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Volumn 59, Issue 4, 2010, Pages 465-476

Sampling trees from evolutionary models

Author keywords

Algorithms; Distribution; Evolutionary models; Phylogenetic trees; Sampling; Simulating

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EPIDEMIOLOGY; EVOLUTION; SPECIES DIFFERENTIATION; SELECTION BIAS;

EID: 77953743320     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syq026     Document Type: Article
Times cited : (65)

References (46)
  • 2
    • 31944437577 scopus 로고    scopus 로고
    • A critical branching process model for biodiversity
    • Aldous D., Popovic L. 2005. A critical branching process model for biodiversity. Adv. Appl. Probab. 37:1094-1115.
    • (2005) Adv. Appl. Probab , vol.37 , pp. 1094-1115
    • Aldous, D.1    Popovic, L.2
  • 3
    • 0030595819 scopus 로고    scopus 로고
    • Constant extinction, constrained diversifcation, and uncoordinated stasis in North American mammals
    • Alroy J. 1996. Constant extinction, constrained diversifcation, and uncoordinated stasis in North American mammals. Palaeogeogr. Palaeoclimatol. Palaeoecol. 127:285-311.
    • (1996) Palaeogeogr. Palaeoclimatol. Palaeoecol , vol.127 , pp. 285-311
    • Alroy, J.1
  • 4
    • 50049122138 scopus 로고    scopus 로고
    • Dynamics of origination and extinction in the marine fossil record
    • Alroy J. 2008. Dynamics of origination and extinction in the marine fossil record. Proc. Natl. Acad. Sci. USA. 105:11536.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 11536
    • Alroy, J.1
  • 6
    • 33750245951 scopus 로고    scopus 로고
    • Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance
    • Blum M., Francois O. 2006. Which random processes describe the tree of life? A large-scale study of phylogenetic tree imbalance. Syst. Biol. 55:685.
    • (2006) Syst. Biol , vol.55 , pp. 685
    • Blum, M.1    Francois, O.2
  • 7
    • 0032950511 scopus 로고    scopus 로고
    • Accounting for mode of speciation increases power and realism of tests of phylogenetic asymmetry
    • Chan K.M.A., Moore B.R. 1999. Accounting for mode of speciation increases power and realism of tests of phylogenetic asymmetry. Am. Nat. 153:332-346.
    • (1999) Am. Nat , vol.153 , pp. 332-346
    • Chan, K.M.A.1    Moore, B.R.2
  • 8
    • 0036959868 scopus 로고    scopus 로고
    • Whole-tree methods for detecting differential diversifcation rates
    • Chan K.M.A., Moore B.R. 2002. Whole-tree methods for detecting differential diversifcation rates. Syst. Biol. 51:855-865.
    • (2002) Syst. Biol , vol.51 , pp. 855-865
    • Chan, K.M.A.1    Moore, B.R.2
  • 9
    • 48049107322 scopus 로고    scopus 로고
    • The conditioned reconstructed process
    • Gernhard T. 2008. The conditioned reconstructed process. J. Theor. Biol. 253:769-778.
    • (2008) J. Theor. Biol , vol.253 , pp. 769-778
    • Gernhard, T.1
  • 10
    • 23744452485 scopus 로고    scopus 로고
    • Estimating the tempo and modeof gene family evolution from comparative genomic data
    • Hahn M., De Bie T., Stajich J., Nguyen C., Cristianini N. 2005. Estimating the tempo and modeof gene family evolution from comparative genomic data. Genome Res. 15:1153.
    • (2005) Genome Res , vol.15 , pp. 1153
    • Hahn, M.1    De Bie, T.2    Stajich, J.3    Nguyen, C.4    Cristianini, N.5
  • 11
    • 0001996348 scopus 로고
    • The probabilities of rooted tree-shapes generated by random bifurcation
    • Harding E.F. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Probab. 3:44-77.
