Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions

Nature Communications

Volumn 6, Issue , 2015, Pages

  Qiu, Qiang ^a   Wang, Lizhong ^a   Wang, Kun ^b   Yang, Yongzhi ^a   Ma, Tao ^b   Wang, Zefu ^a   Zhang, Xiao ^a   Ni, Zhengqiang ^a   Hou, Fujiang ^a   Long, Ruijun ^a   Abbott, Richard ^c   Lenstra, Johannes ^d   Liu, Jianquan ^a,b  

^a LANZHOU UNIVERSITY   (China)

^b SICHUAN UNIVERSITY   (China)

^c UNIVERSITY OF ST ANDREWS   (United Kingdom)

^d UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DOMESTIC SPECIES; DOMESTICATION; GENE; GENETIC ANALYSIS; GENETIC VARIATION; HUMAN SETTLEMENT; NEOLITHIC; NOMADIC PEOPLE; OCCUPATION; POPULATION SIZE; PREHISTORIC; RANGE EXPANSION; WILD POPULATION;

BEHAVIOR; CHINA; DOMESTICATION; GENOME; HUMAN; LATE HOLOCENE; NEOLITHIC; OCCUPATION; POPULATION SIZE; YAK; ANIMAL; ANIMAL DISPERSAL; BOVINE; DOMESTIC ANIMAL; GENETIC VARIATION; GENETICS; GENOMICS; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; POPULATION DYNAMICS;

CHINA; QINGHAI-XIZANG PLATEAU;

BOS GRUNNIENS;

ANIMAL DISTRIBUTION; ANIMALS; ANIMALS, DOMESTIC; CATTLE; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOMICS; PHYLOGENY; POPULATION DYNAMICS;

EID: 84951334878     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms10283     Document Type: Article

References (58)

