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Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions
Open accessAbstract
Yak domestication represents an important episode in the early human occupation of the high-altitude Qinghai-Tibet Plateau (QTP). The precise timing of domestication is debated and little is known about the underlying genetic changes that occurred during the process. Here we investigate genome variation of wild and domestic yaks. We detect signals of selection in 209 genes of domestic yaks, several of which relate to behaviour and tameness. We date yak domestication to 7,300 years before present (yr BP), most likely by nomadic people, and an estimated sixfold increase in yak population size by 3,600 yr BP. These dates coincide with two early human population expansions on the QTP during the early-Neolithic age and the late-Holocene, respectively. Our findings add to an understanding of yak domestication and its importance in the early human occupation of the QTP.
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Cites
Molecular Cloning: A Laboratory Manual
Sambrook, J., Fritsch, E., & Maniatis, T. (1989) · UCLA - Biblioteca de Ciencias de la Salud · Cited by 133,589
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 39,969
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R., Garimella, K. V., Maguire, J. R., Hartl, C., Philippakis, A. A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,456
Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,486
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
Browning, S. R., & Browning, B. L. (2007) · The American Journal of Human Genetics · doi:10.1086/521987 · Cited by 3,210
ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982
Inference of human population history from individual whole-genome sequences
Li, H., & Durbin, R. (2011) · Nature · doi:10.1038/nature10231 · Cited by 2,590
Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics
Conesa, A., & Götz, S. (2008) · International Journal of Plant Genomics · doi:10.1155/2008/619832 · Cited by 2,151
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906
Evolution, consequences and future of plant and animal domestication
Diamond, J. (2002) · Nature · doi:10.1038/nature01019 · Cited by 1,776
Robust Demographic Inference from Genomic and SNP Data
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C., & Foll, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003905 · Cited by 1,466
Human–Mouse Alignments with BLASTZ
Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D., & Miller, W. (2003) · Genome Research · doi:10.1101/gr.809403 · Cited by 1,239
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
Self-citationKeane, T. M., Creevey, C. J., Pentony, M. M., Naughton, T. J., & Mclnerney, J. O. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-29 · Cited by 1,071
The yak genome and adaptation to life at high altitude
Qiu, Q., Zhang, G., Ma, T., Qian, W., Wang, J., Ye, Z., Cao, C., Hu, Q., Kim, J., Larkin, D. M., et al. (2012) · Nature Genetics · doi:10.1038/ng.2343 · Cited by 983
Self-citationThe genomic signature of dog domestication reveals adaptation to a starch-rich diet
Axelsson, E., Ratnakumar, A., Arendt, M.-L., Maqbool, K., Webster, M. T., Perloski, M., Liberg, O., Arnemo, J. M., Hedhammar, Å., & Lindblad-Toh, K. (2013) · Nature · doi:10.1038/nature11837 · Cited by 963
Current perspectives and the future of domestication studies
Larson, G., Piperno, D. R., Allaby, R. G., Purugganan, M. D., Andersson, L., Arroyo-Kalin, M., Barton, L., Climer Vigueira, C., Denham, T., Dobney, K., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323964111 · Cited by 875
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds
The Bovine HapMap Consortium, Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., et al. (2009) · Science · doi:10.1126/science.1167936 · Cited by 868
Post-traumatic stress disorder is associated with PACAP and the PAC1 receptor
Ressler, K. J., Mercer, K. B., Bradley, B., Jovanovic, T., Mahan, A., Kerley, K., Norrholm, S. D., Kilaru, V., Smith, A. K., Myers, A. J., et al. (2011) · Nature · doi:10.1038/nature09856 · Cited by 800
Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.
