메뉴 건너뛰기




Volumn 3, Issue 5, 2013, Pages 795-806

Distribution of long-range linkage disequilibrium and tajima's d values in scandinavian populations of norway spruce (picea abies)

Author keywords

Conifer; Disequilibrium; Linkage; Recombination; Resampling; Tajima's D

Indexed keywords

NUCLEOTIDE;

EID: 84883250084     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.005462     Document Type: Article
Times cited : (26)

References (49)
  • 2
    • 67650795862 scopus 로고    scopus 로고
    • The distribution of late-Quaternary woody taxa in northern Eurasia: evidence from a new macrofossil database
    • Binney, H. A., K. J. Willis, M. E. Edwards, S. A. Bhagwat, P. M. Anderson et al., 2009 The distribution of late-Quaternary woody taxa in northern Eurasia: evidence from a new macrofossil database. Quat. Sci. Rev. 28: 2445-2464.
    • (2009) Quat. Sci. Rev. , vol.28 , pp. 2445-2464
    • Binney, H.A.1    Willis, K.J.2    Edwards, M.E.3    Bhagwat, S.A.4    Anderson, P.M.5
  • 4
    • 73349130751 scopus 로고    scopus 로고
    • New insights on the speciation history and nucleotide diversity of three boreal spruce species and a tertiary relict
    • Chen, J., T. Källman, N. Gyllenstrand, and M. Lascoux, 2010 New insights on the speciation history and nucleotide diversity of three boreal spruce species and a tertiary relict. Heredity 104: 3-14.
    • (2010) Heredity , vol.104 , pp. 3-14
    • Chen, J.1    Källman, T.2    Gyllenstrand, N.3    Lascoux, M.4
  • 5
    • 84863865175 scopus 로고    scopus 로고
    • Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies)
    • Chen, J., T. Källman, X. Ma, N. Gyllenstrand, G. Zaina et al., 2012 Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies). Genetics 191: 865-881.
    • (2012) Genetics , vol.191 , pp. 865-881
    • Chen, J.1    Källman, T.2    Ma, X.3    Gyllenstrand, N.4    Zaina, G.5
  • 6
    • 84862792463 scopus 로고    scopus 로고
    • Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity
    • Cutter, A. D., G. X. Wang, H. Ai, and Y. Peng, 2012 Influence of finite-sites mutation, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity. Mol. Ecol. 21: 1345-1359.
    • (2012) Mol. Ecol. , vol.21 , pp. 1345-1359
    • Cutter, A.D.1    Wang, G.X.2    Ai, H.3    Peng, Y.4
  • 7
    • 21244479740 scopus 로고    scopus 로고
    • Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    • Evanno, G., S. Regnaut, and J. Goudet, 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611-2620.
    • (2005) Mol. Ecol. , vol.14 , pp. 2611-2620
    • Evanno, G.1    Regnaut, S.2    Goudet, J.3
  • 8
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred
    • Ewing, B., and P. Green, 1998 Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
    • (1998) II. Error probabilities. Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 10
    • 77953032930 scopus 로고    scopus 로고
    • Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
    • Excoffier, L., and H. E. L. Lischer, 2010 Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10: 564-567.
    • (2010) Mol. Ecol. Res. , vol.10 , pp. 564-567
    • Excoffier, L.1    Lischer, H.E.L.2
  • 11
    • 33845768012 scopus 로고    scopus 로고
    • Recombination: an underappreciated factor in the evolution of plant genomes
    • Gaut, B. S., S. I. Wright, C. Rizzon, J. Dvorak, and L. K. Andersson, 2007 Recombination: an underappreciated factor in the evolution of plant genomes. Nat. Rev. Genet. 8: 77-84.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 77-84
    • Gaut, B.S.1    Wright, S.I.2    Rizzon, C.3    Dvorak, J.4    Andersson, L.K.5
  • 12
    • 33645219360 scopus 로고    scopus 로고
    • DNA sequence variation and selection of tag singlenucleotide polymorphisms at candidate genes for dought-stress response in Pinus taeda L
    • González-Martínez, S. C., E. Ersoz, G. R. Brown, N. C. Wheeler, and D. B. Neale, 2006 DNA sequence variation and selection of tag singlenucleotide polymorphisms at candidate genes for dought-stress response in Pinus taeda L. Genetics 172: 1915-1926.
    • (2006) Genetics , vol.172 , pp. 1915-1926
    • González-Martínez, S.C.1    Ersoz, E.2    Brown, G.R.3    Wheeler, N.C.4    Neale, D.B.5
  • 13
    • 0031955116 scopus 로고    scopus 로고
    • Consed: a graphical tool for sequence finishing
    • Gordon, D., C. Abajian, and P. Green, 1998 Consed: a graphical tool for sequence finishing. Genome Res. 8: 195-202.
