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Volumn 58, Issue 2, 2015, Pages 379-389

Strap: An R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

Author keywords

Computer program; Phylogeny; R; Stratigraphy

Indexed keywords

BIOSTRATIGRAPHY; FOSSIL; PALEONTOLOGY; PHYLOGENY; SOFTWARE; TOPOLOGY;

EID: 84924065334     PISSN: 00310239     EISSN: 14754983     Source Type: Journal    
DOI: 10.1111/pala.12142     Document Type: Article
Times cited : (240)

References (50)
  • 1
    • 0035722732 scopus 로고    scopus 로고
    • Preliminary phylogenetic analysis and stratigraphic congruence of the dicynodont anomodonts (Synapsida: Therapsida)
    • Angielczyk, K. D. 2001. Preliminary phylogenetic analysis and stratigraphic congruence of the dicynodont anomodonts (Synapsida: Therapsida). Palaeontologia Africana, 37, 53-79.
    • (2001) Palaeontologia Africana , vol.37 , pp. 53-79
    • Angielczyk, K.D.1
  • 2
    • 84875234698 scopus 로고    scopus 로고
    • paleotree: an R package for paleontological and phylogenetic analyses of evolution
    • Bapst, D. W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology & Evolution, 3, 803-807.
    • (2012) Methods in Ecology & Evolution , vol.3 , pp. 803-807
    • Bapst, D.W.1
  • 3
    • 84903524827 scopus 로고    scopus 로고
    • Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record
    • Bapst, D. W. 2014. Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Paleobiology, 40, 331-351.
    • (2014) Paleobiology , vol.40 , pp. 331-351
    • Bapst, D.W.1
  • 5
    • 84861958388 scopus 로고    scopus 로고
    • Cope's rule in the Ordovician trilobite Family Asaphidae (Order Asaphida): patterns across multiple most parsimonious trees
    • Bell, M. A. and Braddy, S. J. 2012. Cope's rule in the Ordovician trilobite Family Asaphidae (Order Asaphida): patterns across multiple most parsimonious trees. Historical Biology, 24, 223-230.
    • (2012) Historical Biology , vol.24 , pp. 223-230
    • Bell, M.A.1    Braddy, S.J.2
  • 6
    • 84924027055 scopus 로고    scopus 로고
    • Data from: strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence
    • Bell, M. A. and Lloyd, G. T. 2014. Data from: strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Dryad Digital Repository, doi:10.5061/dryad.4k078.
    • (2014) Dryad Digital Repository
    • Bell, M.A.1    Lloyd, G.T.2
  • 7
    • 84874984004 scopus 로고
    • Testing the quality of the fossil record: paleontological knowledge is improving
    • Benton, M. J. and Storrs, G. W. 1994. Testing the quality of the fossil record: paleontological knowledge is improving. Geology, 22, 111-114.
    • (1994) Geology , vol.22 , pp. 111-114
    • Benton, M.J.1    Storrs, G.W.2
  • 8
    • 0033183799 scopus 로고    scopus 로고
    • Assessing congruence between cladistic and stratigraphic data
    • Benton, M. J., Hitchin, R. and Wills, M. A. 1999. Assessing congruence between cladistic and stratigraphic data. Systematic Biology, 48, 581-596.
    • (1999) Systematic Biology , vol.48 , pp. 581-596
    • Benton, M.J.1    Hitchin, R.2    Wills, M.A.3
  • 9
    • 0034598807 scopus 로고    scopus 로고
    • Quality of the fossil record through time
    • Benton, M. J., Wills, M. A. and Hitchin, R. 2000. Quality of the fossil record through time. Nature, 403, 534-537.
    • (2000) Nature , vol.403 , pp. 534-537
    • Benton, M.J.1    Wills, M.A.2    Hitchin, R.3
  • 10
    • 78650766455 scopus 로고    scopus 로고
