TY - JOUR AU - Giuffra, E. AU - Kijas, J. M. H. AU - Amarger, V. AU - Carlborg, Ö. AU - Jeon, J. -. T. AU - Andersson, L. PY - 2000 DA - 2000// TI - The origin of the domestic pig: independent domestication and subsequent introgression JO - Genetics VL - 154 ID - Giuffra2000 ER - TY - JOUR AU - Petersen, J. L. AU - Mickelson, J. R. AU - Cothran, E. G. AU - Andersson, L. S. AU - Axelsson, J. AU - Bailey, E. PY - 2013 DA - 2013// TI - Genetic diversity in the modern horse illustrated from genome-wide SNP data JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0054997 DO - 10.1371/journal.pone.0054997 ID - Petersen2013 ER - TY - JOUR AU - Larkin, D. M. AU - Daetwyler, H. D. AU - Hernandez, A. G. AU - Wright, C. L. AU - Hetrick, L. A. AU - Boucek, L. PY - 2012 DA - 2012// TI - Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1114546109 DO - 10.1073/pnas.1114546109 ID - Larkin2012 ER - TY - JOUR AU - Ernst, C. W. AU - Steibel, J. P. PY - 2013 DA - 2013// TI - Molecular advances in QTL discovery and application in pig breeding JO - Trends Genet VL - 29 UR - https://doi.org/10.1016/j.tig.2013.02.002 DO - 10.1016/j.tig.2013.02.002 ID - Ernst2013 ER - TY - JOUR AU - Stinchcombe, J. R. AU - Hoekstra, H. E. PY - 2007 DA - 2007// TI - Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits JO - Heredity VL - 100 UR - https://doi.org/10.1038/sj.hdy.6800937 DO - 10.1038/sj.hdy.6800937 ID - Stinchcombe2007 ER - TY - JOUR AU - Goddard, M. E. AU - Hayes, B. J. PY - 2007 DA - 2007// TI - Genomic selection JO - J Anim Breed Genet VL - 124 UR - https://doi.org/10.1111/j.1439-0388.2007.00702.x DO - 10.1111/j.1439-0388.2007.00702.x ID - Goddard2007 ER - TY - JOUR AU - Dekkers, J. C. PY - 2004 DA - 2004// TI - Commercial application of marker- and gene-assisted selection in livestock: strategies and lessons JO - J Anim Sci VL - 82 ID - Dekkers2004 ER - TY - JOUR AU - Notter, D. R. PY - 1999 DA - 1999// TI - The importance of genetic diversity in livestock populations of the future JO - J Anim Sci VL - 77 ID - Notter1999 ER - TY - JOUR AU - Ajmone‐Marsan, P. PY - 2010 DA - 2010// TI - A global view of livestock biodiversity and conservation–GLOBALDIV JO - Anim Genet VL - 41 UR - https://doi.org/10.1111/j.1365-2052.2010.02036.x DO - 10.1111/j.1365-2052.2010.02036.x ID - Ajmone‐Marsan2010 ER - TY - STD TI - Rare Breeds Survival Trust. [https://www.rbst.org.uk/]. accessed 2014. UR - https://www.rbst.org.uk/ ID - ref10 ER - TY - JOUR AU - Kijas, J. W. AU - Lenstra, J. A. AU - Hayes, B. AU - Boitard, S. AU - Porto Neto, L. R. AU - San Cristobal, M. PY - 2012 DA - 2012// TI - Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection JO - PLoS Biol VL - 10 UR - https://doi.org/10.1371/journal.pbio.1001258 DO - 10.1371/journal.pbio.1001258 ID - Kijas2012 ER - TY - JOUR PY - 2009 DA - 2009// TI - Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds JO - Science VL - 324 UR - https://doi.org/10.1126/science.1167936 DO - 10.1126/science.1167936 ID - ref12 ER - TY - JOUR AU - Elsik, C. G. AU - Tellam, R. L. AU - Worley, K. C. PY - 2009 DA - 2009// TI - The genome sequence of taurine cattle: a window to ruminant biology and evolution JO - Science VL - 324 UR - https://doi.org/10.1126/science.1169588 DO - 10.1126/science.1169588 ID - Elsik2009 ER - TY - JOUR AU - Groenen, M. A. M. AU - Archibald, A. L. AU - Uenishi, H. AU - Tuggle, C. K. AU - Takeuchi, Y. AU - Rothschild, M. F. PY - 2012 DA - 2012// TI - Analyses of pig genomes provide insight into porcine demography and evolution JO - Nature VL - 491 UR - https://doi.org/10.1038/nature11622 DO - 10.1038/nature11622 ID - Groenen2012 ER - TY - BOOK AU - Trow-Smith, R. PY - 1957 DA - 1957// TI - A History of British Livestock Husbandry to 1700 PB - Routledge and Paul CY - Oxford ID - Trow-Smith1957 ER - TY - BOOK AU - Trow-Smith, R. PY - 1959 DA - 1959// TI - A history of british livestock husbandry, 1700–1900 PB - K. Paul Ltd. CY - London ID - Trow-Smith1959 ER - TY - STD TI - Illumina. OvineSNP50 Genotyping Beadchip. http://www.illumina.com/documents//products/datasheets/datasheet_ovinesnp50.pdf 2010. UR - http://www.illumina.com/documents//products/datasheets/datasheet_ovinesnp50.pdf ID - ref17 ER - TY - STD TI - QIAGEN Genomic DNA Handbook. [http://www.qiagen.com/knowledge-and-support/resource-center/resource-download.aspx?id=402bb209-4104-4956-a005-6226ff0b67d5&lang=en]. UR - http://www.qiagen.com/knowledge-and-support/resource-center/resource-download.aspx?id=402bb209-4104-4956-a005-6226ff0b67d5&lang=en ID - ref18 ER - TY - JOUR AU - Purcell, S. AU - Neale, B. AU - Todd-Brown, K. AU - Thomas, L. AU - Ferreira, M. A. AU - Bender, D. PY - 2007 DA - 2007// TI - PLINK: a tool set for whole-genome association and population-based linkage analyses JO - Am J Hum Genet VL - 81 UR - https://doi.org/10.1086/519795 DO - 10.1086/519795 ID - Purcell2007 ER - TY - JOUR AU - Price, A. L. AU - Patterson, N. J. AU - Plenge, R. M. AU - Weinblatt, M. E. AU - Shadick, N. A. AU - Reich, D. PY - 2006 DA - 2006// TI - Principal components analysis corrects for stratification in genome-wide association studies JO - Nat Genet VL - 38 UR - https://doi.org/10.1038/ng1847 DO - 10.1038/ng1847 ID - Price2006 ER - TY - JOUR AU - Patterson, N. AU - Price, A. L. AU - Reich, D. PY - 2006 DA - 2006// TI - Population structure and eigenanalysis JO - PLoS Genet VL - 2 UR - https://doi.org/10.1371/journal.pgen.0020190 DO - 10.1371/journal.pgen.0020190 ID - Patterson2006 ER - TY - JOUR AU - Tenesa, A. AU - Navarro, P. AU - Hayes, B. J. AU - Duffy, D. L. AU - Clarke, G. M. AU - Goddard, M. E. PY - 2007 DA - 2007// TI - Recent human effective population size estimated from linkage disequilibrium JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6023607 DO - 10.1101/gr.6023607 ID - Tenesa2007 ER - TY - JOUR AU - Lischer, H. E. L. AU - Excoffier, L. PY - 2012 DA - 2012// TI - PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/btr642 DO - 10.1093/bioinformatics/btr642 ID - Lischer2012 ER - TY - JOUR AU - Pritchard, J. K. AU - Stephens, M. AU - Donnelly, P. PY - 2000 DA - 2000// TI - Inference of population structure using multilocus genotype data JO - Genetics VL - 155 ID - Pritchard2000 ER - TY - JOUR AU - Falush, D. AU - Stephens, M. AU - Pritchard, J. K. PY - 2003 DA - 2003// TI - Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies JO - Genetics VL - 164 ID - Falush2003 ER - TY - JOUR AU - Falush, D. AU - Stephens, M. AU - Pritchard, J. K. PY - 2007 DA - 2007// TI - Inference of population structure using multilocus genotype data: dominant markers and null alleles JO - Mol Ecol Notes VL - 7 UR - https://doi.org/10.1111/j.1471-8286.2007.01758.x DO - 10.1111/j.1471-8286.2007.01758.x ID - Falush2007 ER - TY - JOUR AU - Hubisz, M. J. AU - Falush, D. AU - Stephens, M. AU - Pritchard, J. K. PY - 2009 DA - 2009// TI - Inferring weak population structure with the assistance of sample group information JO - Mol Ecol Resour VL - 9 UR - https://doi.org/10.1111/j.1755-0998.2009.02591.x DO - 10.1111/j.1755-0998.2009.02591.x ID - Hubisz2009 ER - TY - JOUR AU - Jakobsson, M. AU - Rosenberg, N. A. PY - 2007 DA - 2007// TI - CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm233 DO - 10.1093/bioinformatics/btm233 ID - Jakobsson2007 ER - TY - JOUR AU - Rosenberg, N. A. PY - 2004 DA - 2004// TI - Distruct: a program for the graphical display of population structure JO - Mol Ecol Notes VL - 4 UR - https://doi.org/10.1046/j.1471-8286.2003.00566.x DO - 10.1046/j.1471-8286.2003.00566.x ID - Rosenberg2004 ER - TY - STD TI - Team RDC. R: a language and environment for statistical computing. R foundation for statistical computing. Vienna, Austria; 2005 http://cran.r-project.org/doc/FAQ/R-FAQ.html. UR - http://cran.r-project.org/doc/FAQ/R-FAQ.html ID - ref30 ER - TY - JOUR AU - Felsenstein, J. PY - 1989 DA - 1989// TI - PHYLIP-phylogeny interference package (version 3.2) JO - Cladistics VL - 5 ID - Felsenstein1989 ER - TY - STD TI - Rambaut A. FigTree v1. 4.0. A graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree/, accessed 2012. UR - http://tree.bio.ed.ac.uk/software/figtree/ ID - ref32 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2011 DA - 2011// TI - Inference of human population history from individual whole-genome sequences JO - Nature VL - 475 UR - https://doi.org/10.1038/nature10231 DO - 10.1038/nature10231 ID - Li2011 ER - TY - JOUR AU - MacLeod, I. M. AU - Larkin, D. M. AU - Lewin, H. A. AU - Hayes, B. J. AU - Goddard, M. E. PY - 2013 DA - 2013// TI - Inferring demography from runs of homozygosity in whole-genome sequence, with correction for sequence errors JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst125 DO - 10.1093/molbev/mst125 ID - MacLeod2013 ER - TY - JOUR AU - MacLeod, I. M. AU - Meuwissen, T. H. E. AU - Hayes, B. J. AU - Goddard, M. E. PY - 2009 DA - 2009// TI - A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors JO - Genet Res VL - 91 UR - https://doi.org/10.1017/S0016672309990358 DO - 10.1017/S0016672309990358 ID - MacLeod2009 ER - TY - JOUR AU - Heaton, M. P. AU - Leymaster, K. A. AU - Kalbfleisch, T. S. AU - Kijas, J. W. AU - Clarke, S. M. AU - McEwan, J. PY - 2014 DA - 2014// TI - SNPs for parentage testing and traceability in globally diverse breeds of sheep JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0094851 DO - 10.1371/journal.pone.0094851 ID - Heaton2014 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows–Wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Marth, G. T. AU - Korf, I. AU - Yandell, M. D. AU - Yeh, R. T. AU - Gu, Z. AU - Zakeri, H. PY - 1999 DA - 1999// TI - A general approach to single-nucleotide polymorphism discovery JO - Nat Genet VL - 23 UR - https://doi.org/10.1038/70570 DO - 10.1038/70570 ID - Marth1999 ER - TY - JOUR AU - Roach, J. C. AU - Glusman, G. AU - Smit, A. F. AU - Huff, C. D. AU - Hubley, R. AU - Shannon, P. T. PY - 2010 DA - 2010// TI - Analysis of genetic inheritance in a family quartet by whole-genome sequencing JO - Science VL - 328 UR - https://doi.org/10.1126/science.1186802 DO - 10.1126/science.1186802 ID - Roach2010 ER - TY - JOUR AU - Scally, A. AU - Durbin, R. PY - 2012 DA - 2012// TI - Revising the human mutation rate: implications for understanding human evolution JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3295 DO - 10.1038/nrg3295 ID - Scally2012 ER - TY - JOUR AU - Abecasis, G. R. AU - Altshuler, D. AU - Auton, A. AU - Brooks, L. D. AU - Durbin, R. M. AU - Gibbs, R. A. PY - 2010 DA - 2010// TI - A map of human genome variation from population-scale sequencing JO - Nature VL - 467 UR - https://doi.org/10.1038/nature09534 DO - 10.1038/nature09534 ID - Abecasis2010 ER - TY - JOUR AU - Nei, M. PY - 1973 DA - 1973// TI - Analysis of gene diversity in subdivided populations JO - Proc Natl Acad Sci VL - 70 UR - https://doi.org/10.1073/pnas.70.12.3321 DO - 10.1073/pnas.70.12.3321 ID - Nei1973 ER - TY - STD TI - Pollott G. The breeding structure of the British sheep industry 2012. Kenilworth, Warwickshire: EBLEX; 2012. ID - ref43 ER - TY - JOUR AU - Kim, Y. AU - Ryu, J. AU - Woo, J. AU - Kim, J. B. AU - Kim, C. Y. AU - Lee, C. PY - 2011 DA - 2011// TI - Genome-wide association study reveals five nucleotide sequence variants for carcass traits in beef cattle JO - Anim Genet VL - 42 UR - https://doi.org/10.1111/j.1365-2052.2010.02156.x DO - 10.1111/j.1365-2052.2010.02156.x ID - Kim2011 ER - TY - JOUR AU - Snelling, W. M. AU - Allan, M. F. AU - Keele, J. W. AU - Kuehn, L. A. AU - McDaneld, T. AU - Smith, T. P. L. PY - 2010 DA - 2010// TI - Genome-wide association study of growth in crossbred beef cattle JO - J Anim Sci VL - 88 UR - https://doi.org/10.2527/jas.2009-2257 DO - 10.2527/jas.2009-2257 ID - Snelling2010 ER - TY - JOUR AU - Kim, K. S. AU - Larsen, N. AU - Short, T. AU - Plastow, G. AU - Rothschild, M. F. PY - 2000 DA - 2000// TI - A missense variant of the porcine melanocortin-4 receptor (MC4R) gene is associated with fatness, growth, and feed intake traits JO - Mamm Genome VL - 11 UR - https://doi.org/10.1007/s003350010025 DO - 10.1007/s003350010025 ID - Kim2000 ER - TY - JOUR AU - Diamond, J. PY - 2002 DA - 2002// TI - Evolution, consequences and future of plant and animal domestication JO - Nature VL - 418 UR - https://doi.org/10.1038/nature01019 DO - 10.1038/nature01019 ID - Diamond2002 ER - TY - JOUR AU - Zeder, M. A. PY - 2008 DA - 2008// TI - Domestication and early agriculture in the Mediterranean Basin: origins, diffusion, and impact JO - Proc Natl Acad Sci VL - 105 UR - https://doi.org/10.1073/pnas.0801317105 DO - 10.1073/pnas.0801317105 ID - Zeder2008 ER - TY - JOUR AU - Bruford, M. W. AU - Bradley, D. G. AU - Luikart, G. PY - 2003 DA - 2003// TI - DNA markers reveal the complexity of livestock domestication JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg1203 DO - 10.1038/nrg1203 ID - Bruford2003 ER - TY - JOUR AU - Feulner, P. G. D. AU - Gratten, J. AU - Kijas, J. W. AU - Visscher, P. M. AU - Pemberton, J. M. AU - Slate, J. PY - 2013 DA - 2013// TI - Introgression and the fate of domesticated genes in a wild mammal population JO - Mol Ecol VL - 22 UR - https://doi.org/10.1111/mec.12378 DO - 10.1111/mec.12378 ID - Feulner2013 ER - TY - JOUR AU - Johnston, S. E. AU - Gratten, J. AU - Berenos, C. AU - Pilkington, J. G. AU - Clutton-Brock, T. H. AU - Pemberton, J. M. PY - 2013 DA - 2013// TI - Life history trade-offs at a single locus maintain sexually selected genetic variation JO - Nature VL - 502 UR - https://doi.org/10.1038/nature12489 DO - 10.1038/nature12489 ID - Johnston2013 ER - TY - JOUR AU - Kijas, J. W. AU - Townley, D. AU - Dalrymple, B. P. AU - Heaton, M. P. AU - Maddox, J. F. AU - McGrath, A. PY - 2009 DA - 2009// TI - A genome wide survey of SNP variation reveals the genetic structure of sheep breeds JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0004668 DO - 10.1371/journal.pone.0004668 ID - Kijas2009 ER - TY - JOUR AU - Wolf, B. AU - Smith, C. AU - Sales, D. PY - 1980 DA - 1980// TI - Growth and carcass composition in the crossbred progeny of six terminal sire breeds of sheep JO - Anim Prod VL - 31 UR - https://doi.org/10.1017/S0003356100024648 DO - 10.1017/S0003356100024648 ID - Wolf1980 ER - TY - JOUR AU - Leymaster, K. A. AU - Jenkins, T. G. PY - 1993 DA - 1993// TI - Comparison of Texel- and Suffolk-sired crossbred lambs for survival, growth, and compositional traits JO - J Anim Sci VL - 71 ID - Leymaster1993 ER - TY - STD TI - National Sheep Association (NSA). British Sheep, vol. 9. Malvern; 1998. ID - ref55 ER - TY - JOUR AU - Oltenacu, E. A. AU - Boylan, W. J. PY - 1981 DA - 1981// TI - Productivity of purebred and crossbred finnsheep. I. Reproductive traits of ewes and lamb survival JO - J Anim Sci VL - 52 ID - Oltenacu1981 ER - TY - STD TI - Leslie S, Winney B, Hellenthal G, Davison D, Boumertit A, Day T, et al. The fine-scale genetic structure of the British population. Nature. 