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High levels of nucleotide diversity in the European rabbit (Oryctolagus cuniculus) SRY gene","volume":"36","author":"A Geraldes","year":"2005","journal-title":"Animal Genetics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1126\/science.1253714","article-title":"Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication","volume":"345","author":"M Carneiro","year":"2014","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1093\/molbev\/msr003","article-title":"The genetic structure of domestic rabbits","volume":"28","author":"M Carneiro","year":"2011","journal-title":"Molecular Biology and Evolution"},{"key":"ref16","unstructured":"Lebas F, Coudert P, de Rochambeau H, Thebault RG. The Rabbit: Husbandry, Health, and Production. Health and Production. FAO, Rome, Italy; 1997."},{"key":"ref17","first-page":"165","article-title":"Genome Mapping and Genomics in Domestic Animals","author":"C Rogel Gaillard","year":"2009"},{"key":"ref18","first-page":"49","article-title":"Rabbit Biotechnology","author":"M Shiomi","year":"2009"},{"key":"ref19","unstructured":"Bolet G, Brun JM, Monnerot M, Abeni F, Arnal C, Arnold J, et al. Evaluation and conservation of European rabbit (Oryctolagus cuniculus) genetic resources. First results and inferences. Valencia, Spain, 4\u20137 July; 1999. pp. 281\u2013315."},{"key":"ref20","article-title":"Molecular Cloning: A Laboratory Manual","author":"J Sambrook","year":"1989"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1159\/000076310","article-title":"133 new gene localizations on the rabbit cytogenetic map","volume":"103","author":"C Chantry-Darmon","year":"2003","journal-title":"Cytogenet Genome Res"},{"key":"ref22","first-page":"58","article-title":"Nine polymorphic microsatellite loci in the rabbit, Oryctolagus cuniculus","volume":"28","author":"F Mougel","year":"1997","journal-title":"Animal Genetics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"226","DOI":"10.2144\/04372ST03","article-title":"AutoDimer: a screening tool for primer-dimer and hairpin structures","volume":"37","author":"PM Vallone","year":"2004","journal-title":"BioTechniques"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1111\/j.1471-8286.2004.00684.x","article-title":"MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data","volume":"4","author":"C van Oosterhout","year":"2004","journal-title":"Mol Ecol Notes"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1111\/j.1755-0998.2010.02847.x","article-title":"Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows","volume":"10","author":"L Excoffier","year":"2010","journal-title":"Molecular Ecology Resources"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1111\/j.1471-8286.2005.01155.x","article-title":"GENALEX 6: genetic analysis in Excel. 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Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. 1992;131: 479\u2013491.","DOI":"10.1093\/genetics\/131.2.479"},{"key":"ref30","first-page":"233","article-title":"Phylogenetic analysis. Models and estimation procedures","volume":"19","author":"LL Cavalli-Sforza","year":"1967","journal-title":"Am J Hum Genet"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/368455a0","article-title":"High resolution of human evolutionary trees with polymorphic microsatellites","volume":"368","author":"AM Bowcock","year":"1994","journal-title":"Nature"},{"key":"ref32","unstructured":"Langella O. Populations 1.2.32 (02\/13\/2011): a population genetic software. CNRS UPR9034. Available at <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/bioinformatics.org\/~tryphon\/populations\/\" xlink:type=\"simple\">http:\/\/bioinformatics.org\/~tryphon\/populations\/<\/ext-link>. 1999."},{"key":"ref33","unstructured":"Gao L-Z, Innan H. Nonindependent domestication of the two rice subspecies, Oryza sativa ssp. indica and ssp. japonica, demonstrated by multilocus microsatellites. 2008;179: 965\u2013976."},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1126\/science.1097406","article-title":"Genetic structure of the purebred domestic dog","volume":"304","author":"HG Parker","year":"2004","journal-title":"Science"},{"key":"ref35","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"N Saitou","year":"1987","journal-title":"Molecular Biology and Evolution"},{"key":"ref36","article-title":"Distributed by the author Department of Genome Sciences","author":"J Felsenstein","year":"2005"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1046\/j.1471-8286.2003.00351.x","article-title":"Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets","volume":"3","author":"D Dieringer","year":"2003","journal-title":"Mol Ecol Notes"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1126\/science.155.3760.279","article-title":"Construction of phylogenetic trees","volume":"155","author":"WM Fitch","year":"1967","journal-title":"Science"},{"key":"ref39","doi-asserted-by":"crossref","unstructured":"Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. 