Out of southern East Asia: The natural history of domestic dogs across the world

Cell Research

Volumn 26, Issue 1, 2016, Pages 21-33

  Wang, Guo Dong ^a   Zhai, Weiwei ^b   Yang, He Chuan ^a,b,c   Wang, Lu ^d   Zhong, Li ^d   Liu, Yan Hu ^d   Fan, Ruo Xi ^d   Yin, Ting Ting ^a,e   Zhu, Chun Ling ^a   Poyarkov, Andrei D ^f   Irwin, David M ^g   Hytönen, Marjo K ^h   Lohi, Hannes ^h   Wu, Chung I ⁱ   Savolainen, Peter ^j   Zhang, Ya Ping ^a,d  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d YUNNAN UNIVERSITY   (China)

^e INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^f SEVERTSOV INSTITUTE OF ECOLOGY AND EVOLUTION   (Russian Federation)

^g UNIVERSITY OF TORONTO   (Canada)

^h UNIVERSITY OF HELSINKI   (Finland)

ⁱ UNIVERSITY OF CHICAGO   (United States)

^j ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

more..

Author keywords

artificial selection; Chinese indigenous dog; demography; dog domestication; gene flow

Indexed keywords

AFRICA; ANIMAL; CHINA; DOG; DOMESTIC ANIMAL; EUROPE; EVOLUTION; GENE FLOW; GENETIC VARIATION; GENETICS; GENOME; MIDDLE EAST; PHYLOGENY; POPULATION MIGRATION; SOUTHEAST ASIA; WOLF;

AFRICA; ANIMAL MIGRATION; ANIMALS; ANIMALS, DOMESTIC; ASIA, SOUTHEASTERN; BIOLOGICAL EVOLUTION; CHINA; DOGS; EUROPE; GENE FLOW; GENETIC VARIATION; GENOME; MIDDLE EAST; PHYLOGENY; WOLVES;

EID: 84953360034     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2015.147     Document Type: Article

References (61)

