메뉴 건너뛰기




Volumn 22, Issue 5, 2013, Pages 1383-1399

Detecting selection along environmental gradients: Analysis of eight methods and their effectiveness for outbreeding and selfing populations

Author keywords

adaptation; Bayesian methods; detection of selection; F ST; genome scan

Indexed keywords

ADAPTATION; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; ENVIRONMENT; GENE LOCUS; GENETIC DATABASE; GENETIC DRIFT; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; POPULATION GENETICS; STATISTICAL MODEL;

EID: 84874409839     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12182     Document Type: Article
Times cited : (284)

References (51)
  • 1
    • 80054759105 scopus 로고    scopus 로고
    • Molecular spandrels: Tests of adaptation at the genetic level
    • Barrett RDH, Hoekstra HE, (2011) Molecular spandrels: tests of adaptation at the genetic level. Nature Reviews Genetics, 12, 767-780.
    • (2011) Nature Reviews Genetics , vol.12 , pp. 767-780
    • Barrett, R.D.H.1    Hoekstra, H.E.2
  • 2
    • 1642269679 scopus 로고    scopus 로고
    • Identifying adaptive genetic divergence among populations from genome scans
    • Beaumont MA, Balding DJ, (2004) Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology, 13, 969-980.
    • (2004) Molecular Ecology , vol.13 , pp. 969-980
    • Beaumont, M.A.1    Balding, D.J.2
  • 5
    • 77958565484 scopus 로고    scopus 로고
    • The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population
    • Bierne N, (2011) The distinctive footprints of local hitchhiking in a varied environment and global hitchhiking in a subdivided population. Evolution, 64, 3254-3272.
    • (2011) Evolution , vol.64 , pp. 3254-3272
    • Bierne, N.1
  • 6
    • 79955577378 scopus 로고    scopus 로고
    • The coupling hypothesis: Why genome scans may fail to map local adaptation genes
    • Bierne N, Welch J, Loire E, Bonhomme F, David P, (2011) The coupling hypothesis: why genome scans may fail to map local adaptation genes. Molecular Ecology, 20, 2044-2072.
    • (2011) Molecular Ecology , vol.20 , pp. 2044-2072
    • Bierne, N.1    Welch, J.2    Loire, E.3    Bonhomme, F.4    David, P.5
  • 7
    • 78751653688 scopus 로고    scopus 로고
    • Detecting selection in population trees: The Lewontin and Krakauer test extended
    • Bonhomme M, Chevalet C, Servin B, et al,. (2010) Detecting selection in population trees: the Lewontin and Krakauer test extended. Genetics, 186, 241-262.
    • (2010) Genetics , vol.186 , pp. 241-262
    • Bonhomme, M.1    Chevalet, C.2    Servin, B.3
  • 9
    • 77956491134 scopus 로고    scopus 로고
    • Using environmental correlations to identify loci underlying local adaptation
    • Coop G, Witonsky D, Di Rienzo A, Pritchard JK, (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics, 185, 1411-1423.
    • (2010) Genetics , vol.185 , pp. 1411-1423
    • Coop, G.1    Witonsky, D.2    Di Rienzo, A.3    Pritchard, J.K.4
  • 10
    • 0032510734 scopus 로고    scopus 로고
    • Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): An evaluation of the background selection hypothesis
    • Cummings M, Clegg MT, (1998) Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 95, 5637-5642.
    • (1998) Proceedings of the National Academy of Sciences of the United States of America , vol.95 , pp. 5637-5642
    • Cummings, M.1    Clegg, M.T.2
  • 11
    • 84859499806 scopus 로고    scopus 로고
    • EggLib: Processing, analysis and simulation tools for population genetics and genomics
    • De Mita S, Siol M, (2012) EggLib: processing, analysis and simulation tools for population genetics and genomics. BMC Genetics, 13, 27.
    • (2012) BMC Genetics , vol.13 , pp. 27