    • Exploring the effects of phylogenetic uncertainty and consensus trees on stratigraphic consistency scores: a new program and a standardized method
    • Boyd, C. A., Cleland, T. P., Marrero, N. L. and Clarke, J. A. 2011. Exploring the effects of phylogenetic uncertainty and consensus trees on stratigraphic consistency scores: a new program and a standardized method. Cladistics, 27, 52-60.
    • (2011) Cladistics , vol.27 , pp. 52-60
    • Boyd, C.A.1    Cleland, T.P.2    Marrero, N.L.3    Clarke, J.A.4
  • 12
    • 51749121248 scopus 로고    scopus 로고
    • Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs
    • Brusatte, S. L., Benton, M. J., Ruta, M. and Lloyd, G. T. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science, 321, 1485-1488.
    • (2008) Science , vol.321 , pp. 1485-1488
    • Brusatte, S.L.1    Benton, M.J.2    Ruta, M.3    Lloyd, G.T.4
  • 13
    • 84894025076 scopus 로고    scopus 로고
    • The ICS International Chronostratigraphic Chart
    • Cohen, K. M., Finney, S. C., Gibbard, P. L. and Fan, J.-X. 2013. The ICS International Chronostratigraphic Chart. Episodes, 36, 199-204.
    • (2013) Episodes , vol.36 , pp. 199-204
    • Cohen, K.M.1    Finney, S.C.2    Gibbard, P.L.3    Fan, J.-X.4
  • 15
    • 84959792503 scopus 로고
    • The number of evolutionary trees
    • Felsenstein, J. 1978. The number of evolutionary trees. Systematic Zoology, 27, 27-33.
    • (1978) Systematic Zoology , vol.27 , pp. 27-33
    • Felsenstein, J.1
  • 16
    • 0002603603 scopus 로고
    • Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process
    • In Grande, L and Rieppel, O (eds) Academic press, San Diego, 312
    • Fischer, D. C. 1994. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. 133-171. In Grande, L. and Rieppel, O. (eds). Interpreting the hierarchy of nature. Academic press, San Diego, 312 pp.
    • (1994) Interpreting the hierarchy of nature , pp. 133-171
    • Fischer, D.C.1
  • 17
    • 0002103658 scopus 로고
    • Stratophenetic approach to phylogeny reconstruction in vertebrate paleontology
    • In Cracraft, J and Eldredge, N (eds) Columbia University Press, New York, 233
    • Gingerich, P. D. 1979. Stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. 41-77. In Cracraft, J. and Eldredge, N. (eds). Phylogenetic analysis and paleontology. Columbia University Press, New York, 233 pp.
    • (1979) Phylogenetic analysis and paleontology , pp. 41-77
    • Gingerich, P.D.1
  • 18
    • 45749124657 scopus 로고    scopus 로고
    • TNT, a free program for phylogenetic analysis
    • Goloboff, P. A., Farris, J. S. and Nixon, K. C. 2008. TNT, a free program for phylogenetic analysis. Cladistics, 24, 774-786.
    • (2008) Cladistics , vol.24 , pp. 774-786
    • Goloboff, P.A.1    Farris, J.S.2    Nixon, K.C.3
  • 20
    • 0028575143 scopus 로고
    • Comparing the stratigraphic record to estimates of phylogeny
    • Huelsenbeck, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology, 20, 470-483.
    • (1994) Paleobiology , vol.20 , pp. 470-483
    • Huelsenbeck, J.P.1
  • 21
    • 0030776127 scopus 로고    scopus 로고
    • Maximum likelihood estimation of phylogeny using stratigraphic data
    • Huelsenbeck, J. P. and Rannala, B. 1997. Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology, 23, 174-180.
    • (1997) Paleobiology , vol.23 , pp. 174-180
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 22
    • 0005638576 scopus 로고    scopus 로고
    • Using stratigraphic information in phylogenetics
    • Weins, J J (ed) Smithsonian Institution Press, