Ancient DNA Analysis Affirms the Canid from Altai as a Primitive Dog

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Druzhkova, Anna S ^a   Thalmann, Olaf ^b   Trifonov, Vladimir A ^a   Leonard, Jennifer A ^c   Vorobieva, Nadezhda V ^a   Ovodov, Nikolai D ^d   Graphodatsky, Alexander S ^a   Wayne, Robert K ^e  

^a INSTITUTE OF MOLECULAR AND CELLULAR BIOLOGY   (Russian Federation)

^b UNIVERSITY OF TURKU   (Finland)

^c DEPARTMENT OF CONSERVATION BIOLOGY   (Spain)

^d INSTITUTE OF ARCHAEOLOGY AND ETHNOGRAPHY   (Russian Federation)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ANIMAL TISSUE; ARTICLE; CLADISTICS; DNA DETERMINATION; DNA ISOLATION; DNA SEQUENCE; DOMESTIC ANIMAL; DOMESTICATION; FOSSIL ANIMAL; GENETIC ANALYSIS; HAPLOTYPE; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLEISTOCENE; PLESIOMORPHY; PREHISTORIC PERIOD; REGULATOR GENE; RUSSIAN FEDERATION;

ANIMALS; ASIA; BASE SEQUENCE; DNA; DNA, MITOCHONDRIAL; DOGS; EXTINCTION, BIOLOGICAL; GENOME, MITOCHONDRIAL; GEOGRAPHY; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; WOLVES;

EID: 84874589706     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0057754     Document Type: Article

References (30)

1. Vila C, Savolainen P, Maldonado JE, Amorim IR, Rice JE, et al. (1997) Multiple and ancient origins of the domestic dog. Science 276: 1687-1689.
2. Germonpré M, Sablin MV, Stevens RE, Hedges REM, Hofreiter M, et al. (2009) Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes. Journal of Archaeological Science 36: 473-490.
3. Crockford SJ, Kuzmin YV, (2012) Comments on Germonpre et al., Journal of Archaeological Science 36, 2009 "Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes". and Germonpre, Lazkickova-Galetova, and Sablin, Journal of Archaeological Science 39, 2012 "Palaeolithic dog skulls at the Gravettian Predmosti site, the Czech Republic" Journal of Archaeological Science 39: 2797-2801.
4. Larson G, Karlsson EK, Perri A, Webster MT, Ho SY, et al. (2012) Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc Natl Acad Sci U S A 109: 8878-8883.
5. Germonpré M, Sablin MV, Despres V, Hofreiter M, Laznickova-Galetova M, et al. (2013) Palaeolithic dogs and the early domestication of the wolf: a reply to the comments of Crockford and Kuzmin (2012). Journal of Archaeological Science 40: 786-792.
6. Tchernov E, Valla FF, (1997) Two new dogs, and other Natufian dogs, from the southern Levant. Journal of Archaeological Science 24: 65-95.
7. Sablin MV, Khlopachev GA, (2002) The earliest ice age dogs: Evidence from Eliseevichi I. Current Anthropology. 43: 795-799.
8. Ovodov ND, Crockford SJ, Kuzmin YV, Higham TF, Hodgins GW, et al. (2011) A 33,000-year-old incipient dog from the Altai Mountains of Siberia: evidence of the earliest domestication disrupted by the Last Glacial Maximum. Plos One 6: e22821.
9. Germonpré M, Laznickova-Galetova M, Sablin MV, (2012) Palaeolithic dog skulls at the Gravettian Predmosti site, the Czech Republic. Journal of Archaeological Science 39: 184-202.
10. Pang JF, Kluetsch C, Zou XJ, Zhang AB, Luo LY, et al. (2009) mtDNA data indicate a single origin for dogs south of Yangtze River, less than 16,300 years ago, from numerous wolves. Molecular Biology and Evolution 26: 2849-2864.
11. vonHoldt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902.
12. Yang DY, Eng B, Waye JS, Dudar JC, Saunders SR, (1998) Technical note: Improved DNA extraction from ancient bones using silica-based spin columns. American Journal of Physical Anthropology 105: 539-543.
13. Hofreiter M, Serre D, Poinar HN, Kuch M, Paabo S, (2001) Ancient DNA. Nature Reviews Genetics 2: 353-359.
14. Willerslev E, Cooper A, (2005) Ancient DNA. Proceedings of the Royal Society B-Biological Sciences 272: 3-16.
15. Poulakakis N, Parmakelis A, Lymberakis P, Mylonas M, Zouros E, et al. (2006) Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids. Biol Lett 2: 451-454.
16. Sharma DK, Maldonado JE, Jhala YV, Fleischer RC, (2004) Ancient wolf lineages in India. Proc Biol Sci 271Suppl 3: S1-4.
17. Verginelli F, Capelli C, Coia V, Musiani M, Falchetti M, et al. (2005) Mitochondrial DNA from prehistoric canids highlights relationships between dogs and South-East European wolves. Molecular Biology and Evolution 22: 2541-2551.
18. Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L, (2011) mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 27: 2153-2155.
19. Zhang Z, Schwartz S, Wagner L, Miller W, (2000) A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 7: 203-214.
20. Strimmer K, von Haeseler A, (1997) Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 94: 6815-6819.
21. Bandelt HJ, Forster P, Rohl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.
22. Polzin T, Daneshmand SV, (2003) On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters 31: 12-20.
23. Leonard JA, Wayne RK, Wheeler J, Valadez R, Guillen S, et al. (2002) Ancient DNA evidence for Old World origin of New World dogs. Science 298: 1613-1616.
24. Leonard JA, Vila C, Fox-Dobbs K, Koch PL, Wayne RK, et al. (2007) Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Current Biology 17: 1146-1150.
25. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731-2739.
26. Schmidt HA, Strimmer K, Vingron M, von Haeseler A, (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
27. Hasegawa M, Kishino H, Yano T, (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
28. Stiller M, Green RE, Ronan M, Simons JF, Du L, et al. (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA (vol 103, pg 13578, 2006). Proceedings of the National Academy of Sciences of the United States of America 103: 14977-14977.
29. vonHoldt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR, et al. (2011) A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Research 21: 1294-1305.
30. Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T, (2002) Genetic evidence for an East Asian origin of domestic dogs. Science 298: 1610-1613.