메뉴 건너뛰기




Volumn 4, Issue 6, 2013, Pages 566-572

The mean and variance of phylogenetic diversity under rarefaction

Author keywords

Alpha diversity; Phylogenetic diversity; Rarefaction sampling depth

Indexed keywords

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 84878905185     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12042     Document Type: Article
Times cited : (39)

References (46)
  • 1
    • 70149113478 scopus 로고    scopus 로고
    • A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats
    • Allen, B., Kon, M. & Bar-Yam, Y. (2009) A new phylogenetic diversity measure generalizing the Shannon index and its application to phyllostomid bats. The American Naturalist, 174, 236-243.
    • (2009) The American Naturalist , vol.174 , pp. 236-243
    • Allen, B.1    Kon, M.2    Bar-Yam, Y.3
  • 2
    • 79955456912 scopus 로고    scopus 로고
    • Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood
    • Berger, S.A., Krompass, D. & Stamatakis, A. (2011) Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology, 60, 291-302.
    • (2011) Systematic Biology , vol.60 , pp. 291-302
    • Berger, S.A.1    Krompass, D.2    Stamatakis, A.3
  • 4
    • 66349094682 scopus 로고    scopus 로고
    • Using phylogenetic, functional and trait diversity to understand patterns of plant community of productivity
    • Cadotte, M., Cavender-Bares, J., Tilman, D. & Oakley, T.H. (2009) Using phylogenetic, functional and trait diversity to understand patterns of plant community of productivity. PLOS ONE, 4, e5695.
    • (2009) PLOS ONE , vol.4
    • Cadotte, M.1    Cavender-Bares, J.2    Tilman, D.3    Oakley, T.H.4
  • 5
    • 84861347511 scopus 로고    scopus 로고
    • The Western English Channel contains a persistent microbial seed bank
    • Caporaso, J.G., Paszkiewicz, K., Field, D., Knight, R. & Gilbert, J.A. (2012) The Western English Channel contains a persistent microbial seed bank. ISME Journal, 6, 1089-1093.
    • (2012) ISME Journal , vol.6 , pp. 1089-1093
    • Caporaso, J.G.1    Paszkiewicz, K.2    Field, D.3    Knight, R.4    Gilbert, J.A.5
  • 6
    • 84871737233 scopus 로고    scopus 로고
    • Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size
    • Chao, A. & Jost, L. (2012) Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. Ecology, 93, 2533-2547.
    • (2012) Ecology , vol.93 , pp. 2533-2547
    • Chao, A.1    Jost, L.2
  • 8
    • 49249113020 scopus 로고    scopus 로고
    • Discovering and rediscovering the sample-based rarefaction formula in the ecological literature
    • Chiarucci, A., Bacaro, G., Rocchini, D. & Fattorini, L. (2008) Discovering and rediscovering the sample-based rarefaction formula in the ecological literature. Community Ecology, 9, 121-123.
    • (2008) Community Ecology , vol.9 , pp. 121-123
    • Chiarucci, A.1    Bacaro, G.2    Rocchini, D.3    Fattorini, L.4
  • 9
    • 84862908094 scopus 로고    scopus 로고
    • Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages
    • Colwell, R.K., Chao, A., Gotelli, N.J., Lin, S.Y., Mao, C.X., Chazdon, R.L. & Longino, J.T. (2012) Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. Journal of Plant Ecology, 5, 3-21.
    • (2012) Journal of Plant Ecology , vol.5 , pp. 3-21
    • Colwell, R.K.1    Chao, A.2    Gotelli, N.J.3    Lin, S.Y.4    Mao, C.X.5    Chazdon, R.L.6    Longino, J.T.7
  • 10
    • 33746673919 scopus 로고    scopus 로고
    • Additive partitioning of rarefaction curves and species-area relationships: unifying α-, β-and γ-diversity with sample size and habitat area
    • Crist, T.O. & Veech, J.A. (2006) Additive partitioning of rarefaction curves and species-area relationships: unifying α-, β-and γ-diversity with sample size and habitat area. Ecology Letters, 9, 923-932.
    • (2006) Ecology Letters , vol.9 , pp. 923-932
    • Crist, T.O.1    Veech, J.A.2
  • 12
    • 79960550162 scopus 로고    scopus 로고
    • Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals
    • Davies, T.J & Buckley, L.B. (2011) Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 366, 2414-2425.
    • (2011) Philosophical Transactions of the Royal Society of London B: Biological Sciences , vol.366 , pp. 2414-2425
    • Davies, T.J.1    Buckley, L.B.2
  • 14
    • 0026499429 scopus 로고
    • Conservation evaluation and phylogenetic diversity
    • Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
    • (1992) Biological Conservation , vol.61 , pp. 1-10
    • Faith, D.P.1
  • 15
    • 0000283560 scopus 로고    scopus 로고
    • Conservation priorities and phylogenetic pattern
    • Faith, D.P. (1996) Conservation priorities and phylogenetic pattern. Conservation Biology, 10, 1286-1289.
    • (1996) Conservation Biology , vol.10 , pp. 1286-1289