    • (1998) Genome Res. , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 14
    • 54449091448 scopus 로고    scopus 로고
    • GSDS: a gene structure display server
    • Guo, A. Y., Q. H. Zhu, X. Chen, and J. C. Luo, 2007 GSDS: a gene structure display server. Yi Chuan 29: 1023-1026.
    • (2007) Yi Chuan , vol.29 , pp. 1023-1026
    • Guo, A.Y.1    Zhu, Q.H.2    Chen, X.3    Luo, J.C.4
  • 15
    • 0035711599 scopus 로고    scopus 로고
    • Mutation and linkage disequilibrium in human mtDNA
    • Hedrick, P. W., and S. Kumar, 2001 Mutation and linkage disequilibrium in human mtDNA. Eur. J. Hum. Genet. 9: 969-972.
    • (2001) Eur. J. Hum. Genet. , vol.9 , pp. 969-972
    • Hedrick, P.W.1    Kumar, S.2
  • 16
    • 33845746244 scopus 로고    scopus 로고
    • Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L. Karst].
    • Heuertz, M., E. De Paoli, T. Källman, H. Larsson, I. Jurman et al., 2006 Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) . Karst]. Genetics 174: 2095-2105.
    • (2006) Genetics , vol.174 , pp. 2095-2105
    • Heuertz, M.1    De Paoli, E.2    Källman, T.3    Larsson, H.4    Jurman, I.5
  • 17
    • 33646226097 scopus 로고
    • Linkage disequilibrium in finite populations
    • Hill, W. G., and A. Robertson, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 226-231.
    • (1968) Theor. Appl. Genet. , vol.38 , pp. 226-231
    • Hill, W.G.1    Robertson, A.2
  • 18
    • 0023959349 scopus 로고
    • Variances and covariances of squared linkage disequilibria in finite populations
    • Hill, W. G., and B. S. Weir, 1988 Variances and covariances of squared linkage disequilibria in finite populations. Theor. Popul. Biol. 33: 54-78.
    • (1988) Theor. Popul. Biol. , vol.33 , pp. 54-78
    • Hill, W.G.1    Weir, B.S.2
  • 19
    • 77956566380 scopus 로고    scopus 로고
    • Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests
    • Holliday, J. A., M. Yuen, K. Ritland, and S. N. Aitken, 2010 Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests. Mol. Ecol. 19: 3857-3864.
    • (2010) Mol. Ecol. , vol.19 , pp. 3857-3864
    • Holliday, J.A.1    Yuen, M.2    Ritland, K.3    Aitken, S.N.4
  • 20
    • 34547861256 scopus 로고    scopus 로고
    • CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    • Jakobsson, M., and N. A. Rosenberg, 2007 CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
    • (2007) Bioinformatics , vol.23 , pp. 1801-1806
    • Jakobsson, M.1    Rosenberg, N.A.2
  • 21
    • 77649176976 scopus 로고    scopus 로고
    • The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms
    • Jaramillo-Correa, J. P., M. Verdú, and S. C. González-Martínez, 2010 The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol. Biol. 10: 22.
    • (2010) BMC Evol. Biol. , vol.10 , pp. 22
    • Jaramillo-Correa, J.P.1    Verdú, M.2    González-Martínez, S.C.3
  • 22
    • 84883251357 scopus 로고    scopus 로고
    • Adaptive evolution and demographic history of Norway spruce (Picea abies)
    • Ph.D. Thesis, Uppsala University
    • Källman, T., 2009 Adaptive evolution and demographic history of Norway spruce (Picea abies). Ph.D. Thesis, Uppsala University.
    • (2009)
    • Källman, T.1
  • 23
    • 79961187177 scopus 로고    scopus 로고
    • Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution
    • Karlgren, A., N. Gyllenstrand, T. Källman, J. F. Sundström, D. Moore et al., 2011 Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol. 156: 1967-1977.
    • (2011) Plant Physiol. , vol.156 , pp. 1967-1977
    • Karlgren, A.1    Gyllenstrand, N.2    Källman, T.3    Sundström, J.F.4    Moore, D.5
  • 24
    • 33645130943 scopus 로고    scopus 로고
    • Nucleotide diversity and linkage disequilibrium in cold-hardiness-and wood quality-related candidate genes in Douglas fir
    • Krutovsky, K. V., and D. B. Neale, 2005 Nucleotide diversity and linkage disequilibrium in cold-hardiness-and wood quality-related candidate genes in Douglas fir. Genetics 171: 2029-2041.
    • (2005) Genetics , vol.171 , pp. 2029-2041
    • Krutovsky, K.V.1    Neale, D.B.2
  • 25
    • 84856212134 scopus 로고    scopus 로고
    • Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population
    • Lepoittevin, C., L. Harvengt, C. Plomion, and P. Garnier-Gere, 2012 Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population. Tree Genet. Genomes 8: 113-126.
    • (2012) Tree Genet. Genomes , vol.8 , pp. 113-126
    • Lepoittevin, C.1    Harvengt, L.2    Plomion, C.3    Garnier-Gere, P.4
