基因组水平的选择信号及其检测方法研究进展
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摘要
在进化过程中,自然或人工选择在基因组上留下了各种选择信号的印迹。探究不同物种或同一物种不同种群之间的选择信号有助于我们研究物种的进化历史,筛选优势等位基因并应用于遗传育种之中。本文详细介绍了各种经典的选择信号检测方法及其适用场景,并讨论了各自的优缺点和未来的发展方向。
During evolution, natural or artificial selection leave extensive selection signatures in the genome. Detecting the selection signatures among species or different populations within same species would help elucidate evolutionary history of species, or screen for dominant alleles for their applications in genetic breeding. In the paper,the classical methods for the detection of selection signatures and their application scenarios were summarized in detail.The advantages and disadvantages of the methods as well as the direction of method developments in future were also discussed.
During evolution, natural or artificial selection leave extensive selection signatures in the genome. Detecting the selection signatures among species or different populations within same species would help elucidate evolutionary history of species, or screen for dominant alleles for their applications in genetic breeding. In the paper,the classical methods for the detection of selection signatures and their application scenarios were summarized in detail.The advantages and disadvantages of the methods as well as the direction of method developments in future were also discussed.
引文
[1] VITTI J J,GROSSMAN S R,SABETI P C.Detecting natural selection in genomic data[J].Annu Rev Genet,2013,47:97-120.
[2] KEMPER K E,SAXTON S J,BOLORMAA S,et al.Selection for complex traits leaves little or no classic signatures of selection[J].BMC Genomics,2014,15(1):246.
[3] ANTELOPE C X,MARNETTO D,CASEY F,et al.Leveraging Multiple Populations across Time Helps Define Accurate Models of Human Evolution:A Reanalysis of the Lactase Persistence Adaptation[J].Hum Biol,2017,89(1):81-97.
[4] LUO J,LIU H,ZHOU T,et al.An-1 encodes a basic helix-loop-helix protein that regulates awn development,grain size,and grain number in rice[J].Plant Cell,2013,25(9):3 360-3 376.
[5] ZHAO P,LI J,KANG H,et al.Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs[J].Scientific Reports,2016,6(1):18 501.
[6] WILLIAMSON S H,HUBISZ M J,CLARK A G,et al.Localizing recent adaptive evolution in the human genome[J].PLoS Genet,2007,3(6):e90.
[7] ENARD D,MESSER P W,PETROV D A.Genome-wide signals of positive selection in human evolution[J].Genome Res,2014,24(6):885-895.
[8] DENISOV S V,BAZYKIN G A,SUTORMIN R,et al.Weak negative and positive selection and the drift load at splice sites[J].Genome Biol Evol,2014,6(6):1 437-1 447.
[9] CONNALLON T,CLARK A G.Balancing selection in species with separate sexes:insights from Fisher's geometric model[J].Genetics,2014,197(3):991-1 006.
[10] SLATKIN M.Linkage disequilibrium--understanding the evolutionary past and mapping the medical future[J].Nat Rev Genet,2008,9(6):477-485.
[11] HUDSON R R,KREITMAN M,AGUADE M.A test of neutral molecular evolution based on nucleotide data[J].Genetics,1987,116(1):153-159.
[12] HURST L D.The Ka/Ks ratio:diagnosing the form of sequence evolution[J].Trends Genet,2002,18(9):486.
[13] YANG Z.Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites:approximate methods[J].J Mol Evol,1994,39(3):306-314.
[14] 杨子恒.计算分子进化[M].上海:复旦大学出版社,2008:57-59.
[15] CHEN J,NI P,LI X,et al.Population size may shape the accumulation of functional mutations following domestication[J].BMC Evol Biol,2018,18(1):4.
[16] TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[17] 王建康.数量遗传学[M].北京:科学出版社,2017:120-121.
[18] FUJISAKI I,PEARLSTINE E V,MAZZOTTI F J.The rapid spread of invasive Eurasian Collared Doves Streptopelia decaocto in the continental USA follows human-altered habitats[J].IBIS,2010,152(3):622-632.
[19] OWEN J.The Ecology of a Garden:The First Fifteen Years[M].Cambridge:University Press ,2005.
[20] BAGI Z,DIMOPOULOS E A,LOUKOVITIS D,et al.MtDNA genetic diversity and structure of Eurasian Collared Dove (Streptopelia decaocto)[J].PLoS One,2018,13(3):e193935.
[21] 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.
[22] 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):1 251-1 260.
[23] 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.
[24] VOIGHT B F,KUDARAVALLI S,WEN X,et al.A map of recent positive selection in the human genome[J].PLoS Biol,2006,4(3):e72.
[25] CORONA E,WANG L,KO D,et al.Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility[J].PLoS One,2018,13(5):e196676.
[26] WANG E T,KODAMA G,BALDI P,et al.Global landscape of recent inferred Darwinian selection for Homo sapiens[J].Proc Natl Acad Sci U S A,2006,103(1):135-140.