    • Faith, D.P.1
  • 16
    • 72849129069 scopus 로고    scopus 로고
    • The role of the phylogenetic diversity measure, PD, in bio-informatics: Getting the definition right
    • Faith, D.P. (2006) The role of the phylogenetic diversity measure, PD, in bio-informatics: Getting the definition right. Evolutionary Bioinformatics Online, 2, 277-283.
    • (2006) Evolutionary Bioinformatics Online , vol.2 , pp. 277-283
    • Faith, D.P.1
  • 17
    • 1242310425 scopus 로고    scopus 로고
    • Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment
    • Faith, D.P., Reid, C.A.M. & Hunter, J. (2004) Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment. Conservation Biology, 18, 255-261.
    • (2004) Conservation Biology , vol.18 , pp. 255-261
    • Faith, D.P.1    Reid, C.A.M.2    Hunter, J.3
  • 18
    • 71649105829 scopus 로고    scopus 로고
    • The cladistic basis for the Phylogenetic Diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework
    • Faith, D.P., Lozupone, C.A., Nipperess, D.A. & Knight, R. (2009) The cladistic basis for the Phylogenetic Diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework. International Journal of Molecular Sciences, 10, 4723-4741.
    • (2009) International Journal of Molecular Sciences , vol.10 , pp. 4723-4741
    • Faith, D.P.1    Lozupone, C.A.2    Nipperess, D.A.3    Knight, R.4
  • 19
    • 39749116275 scopus 로고    scopus 로고
    • Distribution of phylogenetic diversity under random extinction
    • Faller, B., Pardi, F. & Steel, M. (2008) Distribution of phylogenetic diversity under random extinction. Journal of Theoretical Biology, 251, 286-296.
    • (2008) Journal of Theoretical Biology , vol.251 , pp. 286-296
    • Faller, B.1    Pardi, F.2    Steel, M.3
  • 20
    • 34247340904 scopus 로고    scopus 로고
    • Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment
    • Ferrier, S., Manion, G., Elith, J. & Richardson, K. (2007) Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Diversity and Distributions, 13, 252-264.
    • (2007) Diversity and Distributions , vol.13 , pp. 252-264
    • Ferrier, S.1    Manion, G.2    Elith, J.3    Richardson, K.4
  • 22
    • 27644443333 scopus 로고    scopus 로고
    • Molecular identification of bacteria associated with bacterial vaginosis
    • Fredricks, D.N., Fiedler, T.L. & Marrazzo, J.M. (2005) Molecular identification of bacteria associated with bacterial vaginosis. New England Journal of Medicine, 353, 1899-1911.
    • (2005) New England Journal of Medicine , vol.353 , pp. 1899-1911
    • Fredricks, D.N.1    Fiedler, T.L.2    Marrazzo, J.M.3
  • 23
    • 0034870192 scopus 로고    scopus 로고
    • Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness
    • Gotelli, N.J. & Colwell, R.K. (2001) Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters, 4, 379-391.
    • (2001) Ecology Letters , vol.4 , pp. 379-391
    • Gotelli, N.J.1    Colwell, R.K.2
  • 24
    • 0000917309 scopus 로고
    • Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size
    • Heck Jr, K.L., van Belle, G. & Simberloff, D. (1975) Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology, 56, 1459-1461.
    • (1975) Ecology , vol.56 , pp. 1459-1461
    • Heck Jr., K.L.1    van Belle, G.2    Simberloff, D.3
  • 25
    • 0000006498 scopus 로고
    • Diversity and evenness: a unifying notation and its consequences
    • Hill, M.O. (1973) Diversity and evenness: a unifying notation and its consequences. Ecology, 54, 427-432.
    • (1973) Ecology , vol.54 , pp. 427-432
    • Hill, M.O.1
  • 26
    • 0000752502 scopus 로고
    • The nonconcept of species diversity: a critique and alternative parameters
    • Hurlbert, S. (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology, 52, 577-586.
    • (1971) Ecology , vol.52 , pp. 577-586
    • Hurlbert, S.1
  • 28
    • 44849128805 scopus 로고    scopus 로고
    • Species divergence and the measurement of microbial diversity
    • Lozupone, C.A. & Knight, R. (2008) Species divergence and the measurement of microbial diversity. FEMS Microbiology Reviews, 32, 557-578.
    • (2008) FEMS Microbiology Reviews , vol.32 , pp. 557-578
    • Lozupone, C.A.1    Knight, R.2
  • 29
    • 77958610660 scopus 로고    scopus 로고
    • pplacer: linear time maximum-likelihood and bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen, F.A., Kodner, R.B. & Armbrust, E.V. (2010) pplacer: linear time maximum-likelihood and bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.
    • (2010) BMC Bioinformatics , vol.11 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.V.3
  • 30
    • 80053623201 scopus 로고    scopus 로고