1. Diamond, J. Evolution, consequences and future of plant and animal domestication. Nature 418, 700-707 (2002).
2. Larson, G. et al. Current perspectives and the future of domestication studies. Proc. Natl Acad. Sci. USA 111, 6139-6146 (2014).
3. Dong, G. et al. Spatial and temporal variety of prehistoric human settlement and its influencing factors in the upper Yellow River valley, Qinghai Province, China. J. Archaeol. Sci. 40, 2538-2546 (2013).
4. Qi, X. et al. Genetic evidence of paleolithic colonization and neolithic expansion of modern humans on the tibetan plateau. Mol. Biol. Evol. 30, 1761-1778 (2013).
5. Qiu, J. Who are the Tibetans? Science 347, 708-711 (2015).
6. Meyer, M. C. et al. Holocene glacier fluctuations and migration of Neolithic yak pastoralists into the high valleys of northwest Bhutan. Quart. Sci. Rev. 28, 1217-1237 (2009).
7. Zhang, R. C. Yak of China (Gansu Scientific and Technical Publishers, 1989).
8. Guo, S. et al. Origin of mitochondrial DNA diversity of domestic yaks. BMC Evol. Biol. 6, 73 (2006).
9. Wang, Z. F. et al. Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal. J. Biogeogr. 37, 2332-2344 (2010).
10. Atlas of Chinese Cultural Relics-Fascicule of the Tibet Autonomous Region (Bureau of National Cultural Relics, Cultural Relics Press, Beijing, 2010).
11. Wiener, G., Jianlin, H. & Ruijun, L. The Yak 2nd edn (FAO Regional Office for Asia and the Pacific Food and Agriculture Organization of the United Nations, Bangkok, Thailand, 2003).
12. Zhang, M. Q., Xu, X. & Luo, S. J. The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens). Anim. Genet. 45, 652-659 (2014).
13. Gibbs, R. A. et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528-532 (2009).
14. Ross-Ibarra, J., Morrell, P. L. & Gaut, B. S. Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc. Natl Acad. Sci. USA 104(Suppl 1): 8641-8648 (2007).
15. Porto-Neto, L. R. et al. Genome-wide detection of signatures of selection in Korean Hanwoo cattle. Anim. Genet. 45, 180-190 (2014).
16. Axelsson, E. et al. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495, 360-364 (2013).
17. Li, M. et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat. Genet. 45, 1431-1438 (2013).
18. Ressler, K. J. et al. Post-traumatic stress disorder is associated with PACAP and the PAC1 receptor. Nature 470, 492-497 (2011).
19. Moreau, M. M. et al. The planar polarity protein Scribble1 is essential for neuronal plasticity and brain function. J. Neurosci. 30, 9738-9752 (2010).
20. Winberg, M. L. et al. Plexin A is a neuronal semaphorin receptor that controls axon guidance. Cell 95, 903-916 (1998).
21. Heyne, H. O. et al. Genetic influences on brain gene expression in rats selected for tameness and aggression. Genetics 198, 1277-1290 (2014).
22. Carneiro, M. et al. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345, 1074-1079 (2014).
23. Montague, M. J. et al. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc. Natl Acad. Sci. USA 111, 17230-17235 (2014).
24. Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493-496 (2011).
25. Zheng, B., Xu, Q. & Shen, Y. The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau: review and speculation. Quat. Int. 97, 93-101 (2002).
26. Zhao, S. et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat. Genet. 45, 67-71 (2013).
27. Zhou, X. et al. Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history. Nat. Genet. 46, 1303-1310 (2014).
28. Excoffier, L. et al. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905 (2013).
29. Cai, D. et al. The origins of Chinese domestic cattle as revealed by ancient DNA analysis. J. Archaeol. Sci. 41, 423-434 (2014).
30. Chen, F. H. et al. Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 BP. Science 347, 248-250 (2015).
31. Zhao, M. et al. Mitochondrial genome evidence reveals successful Late Paleolithic settlement on the Tibetan Plateau. Proc. Natl Acad. Sci. USA 106, 21230-21235 (2009).
32. Aldenderfer, M. Peopling the Tibetan plateau: insights from archaeology. High Alt. Med. Biol. 12, 141-147 (2011).
33. Wang, J. et al. Reindeer Ewenki's fading culture. Science 347, 957 (2015).
34. Green, M. R. & Sambrook, J. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press New York, 2012).
35. Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317 (2010).
36. Schwartz, S. et al. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107 (2003).
37. Qiu, Q. et al. The yak genome and adaptation to life at high altitude. Nat. Genet. 44, 946-949 (2012).
38. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
39. Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
40. DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
41. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993 (2011).
42. Korneliussen, T., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).
43. Skotte, L., Korneliussen, T. S. & Albrechtsen, A. Association testing for next-generation sequencing data using score statistics. Genet. Epidemiol. 36, 430-437 (2012).
44. Kim, S. Y. et al. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 12, 231 (2011).
45. Kawahara-Miki, R. et al. Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi. BMC Genomics 12, 103 (2011).
46. Nielsen, R. et al. SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS ONE 7, e37558 (2012).
47. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
48. Keane, T. M. et al. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6, 29 (2006).
49. Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001).
50. Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
51. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
52. Fumagalli, M. et al. Quantifying population genetic differentiation from next-generation sequencing data. Genetics 195, 979-992 (2013).
53. Fumagalli, M., Vieira, F. G., Linderoth, T. & Nielsen, R. NgsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics 30, 1486-1487 (2014).
54. Korneliussen, T. S., Moltke, I., Albrechtsen, A. & Nielsen, R. Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics 14, 289 (2013).
55. Conesa, A. & Gotz, S. Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 619832 (2008).
56. Hassanin, A. & Ropiquet, A. Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937. Mol. Phylogenet. Evol. 33, 896-907 (2004).
57. Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084-1097 (2007).
58. Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H. & Bustamante, C. D. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5, e1000695 (2009).