2000;155: 945\u2013959.","DOI":"10.1093\/genetics\/155.2.945"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"G Evanno","year":"2005","journal-title":"Mol Ecol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method","volume":"4","author":"DA Earl","year":"2012","journal-title":"Conservation Genet Resour"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1046\/j.1471-8286.2003.00566.x","article-title":"DISTRUCT: a program for the graphical display of population structure","volume":"4","author":"NA Rosenberg","year":"2004","journal-title":"Mol Ecol Notes"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.1093\/bioinformatics\/btm233","article-title":"CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure","volume":"23","author":"M Jakobsson","year":"2007","journal-title":"Bioinformatics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1126\/science.1078311","article-title":"Genetic structure of human populations","volume":"298","author":"NA Rosenberg","year":"2002","journal-title":"Science"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/1471-2156-11-94","article-title":"Discriminant analysis of principal components: a new method for the analysis of genetically structured populations","volume":"11","author":"T Jombart","year":"2010","journal-title":"BMC Genetics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1093\/bioinformatics\/btn129","article-title":"adegenet: a R package for the multivariate analysis of genetic markers","volume":"24","author":"T Jombart","year":"2008","journal-title":"Bioinformatics"},{"key":"ref47","article-title":"R: A Language and Environment for Statistical Computing","year":"2015"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/j.1365-294X.1995.tb00227.x","article-title":"Microsatellite analysis of population structure in Canadian polar bears","volume":"4","author":"D Paetkau","year":"1995","journal-title":"Mol Ecol"},{"key":"ref49","doi-asserted-by":"crossref","unstructured":"Gray MM, Granka JM, Bustamante CD, Sutter NB, Boyko AR, Zhu L, et al. Linkage disequilibrium and demographic history of wild and domestic canids. 2009;181: 1493\u20131505.","DOI":"10.1534\/genetics.108.098830"},{"key":"ref50","article-title":"Lagomorph Biology","author":"JA Chapman","year":"2008"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1111\/j.1365-2907.1992.tb00129.x","article-title":"World distribution of the Rabbit Oryctolagus funiculus on islands","volume":"22","author":"JE Flux","year":"1992","journal-title":"Mammal Review"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1506","DOI":"10.1093\/molbev\/msm077","article-title":"Grinding up wheat: a massive loss of nucleotide diversity since domestication","volume":"24","author":"A Haudry","year":"2007","journal-title":"Molecular Biology and Evolution"},{"key":"ref53","doi-asserted-by":"crossref","unstructured":"Liu A, Burke JM. Patterns of nucleotide diversity in wild and cultivated sunflower. 2006;173: 321\u2013330.","DOI":"10.1534\/genetics.105.051110"},{"key":"ref54","doi-asserted-by":"crossref","unstructured":"Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JSC, et al. An analysis of genetic diversity across the maize genome using microsatellites. 2005;169: 1617\u20131630.","DOI":"10.1534\/genetics.104.032086"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1038\/nrg1203","article-title":"DNA markers reveal the complexity of livestock domestication","volume":"4","author":"MW Bruford","year":"2003","journal-title":"Nature Reviews Genetics"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1111\/j.1469-7998.2006.00042.x","article-title":"Genetics and animal domestication: new windows on an elusive process","volume":"269","author":"K Dobney","year":"2006","journal-title":"J Zoology"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.tig.2005.02.004","article-title":"Genes of domestic mammals augmented by backcrossing with wild ancestors","volume":"21","author":"C Vil\u00e0","year":"2005","journal-title":"Trends Genet"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/sj.hdy.6801039","article-title":"Genetic structure of European sheep breeds","volume":"99","author":"L-J Lawson Handley","year":"2007","journal-title":"Heredity"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/1471-2156-11-76","article-title":"Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia","volume":"11","author":"M Tapio","year":"2010","journal-title":"BMC Genetics"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1186\/1297-9686-33-3-311","article-title":"Genetic diversity measures of local European beef cattle breeds for conservation purposes","volume":"33","author":"J Ca\u00f1on","year":"2001","journal-title":"Genet Sel Evol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1046\/j.1365-2052.1998.295330.x","article-title":"Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers","volume":"29","author":"DE MacHugh","year":"1998","journal-title":"Animal Genetics"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1046\/j.1439-0388.2000.00264.x","article-title":"Genetic structure of Norwegian horse breeds","volume":"117","author":"G Bj\u00f8rnstad","year":"2000","journal-title":"Journal of Animal Breeding and Genetics"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1046\/j.1365-2052.2000.00591.x","article-title":"The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data","volume":"31","author":"J Ca\u00f1on","year":"2000","journal-title":"Animal Genetics"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/j.1365-2052.2006.01461.x","article-title":"Geographical partitioning of goat diversity in Europe and the Middle East","volume":"37","author":"J Ca\u00f1on","year":"2006","journal-title":"Animal 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