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All issues Volume 39 / No 5 (September-October 2007) Genet. Sel. Evol., 39 5 (2007) 545-567 References
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Issue
Genet. Sel. Evol.
Volume 39, Number 5, September-October 2007
Page(s) 545 - 567
DOI https://doi.org/10.1051/gse:2007021
Published online 27 September 2007
References of  Genet. Sel. Evol. 39 (2007) 545-567
  1. Aitchison J., Principal component analysis of compositional data, Biometrika 70 (1983) 57-65 [CrossRef] [MathSciNet].
  2. Aitchison J., Logratios and natural laws in compositional data analysis, Math. Geol. 31 (1999) 563-589 [CrossRef].
  3. Aitchison J., Greenacre M., Biplot of compositional data, Appl. Stat. 51 (2002) 375-392.
  4. Bady P., Dolédec S., Dumont B., Fruget J.-F., Multiple co-inertia analysis: a tool for assessing synchrony in the temporal variability of aquatic communities, C. R. Biol. 327 (2004) 29-36 [CrossRef] [PubMed].
  5. Baumung R., Simianer H., Hoffmann I., Genetic diversity studies in farm animals - a survey, J. Anim. Breed. Genet. 121 (2004) 361-373.
  6. Baumung R., Cubric-Curik V., Schwend K., Achmann R., Solkner J., Genetic characterisation and breed assignment in Austrian sheep breeds using microsatellite marker information, J. Anim. Breed. Genet. 123 (2006) 265-271 [PubMed].
  7. Beaumont M.A., Recent developments in genetic data analysis: what can they tell us about human demographic history? Heredity 92 (2004) 365-379 [CrossRef] [PubMed].
  8. Beja-Pereira A., Alexandrino P., Bessa I., Carretero Y., Dunner S., Ferrand N., Jordana J., Laloë D., Moazami-Goudarzi K., Sanchez A., Canon J., Genetic characterization of southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites, J. Hered. 94 (2003) 243-250 [CrossRef] [PubMed].
  9. Beja-Pereira A., Caramelli D., Lalueza-Fox C., Vernesi C., Ferrand N., Casoli A., Goyache F., Royo L.J., Conti S., Lari M., Martini A., Ouragh L., Magid A., Atash A., Zsolnai A., Boscato P., Triantaphylidis C., Ploumi K., Sineo L., Mallegni F., Taberlet P., Erhardt G., Sampietro L., Bertranpetit J., Barbujani G., Luikart G., Bertorelle G., The origin of European cattle: evidence from modern and ancient DNA, Proc. Natl. Acad. Sci. USA 103 (2006) 8113-8118 [CrossRef] [PubMed].
  10. Bennewitz J., Kantanen J., Tapio I., Li M.H., Kalm E., Vilkki J., Ammosov I., Ivanova Z., Kiselyova T., Popov R., Meuwissen T.H., Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures, Genet. Sel. Evol. 38 (2006) 201-220 [CrossRef] [PubMed] [EDP Sciences].
  11. Bruford M.W., Bradley D.G., Luikart G., DNA markers reveal the complexity of livestock domestication, Nat. Rev. Genet. 4 (2003) 900-910 [CrossRef] [PubMed].
  12. Bryant D., A classification of consensus methods for phylogenies, in: Janowitz M., Lapointe F.-J., McMorris F.R., Mirkin B., Roberts F.S. (Eds.), Bioconsensus, DIMACS, AMS, 2003, pp. 163-184.
  13. Canon J., Alexandrino P., Bessa I., Carleos C., Carretero Y., Dunner S., Ferran N., Garcia D., Jordana J., Laloë D., Pereira A., Sanchez A., Moazami-Goudarzi K., Genetic diversity measures of local European beef cattle breeds for conservation purposes, Genet. Sel. Evol. 33 (2001) 311-332 [CrossRef] [PubMed] [EDP Sciences].
  14. Cavalli-Sforza L.L., The Human Genome Diversity Project: past, present and future, Nat. Rev. Genet. 6 (2005) 333-340 [CrossRef] [PubMed].
  15. Cavalli-Sforza L.L., Menozzi P., Piazza A., The history and geography of human genes, Princeton University Press, 1994, 1088 p.
