메뉴 건너뛰기




Volumn 7, Issue 11, 2012, Pages

Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DNA FLANKING REGION; DNA FOOTPRINTING; DNA SEQUENCE; GENE CONSTRUCT; GENE FLOW; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENEALOGY; GENETIC ALGORITHM; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; SACCHAROMYCES CEREVISIAE;

EID: 84870619916     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046947     Document Type: Article
Times cited : (5)

References (37)
  • 2
    • 56449108529 scopus 로고    scopus 로고
    • Regulatory genes control a key morphological and ecological trait transferred between species
    • Kim M, Cui ML, Cubas P, Gillies A, Lee K, et al. (2008) Regulatory genes control a key morphological and ecological trait transferred between species. Science 322: 1116-1119.
    • (2008) Science , vol.322 , pp. 1116-1119
    • Kim, M.1    Cui, M.L.2    Cubas, P.3    Gillies, A.4    Lee, K.5
  • 3
    • 62149151949 scopus 로고    scopus 로고
    • Molecular and evolutionary history of melanism in North American gray wolves
    • Anderson TM, vonHoldt BM, Candille SI, Musiani M, Greco C, et al. (2009) Molecular and evolutionary history of melanism in North American gray wolves. Science 323: 1339-1343.
    • (2009) Science , vol.323 , pp. 1339-1343
    • Anderson, T.M.1    vonHoldt, B.M.2    Candille, S.I.3    Musiani, M.4    Greco, C.5
  • 4
    • 77954241323 scopus 로고    scopus 로고
    • Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control
    • Neafsey DE, Barker BM, Sharpton TJ, Stajich JE, Park DJ, et al. (2010) Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Genome Research 20: 938-946.
    • (2010) Genome Research , vol.20 , pp. 938-946
    • Neafsey, D.E.1    Barker, B.M.2    Sharpton, T.J.3    Stajich, J.E.4    Park, D.J.5
  • 5
    • 58749092473 scopus 로고    scopus 로고
    • Divergent selection and heterogeneous genomic divergence
    • Nosil P, Funk DJ, Ortiz-Barrientos D, (2009) Divergent selection and heterogeneous genomic divergence. Molecular Ecology 18: 375-402.
    • (2009) Molecular Ecology , vol.18 , pp. 375-402
    • Nosil, P.1    Funk, D.J.2    Ortiz-Barrientos, D.3
  • 6
    • 0036215045 scopus 로고    scopus 로고
    • Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives
    • Machado CA, Kliman RM, Markert JA, Hey J, (2002) Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology and Evolution 19: 472-488.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 472-488
    • Machado, C.A.1    Kliman, R.M.2    Markert, J.A.3    Hey, J.4
  • 8
    • 18944369385 scopus 로고    scopus 로고
    • Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
    • Macleod D, Charlebois RL, Doolittle F, Bapteste E, (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evolutionary Biology 5: 27.
    • (2005) BMC Evolutionary Biology , vol.5 , pp. 27
    • Macleod, D.1    Charlebois, R.L.2    Doolittle, F.3    Bapteste, E.4
  • 10
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254-267.
    • (2006) Molecular Biology and Evolution , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 12
    • 33645096818 scopus 로고    scopus 로고
    • Evidence for domesticated and wild populations of Saccharomyces cerevisiae
    • Fay JC, Benavides JA, (2005) Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genetics 1: e5.
    • (2005) PLoS Genetics , vol.1
    • Fay, J.C.1    Benavides, J.A.2
  • 13
    • 33748288159 scopus 로고    scopus 로고
    • Population genomic analysis of outcrossing and recombination in yeast
    • Ruderfer DM, Pratt SC, Seidel HS, Kruglyak L, (2006) Population genomic analysis of outcrossing and recombination in yeast. Nature Genetics 38: 1077-1081.
