Establishing the validity of domestication genes using DNA from ancient chickens

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 17, 2014, Pages 6184-6189

  Flink, Linus Girdland ^a,g   Allen, Richard ^a   Barnett, Ross ^a   Malmström, Helena ^b   Peters, Joris ^c,d   Eriksson, Jonas ^e   Andersson, Leif ^e,f   Dobney, Keith ^g   Larson, Greger ^a  

^a DURHAM UNIVERSITY   (United Kingdom)

^b UPPSALA UNIVERSITY   (Sweden)

^c UNIVERSITY OF MUNICH   (Germany)

^d BAVARIAN NATURAL HISTORY COLLECTIONS   (Germany)

^e UPPSALA UNIVERSITY   (Sweden)

^f SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^g UNIVERSITY OF ABERDEEN   (United Kingdom)

Author keywords

Animal domestication; Breed formation; Cultural history; Gallus gallus; Selective sweep

Indexed keywords

BETA CAROTENE 15,15' MONOOXYGENASE; BETA CAROTENE DIOXYGENASE 2; DNA; THYROTROPIN RECEPTOR; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARCHEOLOGY; ARTICLE; BREEDING; CHICKEN; CONTROLLED STUDY; DOMESTICATION; EUROPE; GENE; GENE EXPRESSION; GENE LOCUS; GENETIC DIFFERENCE; GENETIC VARIABILITY; MITOCHONDRION; NONHUMAN; PHOTOPERIODICITY; PHYLOGENETIC TREE; POPULATION GENETICS; PRIORITY JOURNAL; SKIN COLOR; VALIDITY;

ANIMAL DOMESTICATION; BREED FORMATION; CULTURAL HISTORY; GALLUS GALLUS; SELECTIVE SWEEP;

ANIMALS; ANIMALS, DOMESTIC; CHICKENS; DNA; DNA, MITOCHONDRIAL; EUROPE; GEOGRAPHY; HAPLOTYPES; HISTORY, ANCIENT; HUMANS; MOLECULAR SEQUENCE DATA; REPRODUCIBILITY OF RESULTS;

EID: 84899620497     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1308939110     Document Type: Article

References (51)