2015;519(7543):309–314. ID - ref57 ER - TY - JOUR AU - Ryder, M. PY - 1981 DA - 1981// TI - A survey of European primitive breeds of sheep JO - Genet Sel Evol VL - 13 UR - https://doi.org/10.1186/1297-9686-13-4-381 DO - 10.1186/1297-9686-13-4-381 ID - Ryder1981 ER - TY - JOUR AU - Dýrmundsson, Ó. R. AU - Niżnikowski, R. PY - 2010 DA - 2010// TI - North European short-tailed breeds of sheep: a review JO - Anim VL - 4 UR - https://doi.org/10.1017/S175173110999156X DO - 10.1017/S175173110999156X ID - Dýrmundsson2010 ER - TY - STD TI - History of the Lleyn. [http://www.lleynsheep.com/society/history/]. UR - http://www.lleynsheep.com/society/history/ ID - ref60 ER - TY - JOUR AU - Álvarez, I. AU - Royo, L. AU - Fernandez, I. AU - Gutiérrez, J. AU - Gómez, E. AU - Goyache, F. PY - 2004 DA - 2004// TI - Genetic relationships and admixture among sheep breeds from Northern Spain assessed using microsatellites JO - J Anim Sci VL - 82 ID - Álvarez2004 ER - TY - JOUR AU - Gautier, M. AU - Laloë, D. AU - Moazami-Goudarzi, K. PY - 2010 DA - 2010// TI - Insights into the genetic history of french cattle from dense SNP data on 47 worldwide breeds JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0013038 DO - 10.1371/journal.pone.0013038 ID - Gautier2010 ER - TY - BOOK AU - Williams-Davies, J. PY - 1981 DA - 1981// TI - Welsh sheep and their wool PB - Gomer Press CY - Dyfed ID - Williams-Davies1981 ER - TY - JOUR AU - Jones, C. AU - Davies, S. AU - Macdonald, N. PY - 2012 DA - 2012// TI - Examining the social consequences of extreme weather: the outcomes of the 1946/1947 winter in upland Wales, UK JO - Clim Change VL - 113 UR - https://doi.org/10.1007/s10584-012-0413-9 DO - 10.1007/s10584-012-0413-9 ID - Jones2012 ER - TY - STD TI - Alderson L. Rare Breeds. In: A shire book. Tarxien Malta: Gutenberg Press; 2001. ID - ref65 ER - TY - STD TI - Watchlist. 2014. [https://www.rbst.org.uk/watchlist-2014.pdf] accessed 2014 UR - https://www.rbst.org.uk/watchlist-2014.pdf ID - ref66 ER - TY - JOUR AU - Ma, L. AU - Wiggans, G. R. AU - Wang, S. AU - Sonstegard, T. S. AU - Yang, J. AU - Crooker, B. A. PY - 2012 DA - 2012// TI - Effect of sample stratification on dairy GWAS results JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-536 DO - 10.1186/1471-2164-13-536 ID - Ma2012 ER - TY - JOUR AU - Clark, P. U. AU - Dyke, A. S. AU - Shakun, J. D. AU - Carlson, A. E. AU - Clark, J. AU - Wohlfarth, B. PY - 2009 DA - 2009// TI - The last glacial maximum JO - Science VL - 325 UR - https://doi.org/10.1126/science.1172873 DO - 10.1126/science.1172873 ID - Clark2009 ER - TY - JOUR AU - Tian, C. AU - Gregersen, P. K. AU - Seldin, M. F. PY - 2008 DA - 2008// TI - Accounting for ancestry: population substructure and genome-wide association studies JO - Hum Mol Genet VL - 17 UR - https://doi.org/10.1093/hmg/ddn268 DO - 10.1093/hmg/ddn268 ID - Tian2008 ER - TY - JOUR AU - Goddard, M. E. AU - Hayes, B. J. PY - 2009 DA - 2009// TI - Mapping genes for complex traits in domestic animals and their use in breeding programmes JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2575 DO - 10.1038/nrg2575 ID - Goddard2009 ER -