A dig into the past mitochondrial diversity of corsican goats reveals the influence of secular herding practices

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Hughes, Sandrine ^a   Fernández, Helena ^b   Cucchi, Thomas ^c,d   Duffraisse, Marilyne ^a   Casabianca, François ^e   Istria, Daniel ^f   Pompanon, François ^b   Vigne, Jean Denis ^c   Hänni, Catherine ^a   Taberlet, Pierre ^b  

^a Univ Lyon 1   (France)

^b UNIVERSITÉ JOSEPH FOURIER   (France)

^c MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

^d UNIVERSITY OF ABERDEEN   (United Kingdom)

^e INRA SAD   (France)

^f CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREEDING METHOD; CONTROLLED STUDY; ENDEMIC SPECIES; GENETIC VARIABILITY; GENOMIC FRAGMENT; GOAT; HAPLOTYPE; HERD; MIDDLE AGES; MITOCHONDRIAL GENETICS; NEOLITHIC; NONHUMAN; SPECIES CONSERVATION; AGRICULTURE; ANIMAL; ANIMAL HUSBANDRY; ARCHEOLOGY; DNA SEQUENCE; DOMESTIC ANIMAL; FEMALE; FRANCE; GENETICS; HISTORY; MALE; METHODOLOGY; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY;

ANIMALIA; CAPRA AEGAGRUS; CAPRA HIRCUS;

MITOCHONDRIAL DNA;

AGRICULTURE; ANIMAL HUSBANDRY; ANIMALS; ANIMALS, DOMESTIC; ARCHAEOLOGY; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FEMALE; FRANCE; GENETIC VARIATION; GOATS; HISTORY, 21ST CENTURY; HISTORY, ANCIENT; MALE; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84856402431     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030272     Document Type: Article

References (57)