1. Andersson L (2013) Molecular consequences of animal breeding. Curr Opin Genet Dev 23(3):295-301.
2. Olsen K-M, Wendel J-F (2013) A bountiful harvest: Genomic insights into crop domestication phenotypes. Annu Rev Plant Biol 64:47-70.
3. Andersson L (2012) How selective sweeps in domestic animals provide new insight into biological mechanisms. J Intern Med 271(1):1-14.
4. Wayne RK, vonHoldt BM (2012) Evolutionary genomics of dog domestication. Mamm Genome 23(1-2):3-18.
5. Drögemüller C, et al. (2008) A mutation in hairless dogs implicates FOXI3 in ectodermal development. Science 321(5895):1462.
6. Salmon Hillbertz NHC, et al. (2007) Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs. Nat Genet 39(11):1318-1320.
7. Olsson M, et al. (2011) A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs. PLoS Genet 7(3):e1001332.
8. McPherron AC, Lee S-J (1997) Double muscling in cattle due to mutations in the myostatin gene. Proc Natl Acad Sci USA 94(23):12457-12461.
9. Filler S, et al. (2012) Selkirk Rex: Morphological and genetic characterization of a new cat breed. J Hered 103(5):727-733.
10. Rosengren Pielberg G, et al. (2008) A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the horse. Nat Genet 40(8):1004-1009.
11. Andersson LS, et al. (2012) Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488(7413):642-646.
12. Bannasch D, et al. (2010) Localization of canine brachycephaly using an across breed mapping approach. PLoS ONE 5(3):e9632.
13. Van Laere A-S, et al. (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425(6960):832-836.
14. Gray MM, Sutter NB, Ostrander EA, Wayne RK (2010) The IGF1 small dog haplotype is derived from Middle Eastern grey wolves. BMC Biol 8(1):16.
15. Sutter NB, et al. (2007) A single IGF1 allele is a major determinant of small size in dogs. Science 316(5821):112-115.
16. Parker HG, et al. (2009) An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325(5943):995-998.
17. Wright D, et al. (2009) Copy number variation in intron 1 of SOX5 causes the Peacomb phenotype in chickens. PLoS Genet 5(6):e1000512.
18. Axelsson E, et al. (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495(7441):360-364.
19. Liu Y-P, et al. (2006) Multiple maternal origins of chickens: Out of the Asian jungles. Mol Phylogenet Evol 38(1):12-19.
20. West B, Zhou B-X (1988) Did chickens go north? New evidence for domestication. J Archaeol Sci 15(5):515-533.
21. Chow BS (1981) The animal remains discovered at Cishan village, Wu'an, Hebei Province. Kaogu Xuebao 62(3):339-348. Chinese.
22. Chow BS (1983) The animal remains discovered at Baiyingsite, Tangyin, Henan Province. Papers on Chinese Archaeology 3:48-50. Chinese.
23. Deng H, Yuan J, Song G-D, Wang C-S, Masaki E (2013) The re-examination of the Domestic Chicken in Ancient China. Archaeology 6(6):83-96. Chinese.
24. Peters J (1998) Römische Tierhaltung und Tierzucht. Eine Synthese aus archäozoologischer Untersuchung und schriftlich-bildlicher Überlieferung. Passauer Universitätsschriften zur Archä ologie(Marie Leidorf, Rahden, Westfalen, Germany)
25. Eriksson J, et al. (2008) Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 4(2):e1000010.
26. Kiefer C, et al. (2001) Identification and characterization of a mammalian enzyme catalyzing the asymmetric oxidative cleavage of provitamin A. J Biol Chem 276(17): 14110-14116.
27. Tegetmeier WB (1867) The Poultry Book: Comprising the Breeding and Management of Profitable and Ornamental Poultry, Their Qualities and Characteristics; To Which is added "The Standard of Excellence in Exhibition Birds," Authorized by the Poultry (G. Routledge and Sons, London).
28. McGowan PJK (1994) Phasianidae (Pheasants and Partridges). Handbook of the Birds of the World, eds del Hoyo J, Elliott A, Sargatal J (Lynx Edicions, Barcelona, Spain), pp 434-552.
29. Rubin C-J, et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464(7288):587-591.
30. Benecke N (1994) Archäozoologische Studien zur Entwicklung der Haustierhaltung in Mitteleuropa und Südskandinavien von den Anfängen bis zum ausgehenden Mittelalter (Akademie, Berlin).
31. Carrasquila Hernández F (1992) Some comments on the introduction of domestic fowl in Iberia. Archaeofauna 1:45-93.
32. Dana N, et al. (2010) East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis. Anim Genet 42(2):125-133.
33. Storey AA, et al. (2007) Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile. Proc Natl Acad Sci USA 104(25): 10335-10339.
34. Storey AA, et al. (2012) Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures. PLoS ONE 7(7):e39171.
35. Miao YW, et al. (2013) Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity (Edinb) 110(3):277-282.
36. Roaf M (1990) Cultural Atlas of Mesopotamia and the Ancient Near East (Equinox, Facts on File, New York).
37. Aldrovandi U (1600) Ornithologiae Tomus Alter cum Indice Copiosissimo Variarum Linguarum (Giovanni Battista Bellagamba, Bologna).
38. Gongora J, et al. (2008) Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proc Natl Acad Sci USA 105(30):10308-10313.
39. Revay T, Bodzsar N, Mobegi VE, Hanotte O, Hidas A (2010) Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequences. Anim Genet 41(5):548-550.
40. Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314(5803):1298-1301.
41. Asplund L, Hagenblad J, Leino MW (2010) Re-evaluating the history of the wheat domestication gene NAM-B1 using historical plant material. J Archaeol Sci 37(9):2303-2307.
42. Jaenicke-Després V, et al. (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302(5648):1206-1208.
43. Malmström H, et al. (2008) Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evol Biol 8:71.
44. Ottoni C, et al. (2013) Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics. Mol Biol Evol 30(4):824-832.
45. Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A (2002) Dynamics of Pleistocene population extinctions in Beringian brown bears. Science 295(5563):2267-2270.
46. Shapiro B, et al. (2004) Rise and fall of the Beringian steppe bison. Science 306(5701): 1561-1565.
47. Larson G, et al. (2012) Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc Natl Acad Sci USA 109(23):8878-8883.
48. Boessneck J (1988) Die Tierwelt des Alten Ägypten (C. H. Beck, Munich).
49. Cooper A, Poinar HN (2000) Ancient DNA: Do it right or not at all. Science 289(5482):1139.
50. Gilbert MT, Bandelt HJ, Hofreiter M, Barnes I (2005) Assessing ancient DNA studies. Trends Ecol Evol 20(10):541-544.
51. Drummond AJ, et al. (2011) Geneious v5.4, Available from www.geneious.com/. Accessed July 1, 2011.