  16. Chenyambuga S.W., Hanotte O., Hirbo J., Watts P.C., Kemp S.J., Kifaro G.C., Gwakisa P.S., Peterson P.H., Rege J.E.O., Genetic characterization of indigenous goats of Sub-Saharan Africa using microsatellite DNA markers, Asian-Australas. J. Anim. Sci. 17 (2004) 445-452.
  17. Chessel D., Hanafi M., Analyses de la co-inertie de K nuages de points, Rev. Stat. Appl. 44 (1996) 35-60.
  18. Chessel D., Dufour A.B., Thioulouse J., The ade4 package - I: One-table methods, R-News 4 (2004) 5-10.
  19. De Crespin de Billy V., Dolédec S., Chessel D., Biplot presentation of diet composition data: an alternative for fish stomach contents analysis, J. Fish Biol. 56 (2000) 961-973.
  20. DeYoung R.W., Demarais S., Honeycutt R.L., Rooney A.P., Gonzales R.A., Gee K.L., Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi, Mol. Ecol. 12 (2003) 3237-3252 [PubMed].
  21. Excoffier L., Heckel G., Computer programs for population genetics data analysis: a survival guide, Nat. Rev. Genet. 7 (2006) 745-758 [CrossRef] [PubMed].
  22. Fabuel E., Barragan C., Silio L., Rodriguez M.C., Toro M.A., Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers, Heredity 93 (2004) 104-113 [CrossRef] [PubMed].
  23. Fang M., Hu X., Jiang T., Braunschweig M., Hu L., Du Z., Feng J., Zhang Q., Wu C., Li N., The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers, Anim. Genet. 36 (2005) 7-13 [PubMed].
  24. FAO, Secondary Guidelines for Development of National Farm Animal Genetics Resources Management Plans. Measurement of Domestic Animal Diversity (MoDAD), Original Working Group Report, FAO, Rome, 1998.
  25. Felsenstein J., How can we infer geography and history from gene frequencies? J. Theor. Biol. 96 (1982) 9-20 [CrossRef] [PubMed].
  26. Freeman A.R., Meghen C.M., Machugh D.E., Loftus R.T., Achukwi M.D., Bado A., Sauveroche B., Bradley D.G., Admixture and diversity in West African cattle populations, Mol. Ecol. 13 (2004) 3477-3487 [PubMed].
  27. Gabriel K.R., The biplot graphic display of matrices with application to principal component analysis, Biometrika 58 (1971) 453-467 [CrossRef] [MathSciNet].
  28. Hanotte O., Bradley D.G., Ochieng J.W., Verjee Y., Hill E.W., Rege J.E., African pastoralism: genetic imprints of origins and migrations, Science 296 (2002) 336-339 [CrossRef].
  29. Healy M.J.R., Drawing a probability ellipse, J. R. Stat. Soc. Ser. C-Appl. Stat. 21 (1972) 202-204.
  30. Hedde M., Lavelle P., Joffre R., Jiménez J.J., Decaëns T., Specific functional signature in soil macro-invertebrate biostructures, Funct. Ecol. 19 (2005) 785-793.
  31. Hillel J., Groenen M.A., Tixier-Boichard M., Korol A.B., David L., Kirzhner V.M., Burke T., Barre-Dirie A., Crooijmans R.P., Elo K., Feldman M.W., Freidlin P.J., Maki-Tanila A., Oortwijn M., Thomson P., Vignal A., Wimmers K., Weigend S., Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools, Genet. Sel. Evol. 35 (2003) 533-557 [CrossRef] [PubMed] [EDP Sciences].
  32. Holmes S., Multivariate Data Analysis: The French Way, to appear in Festchrift for David Freeman, IMS lecture notes (2006) http://www-stat.stanford.edu/$\sim $susan/papers/dfc.pdf [consulted: 20 March 2007].
  33. Hotelling H., Analysis of a complex of statistical variables into principal components, J. Educ. Psychol. 24 (1933) 417-441 [CrossRef].
  34. Hotelling H., Analysis of a complex of statistical variables into principal components (continued from September issue), J. Educ. Psychol. 24 (1933) 498-520 [CrossRef].
