Morphological and genetic evidence for early Holocene cattle management in northeastern China

Nature Communications

Volumn 4, Issue , 2013, Pages

  Zhang, Hucai ^a   Paijmans, Johanna L A ^b,h   Chang, Fengqin ^a   Wu, Xiaohong ^c   Chen, Guangjie ^a   Lei, Chuzhao ^d   Yang, Xiujuan ^e   Wei, Zhenyi ^e   Bradley, Daniel G ^f   Orlando, Ludovic ^g   O'Connor, Terry ^b   Hofreiter, Michael ^b,h  

^a YUNNAN NORMAL UNIVERSITY   (China)

^b UNIVERSITY OF YORK   (United Kingdom)

^c PEKING UNIVERSITY   (China)

^d NORTHWEST A F UNIVERSITY   (China)

^e Heilongjiang Province Hospital   (China)

^f TRINITY COLLEGE DUBLIN   (Ireland)

^g UNIVERSITY OF COPENHAGEN   (Denmark)

^h UNIVERSITY OF POTSDAM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON 14;

CATTLE; DATA ACQUISITION; DNA; DOMESTICATION; GENETIC ANALYSIS; HOLOCENE; HUMAN BEHAVIOR; HYBRIDIZATION; LIVESTOCK FARMING; MITOCHONDRION; MORPHOLOGY;

ALVEOLAR BONE; ARTICLE; CATTLE; CHINA; CONSENSUS SEQUENCE; DENTIN; DNA DAMAGE; DNA HYBRIDIZATION; DOMESTICATION; GENETIC ANALYSIS; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HOLOCENE; MANDIBLE; MASS SPECTROMETRY; MOLAR TOOTH; MORPHOLOGICAL TRAIT; NONHUMAN; PHYLOGENY; PREMOLAR TOOTH; RADIOMETRIC DATING; UPPER PLEISTOCENE;

CHINA;

BOS; BOS INDICUS; BOS TAURUS;

ANIMAL HUSBANDRY; ANIMALS; CATTLE; CHINA; DNA; GENOME, MITOCHONDRIAL; HISTORY, ANCIENT; HUMANS; MANDIBLE; PHYLOGENY;

EID: 84889251111     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3755     Document Type: Article

References (57)