    • (1971) Adv. Appl. Probab , vol.3 , pp. 44-77
    • Harding, E.F.1
  • 12
    • 77953794183 scopus 로고    scopus 로고
    • Hobart, Australia: Tasmanian Aqua-culture and Fisheries Institute, University of Tasmania
    • Hartmann K. 2010. Tree sample. Hobart, Australia: Tasmanian Aqua-culture and Fisheries Institute, University of Tasmania. Available from: http://treesample.googlecode.com.
    • (2010) Tree Sample
    • Hartmann, K.1
  • 13
    • 0028561478 scopus 로고
    • Phylogenies without fossils
    • Harvey P.H., May R.M., Nee S. 1994. Phylogenies without fossils. Evolution. 48:523-529.
    • (1994) Evolution , vol.48 , pp. 523-529
    • Harvey, P.H.1    May, R.M.2    Nee, S.3
  • 14
    • 0030484686 scopus 로고    scopus 로고
    • Patterns in phylogenetic tree balance with variable and evolving speciation rates
    • Heard S.B. 1996. Patterns in phylogenetic tree balance with variable and evolving speciation rates. Evolution. 50:2141-2148.
    • (1996) Evolution , vol.50 , pp. 2141-2148
    • Heard, S.B.1
  • 15
    • 0026540732 scopus 로고
    • Using phylogenetic trees to study speciation and extinction
    • Hey J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution. 46:627-640.
    • (1992) Evolution , vol.46 , pp. 627-640
    • Hey, J.1
  • 16
    • 34447260522 scopus 로고    scopus 로고
    • Is multiple-sequence alignment required for accurate inference of phylogeny?
    • Hohl M., Ragan M.A. 2007. Is multiple-sequence alignment required for accurate inference of phylogeny? Syst. Biol. 56:206-221.
    • (2007) Syst. Biol , vol.56 , pp. 206-221
    • Hohl, M.1    Ragan, M.A.2
  • 17
    • 0142148213 scopus 로고    scopus 로고
    • Simple stochastic birth and death models of genome evolution: Was there enough time for us to evolve?
    • Karev G.P., Wolf Y.I., Koonin E.V. 2003. Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve? Bioinformatics. 19:1889-1900.
    • (2003) Bioinformatics , vol.19 , pp. 1889-1900
    • Karev, G.P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 18
    • 0002743467 scopus 로고
    • Exchangeability and the evolution of large populations
    • Koch G., Spizzichino F., editors Amsterdam-New York: North-Holland
    • Kingman J.F.C. 1982a. Exchangeability and the evolution of large populations. In: Koch G., Spizzichino F., editors. Exchangeability in probability and statistics. Amsterdam-New York: North-Holland. p. 97-112.
    • (1982) Exchangeability in Probability and Statistics , pp. 97-112
    • Kingman, J.F.C.1
  • 19
    • 0002556819 scopus 로고
    • On the genealogy of large populations
    • Kingman J.F.C. 1982b. On the genealogy of large populations. J. Appl. Probab. 19A:27-43.
    • (1982) J. Appl. Probab. , vol.19 A , pp. 27-43
    • Kingman, J.F.C.1
  • 21
    • 0034765180 scopus 로고    scopus 로고
    • Absolute diversifcation rates in an-giosperm clades
    • Magallón S., Sanderson M. 2001. Absolute diversifcation rates in an-giosperm clades. Evolution. 55:1762-1780
    • (2001) Evolution , vol.55 , pp. 1762-1780
    • Magallón, S.1    Sanderson, M.2
  • 23
    • 0002638760 scopus 로고    scopus 로고
    • Inferring evolutionary process from phylogenetic tree shape
    • Mooers A.Ø., Heard S.B. 1997. Inferring evolutionary process from phylogenetic tree shape. Q. Rev. Biol. 72:31-54.
    • (1997) Q. Rev. Biol , vol.72 , pp. 31-54
    • Mooers A.Ø1    Heard, S.B.2
  • 24
    • 0001733997 scopus 로고
    • A general theory of the distribution of gene frequencies. I. Overlapping generations