    • De Mita, S.1    Siol, M.2
  • 13
    • 77952095479 scopus 로고    scopus 로고
    • Utility of computer simulations in landscape genetics
    • Epperson BK, McRae BH, Scribner K, et al,. (2010) Utility of computer simulations in landscape genetics. Molecular Ecology, 19, 3549-3564.
    • (2010) Molecular Ecology , vol.19 , pp. 3549-3564
    • Epperson, B.K.1    McRae, B.H.2    Scribner, K.3
  • 14
    • 70349506039 scopus 로고    scopus 로고
    • Detecting loci under selection in a hierarchically structured population
    • Excoffier L, Hofer T, Foll M, (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285-298.
    • (2009) Heredity , vol.103 , pp. 285-298
    • Excoffier, L.1    Hofer, T.2    Foll, M.3
  • 15
    • 58149347836 scopus 로고    scopus 로고
    • A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective
    • Foll M, Gaggiotti O, (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180, 977-993.
    • (2008) Genetics , vol.180 , pp. 977-993
    • Foll, M.1    Gaggiotti, O.2
  • 16
    • 0005787099 scopus 로고
    • Linkage disequilibrium in a finite population that is partially selfing
    • Golding GB, Strobeck C, (1980) Linkage disequilibrium in a finite population that is partially selfing. Genetics, 94, 777-789.
    • (1980) Genetics , vol.94 , pp. 777-789
    • Golding, G.B.1    Strobeck, C.2
  • 18
    • 84858080216 scopus 로고    scopus 로고
    • Monitoring adaptive genetic responses to environmental change
    • GeM Working Group.
    • Hansen MM, Olivieri I, Waller DM, Nielsen EE, GeM Working Group (2012) Monitoring adaptive genetic responses to environmental change. Molecular Ecology, 21, 1311-1329.
    • (2012) Molecular Ecology , vol.21 , pp. 1311-1329
    • Hansen, M.M.1    Olivieri, I.2    Waller, D.M.3    Nielsen, E.E.4
  • 19
    • 0003414592 scopus 로고
    • 3rd edn. Oxford University Press, Oxford.
    • Jeffreys H, (1961) Theory of Probability, 3rd edn. Oxford University Press, Oxford.
    • (1961) Theory of Probability
    • Jeffreys, H.1
  • 20
    • 34548587106 scopus 로고    scopus 로고
    • A spatial analysis method (SAM) to detect candidate loci for selection: Towards a landscape genomics approach to adaptation
    • Joost S, Bonin A, Bruford MW, et al,. (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology, 16, 3955-3969.
    • (2007) Molecular Ecology , vol.16 , pp. 3955-3969
    • Joost, S.1    Bonin, A.2    Bruford, M.W.3
  • 22
    • 0015879546 scopus 로고
    • Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms
    • Lewontin RC, Krakauer J, (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 74, 175-195.
    • (1973) Genetics , vol.74 , pp. 175-195
    • Lewontin, R.C.1    Krakauer, J.2
  • 23
    • 0032922271 scopus 로고    scopus 로고
    • The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia
    • Liu F, Charlesworth D, Kreitman M, (1999) The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics, 151, 343-357.
    • (1999) Genetics , vol.151 , pp. 343-357
    • Liu, F.1    Charlesworth, D.2    Kreitman, M.3
  • 25
    • 74049151878 scopus 로고    scopus 로고
    • Genome scan to assess the respective role of host-plant and environmental constraints on the adaptation of a widespread insect
    • Manel S, Conord C, Després L, (2009) Genome scan to assess the respective role of host-plant and environmental constraints on the adaptation of a widespread insect. BMC Evolutionary Biology, 9, 288.
    • (2009) BMC Evolutionary Biology , vol.9 , pp. 288
    • Manel, S.1    Conord, C.2    Després, L.3
  • 26
    • 77956087880 scopus 로고    scopus 로고
    • Perspective on the use of landscape genetics to detect genetic adaptive variation in the field
