[1] QANBARI S,SIMIANER H.Mapping signatures of positive selection in the genome of livestock[J].Livest Sci,2014,166:133-143.
[2] LARSON G,PIPERNO D R,ALLABY R G,et al.Current perspectives and the future of domestication studies[J].Proc Natl Acad Sci U S A,2014,111(17):6139-6146.
[3] ANDERSSON L.How selective sweeps in domestic animals provide new insight into biological mechanisms[J].J Intern Med,2012,271(1):1-14.
[4] 潘章源,贺小云,王翔宇,等.家养动物选择信号研究进展[J].遗传,2016,38(12):1069-1080.
PAN Z Y,HE X Y,WANG X Y,et al.Selection signatures in domesticated animals[J].Hereditas (Beijing),2016,38(12):1069-1080. (in Chinese)
[5] SUZUKI Y.Statistical methods for detecting natural selection from genomic data[J].Genes Genet Syst,2010,85(6):359-376.
[6] BISWAS S,AKEY J M.Genomic insights into positive selection[J].Trends Genet,2006,22(8):437-446.
[7] SABETI P C,VARILLY P,FRY B,et al.Genome-wide detection and characterization of positive selection in human populations[J].Nature,2007,449(7164):913-918.
[8] PENNINGS P S,HERMISSON J.Soft sweeps Ⅱ-molecular population genetics of adaptation from recurrent mutation or migration[J].Mol Biol Evol,2006,23(5):1076-1084.
[9] DE SIMONI GOUVEIA J J,DA SILVA M V G B,PAIVA S R,et al.Identification of selection signatures in livestock species[J].Genet Mol Biol,2014,37(2):330-342.
[10] 刘真,王慧华,刘瑞凿,等.不同尾型绵羊全基因组选择信号检测[J].畜牧兽医学报,2015,46(10):1721-1732.
LIU Z,WANG H H,LIU R Z,et al.Genome-wide detection of selection signatures of distinct tail types in sheep populations[J].Acta Veterinaria et Zootechnica Sinica,2015,46(10):1721-1732. (in Chinese)
[11] 王光凯,曾滔,王慧华,等.苏尼特羊全基因组选择信号检测[J].中国农业科学,2014,47(6):1190-1199.
WANG G K,ZENG T,WANG H H,et al.Genome-wide detection of selection signature on sunite sheep[J].Scientia Agricultura Sinica,2014,47(6):1190-1199. (in Chinese)
[12] 马云龙,张勤,丁向东.利用高密度SNP检测不同猪品种间X染色体选择信号[J].遗传,2012,34(10):1251-1260.
MA Y L,ZHANG Q,DING X D.Detecting selection signatures on X chromosome in pig through high density SNPs[J].Hereditas (Beijing),2012,34(10):1251-1260. (in Chinese)
[13] HERMISSON J,PENNINGS P S.Soft sweeps:Molecular population genetics of adaptation from standing genetic variation[J].Genetics,2005,169(4):2335-2352.
[14] BARRETT R D H,SCHLUTER D.Adaptation from standing genetic variation[J].Trends Ecol Evol,2008,23(1):38-44.
[15] NIELSEN R.Molecular signatures of natural selection[J].Annu Rev Genet,2005,39:197-218.
[16] LOHMUELLER K E,BUSTAMANTE C D,CLARK A G.Detecting directional selection in the presence of recent admixture in African-Americans[J].Genetics,2011,187(3):823-835.
[17] PERSI E,WOLF Y I,KOONIN E V.Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins[J].Nat Commun,2016,7:13570.
[18] FIJARCZYK A,BABIK W.Detecting balancing selection in genomes:limits and prospects[J].Mol Ecol,2015,24(14):3529-3545.
[19] QANBARI S,SEIDEL M,STROM T M,et al.Parallel selection revealed by population sequencing in chicken[J].Genome Biol Evol,2015,7(12):3299-3306.
[20] SHENG Z Y,PETTERSSON M E,HONAKER C F,et al.Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment[J].Genome Biol,2015,16:219.
[21] ZHU L,BUSTAMANTE C D.A composite-likelihood approach for detecting directional selection from DNA sequence data[J].Genetics,2005,170(3):1411-1421.
[22] TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[23] NIELSEN R,WILLIAMSON S,KIM Y,et al.Genomic scans for selective sweeps using SNP data[J].Genome Res,2005,15(11):1566-1575.
[24] RUBIN C J,ZODY M C,ERIKSSON J,et al.Whole-genome resequencing reveals loci under selection during chicken domestication[J].Nature,2010,464(7288):587-591.
[25] MA Y,DING X,QANBARI S,et al.Properties of different selection signature statistics and a new strategy for combining them[J].Heredity,2015,115(5):426-436.
[26] SABETI P C,REICH D E,HIGGINS J M,et al.Detecting recent positive selection in the human genome from haplotype structure[J].Nature,2002,419(6909):832-837.
[27] VOIGHT B F,KUDARAVALLI S,WEN X Q,et al.A map of recent positive selection in the human genome[J].PLoS Biol,2006,4(3):e72.
[28] ALACHIOTIS N,PAVLIDIS P.Scalable linkage-disequilibrium-based selective sweep detection:a performance guide[J].Gigascience,2016,5:7.