Chen, F. H., Dong, G. H., Zhang, D. J., Liu, X. Y., Jia, X., An, C. B., Ma, M. M., Xie, Y. W., Barton, L., Ren, X. Y., et al. (2015) · Science · doi:10.1126/science.1259172 · Cited by 725
Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars
Li, M., Tian, S., Jin, L., Zhou, G., Li, Y., Zhang, Y., Wang, T., Yeung, C. K. L., Chen, L., Ma, J., et al. (2013) · Nature Genetics · doi:10.1038/ng.2811 · Cited by 556
Self-citationPlant domestication, a unique opportunity to identify the genetic basis of adaptation
Ross-Ibarra, J., Morrell, P. L., & Gaut, B. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700643104 · Cited by 475
Plexin A Is a Neuronal Semaphorin Receptor that Controls Axon Guidance
Winberg, M. L., Noordermeer, J. N., Tamagnone, L., Comoglio, P. M., Spriggs, M. K., Tessier-Lavigne, M., & Goodman, C. S. (1998) · Cell · doi:10.1016/s0092-8674(00)81715-8 · Cited by 470
Nielsen, R., Korneliussen, T., Albrechtsen, A., Li, Y., & Wang, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037558 · Cited by 424 · cited 1×
“46) programme in order the estimate the SFS. Genotypes were called using the full set of genotype likelihoods data.”
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
Carneiro, M., Rubin, C.-J., Di Palma, F., Albert, F. W., Alföldi, J., Barrio, A. M., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., et al. (2014) · Science · doi:10.1126/science.1253714 · Cited by 404
Zhao, S., Zheng, P., Dong, S., Zhan, X., Wu, Q., Guo, X., Hu, Y., He, W., Zhang, S., Fan, W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2494 · Cited by 355
Self-citationZheng, B., Xu, Q., & Shen, Y. (2002) · Quaternary International · doi:10.1016/s1040-6182(02)00054-x · Cited by 349
Montague, M. J., Li, G., Gandolfi, B., Khan, R., Aken, B. L., Searle, S. M. J., Minx, P., Hillier, L. W., Koboldt, D. C., Davis, B. W., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1410083111 · Cited by 340
Korneliussen, T. S., Moltke, I., Albrechtsen, A., & Nielsen, R. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-289 · Cited by 269
Mitochondrial genome evidence reveals successful Late Paleolithic settlement on the Tibetan Plateau
Zhao, M., Kong, Q.-P., Wang, H.-W., Peng, M.-S., Xie, X.-D., Wang, W.-Z., Jiayang, Duan, J.-G., Cai, M.-C., Zhao, S.-N., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907844106 · Cited by 264
ngsTools: methods for population genetics analyses from next-generation sequencing data
Fumagalli, M., Vieira, F. G., Linderoth, T., & Nielsen, R. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu041 · Cited by 251
Estimation of allele frequency and association mapping using next-generation sequencing data
Kim, S. Y., Lohmueller, K. E., Albrechtsen, A., Li, Y., Korneliussen, T., Tian, G., Grarup, N., Jiang, T., Andersen, G., Witte, D., et al. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-231 · Cited by 217
Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data
Fumagalli, M., Vieira, F. G., Korneliussen, T. S., Linderoth, T., Huerta-Sánchez, E., Albrechtsen, A., & Nielsen, R. (2013) · Genetics · doi:10.1534/genetics.113.154740 · Cited by 207
Zhou, X., Wang, B., Pan, Q., Zhang, J., Kumar, S., Sun, X., Liu, Z., Pan, H., Lin, Y., Liu, G., et al. (2014) · Nature Genetics · doi:10.1038/ng.3137 · Cited by 205
Qi, X., Cui, C., Peng, Y., Zhang, X., Yang, Z., Zhong, H., Zhang, H., Xiang, K., Cao, X., Wang, Y., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst093 · Cited by 196
Self-citationPeopling the Tibetan Plateau: Insights from Archaeology