1. Zeder MA, Hesse B, (2000) The initial domestication of goats (Capra hircus) in the Zagros mountains 10,000 years ago. Science 287: 2254-2257.
2. Peters J, von den Driesch A, Helmer D, (2005) The First Steps of Animal Domestication. New Archaeological Approaches Oxford, UK Oxbow Books.
3. Naderi S, Rezaei HR, Pompanon F, Blum MG, Negrini R, et al. (2008) The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proc Natl Acad Sci U S A 105: 17659-17664.
4. Vigne JD, (2011) The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere. C R Biol 334: 171-181.
5. Guilaine J, (2003) De la vague à la tombe. La conquête néolithique de la Méditerranée. Paris.
6. Tresset A, Bollongino R, Edwards CJ, Hughes S, Vigne JD, (2009) Early diffusion of domestic bovids in Europe: an indicator for human contacts, exchanges and migrations? In: Hombert J-MadE, F., editors. The Origin of Man, Language and Languages Cambridge McDonald Institute Monograph Series pp. 69-90.
7. FAOSTAT (2009) Preliminary data for production of Live Animals in 2009 in the World. FAOSTAT website. Available: http://faostat.fao.org/ Accessed 2011 May 10.
8. Luikart G, Gielly L, Excoffier L, Vigne JD, Bouvet J, et al. (2001) Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc Natl Acad Sci U S A 98: 5927-5932.
9. Azor PJ, Monteagudo LV, Luque M, Tejedor MT, Rodero E, et al. (2005) Phylogenetic relationships among Spanish goats breeds. Anim Genet 36: 423-425.
10. Chen SY, Su YH, Wu SF, Sha T, Zhang YP, (2005) Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mol Phylogenet Evol 37: 804-814.
11. Pereira F, Pereira L, Van Asch B, Bradley DG, Amorim A, (2005) The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Mol Ecol 14: 2313-2318.
12. Sardina MT, Ballester M, Marmi J, Finocchiaro R, van Kaam JB, et al. (2006) Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Anim Genet 37: 376-378.
13. Fan B, Chen S-L, Kijas JH, Liu B, Yu M, et al. (2007) Phylogenetic relationships among Chinese indigenous goat breds inferred from mitochondrial control region sequence. Small Ruminant Research 73: 262-266.
14. Naderi S, Rezaei HR, Taberlet P, Zundel S, Rafat SA, et al. (2007) Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One 2: e1012.
15. Wang J, Chen YL, Wang XL, Yang ZX, (2008) The genetic diversity of seven indigenous Chinese goat breds. Small Ruminant Research 74: 231-237.
16. Pereira F, Queiros S, Gusmao L, Nijman IJ, Cuppen E, et al. (2009) Tracing the history of goat pastoralism: new clues from mitochondrial and Y chromosome DNA in North Africa. Mol Biol Evol 26: 2765-2773.
17. Vacca GM, Daga C, Pazzola M, Carcangiu V, Dettori ML, et al. (2010) D-loop sequence mitochondrial DNA variability of Sarda goat and other goat breeds and populations reared in the Mediterranean area. Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 127: 352-360.
18. Vigne JD, (1999) The large "true" Mediterranean islands as a model for the Holocene human impact on the European vertebrate fauna? Recent data and new reflections. In: Benecke N, editors. The Holocene history of the European vertebrate fauna Modern aspects of research Berlin Deutsches Archäologisches Institut, Eurasien-Abteilung (Archäologie in Eurasien, 6) pp. 295-322.
19. Vigne JD, (1988) Les Mammifères post-glaciaires de Corse, étude Archéozoologique (XXVIe suppl. à Gallia Préhistoire); CNRS, editor. Paris.
20. Ravis-Giordani G, (1983) Bergers corses. Communautés villageoises du Niolu. Aix-en-Provence: Edisud.
21. Bouche R, Aragni CHJ, Bordeaux C, (2009) Caprin extensif en Corse: Savoirs durables en quête de développement. Options Méditerranéennes, A 91: 209-213.
22. Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, et al. (2008) Are cattle, sheep, and goats endangered species? Mol Ecol 17: 275-284.
23. Pernet F, Lenclud G, (1977) Berger en Corse. Essai sur la question pastorale Grenoble Presses universitaires de Grenoble.
24. Istria D, (2005) Pouvoirs et fortifications dans le Nord de la Corse, XIe-XIVe siècle. Ajaccio Editions Alain Piazzola.
25. Cucchi T, (2003) Production et distribution de biens d'origine animale en contexte seigneurial de Haute-Corse: la faune mammalienne de la salle 1 du castrum de Rostino (XIIIe-XIVe siècles). Bulletin d'Archéologie et d'Histoire de la Corse 1: 70-93.
26. Payne S, (1985) Morphological distinction between the mandibular teeth of young sheep, Ovis and goats, Capra. Journal of Archaeological Science 12: 139-147.
27. Helmer D, (2000) Discrimination des genres Ovis et Capra à l'aide des prémolaires inférieures 3 et 4 et interprétation des âges d'abattage: l'exemple de Dikili Tash (Grèce). Anthropozoologica 31.
28. Boessneck J, (1969) Oesteological differences beetween sheep (Ovis aries Linne) and goat (Capra hircus Linne). In: D HEB, editors. Science in Archaeology Londres Thames and Huston pp. 331-358.
29. Clutton-Brock J, Dennis-Brian K, Armitage P-A, Jewel P, (1990) Osteology of the Soay sheep. Bull Br Mus Nat Hist 56: 1-56.
30. Helmer D, Rocheteau M, (1994) Atlas du squelette appendiculaire des principaux genres holocènes de petits ruminants du nord de la méditerranée et du Proche-Orient; APDCA, editor. Juan-les-Pins.
31. Poplin F, (1979) Origine du Mouflon de Corse dans une nouvelle perspective paléontologique: par marronnage. Annales de Génétique et Sélection Animale 11: 133-143.
32. Loreille O, Vigne JD, Hardy C, Callou C, Treinen-Claustre F, et al. (1997) First distinction of sheep and goat archaeological bones by the means of their fossil mtDNA. Journal of Archaeological Science 24: 33-37.
33. Collins M, Buckley M, Grundy HH, Thomas-Oates J, Wilson J, et al. (2010) ZooMS: the collagen barcode and fingerprints. Spectroscopy Europe 22: 11-13.
34. Hughes S, Hayden TJ, Douady CJ, Tougard C, Germonpre M, et al. (2006) Molecular phylogeny of the extinct giant deer, Megaloceros giganteus. Mol Phylogenet Evol 40: 285-291.
35. Calvignac S, Hughes S, Tougard C, Michaux J, Thevenot M, et al. (2008) Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times. Mol Ecol 17: 1962-1970.
36. Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, et al. (2001) Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr Biol 11: 200-203.
37. Orlando L, Bonjean D, Bocherens H, Thenot A, Argant A, et al. (2002) Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol Biol Evol 19: 1920-1933.
38. Fernández H, Hughes S, Vigne JD, Helmer D, Hodgins G, et al. (2006) Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas. Proc Natl Acad Sci U S A 103: 15375-15379.
39. Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Paabo S, (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29: 4793-4799.
40. Gouy M, Guindon S, Gascuel O, (2010) SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 27: 221-224.
41. Villesen P, (2007) FaBox: an online toolbox for fasta sequences. Mol Ecol Notes 7: 965-968.
42. Posada D, (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
43. Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
44. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
45. Bandelt HJ, Forster P, Rohl A, (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
46. 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.
47. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
48. Excoffier L, Lischer HEL, (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Ressources 10: 564-567.
49. Orlando L, Calvignac S, Schnebelen C, Douady CJ, Godfrey LR, et al. (2008) DNA from extinct giant lemurs links archaeolemurids to extant indriids. BMC Evol Biol 8: 121.
50. Calvignac S, Hughes S, Hänni C, (2009) Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. Diversity and Distributions 15: 742-750.
51. Ruas M-P, Vigne JD, (1995) Perspectives archéobotaniques et archéozoologiques pour les périodes historiques en Corse. pp. 113-126 Patrimoine d'une île, 1: Recherches récentes d'archéologie médiévale en Corse: Ajaccio: Soc. Archéol. Corse-du-Sud.
52. Charlet P, Le Jaouen JC, (1977) Les populations caprines du bassin méditerranéen. Aptitudes et évolution. Options Méditerranéennes, A 35: 45-53.
53. Bruford MW, Bradley DG, Luikart G, (2003) DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 4: 900-910.
54. Pariset L, Cuteri A, Ligda C, Ajmone-Marsan P, Valentini A, (2009) Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms. BMC Ecol 9: 20.
55. Canon J, Garcia D, Garcia-Atance MA, Obexer-Ruff G, Lenstra JA, et al. (2006) Geographical partitioning of goat diversity in Europe and the Middle East. Anim Genet 37: 327-334.
56. Bouche R, Gambotti JY, Maestrini O, (2004) L'avenir c'est de durer... Quand le changement en élevage extensif nécessite le maintien ou la réinvention de systèmes collectifs. Cas des caprins corses. L'évolution des systèmes de production ovine et caprine: Avenir des systèmes extensifs face au changement de la société, Alghero (ITA) Montpellier, France CIHEAM pp. 319-327.
57. Hugot S, Bouche R, (1999) Regards sur les pratiques de l'élevage extensif de la chèvre corse: Préalable à la mise en place d'un schéma de sélection. Options Méditerranéennes, A 38: 137-143.