    • Moran P. 1958. A general theory of the distribution of gene frequencies. I. Overlapping generations. Proc. R. Soc. Lond. B. 149:102-112.
    • (1958) Proc. R. Soc. Lond. B. , vol.149 , pp. 102-112
    • Moran, P.1
  • 26
    • 33746878289 scopus 로고    scopus 로고
    • Repression and loss of gene expression outpaces activation and gain in recently duplicated fy genes
    • Oakley T., Ostman B., Wilson A. 2006. Repression and loss of gene expression outpaces activation and gain in recently duplicated fy genes. Proc. Natl. Acad. Sci. USA. 103:11637.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 11637
    • Oakley, T.1    Ostman, B.2    Wilson, A.3
  • 27
    • 0028994998 scopus 로고
    • A hierarchical branching model of evolutionary radiations
    • Patzkowsky M. 1995. A hierarchical branching model of evolutionary radiations. Paleobiology. 21:440-460. (Pubitemid 3025383)
    • (1995) Paleobiology , vol.21 , Issue.4 , pp. 440-460
    • Patzkowsky, M.E.1
  • 28
    • 26844542229 scopus 로고    scopus 로고
    • Asymptotic genealogy of a critical branching process
    • Popovic L. 2004. Asymptotic genealogy of a critical branching process. Ann. Appl. Probab. 14:2120-2148.
    • (2004) Ann. Appl. Probab , vol.14 , pp. 2120-2148
    • Popovic, L.1
  • 29
    • 0032434606 scopus 로고    scopus 로고
    • An evaluation of a hierarchical branching process as a model for species diversifcation
    • Przeworski M., Wall J. 1998. An evaluation of a hierarchical branching process as a model for species diversifcation. Paleobiology. 24: 498-511.
    • (1998) Paleobiology , vol.24 , pp. 498-511
    • Przeworski, M.1    Wall, J.2
  • 30
    • 16544372620 scopus 로고    scopus 로고
    • Evolution: How do characters evolve?
    • Purvis A. 2004. Evolution: how do characters evolve? Nature. 432:7014.
    • (2004) Nature , vol.432 , pp. 7014
    • Purvis, A.1
  • 31
    • 0034703844 scopus 로고    scopus 로고
    • Testing macro-evolutionary models using incomplete molecular phylogenies
    • Pybus O., Harvey P. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. Lond. B. 267: 2267-2272.
    • (2000) Proc. R. Soc. Lond. B , vol.267 , pp. 2267-2272
    • Pybus, O.1    Harvey, P.2
  • 32
    • 0242488262 scopus 로고    scopus 로고
    • Department of Zoology, University of Oxford, Oxford, UK
    • Rambaut A. 2002. PhyloGen: phylogenetic tree simulator package. Department of Zoology, University of Oxford, Oxford, UK. Available from: http://tree.bio.ed.ac.uk/software/phylogen/.
    • (2002) PhyloGen: Phylogenetic Tree Simulator Package
    • Rambaut, A.1
  • 33
    • 0026358333 scopus 로고
    • A kill curve for phanerozoic marine species
    • Raup D. 1991. A kill curve for phanerozoic marine species. Paleobiol-ogy. 17:37-48.
    • (1991) Paleobiol-ogy , vol.17 , pp. 37-48
    • Raup, D.1
  • 34
    • 0242552327 scopus 로고    scopus 로고
    • Global diversifcation rates of passerine birds
    • Ricklefs R. 2003. Global diversifcation rates of passerine birds. Proc. R. Soc. Lond. B. 270:2285-2291.
    • (2003) Proc. R. Soc. Lond. B , vol.270 , pp. 2285-2291
    • Ricklefs, R.1
  • 35
    • 3142696271 scopus 로고    scopus 로고
    • Cladogenesis and morphological diversifcation in passerine birds
    • Ricklefs R. 2004. Cladogenesis and morphological diversifcation in passerine birds. Nature. 430:338-341.
    • (2004) Nature , vol.430 , pp. 338-341
    • Ricklefs, R.1
  • 36
    • 0020343631 scopus 로고
    • Mass extinctions in the Phanerozoic oceans: A review
