R400-R402.
10. Lindqvist C, et al. (2010) Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci USA 107(11):5053-5057.
11. Valdiosera C, et al. (2006) Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA. Biol Lett 2(4):601-603.
12. Krause J, et al. (2010) A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol 20(3):231-236.
13. Miller W, et al. (2008) Sequencing the nuclear genome of the extinct woolly mammoth. Nature 456(7220):387-390.
14. Rasmussen M, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463(7282):757-762.
15. Green RE, et al. (2010) A draft sequence of the Neandertal genome. Science 328(5979):710-722.
16. Meyer M, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338(6104):222-226.
17. Keller A, et al. (2012) New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3:698.
18. Rohland N, Hofreiter M (2007) Ancient DNA extraction from bones and teeth. Nat Protoc 2(7):1756-1762.
19. Rohland N, Hofreiter M (2007) Comparison and optimization of ancient DNA extraction. Biotechniques 42(3):343-352.
20. Reich D, et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468(7327):1053-1060.
21. Gansauge MT, Meyer M (2013) Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8(4):737-748.
22. Maricic T, Whitten M, Pääbo S (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS ONE 5(11):e14004.
23. Fu Q, et al. (2013) DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci USA 110(6):2223-2227.
24. Krause J, et al. (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol 8:220.
25. Orlando L, et al. (2011) True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res 21(10):1705-1719.
26. Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402.
27. Garcia N, Arsuaga JL (2001) Ursus dolinensis: A new species of early pleistocene ursid from Trinchera Dolina, Atapuerca (Spain). Cr Acad Sci Ii A 332(11):717-725.
28. Carbonell E, et al. (2008) The first hominin of Europe. Nature 452(7186):465-469.
29. Garcia N (2004) New results on the remains of Ursidae from Untermassfeld: Comparisons with Ursus dolinensis from Atapuerca and other early and middle Pleistocene sites. Late Neogene and Quaternary Biodiversity and Evolution: Regional Developments and Interregional Correlations Conference, 18th International Senckenberg Conference, Weimar, Germany, eds Kahlke R-D, Maul LC, Mazza PP (Terra Nostra, Schriften der Alfred-Wegener-Stiftung, Berlin), pp 112-113.
30. Kahlke R-D (2006) Untermassfeld: A Late Early Pleistocene (Epivillafranchian) Fossil Site Near Meiningen (Thuringia, Germany) and its Position in the Development of the European Mammal Fauna (Archaeopress, Oxford).
31. García N, Arsuaga JL, Torres T (1997) The carnivore remains from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain). J Hum Evol 33(2-3): 155-174.
32. Pacher M, Stuart AJ (2009) Extinction chronology and palaeobiology of the cave bear (Ursus spelaeus). Boreas 38(2):189-206.
33. Hofreiter M, et al. (2004) Evidence for reproductive isolation between cave bear populations. Curr Biol 14(1):40-43.
34. Baryshnikov G (1998) Cave bears from the Paleolithic of the Greater Caucasus. Quaternary Paleozoology in the Northern Hemisphere, eds Saunders JJ, Styles BW, Baryshnikov GF (Illinois State Museum, Springfield, IL), pp 69-118.
35. Knapp M, et al. (2009) First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Mol Ecol 18(6):1225-1238.
36. Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M (2009) Direct multiplex sequencing (DMPS)-a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res 19(10):1843-1848.
37. Bon C, et al. (2008) Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet. Proc Natl Acad Sci USA 105(45):17447-17452.
38. Bischoff JL, et al. (1997) Geology and preliminary dating of the hominid-bearing sedimentary fill of the Sima de los Huesos Chamber, Cueva Mayor of the Sierra de Atapuerca, Burgos, Spain. J Hum Evol 33(2-3):129-154.
39. Garcia N, Arsuaga JL (2011) The Sima de los Huesos (Burgos, northern Spain): Palaeoenvironment and habitats of Homo heidelbergensis during the Middle Pleistocene. Quat Sci Rev 30(11-12):1413-1419.
40. Shapiro B, et al. (2011) A Bayesian phylogenetic method to estimate unknown sequence ages. Mol Biol Evol 28(2):879-887.
41. Bischoff JL, et al. (2007) High-resolution U-series dates from the Sima de los Huesos hominids yields: Implications for the evolution of the early Neanderthal lineage. J Archaeol Sci 34(5):763-770.
42. Arsuaga JL, et al. (1997) Sima de los Huesos (Sierra de Atapuerca, Spain). The site. J Hum Evol 33(2-3):109-127.
43. Dabney J, Meyer M (2012) Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52(2):87-94.
44. Kircher M, Sawyer S, Meyer M (2012) Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40(1):e3.
45. Kircher M, Heyn P, Kelso J (2011) Addressing challenges in the production and analysis of Illumina sequencing data. BMC Genomics 12:382.
46. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754-1760.
47. Kircher M (2012) Analysis of high-throughput ancient DNA sequencing data. Methods Mol Biol 840:197-228.
48. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 30(4):772-780.
49. Keis M (2013) Brown bear (Ursus arctos) phylogeography in northern Eurasia. Doctoral dissertation (Univ of Tartu, Tartu, Estonia).