[27] HAN L,ABNEY M.Using identity by descent estimation with dense genotype data to detect positive selection[J].Eur J Hum Genet,2013,21(2):205-211.
[28] PRITCHARD J K,PICKRELL J K,COOP G.The genetics of human adaptation:hard sweeps,soft sweeps,and polygenic adaptation[J].Curr Biol,2010,20(4):R208-R215.
[29] WRIGHT S.Genetical structure of populations[J].Nature,1950,166(4215):247-249.
[30] WRIGHT S.The genetical structure of populations[J].Ann Eugen,1951,15(4):323-354.
[31] SHRIVER M D,KENNEDY G C,PARRA E J,et al.The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs[J].Hum Genomics,2004,1(4):274-286.
[32] MATOS-CRUZ V,SCHNEIDER E R,MASTROTTO M,et al.Molecular Prerequisites for Diminished Cold Sensitivity in Ground Squirrels and Hamsters[J].Cell Rep,2017,21(12):3 329-3 337.
[33] KEY F M,ABDUL-AZIZ M A,MUNDRY R,et al.Human local adaptation of the TRPM8 cold receptor along a latitudinal cline[J].PLoS Genet,2018,14(5):e1007298.
[34] CHEN H,PATTERSON N,REICH D.Population differentiation as a test for selective sweeps[J].Genome Research,2010,20(3):393-402.
[35] MWAI O,HANOTTE O,KWON Y J,et al.African Indigenous Cattle:Unique Genetic Resources in a Rapidly Changing World[J].Asian-Australas J Anim Sci,2015,28(7):911-921.
[36] TAYE M,KIM J,YOON S H,et al.Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef[J].BMC Genet,2017,18(1):11.
[37] GROSSMAN S R,SHLYAKHTER 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.
[38] 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.
[39] 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.
[40] PENNINGS P S,HERMISSON J.Soft sweeps III:the signature of positive selection from recurrent mutation[J].PLoS Genet,2006,2(12):e186.
[41] 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):1 076-1 084.
[42] HERMISSON J,PENNINGS P S.Soft sweeps:molecular population genetics of adaptation from standing genetic variation[J].Genetics,2005,169(4):2 335-2 352.
[43] CRISCI J L,DEAN M D,RALPH P.Adaptation in isolated populations:when does it happen and when can we tell?[J].Mol Ecol,2016,25(16):3 901-3 911.
[44] GARUD N R,MESSER P W,BUZBAS E O,et al.Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps[J].PLoS Genet,2015,11(2):e1005004.
[45] KERN A D,SCHRIDER D R.diploS/HIC:An Updated Approach to Classifying Selective Sweeps[J].G3 (Bethesda),2018,8(6):1 959-1 970.
[46] SCHRIDER D R,KERN A D.S/HIC:Robust Identification of Soft and Hard Sweeps Using Machine Learning[J].PLoS Genet,2016,12(3):e1005928.
[47] WANG J,ZOU H,CHEN L,et al.Convergent and divergent genetic changes in the genome of Chinese and European pigs[J].Sci Rep,2017,7(1):8 662-8 674.
[2] KEMPER K E,SAXTON S J,BOLORMAA S,et al.Selection for complex traits leaves little or no classic signatures of selection[J].BMC Genomics,2014,15(1):246.
[3] ANTELOPE C X,MARNETTO D,CASEY F,et al.Leveraging Multiple Populations across Time Helps Define Accurate Models of Human Evolution:A Reanalysis of the Lactase Persistence Adaptation[J].Hum Biol,2017,89(1):81-97.
[4] LUO J,LIU H,ZHOU T,et al.An-1 encodes a basic helix-loop-helix protein that regulates awn development,grain size,and grain number in rice[J].Plant Cell,2013,25(9):3 360-3 376.
[5] ZHAO P,LI J,KANG H,et al.Structural Variant Detection by Large-scale Sequencing Reveals New Evolutionary Evidence on Breed Divergence between Chinese and European Pigs[J].Scientific Reports,2016,6(1):18 501.
[6] WILLIAMSON S H,HUBISZ M J,CLARK A G,et al.Localizing recent adaptive evolution in the human genome[J].PLoS Genet,2007,3(6):e90.
[7] ENARD D,MESSER P W,PETROV D A.Genome-wide signals of positive selection in human evolution[J].Genome Res,2014,24(6):885-895.
[8] DENISOV S V,BAZYKIN G A,SUTORMIN R,et al.Weak negative and positive selection and the drift load at splice sites[J].Genome Biol Evol,2014,6(6):1 437-1 447.
[9] CONNALLON T,CLARK A G.Balancing selection in species with separate sexes:insights from Fisher's geometric model[J].Genetics,2014,197(3):991-1 006.
[10] SLATKIN M.Linkage disequilibrium--understanding the evolutionary past and mapping the medical future[J].Nat Rev Genet,2008,9(6):477-485.
[11] HUDSON R R,KREITMAN M,AGUADE M.A test of neutral molecular evolution based on nucleotide data[J].Genetics,1987,116(1):153-159.