    • (2006) Nature Genetics , vol.38 , pp. 1077-1081
    • Ruderfer, D.M.1    Pratt, S.C.2    Seidel, H.S.3    Kruglyak, L.4
  • 14
    • 62649126517 scopus 로고    scopus 로고
    • Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae
    • Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L, (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345.
    • (2009) Nature , vol.458 , pp. 342-345
    • Schacherer, J.1    Shapiro, J.A.2    Ruderfer, D.M.3    Kruglyak, L.4
  • 15
    • 30744479464 scopus 로고    scopus 로고
    • Minimum recombination histories by branch and bound
    • Berlin, Germany: Springer-Verlag LNCS, The kwarg software package is available from
    • Lyngsø RB, Song YS, Hein J (2005) Minimum recombination histories by branch and bound. In: Proc. of 2005 Workshop on Algorithms in Bioinformatics. Berlin, Germany: Springer-Verlag LNCS, pp. 239-250. The kwarg software package is available from http://www.stats.ox.ac.uk/~lyngsoe/section26/.
    • (2005) Proc. of 2005 Workshop on Algorithms in Bioinformatics , pp. 239-250
    • Lyngsø, R.B.1    Song, Y.S.2    Hein, J.3
  • 16
    • 33751112507 scopus 로고    scopus 로고
    • Mapping trait loci by use of inferred ancestral recombination graphs
    • Minichiello M, Durbin R, (2006) Mapping trait loci by use of inferred ancestral recombination graphs. American Journal of Human Genetics 79: 910-922.
    • (2006) American Journal of Human Genetics , vol.79 , pp. 910-922
    • Minichiello, M.1    Durbin, R.2
  • 17
    • 0034815265 scopus 로고    scopus 로고
    • A simulation study of the reliability of recombination detection methods
    • Wiuf C, Christensen T, Hein J, (2001) A simulation study of the reliability of recombination detection methods. Molecular Biology and Evolution 18: 1929-1939.
    • (2001) Molecular Biology and Evolution , vol.18 , pp. 1929-1939
    • Wiuf, C.1    Christensen, T.2    Hein, J.3
  • 18
    • 0026709389 scopus 로고
    • Estimation of levels of gene flow from dna sequence data
    • Hudson RR, Slatkin M, Maddison WP, (1992) Estimation of levels of gene flow from dna sequence data. Genetics 132: 583-589.
    • (1992) Genetics , vol.132 , pp. 583-589
    • Hudson, R.R.1    Slatkin, M.2    Maddison, W.P.3
  • 19
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 20
    • 79957950801 scopus 로고    scopus 로고
    • SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
    • Le SQ, Durbin R, (2011) SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Research 21: 952-960.
    • (2011) Genome Research , vol.21 , pp. 952-960
    • Le, S.Q.1    Durbin, R.2
  • 21
    • 0024341852 scopus 로고
    • A cladistic measure of gene flow inferred from the phylogenies of alleles
    • Slatkin M, Maddison WP, (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613.
    • (1989) Genetics , vol.123 , pp. 603-613
    • Slatkin, M.1    Maddison, W.P.2
  • 22
    • 33947673770 scopus 로고    scopus 로고
    • Roberts & Company Publishers, Greenwood Village, Colorado
    • Wakeley J (2008) Coalescent theory: an introduction. Roberts & Company Publishers, Greenwood Village, Colorado.
    • (2008) Coalescent theory: An introduction
    • Wakeley, J.1
  • 23
    • 1642320098 scopus 로고    scopus 로고
    • Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations
    • Beerli P, (2004) Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology 13: 827-836.
    • (2004) Molecular Ecology , vol.13 , pp. 827-836
    • Beerli, P.1
  • 24
    • 74549151043 scopus 로고    scopus 로고
    • How robust are \isolation with migration" analyses to violations of the IM model? A simulation study
    • Strasburg JL, Rieseberg LH, (2010) How robust are \isolation with migration" analyses to violations of the IM model? A simulation study. Molecular Biology and Evolution 27: 297-310.
