메뉴 건너뛰기




Volumn 3, Issue 6, 2012, Pages 1084-1092

Diversitree: Comparative phylogenetic analyses of diversification in R

Author keywords

Birth death process; Comparative methods; Extinction; Macroevolution; Speciation

Indexed keywords


EID: 84871008957     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2012.00234.x     Document Type: Article
Times cited : (715)

References (39)
  • 2
    • 79251485306 scopus 로고    scopus 로고
    • Origins and consequences of serpentine endemism in the California flora
    • Anacker, B.L., Whittall, J.B., Goldberg, E.E. & Harrison, S.P. (2010) Origins and consequences of serpentine endemism in the California flora. Evolution, 65, 365-376.
    • (2010) Evolution , vol.65 , pp. 365-376
    • Anacker, B.L.1    Whittall, J.B.2    Goldberg, E.E.3    Harrison, S.P.4
  • 3
    • 54849411673 scopus 로고    scopus 로고
    • Detection of ''punctuated equilibrium'' by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny
    • Bokma, F. (2008) Detection of ''punctuated equilibrium'' by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution, 62, 2718-2726.
    • (2008) Evolution , vol.62 , pp. 2718-2726
    • Bokma, F.1
  • 4
    • 33645029984 scopus 로고    scopus 로고
    • SIMMAP: Stochastic character mapping of discrete traits on phylogenies
    • Bollback, J.P. (2006) SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.
    • (2006) BMC Bioinformatics , vol.7 , pp. 88
    • Bollback, J.P.1
  • 5
    • 84857117210 scopus 로고    scopus 로고
    • When are adaptive radiations replicated in areas? Ecological opportunity and unexceptional diversification in West Indian dipsadine snakes (Colubridae: Alsophiini)
    • Burbrink, F.T., Ruane, S. & Pyron, R.A. (2012) When are adaptive radiations replicated in areas? Ecological opportunity and unexceptional diversification in West Indian dipsadine snakes (Colubridae: Alsophiini). Journal of Biogeography, 39, 465-475.
    • (2012) Journal of Biogeography , vol.39 , pp. 465-475
    • Burbrink, F.T.1    Ruane, S.2    Pyron, R.A.3
  • 7
    • 82855161365 scopus 로고    scopus 로고
    • A novel comparative method for identifying shifts in the rate of character evolution on trees
    • Eastman, J.M., Alfaro, M.E., Joyce, P., Hipp, A.L. & Harmon, L.J. (2011) A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution, 65, 3578-3589.
    • (2011) Evolution , vol.65 , pp. 3578-3589
    • Eastman, J.M.1    Alfaro, M.E.2    Joyce, P.3    Hipp, A.L.4    Harmon, L.J.5
  • 8
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: a maximum likelihood approach
    • Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 9
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein, J. (1985) Phylogenies and the comparative method. The American Naturalist, 125, 1-15.
    • (1985) The American Naturalist , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 10
    • 78650666284 scopus 로고    scopus 로고
    • Quantitative traits and diversification
    • FitzJohn, R.G. (2010) Quantitative traits and diversification. Systematic Biology, 59, 619-633.
    • (2010) Systematic Biology , vol.59 , pp. 619-633
    • FitzJohn, R.G.1
  • 11
    • 72849125317 scopus 로고    scopus 로고
    • Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies
    • FitzJohn, R.G., Maddison, W.P. & Otto, S.P. (2009) Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Systematic Biology, 58, 595-611.
    • (2009) Systematic Biology , vol.58 , pp. 595-611
    • FitzJohn, R.G.1    Maddison, W.P.2    Otto, S.P.3
  • 12
    • 20744449792 scopus 로고    scopus 로고
    • The design and implementation of FFTW3
    • Frigo, M. & Johnson, S.G. (2005) The design and implementation of FFTW3. Procedings of the IEEE, 93, 216-231.
