Akey J M. 2009. Constructing genomic maps of positiveselection in humans: Where do we go from here? GenomeResearch, 19, 711-722Akey J M, Zhang G, Zhang K, Jin L, Shriver M D. 2002.Interrogating a high-density SNP map for signatures ofnatural selection. Genome Research, 12, 1805-1814Biswas S, Akey J M. 2006. Genomic insights into positiveselection. Trends in Genetics, 22, 437-446Browning S R, Browning B L. 2007. Rapid and accuratehaplotype phasing and missing-data inference for wholegenomeassociation studies by use of localized haplotypeclustering. American Journal of Human Genetics, 81,1084-1097Browning S R, Weir B S. 2010. Population structure withlocalized haplotype clusters. Genetics, 185, 1337-1344Chen H, Patterson N, Reich D. 2010. Population differentiationas a test for selective sweeps. Genome Research, 20,393-402Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F,Mainland I, Kao R R, Pemberton J M, Beraldi D, Stear M J.2009. Revealing the history of sheep domestication usingretrovirus integrations. Science, 324, 532-536CNCAGR (China National Commission of Animal GeneticResources). 2012. Animal Genetic Resources in China- Sheep and Goats. China Agriculture Press, China. (inChinese)Conrad D F, Jakobsson M, Coop G, Wen X, Wall J D,Rosenberg N A, Pritchard J K. 2006. A worldwide survey ofhaplotype variation and linkage disequilibrium in the humangenome. Nature Genetics, 38, 1251-1260Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. 2009. GOrilla:A tool for discovery and visualization of enriched GO termsin ranked gene lists. BMC Bioinformatics, 10, 48.Fan H, Wu Y, Qi X, Zhang J, Li J, Gao X, Zhang L, Li J, GaoH. 2014. Genome-wide detection of selective signaturesin Simmental cattle. Journal of Applied Genetics, 55, 1-9Fay J C, Wu C I. 2000. Hitchhiking under positive Darwinianselection. Genetics, 155, 1405-1413Gu J, Orr N, Park S D, Katz L M, Sulimova G, MacHugh D E,Hill E W. 2009. A genome scan for positive selection inthoroughbred horses. PLoS ONE, 4, e5767.Kijas J W, Lenstra J A, Hayes B, Boitard S, Neto L R P, SanCristobal M, Servin B, McCulloch R, Whan V, Gietzen K.2012. Genome-wide analysis of the world’s sheep breedsreveals high levels of historic mixture and strong recentselection. PLoS Biology, 10, e1001258.Lewontin R, Krakauer J. 1973. Distribution of gene frequencyas a test of the theory of the selective neutrality ofpolymorphisms. Genetics, 74, 175-195Lynch M, Walsh B. 1998. Genetics and Analysis of QuantitativeTraits. Sinauer Associates, Sunderland, MA.Pan D, Zhang S, Jiang J, Jiang L, Zhang Q, Liu J. 2013.Genome-wide detection of selective signature in Chineseholstein. PLOS ONE, 8, e60440.Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, MooreS, Thaller G, Simianer H. 2011. Application of site andhaplotype-frequency based approaches for detectingselection signatures in cattle. BMC Genomics, 12, 318.Qanbari S, Pimentel E, Tetens J, Thaller G, Lichtner P, SharifiA, Simianer H. 2010. A genome-wide scan for signaturesof recent selection in Holstein cattle. Animal Genetics, 41,377-389Rubin C J, Zody M C, Eriksson J, Meadows J R, Sherwood E,Webster M T, Jiang L, Ingman M, Sharpe T, Ka S. 2010.Whole-genome resequencing reveals loci under selectionduring chicken domestication. Nature, 464, 587-591 Sabeti P C, Reich D E, Higgins J M, Levine H Z P, Richter DJ, Schaffner S F, Gabriel S B, Platko J V, Patterson N J,McDonald G J. 2002. Detecting recent positive selectionin the human genome from haplotype structure. Nature,419, 832-837Sabeti P C, Varilly P, Fry B, Lohmueller J, Hostetter E, CotsapasC, Xie X, Byrne E H, McCarroll S A, Gaudet R. 2007.Genome-wide detection and characterization of positiveselection in human populations. Nature, 449, 913-918Tajima F. 1989. Statistical method for testing the neutralmutation hypothesis by DNA polymorphism. Genetics,123, 585-595Tang K, Thornton K R, Stoneking M. 2007. A new approach forusing genome scans to detect recent positive selection inthe human genome. PLoS Biology, 5, e171.Voight B F, Kudaravalli S, Wen X, Pritchard J K. 2006. A mapof recent positive selection in the human genome. PLoSBiology, 4, e72.Weir B S, Cardon L R, Anderson A D, Nielsen D M, Hill WG. 2005. Measures of human population structure showheterogeneity among genomic regions. Genome Research,15, 1468-1476Wright S. 1949. The genetical structure of populations. Annalsof Eugenics, 15, 323-354Zhang H, Wang S Z, Wang Z P, Da Y, Wang N, Hu X X, Zhang YD, Wang Y X, Leng L, Tang Z Q. 2012. A genome-wide scanof selective sweeps in two broiler chicken lines divergentlyselected for abdominal fat content. BMC Genomics, 13, 704.Zhang L, Liu J, Zhao F, Ren H, Xu L, Lu J, Zhang S, Zhang X,Wei C, Lu G. 2013. Genome-wide association studies forgrowth and meat production traits in sheep. PLOS ONE,8, e66569.Zhao F, Wang G, Zeng T, Wei C, Zhang L, Wang H, Zhang S,Liu R, Liu Z, Du L. 2014. Estimations of genomic linkagedisequilibrium and effective population sizes in three sheeppopulations. Livestock Science, 170, 22-29 |