    • (2010) Molecular Biology and Evolution , vol.27 , pp. 297-310
    • Strasburg, J.L.1    Rieseberg, L.H.2
  • 25
    • 33748315349 scopus 로고    scopus 로고
    • Genomewide evolutionary rates in laboratory and wild yeast
    • Ronald J, Tang H, Brem RB, (2006) Genomewide evolutionary rates in laboratory and wild yeast. Genetics 174: 541-544.
    • (2006) Genetics , vol.174 , pp. 541-544
    • Ronald, J.1    Tang, H.2    Brem, R.B.3
  • 27
    • 0036224855 scopus 로고    scopus 로고
    • Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species
    • de Barros Lopes M, Bellon JR, Shirley NJ, Ganter PF, (2002) Evidence for multiple interspecific hybridization in Saccharomyces sensu stricto species. FEMS Yeast Research 1: 323-331.
    • (2002) FEMS Yeast Research , vol.1 , pp. 323-331
    • de Barros Lopes, M.1    Bellon, J.R.2    Shirley, N.J.3    Ganter, P.F.4
  • 28
    • 28044456330 scopus 로고    scopus 로고
    • Molecular genetic study of introgression between Saccharomyces bayanus and S. cerevisiae
    • Naumova ES, Naumov GI, Masneuf-Pomarède I, Aigle M, (2005) Molecular genetic study of introgression between Saccharomyces bayanus and S. cerevisiae. Yeast 22: 1099-1115.
    • (2005) Yeast , vol.22 , pp. 1099-1115
    • Naumova, E.S.1    Naumov, G.I.2    Masneuf-Pomarède, I.3    Aigle, M.4
  • 29
    • 33750437730 scopus 로고    scopus 로고
    • Sequence diversity, reproductive isolation and species concepts in Saccharomyces
    • Liti G, Barton DB, Louis EJ, (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174: 839-850.
    • (2006) Genetics , vol.174 , pp. 839-850
    • Liti, G.1    Barton, D.B.2    Louis, E.J.3
  • 32
    • 58149339807 scopus 로고    scopus 로고
    • A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae
    • Muller LAH, McCusker JH, (2009) A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae. FEMS Yeast Research 9: 143-152.
    • (2009) FEMS Yeast Research , vol.9 , pp. 143-152
    • Muller, L.A.H.1    McCusker, J.H.2
  • 34
    • 0008726933 scopus 로고
    • Yeasts associated with pollinating bees and ower nectar
    • Sandhu DK, Waraich MK, (1985) Yeasts associated with pollinating bees and ower nectar. Microbial Ecology 11: 51-58.
    • (1985) Microbial Ecology , vol.11 , pp. 51-58
    • Sandhu, D.K.1    Waraich, M.K.2
  • 35
    • 78649310938 scopus 로고    scopus 로고
    • Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species
    • Elyashiv E, Bullaughey K, Sattath S, Rinott Y, Przeworski M, et al. (2010) Shifts in the intensity of purifying selection: an analysis of genome-wide polymorphism data from two closely related yeast species. Genome Research 20: 1558-1573.
    • (2010) Genome Research , vol.20 , pp. 1558-1573
    • Elyashiv, E.1    Bullaughey, K.2    Sattath, S.3    Rinott, Y.4    Przeworski, M.5
  • 36
    • 80052149129 scopus 로고    scopus 로고
    • Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus
    • Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S, (2011) Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution 28: 2615-2627.
    • (2011) Molecular Biology and Evolution , vol.28 , pp. 2615-2627
    • Vishnoi, A.1    Sethupathy, P.2    Simola, D.3    Plotkin, J.B.4    Hannenhalli, S.5
  • 37
    • 0034274870 scopus 로고    scopus 로고
    • An open graph visualization system and its applications to software engineering
    • Gansner ER, North SC, (2000) An open graph visualization system and its applications to software engineering. Software: Practice and Experience 30: 1203-1233.
    • (2000) Software: Practice and Experience , vol.30 , pp. 1203-1233
    • Gansner, E.R.1    North, S.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.