    • (2005) Procedings of the IEEE , vol.93 , pp. 216-231
    • Frigo, M.1    Johnson, S.G.2
  • 13
    • 84870546247 scopus 로고    scopus 로고
    • Tempo and mode in plant breeding system evolution
    • (in press), DOI: 10.1111/j.1558-5646.2012.01730.x.
    • Goldberg, E.E. & Igić, B. (in press) Tempo and mode in plant breeding system evolution. Evolution, DOI: 10.1111/j.1558-5646.2012.01730.x.
    • Evolution
    • Goldberg, E.E.1    Igić, B.2
  • 14
    • 79959436449 scopus 로고    scopus 로고
    • Phylogenetic inference of reciprocal effects between geographic range evolution and diversification
    • Goldberg, E.E., Lancaster, L.T. & Ree, R.H. (2011) Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. Systematic Biology, 60, 451-465.
    • (2011) Systematic Biology , vol.60 , pp. 451-465
    • Goldberg, E.E.1    Lancaster, L.T.2    Ree, R.H.3
  • 15
    • 84862860504 scopus 로고    scopus 로고
    • Mutualism with plants drives Primate diversification
    • Gómez, J.M. & Verdú, M. (2012) Mutualism with plants drives Primate diversification. Systematic Biology, 61, 567-577.
    • (2012) Systematic Biology , vol.61 , pp. 567-577
    • Gómez, J.M.1    Verdú, M.2
  • 17
    • 80054922044 scopus 로고    scopus 로고
    • Loss of sexual recombination and segregation is associated with increased diversification in evening primroses
    • Johnson, M.T.J., FitzJohn, R.G., Smith, S.D., Rausher, M.D. & Otto, S.P. (2011) Loss of sexual recombination and segregation is associated with increased diversification in evening primroses. Evolution, 65, 3230-3240.
    • (2011) Evolution , vol.65 , pp. 3230-3240
    • Johnson, M.T.J.1    FitzJohn, R.G.2    Smith, S.D.3    Rausher, M.D.4    Otto, S.P.5
  • 19
    • 0035527396 scopus 로고    scopus 로고
    • A likelihood approach to estimating phylogeny from discrete morphological character data
    • Lewis, P.O. (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50, 913-925.
    • (2001) Systematic Biology , vol.50 , pp. 913-925
    • Lewis, P.O.1
  • 20
    • 79957542188 scopus 로고    scopus 로고
    • Seeing the forest for the trees: the limitations of phylogenies in comparative biology
    • Losos, J. (2011) Seeing the forest for the trees: the limitations of phylogenies in comparative biology. The American Naturalist, 177, 709-727.
    • (2011) The American Naturalist , vol.177 , pp. 709-727
    • Losos, J.1
  • 21
    • 33750588239 scopus 로고    scopus 로고
    • Confounding asymmetries in evolutionary diversification and character change
    • Maddison, W.P. (2006) Confounding asymmetries in evolutionary diversification and character change. Evolution, 60, 1743-1746.
    • (2006) Evolution , vol.60 , pp. 1743-1746
    • Maddison, W.P.1
  • 22
    • 84871017869 scopus 로고    scopus 로고
    • Mesquite: a modular system for evolutionary analysis. Version 2.5.
    • Maddison, W.P. & Maddison, D.R. (2008) Mesquite: a modular system for evolutionary analysis. Version 2.5. http://www.mesquiteproject.org
    • (2008)
    • Maddison, W.P.1    Maddison, D.R.2
  • 23
    • 0031350056 scopus 로고    scopus 로고
    • NEXUS: an extensible file format for systematic information
    • Maddison, D.R., Swofford, D.L. & Maddison, W.P. (1997) NEXUS: an extensible file format for systematic information. Systematic Biology, 46, 590-621.
    • (1997) Systematic Biology , vol.46 , pp. 590-621
    • Maddison, D.R.1    Swofford, D.L.2    Maddison, W.P.3
  • 24
    • 34548657597 scopus 로고    scopus 로고
    • Estimating a binary character's effect on speciation and extinction
    • Maddison, W.P., Midford, P.E. & Otto, S.P. (2007) Estimating a binary character's effect on speciation and extinction. Systematic Biology, 56, 701-710.