1. Diamond, J. Evolution, consequences and future of plant and animal domestication. Nature 418, 700-707 (2002)
2. Zeder, M. A. Central questions in the domestication of plants and animals. Evol. Anthropol. 15, 105-117 (2006)
3. Sherratt, A. The Secondary exploitation of animals in the Old World. World Archaeol. 15, 90-104 (1983)
4. Helmer, D., Gourichon, L., Monchot, H., Peters, J. & Sana Segui, M. In The First Steps of Animal Domestication. (eds Vigne, J.-D., Peters, J. & Helmer, D.) 86-95 (Oxbow Books, 2005)
5. Meadow, R. H. In Harappan Civilization. (ed Possehl, G. L.) 295-320 (Oxford and IBH, 1993)
6. Achilli, A. et al. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr. Biol. 18, R157-R158 (2008)
7. Stock, F. et al. Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations. Anim. Genet. 40, 694-700 (2009)
8. Achilli, A. et al. The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS One 4, e5753 (2009)
9. Bonfiglio, S. et al. The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy? PLoS One 5, e15760 (2010)
10. Edwards, C. J. et al. Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc. R. Soc. B Biol. Sci. 274, 1377-1385 (2007)
11. Fuller, D. Q., Willcox, G. & Allaby, R. G. Early agricultural pathways: moving outside the core area hypothesis in Southwest Asia. J. Exp. Bot. 63, 617-633 (2012)
12. Vuure, C. v. Retracing the Aurochs: History, Morphology and Ecology of an Extinct Wild Ox (Sofia-Moscow: Pensoft 41-52, 2005)
13. Ambrose, S. H. Preparation and characterization of bone and tooth collagen for isotopic analysis. J. Archaeol. Sci. 17, 431-451 (1990)
14. Jones, G. G. & Sadler, P. Age at death in cattle: methods, older cattle and known-age reference material. Environ. Archaeol. 17, 11-28 (2012)
15. Lari, M. et al. The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy. BMC Evol. Biol. 11, 32 (2011)
16. Paijmans, J. L., Gilbert, M. T. & Hofreiter, M. Mitogenomic analyses from ancient DNA. Mol. Phylogenet. Evol. 69, 404-416 (2013)
17. Rohland, N., Siedel, H. & Hofreiter, M. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol. Ecol. Resour. 10, 677-683 (2010)
18. Knapp, M., Clarke, A. C., Horsburgh, K. A. & Matisoo-Smith, E. A. Setting the stage-building and working in an ancient DNA laboratory. Ann. Anat. 194, 3-6 (2012)
19. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 1-7 (2010)
20. Horn, S. in Ancient DNA: Methods And Protocols. (eds Shapiro, B. & Hofreiter, M.) 177-188 (Humana Press, 2012)
21. Horn, S. et al. Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in Beavers (Castor), one of the largest rodent species. PLoS One 6, e14622 (2011)
22. Maricic, T., Whitten, M. & Paabo, S. Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One 5, e14004 (2010)
23. Lu, H. et al. Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago. Proc. Natl Acad. Sci. USA 106, 7367-7372 (2009)
24. Yang, X. et al. Early millet use in northern China. Proc. Natl Acad. Sci. USA 109, 3726-3730 (2012)
25. Cucchi, T., Hulme-Beaman, A., Yuan, J. & Dobney, K. Early Neolithic pig domestication at Jiahu, Henan Province, China: clues from molar shape analyses using geometric morphometric approaches. J. Archaeol. Sci. 38, 11-22 (2011)
26. Larson, G. et al. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc. Natl Acad. Sci. USA 107, 7686-7691 (2010)
27. Wickens, C. L. & Heleski, C. R. Crib-biting behavior in horses: a review. Appl. Anim. Behav. Sci. 128, 1-9 (2010)
28. Ishiwata, T., Uetake, K., Kilgour, R. J., Eguchi, Y. & Tanaka, T. Comparison of time budget of behaviors between penned and ranged young cattle focused on general and oral behaviors. Anim. Sci. J. 79, 518-525 (2008)
29. Redbo, I. & Nordblad, A. Stereotypies in heifers are affected by feeding regime. Appl. Anim. Behav. Sci. 53, 193-202 (1997)
30. Tuyttens, F. A. M. The importance of straw for pig and cattle welfare: a review. Appl. Anim. Behav. Sci. 92, 261-282 (2005)
31. Redbo, I. The influence of restraint on the occurrence of oral stereotypies in dairy-cows. Appl. Anim. Behav. Sci. 35, 115-123 (1992)
32. Keeling, L. & Jensen, P. In The Ethology of Domestic Animals. (ed Jensen, P.) 85-101 (CABI Publishing, 2009)
33. Payne, W. J. A. & Hodges, J. Tropical Cattle, Origins, Breeds and Breeding Policies (Wiley-Blackwell, 1997)
34. Fuller, D. Q., Asouti, E. & Purugganan, M. D. Cultivation as slow evolutionary entanglement: comparative data on rate and sequence of domestication. Veget. Hist. Archaeobot. 21, 131-145 (2012)
35. Vigne, J. D. The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere. C R Biol. 334, 171-181 (2011)
36. Purugganan, M. D. & Fuller, D. Q. Archaeological data reveal slow rates of evolution during plant domestication. Evolution 65, 171-183 (2011)
37. Driscoll, C. A., Macdonald, D. W. & OBrien, S. J. From wild animals to domestic pets, an evolutionary view of domestication. Proc. Natl Acad. Sci. USA 106 (Suppl): 9971-9978 (2009)
38. Druzhkova, A. S. et al. Ancient DNA analysis affirms the Canid from Altai as a primitive dog. PLoS One 8, e57754 (2013)
39. Germonpre, M., Laznickova-Galetova, M. & Sablin, M. V. Palaeolithic dog skulls at the Gravettian Predmosti site, the Czech Republic. J. Archaeol. Sci. 39, 184-202 (2012)
40. Germonpre, M. et al. Fossil dogs and wolves from Palaeolithic sites in Belgium, the Ukraine and Russia: osteometry, ancient DNA and stable isotopes. J. Archaeol. Sci. 36, 473-490 (2009)
41. Ovodov, N. D. et al. 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 (2011)
42. Crockford, S. J. & Kuzmin, Y. V. Comments on Germonpre et al., Journal of Archaeological Science 36, 2009
43. Ardalan, A. et al. Comprehensive study of mtDNA among Southwest Asian dogs contradicts independent domestication of wolf, but implies dog-wolf hybridization. Ecol. Evol. 1, 373-385 (2011)
44. Vigne, J. D. et al. Pre-Neolithic wild boar management and introduction to Cyprus more than 11,400 years ago. Proc. Natl Acad. Sci. USA 106, 16135-16138 (2009)
45. Pang, J. F. et al. mtDNA data indicate a single origin for dogs south of Yangtze river, less than 16,300 years ago, from numerous wolves. Mol. Biol. Evol. 26, 2849-2864 (2009)
46. Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012)
47. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25, 1754-1760 (2009)
48. Schubert, M. et al. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics 13, 178 (2012)
49. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004)
50. Ginolhac, A., Rasmussen, M., Gilbert, M. T. P., Willerslev, E. & Orlando, L. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics 27, 2153-2155 (2011)
51. Bernt, M. et al. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol. 69, 313-319 (2013)
52. Gouy, M., Guindon, S. & Gascuel, O. SeaView Version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221-224 (2010)
53. Posada, D. jModel Test: phylogenetic model averaging. Mol. Biol. Evol. 25, 1253-1256 (2008)
54. Guindon, S. et al. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol 59, 307-321 (2010)
55. Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001)
56. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003)
57. Drummond, A. J., Suchard, M. A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973 (2012)