[12] HURST L D.The Ka/Ks ratio:diagnosing the form of sequence evolution[J].Trends Genet,2002,18(9):486.
[13] YANG Z.Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites:approximate methods[J].J Mol Evol,1994,39(3):306-314.
[14] 杨子恒.计算分子进化[M].上海:复旦大学出版社,2008:57-59.
[15] CHEN J,NI P,LI X,et al.Population size may shape the accumulation of functional mutations following domestication[J].BMC Evol Biol,2018,18(1):4.
[16] TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[17] 王建康.数量遗传学[M].北京:科学出版社,2017:120-121.
[18] FUJISAKI I,PEARLSTINE E V,MAZZOTTI F J.The rapid spread of invasive Eurasian Collared Doves Streptopelia decaocto in the continental USA follows human-altered habitats[J].IBIS,2010,152(3):622-632.
[19] OWEN J.The Ecology of a Garden:The First Fifteen Years[M].Cambridge:University Press ,2005.
[20] BAGI Z,DIMOPOULOS E A,LOUKOVITIS D,et al.MtDNA genetic diversity and structure of Eurasian Collared Dove (Streptopelia decaocto)[J].PLoS One,2018,13(3):e193935.
[21] 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.
[22] 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):1 251-1 260.
[23] 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.
[24] VOIGHT B F,KUDARAVALLI S,WEN X,et al.A map of recent positive selection in the human genome[J].PLoS Biol,2006,4(3):e72.
[25] CORONA E,WANG L,KO D,et al.Systematic detection of positive selection in the human-pathogen interactome and lasting effects on infectious disease susceptibility[J].PLoS One,2018,13(5):e196676.
[26] WANG E T,KODAMA G,BALDI P,et al.Global landscape of recent inferred Darwinian selection for Homo sapiens[J].Proc Natl Acad Sci U S A,2006,103(1):135-140.
[27] HAN L,ABNEY M.Using identity by descent estimation with dense genotype data to detect positive selection[J].Eur J Hum Genet,2013,21(2):205-211.
[28] PRITCHARD J K,PICKRELL J K,COOP G.The genetics of human adaptation:hard sweeps,soft sweeps,and polygenic adaptation[J].Curr Biol,2010,20(4):R208-R215.
[29] WRIGHT S.Genetical structure of populations[J].Nature,1950,166(4215):247-249.
[30] WRIGHT S.The genetical structure of populations[J].Ann Eugen,1951,15(4):323-354.
[31] SHRIVER M D,KENNEDY G C,PARRA E J,et al.The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs[J].Hum Genomics,2004,1(4):274-286.
[32] MATOS-CRUZ V,SCHNEIDER E R,MASTROTTO M,et al.Molecular Prerequisites for Diminished Cold Sensitivity in Ground Squirrels and Hamsters[J].Cell Rep,2017,21(12):3 329-3 337.
[33] KEY F M,ABDUL-AZIZ M A,MUNDRY R,et al.Human local adaptation of the TRPM8 cold receptor along a latitudinal cline[J].PLoS Genet,2018,14(5):e1007298.
[34] CHEN H,PATTERSON N,REICH D.Population differentiation as a test for selective sweeps[J].Genome Research,2010,20(3):393-402.
[35] MWAI O,HANOTTE O,KWON Y J,et al.African Indigenous Cattle:Unique Genetic Resources in a Rapidly Changing World[J].Asian-Australas J Anim Sci,2015,28(7):911-921.
[36] TAYE M,KIM J,YOON S H,et al.Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef[J].BMC Genet,2017,18(1):11.
[37] GROSSMAN S R,SHLYAKHTER 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.
[38] 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.
[39] 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.
[40] PENNINGS P S,HERMISSON J.Soft sweeps III:the signature of positive selection from recurrent mutation[J].PLoS Genet,2006,2(12):e186.
[41] 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):1 076-1 084.
[42] HERMISSON J,PENNINGS P S.Soft sweeps:molecular population genetics of adaptation from standing genetic variation[J].Genetics,2005,169(4):2 335-2 352.
[43] CRISCI J L,DEAN M D,RALPH P.Adaptation in isolated populations:when does it happen and when can we tell?[J].Mol Ecol,2016,25(16):3 901-3 911.
[44] GARUD N R,MESSER P W,BUZBAS E O,et al.Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps[J].PLoS Genet,2015,11(2):e1005004.
[45] KERN A D,SCHRIDER D R.diploS/HIC:An Updated Approach to Classifying Selective Sweeps[J].G3 (Bethesda),2018,8(6):1 959-1 970.
[46] SCHRIDER D R,KERN A D.S/HIC:Robust Identification of Soft and Hard Sweeps Using Machine Learning[J].PLoS Genet,2016,12(3):e1005928.
[47] WANG J,ZOU H,CHEN L,et al.Convergent and divergent genetic changes in the genome of Chinese and European pigs[J].Sci Rep,2017,7(1):8 662-8 674.
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