The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

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

Volumn 105, Issue 46, 2008, Pages 17659-17664

  Naderi, Saeid ^a,b   Rezaei, Hamid Reza ^a,c   Pompanon, François ^a   Blum, Michael G B ^d   Negrini, Riccardo ^e   Naghash, Hamid Reza ^a   Balkiz, Özge ^f   Mashkour, Marjan ^d   Gaggiotti, Oscar E ^a   Ajmone Marsan, Paolo ^e   Kence, Aykut ^f   Vigne, Jean Denis ^d   Taberlet, Pierre ^a  

^a UNIVERSITÉ JOSEPH FOURIER   (France)

^b UNIVERSITY OF GUILAN   (Iran)

^c GORGAN UNIVERSITY OF AGRICULTURAL SCIENCES AND NATURAL RESOURCES   (Iran)

^d CNRS   (France)

^e UNIVERSITÀ CATTOLICA DEL SACRO CUORE   (Italy)

^f MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

Author keywords

Livestock origins; Middle east; Neolithic expansion; Phylogeography

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; DNA DETERMINATION; DNA SEQUENCE; DOMESTICATION; GENETIC VARIABILITY; GOAT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLOGEOGRAPHY; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; UNINDEXED SEQUENCE;

AGRICULTURE; ANIMALS; ANIMALS, DOMESTIC; ANIMALS, WILD; BAYES THEOREM; DNA, MITOCHONDRIAL; GENETIC VARIATION; GEOGRAPHY; GOATS; HAPLOTYPES; IRAN; MOLECULAR SEQUENCE DATA; PHYLOGENY; POPULATION DYNAMICS; SEQUENCE ANALYSIS, DNA; TURKEY;

CAPRA HIRCUS; UNGULATA;

EID: 56649112987     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0804782105     Document Type: Article

References (38)

1. Helmer D (1992) La domestication des animaux par l'homme préhistorique (Masson, Paris).
2. Legge T (1996) in The Origins and Spread of Agriculture and Pastoralism in Eurasia, ed. Harris DR (Smithsonian Institution Press, Washington D.C.), pp 238-262.
3. Peters J, von den Driesch A, Helmer D (2005) in The First Steps of Animal Domestication. New Archaeological Approaches, eds Vigne JD, Peters J, Helmer D (Oxbow Books, Oxford, UK), pp 96-124.
4. Zeder MA, Hesse B (2000) The initial domestication of goats (Capra hircus) in the Zagros Mountains 10,000 years ago. Science 287:2254-2257.
5. Peters J, Helmer D, von den Driesch A, Saña-Segui M (1999) Early animal husbandry in the Northern Levant. Paléorient 25(2):27-48.
6. Zeder MA (2005) in The First Steps of Animal Domestication. New Archaeological Approaches, eds Vigne JD, Peters J, Helmer D (Oxbow Books, Oxford, UK), pp 125-146.
7. Zeder MA, Emshwiller E, Smith BD, Bradley DG (2006) Documenting domestication: the intersection of genetics and archaeology. Trends Genet 22:139-155.
8. Horwitz LK, et al. (2000) Animal domestication in the Southern Levant. Paléorient 25(2):63- 80.
9. Meadow RH (1984) in Animals and Archaeology 3. Early Herders and their Flocks, ed Clutton-Brock J & Grigson G (Harris DR (Oxford: British Archaeological Reports S202), pp 309-337.
10. Manceau V, Després L, Bouvet J, Taberlet P (1999) Systematics of the Capra genus inferred from mitochondrial DNA sequence data. Mol Phylogenet Evol 13:504-510.
11. Naderi S, et al. (2007) Large-scale mitochondrial DNA analysis of the domestic goat reveals six maternal lineages with high haplotype diversity. PLoS ONE 10:e1012.
12. Luikart G, et al. (2001) Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc Natl Acad Sci USA 98:5927-5932.
13. Fernández H, et al. (2006) Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas. Proc Natl Acad Sci USA 103:15375-15379.
14. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47-50.
15. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185-1192.
16. Lorenzen ED, De Neergaard R, Arctander P, Siegismund HR (2007) Phylogeography, hybridization and Pleistocene refugia of the kob antelope (Kobus kob). Mol Ecol 16:3241-3252.
17. Questiau S, Eybert MC, Taberlet P (1999) Amplified fragment length polymorphism (AFLP) markers reveal extra-pair parentage in a bird species: the bluethroat (Luscinia svecica). Mol Ecol 8:1331-1339.
18. Ball RM, Freeman S, James FC, Bermingham E, Avise JC (1988) Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA. Proc Natl Acad Sci USA 85:1558-1562.
19. Vigne JD, et al. (2000) in Archaeozoology of the Near East IV, Proceedings of the Fourth International Symposium Archaeozoology of Southwestern Asia and adjacent areas (ASWA; Paris, June 1998), eds Mashkour M, Choyke A, Buitenhuis H, Poplin F (Archaeological Research and Consultancy, Groningen), Vol. Publicaties 32, pp 52-75.
20. Vigne JD, Carrère I, Guilaine J (2003) in Le Néolithique de Chypre, eds Guilaine J, Le Brun A, Vol. Suppl. 43, pp 239-251.
21. Horwitz LK (1989) in Peopleand Culture in Change(Proceedings of the Second Symposium on Upper Palaeolithic, Mesolithic and Neolithic of Europe and the Mediterranean Basin), Part I. British Archaeol. Rep., Int. Ser., ed. Hershkovitz, I., Vol 508, pp 153-181.
22. Redding RW (2005) in The First Steps of Animal Domestication. New Archaeological Approaches, eds Vigne JD, Peters J, Helmer D (Oxbow Books, Oxford, UK), pp 41-48.
23. Arbuckle B (2005) in The First Steps of Animal Domestication. New Archaeological Approaches, eds Vigne JD, Peters J, Helmer D (Oxbow Books, Oxford, UK), pp 18-33.
24. Legge AJ (1972) in Papers in Economic Prehistory, ed Higgs ES (Cambridge Univ Press), pp 119-124.
25. Larson G, et al. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences of the USA 104, 39:15276-15281.
26. Taberlet P, Waits LP, Luikart G (1999) Noninvasive genetic sampling: look before you leap. Trends Ecol Evol 14:321-325.
27. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignement. Brief Bioinform 5:150-163.
28. Parma P, Feligini M, Greeppi G, Enne G (2003) The complete nucleotide sequence of goat (Capra hircus) mitochondrial genome. Goat mitochondrial genome. DNA Seq 14:199-203.
29. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556.
30. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 178:754-755.
31. Posada D, Crandall K (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
32. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 525:696-704.
33. Swofford D (1998) PAUP*: phylogenetic analysis using parsimony (*and other methods), Version 4 (Sinauer Associates, Sunderland, Massachusetts).
34. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
35. Kimura M (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111-120.
36. Kuhner MK (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22:768-770.
37. Rambaut A, Drummond AJ (2007) Tracer v1.4. Available from http://beast.bio.ed.ac.uk/ Tracer. Accessed May 25, 2007.
38. Uerpmann HP (1987) The Ancient Distribution of Ungulate Mammals in the Middle East (Dr. Ludwig Reichert Verlag, Wiesbaden).