    • Sepkoski J.J. 1982. Mass extinctions in the Phanerozoic oceans: a review. Geol. Soc. Am. Spec. Pap. 190:281-289.
    • (1982) Geol. Soc. Am. Spec. Pap , vol.190 , pp. 281-289
    • Sepkoski, J.J.1
  • 37
    • 0242487487 scopus 로고    scopus 로고
    • Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (bryophyta)
    • Shaw A., Cox C., Goffnet B., Buck W., Boles S. 2003. Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (bryophyta). Evolution. 57:2226-2241.
    • (2003) Evolution , vol.57 , pp. 2226-2241
    • Shaw, A.1    Cox, C.2    Goffnet, B.3    Buck, W.4    Boles, S.5
  • 38
    • 56049085351 scopus 로고    scopus 로고
    • Lineages-through-time plots of neutral models for spe-ciation
    • Stadler T. 2008. Lineages-through-time plots of neutral models for spe-ciation. Math. Biosci. 216:163-171.
    • (2008) Math. Biosci , vol.216 , pp. 163-171
    • Stadler, T.1
  • 39
    • 77953760263 scopus 로고    scopus 로고
    • Institute of Integrative Biology, Eid-genössische Technische Hochschule Zürich, Zürich, Switzerland. Available from:
    • Stadler T. 2010. Treesim. Institute of Integrative Biology, Eid-genössische Technische Hochschule Zürich, Zürich, Switzerland. Available from: http://www.tb.ethz.ch/people/tstadler.
    • (2010) Treesim
    • Stadler, T.1
  • 40
    • 0000669426 scopus 로고
    • Natural clades differ from "random" clades: Simulations and analyses
    • Stanley S.M., Signor P.W. III, Lidgard S., Karr A. F. 1981. Natural clades differ from "random" clades: simulations and analyses. Paleobiol-ogy. 7:115-127.
    • (1981) Paleobiology , vol.7 , pp. 115-127
    • Stanley, S.M.1    Signor III, P.W.2    Lidgard, S.3    Karr, A.F.4
  • 41
    • 33746419713 scopus 로고    scopus 로고
    • Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data
    • Tanaka M., Francis A., Luciani F., Sisson S. 2006. Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data. Genetics. 173:1511.
    • (2006) Genetics , vol.173 , pp. 1511
    • Tanaka, M.1    Francis, A.2    Luciani, F.3    Sisson, S.4
  • 42
    • 33749602096 scopus 로고    scopus 로고
    • Detecting the node-density artifact in phylogeny reconstruction
    • Venditti C., Meade A., Pagel M. 2006. Detecting the node-density artifact in phylogeny reconstruction. Syst. Biol. 55:637-643.
    • (2006) Syst. Biol , vol.55 , pp. 637-643
    • Venditti, C.1    Meade, A.2    Pagel, M.3
  • 43
    • 33745230793 scopus 로고    scopus 로고
    • Divergent timing and patterns of species accumulation in lowland and highland neotropical birds
    • Weir J.T. 2006. Divergent timing and patterns of species accumulation in lowland and highland neotropical birds. Evolution. 60:842-855.
    • (2006) Evolution , vol.60 , pp. 842-855
    • Weir, J.T.1
  • 44
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
    • Yang Z., Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 17:717-724.
    • (1997) Mol. Biol. Evol , vol.17 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 45
    • 0001778604 scopus 로고
    • A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S. Philos
    • Yule G.U. 1924. A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F.R.S. Philos. Trans. R. Soc. Lond. B. 213:21-87.
    • (1924) Trans. R. Soc. Lond. B. , Issue.213 , pp. 21-87
    • Yule, G.U.1
  • 46
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • Zwickl D.J., Hillis D.M. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
    • (2002) Syst. Biol , vol.51 , pp. 588-598
    • Zwickl, D.J.1    Hillis, D.M.2


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