  35. Iamartino D., Bruzzone A., Lanza A., Blasi M., Pilla F., Genetic diversity of Southern Italian goat populations assessed by microsatellite markers, Small Ruminant Res. 57 (2005) 249-255 [CrossRef].
  36. Ibeagha-Awemu E.M., Jann O.C., Weimann C., Erhardt G., Genetic diversity, introgression and relationships among West/Central African cattle breeds, Genet. Sel. Evol. 36 (2004) 673-690 [CrossRef] [PubMed] [EDP Sciences].
  37. Jann O.C., Ibeagha-Awemu E.M., Ozbeyaz C., Zaragoza P., Williams J.L., Ajmone-Marsan P., Lenstra J.A., Moazami-Goudarzi K., Erhardt G., Geographic distribution of haplotype diversity at the bovine casein locus, Genet. Sel. Evol. 36 (2004) 243-257 [CrossRef] [PubMed] [EDP Sciences].
  38. Joliffe I.T., Discarding variables in a principal component analysis. I: Artificial data., Appl. Stat. 22 (1972) 373-374.
  39. Knowles L.L., The burgeoning field of statistical phylogeography, J. Evol. Biol. 17 (2004) 1-10 [PubMed].
  40. Krzanowski W.J., A stopping rule for structure-preserving variable selection, Stat. Comput. 6 (1996) 51-56 [CrossRef].
  41. Kumar S., Gupta J., Kumar N., Dikshit K., Navani N., Jain P., Nagarajan M., Genetic variation and relationships among eight Indian riverine buffalo breeds, Mol. Ecol. 15 (2006) 593-600 [PubMed].
  42. Li M.H., Zhao S.H., Bian C., Wang H.S., Wei H., Liu B., Yu M., Fan B., Chen S.L., Zhu M.J., Li S.J., Xiong T.A., Li K., Genetic relationships among twelve Chinese indigenous goat populations based on microsatellite analysis, Genet. Sel. Evol. 34 (2002) 729-744 [CrossRef] [PubMed] [EDP Sciences].
  43. Liron J.P., Peral-Garcia P., Giovambattista G., Genetic characterization of Argentine and Bolivian Creole cattle breeds assessed through microsatellites, J. Hered. 97 (2006) 331-339 [CrossRef] [PubMed].
  44. Luikart G., England P.R., Tallmon D., Jordan S., Taberlet P., The power and promise of population genomics: from genotyping to genome typing, Nat. Rev. Genet. 4 (2003) 981-994 [CrossRef] [PubMed].
  45. MacHugh D.E., Loftus R.T., Cunningham P., Bradley D.G., Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers, Anim. Genet. 29 (1998) 333-340 [PubMed].
  46. Marletta D., Tupac-Yupanqui I., Bordonaro S., Garcia D., Guastella A.M., Criscione A., Canon J., Dunner S., Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers, J. Anim. Breed. Genet. 123 (2006) 315-325 [PubMed].
  47. Martin-Burriel I., Garcia-Muro E., Zaragoza P., Genetic diversity analysis of six Spanish native cattle breeds using microsatellites, Anim. Genet. 30 (1999) 177-182 [PubMed].
  48. Menozzi P., Piazza A., Cavalli-Sforza L.L., Synthetic maps of human gene frequencies in europeans, Science 201 (1978) 786-792 [CrossRef].
  49. Moazami-Goudarzi K., Laloë D., Is a multivariate consensus representation of genetic relationships among populations always meaningful? Genetics 162 (2002) 473-484 [PubMed].
  50. Moazami-Goudarzi K., Laloë D., Furet J.P., Grosclaude F., Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites, Anim. Genet. 28 (1997) 338-345 [PubMed].
  51. Moazami-Goudarzi K., Belemsaga D., Ceriotti G., Laloë D., Fagbohoun F., Kouagou N., Sidibé I., Codjia V., Crimella M., Grosclaude F., Touré S., Caractérisation de la race bovine Somba à l'aide de marqueurs moléculaires, Rev. Elev. Med. Vet. Pays Trop. 54 (2001) 1-10.