Aldenderfer, M. (2011) · High Altitude Medicine & Biology · doi:10.1089/ham.2010.1094 · Cited by 172
Dong, G., Jia, X., Elston, R., Chen, F., Li, S., Wang, L., Cai, L., & An, C. (2012) · Journal of Archaeological Science · doi:10.1016/j.jas.2012.10.002 · Cited by 135
Self-citationHassanin, A., & Ropiquet, A. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.08.009 · Cited by 133
Origin of mitochondrial DNA diversity of domestic yaks
Guo, S., Savolainen, P., Su, J., Zhang, Q., Qi, D., Zhou, J., Zhong, Y., Zhao, X., & Liu, J. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-73 · Cited by 116
Self-citationThe Origins of Chinese Domestic Cattle as Revealed by Ancient DNA Analysis
Cai, D., Sun, Y., Tang, Z., Hu, S., Li, W., Zhao, X., Xiang, H., & Zhou, H. (2014) · Journal of Archaeological Science · doi:10.1016/j.jas.2013.09.003 · Cited by 85
Kawahara‐Miki, R., Tsuda, K., Shiwa, Y., Arai-Kichise, Y., Matsumoto, T., Kanesaki, Y., Oda, S.-I., Ebihara, S., Yajima, S., Yoshikawa, H., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-103 · Cited by 85
Wang, Z., Shen, X., Liu, B., Su, J., Yonezawa, T., Yu, Y., Guo, S., Ho, S. Y. W., Vilà, C., Hasegawa, M., et al. (2010) · Journal of Biogeography · doi:10.1111/j.1365-2699.2010.02379.x · Cited by 79
Self-citationGenetic influences on brain gene expression in rats selected for tameness and aggression
Heyne, H. O., Lautenschläger, S., Nelson, R., Besnier, F., Rotival, M., Cagan, A., Kozhemyakina, R., Plyusnina, I. Z., Trut, L., Carlborg, Ö., et al. (2014) · Genetics · doi:10.1534/genetics.114.168948 · Cited by 72
The planar polarity protein Scribble1 is essential for neuronal plasticity and brain function
Moreau, M. M., Piguel, N., Papouin, T., Koehl, M., Durand, C. M., Rubio, M. E., Loll, F., Richard, E. M., Mazzocco, C., Racca, C., et al. (2010) · Journal of Neuroscience · doi:10.1523/jneurosci.6007-09.2010 · Cited by 69
Meyer, M. C., Hofmann, C.-C., Gemmell, A. M. D., Haslinger, E., Häusler, H., & Wangda, D. (2009) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2008.12.025 · Cited by 67
Association Testing for Next‐Generation Sequencing Data Using Score Statistics
Skotte, L., Korneliussen, T. S., & Albrechtsen, A. (2012) · Genetic Epidemiology · doi:10.1002/gepi.21636 · Cited by 62
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens)
Zhang, M., Xu, X. J., & Luo, S. (2014) · Animal Genetics · doi:10.1111/age.12191 · Cited by 46
Genome‐wide detection of signatures of selection in K orean H anwoo cattle
Porto-Neto, L. R., Lee, S. H., Sonstegard, T. S., Tassell, C. P. V., Lee, H. K., Gibson, J. P., & Gondro, C. (2014) · Animal Genetics · doi:10.1111/age.12119 · Cited by 35
Reindeer Ewenki's fading culture
Wang, J., Sun, J., Aryal, A., et al. (2015) · Science · doi:10.1126/science.347.6225.957-a · Cited by 2
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Zhang, K., Lenstra, J. A., Zhang, S., Liu, W., & Liu, J. (2020) · Animal Genetics · doi:10.1111/age.12974 · Cited by 82
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Metadata
- Authors
- Qiu, Q., Wang, L., Wang, K., Yang, Y., Ma, T., Wang, Z., Zhang, X., Ni, Z., Hou, F., Long, R., Abbott, R., Lenstra, J., & Liu, J.
- Venue
- Nature Communications
- Published
- 2015-12-22
- Volume
- 6
- Issue
- 1
- Pages
- 10283-10283
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2236602350
- Cited by
- 304
- References
- 54
- FWCI
- 8.43
- Type
- journal article
- Language
- en
- Open access
- gold
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