    • Beyond taxonomic diversity patterns: how do α, β and γ components of bird functional and phylogenetic diversity respond to environmental gradients across France?
    • Meynard, C.N., Devictor, V., Mouillot, D., Thuiller, W., Jiguet, F. & Mouquet, N. (2011) Beyond taxonomic diversity patterns: how do α, β and γ components of bird functional and phylogenetic diversity respond to environmental gradients across France? Global Ecology and Biogeography, 20, 893-903.
    • (2011) Global Ecology and Biogeography , vol.20 , pp. 893-903
    • Meynard, C.N.1    Devictor, V.2    Mouillot, D.3    Thuiller, W.4    Jiguet, F.5    Mouquet, N.6
  • 32
    • 77956309163 scopus 로고    scopus 로고
    • Resemblance in phylogenetic diversity among ecological assemblages
    • Nipperess, D.A., Faith, D.P. & Barton, K. (2010) Resemblance in phylogenetic diversity among ecological assemblages. Journal of Vegetation Science, 21, 809-820.
    • (2010) Journal of Vegetation Science , vol.21 , pp. 809-820
    • Nipperess, D.A.1    Faith, D.P.2    Barton, K.3
  • 33
    • 0026088584 scopus 로고
    • Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation
    • Nugent, R.P., Krohn, M.A. & Hillier, S.L. (1991) Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. Journal of Clinical Microbiology, 29, 297-301.
    • (1991) Journal of Clinical Microbiology , vol.29 , pp. 297-301
    • Nugent, R.P.1    Krohn, M.A.2    Hillier, S.L.3
  • 34
    • 84872038980 scopus 로고    scopus 로고
    • Phylogenetic diversity theory sheds light on the structure of microbial communities
    • O'Dwyer, J.P., Kembel, S. W. & Green, J.L. (2012) Phylogenetic diversity theory sheds light on the structure of microbial communities. PLOS Computational Biology 8, e1002832.
    • (2012) PLOS Computational Biology , vol.8
    • O'Dwyer, J.P.1    Kembel, S.W.2    Green, J.L.3
  • 36
    • 0942299969 scopus 로고    scopus 로고
    • A unified mathematical framework for the measurement of richness and evenness within and among multiple communities
    • Olszewski, T.D. (2004) A unified mathematical framework for the measurement of richness and evenness within and among multiple communities. Oikos, 104, 377-387.
    • (2004) Oikos , vol.104 , pp. 377-387
    • Olszewski, T.D.1
  • 37
    • 34548546830 scopus 로고    scopus 로고
    • Resource-aware taxon selection for maximizing phylogenetic diversity
    • Pardi, F. & Goldman, N. (2007) Resource-aware taxon selection for maximizing phylogenetic diversity. Systematic Biology, 56, 431-444.
    • (2007) Systematic Biology , vol.56 , pp. 431-444
    • Pardi, F.1    Goldman, N.2
  • 39
    • 84870338520 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team R: A Language and Environment for Statistical Computing. . URL
    • R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.Rproject.org/.
    • (2010)
  • 40
    • 0003143622 scopus 로고
    • Diversity and dissimilarity coefficients: a unified approach
    • Rao, C.R. (1982) Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology, 21, 24-43.
    • (1982) Theoretical Population Biology , vol.21 , pp. 24-43
    • Rao, C.R.1
  • 41
    • 70349329723 scopus 로고    scopus 로고
    • Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history
    • Rosauer, D., Laffan, S.W., Crisp, M.D., Donnellan, S.C. & Cook, L.G. (2009) Phylogenetic endemism: a new approach for identifying geographical concentrations of evolutionary history. Molecular Ecology, 18, 4061-4072.
    • (2009) Molecular Ecology , vol.18 , pp. 4061-4072
    • Rosauer, D.1    Laffan, S.W.2    Crisp, M.D.3    Donnellan, S.C.4    Cook, L.G.5
  • 42
  • 44
    • 0042196194 scopus 로고    scopus 로고
    • The species-accumulation curve and estimation of species richness
    • Ugland, K.I., Gray, J.S. & Ellingsen, K.E. (2003) The species-accumulation curve and estimation of species richness. Journal of Animal Ecology, 72, 888-897.
    • (2003) Journal of Animal Ecology , vol.72 , pp. 888-897
    • Ugland, K.I.1    Gray, J.S.2    Ellingsen, K.E.3
  • 45
    • 0029477712 scopus 로고
    • New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress
    • Warwick, R.M. & Clarke, K.R., et al. (1995) New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress. Marine Ecology Progress Series, 129, 301-305.
    • (1995) Marine Ecology Progress Series , vol.129 , pp. 301-305
    • Warwick, R.M.1    Clarke, K.R.2
  • 46
    • 84866642478 scopus 로고    scopus 로고
    • Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
    • Yu, D.W., Ji, Y., Emerson, B.C. & Wang, X. (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613-623.
    • (2012) Methods in Ecology and Evolution , vol.3 , pp. 613-623
    • Yu, D.W.1    Ji, Y.2    Emerson, B.C.3    Wang, X.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.