  • 27
    • 65649117685 scopus 로고    scopus 로고
    • DnaSP v5: A software for comprehensive analysis of DNA polymorphism data
    • Librado, P., and J. Rozas, 2009 DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
    • (2009) Bioinformatics , vol.25 , pp. 1451-1452
    • Librado, P.1    Rozas, J.2
  • 28
    • 80052748796 scopus 로고    scopus 로고
    • Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene
    • Marroni, F., S. Pinosio, G. Zaina, F. Fogolari, N. Felice et al., 2011 Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene. Tree Genet. Genomes 7: 1011-1023
    • (2011) Tree Genet. Genomes , vol.7 , pp. 1011-1023
    • Marroni, F.1    Pinosio, S.2    Zaina, G.3    Fogolari, F.4    Felice, N.5
  • 29
    • 0035544521 scopus 로고    scopus 로고
    • What do patterns of genetic variability reveal about mitochondrial recombination?
    • McVean, G A., 2001 What do patterns of genetic variability reveal about mitochondrial recombination?. Heredity 87: 613-620.
    • (2001) Heredity , vol.87 , pp. 613-620
    • McVean, G.A.1
  • 30
    • 0036199914 scopus 로고    scopus 로고
    • A coalescent-based method for detecting and estimating recombination from gene sequences
    • McVean, G. A., P. Awadalla, and P. Fearnhead, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
    • (2002) Genetics , vol.160 , pp. 1231-1241
    • McVean, G.A.1    Awadalla, P.2    Fearnhead, P.3
  • 31
    • 84858185558 scopus 로고    scopus 로고
    • Extended linkage disequilibrium in noncoding regions in a conifer, Cryptomeria japonica
    • Moritsuka, E., Y. Hisataka, M. Tamura, K. Uchiyama, A. Watanabe et al., 2012 Extended linkage disequilibrium in noncoding regions in a conifer, Cryptomeria japonica. Genetics 190: 1145-1148.
    • (2012) Genetics , vol.190 , pp. 1145-1148
    • Moritsuka, E.1    Hisataka, Y.2    Tamura, M.3    Uchiyama, K.4    Watanabe, A.5
  • 32
    • 77954460187 scopus 로고    scopus 로고
    • Molecular evolution of regulatory genes in spruces from different species and continents: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes
    • Namroud, M.-C., C. Guillet-Claude, J. Mackay, N. Isabel, and J. Bousquet, 2010 Molecular evolution of regulatory genes in spruces from different species and continents: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes. J. Mol. Evol. 70: 371-386.
    • (2010) J. Mol. Evol. , vol.70 , pp. 371-386
    • Namroud, M.C.1    Guillet-Claude, C.2    Mackay, J.3    Isabel, N.4    Bousquet, J.5
  • 33
    • 3042745450 scopus 로고    scopus 로고
    • Association genetics of complex traits in conifers
    • Neale, D. B., and O. Savolainen, 2004 Association genetics of complex traits in conifers. Trends Pld O. Savolainen 9: 325-330.
    • (2004) Trends Plant Sci. , vol.9 , pp. 325-330
    • Neale, D.B.1    Savolainen, O.2
  • 34
    • 84863541347 scopus 로고    scopus 로고
    • An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people
    • Nelson, M. R., D. Wegmann, M. G. Ehm, D. Kessner, P. St Jean et al., 2012 An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337: 100-104.
    • (2012) Science , vol.337 , pp. 100-104
    • Nelson, M.R.1    Wegmann, D.2    Ehm, M.G.3    Kessner, D.4    Jean, P.5
  • 35
    • 84857231879 scopus 로고    scopus 로고
    • The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers
    • Pavy, N., M. C. Namroud, F. Gagnon, N. Isabel, and J. Bousquet, 2012 The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers. Heredity 108: 273-284.
    • (2012) Heredity , vol.108 , pp. 273-284
    • Pavy, N.1    Namroud, M.C.2    Gagnon, F.3    Isabel, N.4    Bousquet, J.5
  • 36
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959. Pyhäjärvi, T., M. R. García-Gil, T. KnÜrr, M. Mikkonen, W. Wachowiak et al., 2007 Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 37
    • 37249019973 scopus 로고    scopus 로고
    • Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations
    • Pyhäjärvi, T., M. R. García-Gil, T. Knürr, M. Mikkonen, W. Wachowiak et al., 2007 Demographic history has influenced nucleotide diversity in European Pinus sylvestris populations. Genetics 177: 1713-1724.
    • (2007) Genetics , vol.177 , pp. 1713-1724
    • Pyhäjärvi, T.1    García-Gil, M.R.2    Knürr, T.3    Mikkonen, M.4    Wachowiak, W.5
  • 38
    • 79953027163 scopus 로고    scopus 로고
    • Revisiting protein heterozygosity in plants -nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris
    • Pyhäjärvi, T., S. T. Kujala, and O. Savolainen, 2011 Revisiting protein heterozygosity in plants -nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris. Tree Genet. Genomes 7: 385-397.
    • (2011) Tree Genet. Genomes , vol.7 , pp. 385-397
    • Pyhäjärvi, T.1    Kujala, S.T.2    Savolainen, O.3
  • 39
    • 84863304598 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Development Core Team, Available at:Accessed: March 18, 2013.
    • R Development Core Team, 2012 R: A Language and Environment for Statistical Computing. Available at: http://www.R-project.org. Accessed: March 18, 2013.
    • (2012)
  • 40
    • 67849119548 scopus 로고    scopus 로고
    • The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations
    • Städler, T., B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber, 2009 The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182: 205-216.
    • (2009) Genetics , vol.182 , pp. 205-216
    • Städler, T.1    Haubold, B.2    Merino, C.3    Stephan, W.4    Pfaffelhuber, P.5
  • 41
    • 84883592764 scopus 로고    scopus 로고
    • Impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories
    • St. Onge, K., A. E. Palmé, S. I. Wright, and M. Lascoux, 2012 Impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories. G3 (Bethesda) 2: 803-814.
    • (2012) G3 (Bethesda) , vol.2 , pp. 803-814
    • Onge, K.1    Palmé, A.E.2    Wright, S.I.3    Lascoux, M.4
  • 42
    • 0027986930 scopus 로고
    • Decay of linkage disequilibrium in a finite island model
    • Tachida, H., 1994 Decay of linkage disequilibrium in a finite island model. Genet. Res. 64: 137-144.
    • (1994) Genet. Res. , vol.64 , pp. 137-144
    • Tachida, H.1
  • 43
    • 84864039639 scopus 로고    scopus 로고
    • Linkage disequilibrium in a population undergoing periodic fragmentation and admixture
    • Tachida, H., 2012 Linkage disequilibrium in a population undergoing periodic fragmentation and admixture. Genes Genet. Syst. 87: 125-135.
    • (2012) Genes Genet. Syst. , vol.87 , pp. 125-135
    • Tachida, H.1
  • 44
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA Polymorphism
    • Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA Polymorphism. Genetics 123: 585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 45
    • 0344464730 scopus 로고    scopus 로고
    • libsequence: a C++ class library for evolutionary genetic analysis
    • Thornton, K., 2003 libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
    • (2003) Bioinformatics , vol.19 , pp. 2325-2327
    • Thornton, K.1
  • 46
    • 67349120042 scopus 로고    scopus 로고
    • Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European (Picea abies)
    • Tollefsrud, M. M., J. H. Sonstebo, C. Brochmann, O. Johnsen, T. Skroppa et al., 2009 Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European (Picea abies). Heredity 102: 549-562.
    • (2009) Heredity , vol.102 , pp. 549-562
    • Tollefsrud, M.M.1    Sonstebo, J.H.2    Brochmann, C.3    Johnsen, O.4    Skroppa, T.5
  • 47
    • 79955045330 scopus 로고    scopus 로고
    • Scattered late-glacial and early Holocene tree populations as dispersal nuclei for forest development in north-eastern European Russia
    • Väliranta, M., A. Kaakinen, P. Kuhry, S. Kultti, J. S. Salonen et al., 2011 Scattered late-glacial and early Holocene tree populations as dispersal nuclei for forest development in north-eastern European Russia. J. Biogeogr. 38: 922-932.
    • (2011) J. Biogeogr. , vol.38 , pp. 922-932
    • Väliranta, M.1    Kaakinen, A.2    Kuhry, P.3    Kultti, S.4    Salonen, J.S.5
  • 48
    • 29444451610 scopus 로고    scopus 로고
    • Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes
    • USA
    • Voight, B. F., A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson et al., 2005 Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. Natl. Acad. Sci. USA 102: 18508-18513.
    • (2005) Proc. Natl. Acad. Sci. , vol.102 , pp. 18508-18513
    • Voight, B.F.1    Adams, A.M.2    Frisse, L.A.3    Qian, Y.4    Hudson, R.R.5
  • 49
    • 33751342650 scopus 로고    scopus 로고
    • Statistical tests for detecting positive selection by utilizing high-frequency variants
    • Zeng, K., Y. X. Fu, S. Shi, and C. I. Wu, 2006 Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.
    • (2006) Genetics , vol.174 , pp. 1431-1439
    • Zeng, K.1    Fu, Y.X.2    Shi, S.3    Wu, C.I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.