    • Manel S, Joost S, Epperson BK, et al,. (2010a) Perspective on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19, 3760-3772.
    • (2010) Molecular Ecology , vol.19 , pp. 3760-3772
    • Manel, S.1    Joost, S.2    Epperson, B.K.3
  • 27
    • 77956068779 scopus 로고    scopus 로고
    • Common factors drive adaptive genetic variation at different scales in Arabis alpina
    • Manel S, Poncet BN, Legendre P, Gugerli F, Holderegger R, (2010b) Common factors drive adaptive genetic variation at different scales in Arabis alpina. Molecular Ecology, 19, 2896-2907.
    • (2010) Molecular Ecology , vol.19 , pp. 2896-2907
    • Manel, S.1    Poncet, B.N.2    Legendre, P.3    Gugerli, F.4    Holderegger, R.5
  • 29
    • 47349131008 scopus 로고    scopus 로고
    • Natural selection along an environmental gradient: A classic cline in mouse pigmentation
    • Mullen LM, Hoekstra HE, (2008) Natural selection along an environmental gradient: a classic cline in mouse pigmentation. Evolution, 62, 1555-1569.
    • (2008) Evolution , vol.62 , pp. 1555-1569
    • Mullen, L.M.1    Hoekstra, H.E.2
  • 31
    • 0016516814 scopus 로고
    • Lewontin-Krakauer test for neutral genes - Comment
    • Nei M, Maruyama T, (1975) Lewontin-Krakauer test for neutral genes-comment. Genetics, 80, 395.
    • (1975) Genetics , vol.80 , pp. 395
    • Nei, M.1    Maruyama, T.2
  • 32
    • 46249111534 scopus 로고    scopus 로고
    • QuantiNEMO: An individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
    • Neuenschwander S, Hospital F, Guillaume F, Goudet J, (2008) quantiNEMO: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Bioinformatics, 24, 1552-1553.
    • (2008) Bioinformatics , vol.24 , pp. 1552-1553
    • Neuenschwander, S.1    Hospital, F.2    Guillaume, F.3    Goudet, J.4
  • 33
    • 0033962299 scopus 로고    scopus 로고
    • Linkage disequilibrium, gene trees and selfing: An ancestral recombination graph with partial self-fertilization
    • Nordborg M, (2000) Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics, 154, 923-929.
    • (2000) Genetics , vol.154 , pp. 923-929
    • Nordborg, M.1
  • 34
    • 27844602105 scopus 로고    scopus 로고
    • The geographic spread of the CCR5 Δ32 HIV-resistance allele
    • Novembre J, Galvani AP, Slatkin M, (2005) The geographic spread of the CCR5 Δ32 HIV-resistance allele. PLoS Biology, 3, 1954-1962.
    • (2005) PLoS Biology , vol.3 , pp. 1954-1962
    • Novembre, J.1    Galvani, A.P.2    Slatkin, M.3
  • 35
    • 0035102570 scopus 로고    scopus 로고
    • Akaike's information criterion in generalized estimating equations
    • Pan W, (2001) Akaike's information criterion in generalized estimating equations. Biometrics, 57, 120-125.
    • (2001) Biometrics , vol.57 , pp. 120-125
    • Pan, W.1
  • 36
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of phylogenetics and evolution in R language
    • Paradis E, Claude J, Strimmer K, (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 38
    • 77954554418 scopus 로고    scopus 로고
    • Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina
    • Poncet BN, Herrmann D, Gugerli F, et al,. (2010) Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina. Molecular Ecology, 19, 2896-2907.
    • (2010) Molecular Ecology , vol.19 , pp. 2896-2907
    • Poncet, B.N.1    Herrmann, D.2    Gugerli, F.3
  • 39
    • 79961135005 scopus 로고    scopus 로고
    • R Development Core Team. R Foundation for Statistical Computing, Vienna.
    • R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
    • (2011) R: A Language and Environment for Statistical Computing
  • 40
    • 0016513539 scopus 로고
    • Lewontin-Krakauer test for neutral genes-†comment