  52. Phillips C., Warnow T.J., The asymetric median tree - a new model for building consensus trees, Discrete Appl. Math. 71 (1996) 311-335 [CrossRef] [MathSciNet].
  53. Pompanon F., Bonin A., Bellemain E., Taberlet P., Genotyping errors: causes, consequences and solutions, Nat. Rev. Genet. 6 (2005) 847-859 [CrossRef] [PubMed].
  54. R Development Core Team, R: a Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria (2006), ISBN 3-900051-07-0, http://www.R-project.org.
  55. Reyment R., The statistical analysis of multivariate serological frequency data, Bull. Math. Biol. 67 (2005) 1303-1313 [CrossRef] [PubMed].
  56. Rosenberg N.A., Pritchard J.K., Weber J.L., Cann H.M., Kidd K.K., Zhivotovsky L.A., Feldman M.W., Genetic structure of human populations, Science 298 (2002) 2381-2385 [CrossRef].
  57. Royo L.J., Alvarez I., Beja-Pereira A., Molina A., Fernandez I., Jordana J., Gomez E., Gutierrez J.P., Goyache F., The origins of Iberian horses assessed via mitochondrial DNA, J. Hered. 96 (2005) 663-669 [CrossRef] [PubMed].
  58. Schlötterer C., The evolution of molecular markers-just a matter of fashion? Nat. Rev. Genet. 5 (2004) 63-69 [CrossRef] [PubMed].
  59. Simianer H., Using expected allele number as objective function to design between and within breed conservation of farm animal biodiversity, J. Anim. Breed. Genet. 122 (2005) 177-187 [PubMed].
  60. Simianer H., Meyer J.N., Past and future activities to harmonize farm animal biodiversity studies on global scale, Arch. Zootec. 52 (2003) 193-199.
  61. Takezaki N., Nei M., Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA, Genetics 144 (1996) 389-399 [PubMed].
  62. Talle S.B., Chenyabuga W.S., Fimland E., Syrstad O., Meuwissen T., Klungland H., Use of DNA technologies for the conservation of animal genetic resources: A review, Acta Agric. Scand. Sect. A Anim. Sci. 55 (2005) 1-8.
  63. Tapio M., Miceikiene I., Vilkki J., Kantanen J., Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds, Mol. Ecol. 12 (2003) 2045-2056 [PubMed].
  64. Toro M.A., Caballero A., Characterization and conservation of genetic diversity in subdivided populations, Philos. Trans. R. Soc. Lond. B Biol. Sci. 360 (2005) 1367-1378 [PubMed].
  65. Uzun M., Gutierrez-Gil B., Arranz J.J., San Primitivo F., Saatci M., Kaya M., Bayon Y., Genetic relationships among Turkish sheep, Genet. Sel. Evol. 38 (2006) 513-524 [CrossRef] [PubMed] [EDP Sciences].
  66. Wang A., Gehan E.A., Gene selection for microarray data analysis using principal component analysis., Stat. Med. 24 (2005) 2069-2087 [PubMed] [MathSciNet].
  67. Wiener P., Burton D., Williams J.L., Breed relationships and definition in British cattle: a genetic analysis, Heredity 93 (2004) 597-602 [CrossRef] [PubMed].
  68. Woronow A., Regression and discrimination analysis using raw compositional data - Is it really a problem? in: Proceedings of the 3rd Annual Conference of the International Association for Mathematical Geology, Universitate Politecnica de Catalunya, Barcelona, 1997, pp. 157-162.
  69. Xuebin Q., Jianlin H., Lkhagva B., Chekarova I., Badamdorj D., Rege J.E., Hanotte O., Genetic diversity and differentiation of Mongolian and Russian yak populations, J. Anim. Breed. Genet. 122 (2005) 117-126 [PubMed].
  70. Yue-Hui M., Shao-Qi R., Shen-Jin L., Guan-Yu H., Wei-Jun G., Hong-Bin L., Xia L., Qian-Jun Z., Jun G., Phylogeography and origin of sheep breeds in Northern China, Conserv. Genet. 7 (2006) 117-127 [CrossRef].
  71. Zhang D.X., Hewitt G.M., Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects, Mol. Ecol. 12 (2003) 563-584 [PubMed].