[29] FERRER-ADMETLLA A,LIANG M,KORNELIUSSEN T,et al.On detecting incomplete soft or hard selective sweeps using haplotype structure[J].Mol Biol Evol,2014,31(5):1275-1291.
[30] LEWONTIN R C,KRAKAUER J.Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms[J].Genetics,1973,74(1):175-195.
[31] WRIGHT S.The genetical structure of populations[J].Ann Eugen,1949,15(1):323-354.
[32] WEIR B S,COCKERHAM C C.Estimating F-statistics for the analysis of population structure[J].Evolution,1984,38(6):1358-1370.
[33] AKEY J M,ZHANG G,ZHANG K,et al.Interrogating a high-density SNP map for signatures of natural selection[J].Genome Res,2002,12(12):1805-1814.
[34] GIANOLA D,SIMIANER H,QANBARI S.A two-step method for detecting selection signatures using genetic markers[J].Genet Res,2010,92(2):141-155.
[35] CHEN H,PATTERSON N,REICH D.Population differentiation as a test for selective sweeps[J].Genome Res,2010,20(3):393-402.
[36] FARIELLO M I,BOITARD S,NAYA H,et al.Detecting signatures of selection through haplotype differentiation among hierarchically structured populations[J].Genetics,2013,193(3):929-941.
[37] AI H S,FANG X D,YANG B,et al.Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J].Nat Genet,2015,47(3):217-225.
[38] RACIMO F.Testing for ancient selection using cross-population allele frequency differentiation[J].Genetics,2016,202(2):733-750.
[39] VATSIOU A I,BAZIN E,GAGGIOTTI O E.Detection of selective sweeps in structured populations:a comparison of recent methods[J].Mol Ecol,2016,25(1):89-103.
[40] GROSSMAN S R,SHYLAKHTER I,KARLSSON E K,et al.A composite of multiple signals distinguishes causal variants in regions of positive selection[J].Science,2010,327(5967):883-886.
[41] UTSUNOMIYA Y T,O'BRIEN A M P,SONSTEGARD T S,et al.Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods[J].PLoS One,2013,8(5):e64280.
[42] RANDHAWA I A S,KHATKAR M S,THOMSON P C,et al.Composite selection signals can localize the trait specific genomic regions in multi-breed populations of cattle and sheep[J].BMC Genet,2014,15:34.
[43] KINGMAN J F C.The coalescent[J].Stoch Processes Their Appl,1982,13(2):235-248.
[44] KINGMAN J F C.On the genealogy of large populations[J].J Appl Probab,1982,19(A):27-43.
[45] KINGMAN J F.Origins of the coalescent.1974-1982[J].Genetics,2000,156(4):1461-1463.
[46] SIMIANER H,MA Y L,QANBARI S.Statistical problems in livestock population genomics[C]//Proceedings of the 10th World Congress on Genetics Applied to Livestock Production.Vancouver,BC,Canada:American Society of Animal Science,2014.
[47] HUDSON R R.Generating samples under a Wright-Fisher neutral model of genetic variation[J].Bioinformatics,2002,18(2):337-338.
[48] EWING G,HERMISSON J.MSMS:a coalescent simulation program including recombination,demographic structure and selection at a single locus[J].Bioinformatics,2010,26(16):2064-2065.
[49] PENG B,KIMMEL M.simuPOP:a forward-time population genetics simulation environment[J].Bioinformatics,2005,21(18):3686-3687.
[50] QANBARI S,PAUSCH H,JANSEN S,et al.Classic selective sweeps revealed by massive sequencing in cattle[J].PLoS Genet,2014,10(2):e1004148.
[51] MA Y L,WEI J L,ZHANG Q,et al.A genome scan for selection signatures in pigs[J].PLoS One,2015,10(3):e0116850.
[52] MEYER R S,CHOI J Y,SANCHES M,et al.Domestication history and geographical adaptation inferred from a SNP map of African rice[J].Nat Genet,2016,48(9):1083-1088.
[53] EVANS L M,SLAVOV G T,RODGERS-MELNICK E,et al.Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations[J].Nat Genet,2014,46(10):1089-1096.
[54] CARNEIRO M,RUBIN C J,DI PALMA F,et al.Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication[J].Science,2014,345(6200):1074-1079.
[55] AMARAL A J,FERRETTI L,MEGENS H J,et al.Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA[J].PLoS One,2011,6(4):e14782.
[56] QANBARI S,STROM T M,HABERER G,et al.A high resolution genome-wide scan for significant selective sweeps:an application to pooled sequence data in laying chickens[J].PLoS One,2012,7(11):e49525.
[57] LAAYOUNI H,MONTANUCCI L,SIKORA M,et al.Similarity in recombination rate estimates highly correlates with genetic differentiation in humans[J].PLoS One,2011,6(3):e17913.
[58] BERSAGLIERI T,SABETI P C,PATTERSON N,et al.Genetic signatures of strong recent positive selection at the lactase gene[J].Am J Hum Genet,2004,74(6):1111-1120.
[59] WANG H L,ZHU Z M,WANG H,et al.Molecular characterization and association analysis of porcine CA3[J].Cytogenet Genome Res,2006,115(2):129-133. |