    • Robertson A, (1975) Lewontin-Krakauer test for neutral genes-†comment. Genetics, 80, 396.
    • (1975) Genetics , vol.80 , pp. 396
    • Robertson, A.1
  • 41
    • 84862025426 scopus 로고    scopus 로고
    • Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs
    • Roesti M, Hendry AP, Salzburger W, Berner D, (2012) Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs. Molecular Ecology, 21, 2852-2862.
    • (2012) Molecular Ecology , vol.21 , pp. 2852-2862
    • Roesti, M.1    Hendry, A.P.2    Salzburger, W.3    Berner, D.4
  • 43
    • 77957142014 scopus 로고    scopus 로고
    • The population genomics of plant adaptation
    • Siol M, Wright SI, Barrett SCH, (2010) The population genomics of plant adaptation. New Pythologist, 188, 313-332.
    • (2010) New Pythologist , vol.188 , pp. 313-332
    • Siol, M.1    Wright, S.I.2    Barrett, S.C.H.3
  • 44
    • 38049094991 scopus 로고    scopus 로고
    • Genome-wide patterns of gene flow across a house mouse hybrid zone
    • Teeter KC, Payseur BA, Harris LW, et al,. (2008) Genome-wide patterns of gene flow across a house mouse hybrid zone. Genome Research, 18, 67-76.
    • (2008) Genome Research , vol.18 , pp. 67-76
    • Teeter, K.C.1    Payseur, B.A.2    Harris, L.W.3
  • 45
    • 41149150656 scopus 로고    scopus 로고
    • The quest for adaptive evolution: A theoretical challenge in a maze of data
    • Tenaillon MI, Tiffin PL, (2008) The quest for adaptive evolution: a theoretical challenge in a maze of data. Current Opinion in Plant Biology, 11, 110-115.
    • (2008) Current Opinion in Plant Biology , vol.11 , pp. 110-115
    • Tenaillon, M.I.1    Tiffin, P.L.2
  • 47
    • 33747826265 scopus 로고    scopus 로고
    • The adaptive hypothesis of clinal variation revisited: Single-locus clines as a result of spatially restricted gene flow
    • Vasemägi A, (2006) The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted gene flow. Genetics, 173, 2411-2414.
    • (2006) Genetics , vol.173 , pp. 2411-2414
    • Vasemägi, A.1
  • 48
    • 85027952514 scopus 로고    scopus 로고
    • A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers
    • Vilas A, Pérez-Figueroa A, Caballero A, (2012) A simulation study on the performance of differentiation-based methods to detect selected loci using linked neutral markers. Journal of Evolutionary Biology, 25, 1364-1376.
    • (2012) Journal of Evolutionary Biology , vol.25 , pp. 1364-1376
    • Vilas, A.1    Pérez-Figueroa, A.2    Caballero, A.3
  • 49
    • 84866747543 scopus 로고    scopus 로고
    • DETSEL: A R-package to detect marker loci responding to selection
    • (eds Bonin A. Pompanon F.), Humana Press, New York, New York.
    • Vitalis R, (2012) DETSEL: a R-package to detect marker loci responding to selection. In: Data Production and Analysis in Population Genomics (eds, Bonin A, Pompanon F,), pp. 277-293. Humana Press, New York, New York.
    • (2012) Data Production and Analysis in Population Genomics , pp. 277-293
    • Vitalis, R.1
  • 50
    • 0034856602 scopus 로고    scopus 로고
    • Interpretation of variation across marker loci as evidence of selection
    • Vitalis R, Dawson K, Boursot P, (2001) Interpretation of variation across marker loci as evidence of selection. Genetics, 158, 1811-1823.
    • (2001) Genetics , vol.158 , pp. 1811-1823
    • Vitalis, R.1    Dawson, K.2    Boursot, P.3
  • 51
    • 0021566877 scopus 로고
    • Estimating F-statistics for the analysis for population structure
    • Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis for population structure. Evolution, 38, 1358-1370.
    • (1984) Evolution , vol.38 , pp. 1358-1370
    • Weir, B.S.1    Cockerham, C.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.