1. Coppinger R, Coppinger L. Dogs: A Startling New Understanding of Canine Origin, Behavior & Evolution. 1st Edition, Scribner, 2001.
2. Darwin C. The variation of animals and plants under domestication. O. Judd & company, 1868.
3. Lindblad-Toh K, Wade CM, Mikkelsen TS et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005; 438: 803-819.
4. Wang GD, Xie HB, Peng MS, Irwin D, Zhang YP. Domestication genomics: evidence from animals. Annu Rev Anim Biosci. 2014; 2: 65-84.
5. Wayne RK, Ostrander EA. Lessons learned from the dog genome. Trends Genet. 2007; 23: 557-567.
6. Freedman AH, Gronau I, Schweizer RM, et al. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 2014; 10: e1004016.
7. Pang JF, Kluetsch C, Zou XJ, 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. 2009; 26: 2849-2864.
8. Skoglund P, Ersmark E, Palkopoulou E, Dalen L. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr Biol. 2015; 25: 1515-1519.
9. Skoglund P, Gotherstrom A, Jakobsson M. Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves. Mol Biol Evol. 2011; 28: 1505-1517.
10. Wang GD, Zhai W, Yang HC, et al. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nat Commun. 2013; 4: 1860.
11. Larson G, Karlsson EK, Perri A, et al. Rethinking dog domes tication by integrating genetics, archeology, and biogeography. Proc Natl Acad Sci USA. 2012; 109: 8878-8883.
12. Savolainen P, Zhang YP, Luo J, Lundeberg J, Leitner T. Genetic evidence for an East Asian origin of domestic dogs. Science. 2002; 298: 1610-1613.
13. Thalmann O, Shapiro B, Cui P, et al. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science. 2013; 342: 871-874.
14. Vonholdt BM, Pollinger JP, Lohmueller KE, et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature. 2010; 464: 898-902.
15. Pool JE, Hellmann I, Jensen JD, Nielsen R. Population genetic inference from genomic sequence variation. Genome Res. 2010; 20: 291-300.
16. Crapon de Caprona M-D, Savolainen P. Extensive phenotypic diversity among South Chinese dogs. ISRN Evol Biol. 2013; 2013: 1-8.
17. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43: 491-498.
18. Tang H, Peng J, Wang P, Risch NJ. Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol. 2005; 28: 289-301.
19. Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006; 2: e190.
20. vonHoldt BM, Pollinger JP, Earl DA, et al. A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res. 2011; 21: 1294-1305.
21. Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8: e1002967.
22. Reich D, Thangaraj K, Patterson N, Price AL, Singh L. Reconstructing Indian population history. Nature. 2009; 461: 489-494.
23. Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature. 2011; 475: 493-496.
24. Larson G, Bradley DG. How much is that in dog years? The advent of canine population genomics. PLoS Genet. 2014; 10: e1004093.
25. Kumar S, Subramanian S. Mutation rates in mammalian genomes. Proc Natl Acad Sci USA. 2002; 99: 803-808.
26. Liu GE, Matukumalli LK, Sonstegard TS, Shade LL, Van Tassell CP. Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences. BMC Genomics. 2006; 7: 140.
27. Koch PL, Barnosky AD. Late quaternary extinctions: State of the debate. Annu Rev Ecol Evol S. 2006; 37: 215-250.
28. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009; 5: e1000695.
29. Scott JP. Genetics and the Social Behavior of the Dog: University of Chicago Press 1965.
30. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet. 2011; 43: 1031-1034.
31. Yang Z, Rannala B. Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA. 2010; 107: 9264-9269.
32. Pickrell JK, Reich D. Toward a new history and geography of human genes informed by ancient DNA. Trends Genet. 2014; 30: 377-389.
33. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL. Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA. 2005; 102: 15942-15947.
34. Patterson N, Moorjani P, Luo Y, et al. Ancient admixture in human history. Genetics. 2012; 192: 1065-1093.
35. Yang MA, Malaspinas AS, Durand EY, Slatkin M. Ancient structure in Africa unlikely to explain Neanderthal and non-African genetic similarity. Mol Biol Evol. 2012; 29: 2987-2995.
36. Ding ZL, Oskarsson M, Ardalan A, et al. Origins of domestic dog in southern East Asia is supported by analysis of Y-chromosome DNA. Heredity. 2012; 108: 507-514.
37. Cann RL, Stoneking M, Wilson AC. Mitochondrial DNA and human evolution. Nature. 1987; 325: 31-36.
38. Riehl S, Zeidi M, Conard NJ. Emergence of agriculture in the foothills of the Zagros Mountains of Iran. Science. 2013; 341: 65-67.
39. van Asch B, Zhang AB, Oskarsson MC, Klutsch CF, Amorim A, Savolainen P. Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis. Proc Biol Sci. 2013; 280: 20131142.
40. Price AL, Tandon A, Patterson N, et al. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 2009; 5: e1000519.
41. Koepfli K-P, Pollinger J, Godinho R, et al. Genome-wide evidence reveals that African and Eurasian Golden Jackals are distinct species. Curr Biol. 2015; 25: 2158-2165.
42. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Ges. 2005; 15: 1566-1575.
43. Bliss TV, Collingridge GL. A synaptic model of memory: long-Term potentiation in the hippocampus. Nature. 1993; 361: 31-39.
44. Saltzman B. Dynamical Paleoclimatology, Volume 80: Generalized Theory of Global Climate Change Academic Press; 1 Edition 2001.
45. Vigne JD, Carrere I, Briois F, Guilaine J. The early process of mammal domestication in the Near East. Curr Anthropol. 2011; 52: S255-S271.
46. Zeder MA. Pathways to Animal Domestication. In: Gepts P, Famula TR, Bettinger RL, et al, eds. Biodiversity in Agriculture: Domestication, Evolution, and Sustainability. Cambridge: Cambridge Univ Press, 2012: 227-259.
47. Pinhasi R, Fort J, Ammerman AJ. Tracing the origin and spread of agriculture in Europe. PLoS Biol. 2005; 3: e410.
48. Wang X, Tedford RH. Dogs: Their Fossil Relatives and Evolutionary History. Columbia University Press, 2008.
49. Ovodov ND, Crockford SJ, Kuzmin YV, Higham TF, Hodgins GW, van der Plicht J. 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. 2011; 6: e22821.
50. Boyko AR, Boyko RH, Boyko CM, et al. Complex population structure in African village dogs and its implications for inferring dog domestication history. Proc Natl Acad Sci USA. 2009; 106: 13903-13908.
51. Diamond J. Evolution, consequences and future of plant and animal domestication. Nature. 2002; 418: 700-707.
52. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26: 589-595.
53. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/ Map format and SAMtools. Bioinformatics. 2009; 25: 2078-2079.
54. Browning SR, Browning BL. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81: 1084-1097.
55. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005; 21: 263-265.
56. Sokal R, Michener C. A statistical method for evaluating systematic relationships. Univ Kans Scientif Bull. 1958; 38: 1409-1438.
57. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007; 24: 1586-1591.
58. Hwang DG, Green P. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA. 2004; 101: 13994-14001.
59. Auton A, Rui Li Y, Kidd J, et al. Genetic recombination is targeted towards gene promoter regions in dogs. PLoS Genet. 2013; 9: e1003984.
60. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4: 44-57.
61. Lisiecki LE, Raymo ME. A Pliocene-Pleistocene stack of 57 globally distributed benthic d18O records. Paleoceanography. 2005; 20: PA1003.