    • (2007) Systematic Biology , vol.56 , pp. 701-710
    • Maddison, W.P.1    Midford, P.E.2    Otto, S.P.3
  • 25
    • 84863691195 scopus 로고    scopus 로고
    • Linking the investigations of character evolution and species diversification
    • DOI: 10.1086/666649.
    • Magnuson-Ford, K. & Otto, S.P. (2012) Linking the investigations of character evolution and species diversification. American Naturalist, DOI: 10.1086/666649.
    • (2012) American Naturalist
    • Magnuson-Ford, K.1    Otto, S.P.2
  • 28
    • 0028097770 scopus 로고
    • Detecting correlated evolution on phylogenies: a general method for the comparativ analysis of discrete characters
    • Pagel, M. (1994) Detecting correlated evolution on phylogenies: a general method for the comparativ analysis of discrete characters. Proceedings of the Royal Society of London Series B, 255, 37-45.
    • (1994) Proceedings of the Royal Society of London Series B , vol.255 , pp. 37-45
    • Pagel, M.1
  • 29
    • 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
  • 30
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team., R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
    • R Development Core Team. (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
    • (2012) R: A Language and Environment for Statistical Computing
  • 31
    • 78650630261 scopus 로고    scopus 로고
    • Equilibrium speciation dynamics in a model adaptive radiation of island lizards
    • Rabosky, D.L. & Glor, R.E. (2010) Equilibrium speciation dynamics in a model adaptive radiation of island lizards. Proceedings of the National Acadamy of Sciences, USA, 51, 22178-22183.
    • (2010) Proceedings of the National Acadamy of Sciences, USA , vol.51 , pp. 22178-22183
    • Rabosky, D.L.1    Glor, R.E.2
  • 32
    • 0028932195 scopus 로고
    • Inference from binary comparative data
    • Read, A.F. & Nee, S. (1995) Inference from binary comparative data. Journal of Theoretical Biology, 173, 99-108.
    • (1995) Journal of Theoretical Biology , vol.173 , pp. 99-108
    • Read, A.F.1    Nee, S.2
  • 33
    • 77954721891 scopus 로고    scopus 로고
    • Evolutionary distinctiveness, threat status and ecological oddity in primates
    • Redding, D.W., DeWolff, C. & Mooers, A.Ø. (2010) Evolutionary distinctiveness, threat status and ecological oddity in primates. Conservation Biology, 24, 1052-1058.
    • (2010) Conservation Biology , vol.24 , pp. 1052-1058
    • Redding, D.W.1    DeWolff, C.2    Mooers, A.3
  • 35
    • 59849089846 scopus 로고    scopus 로고
    • Evidence for ecological speciation and its alternative
    • Schluter, D. (2009) Evidence for ecological speciation and its alternative. Science, 323, 737-741.
    • (2009) Science , vol.323 , pp. 737-741
    • Schluter, D.1
  • 36
    • 0031417707 scopus 로고    scopus 로고
    • Likelihood of ancestor states in adaptive radiation
    • Schluter, D., Price, T., Mooers, A.Ø. & Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699-1711.
    • (1997) Evolution , vol.51 , pp. 1699-1711
    • Schluter, D.1    Price, T.2    Mooers, A.3    Ludwig, D.4
  • 38
    • 79955129095 scopus 로고    scopus 로고
    • Effects of gasteroid fruiting body morphology on diversification rates in three independent clades of fungi estimated using binary state speciation and extinction analysis
    • Wilson, A.W., Binder, M. & Hibbett, D.S. (2011) Effects of gasteroid fruiting body morphology on diversification rates in three independent clades of fungi estimated using binary state speciation and extinction analysis. Evolution, 65, 1305-1322.
    • (2011) Evolution , vol.65 , pp. 1305-1322
    • Wilson, A.W.1    Binder, M.2    Hibbett, D.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.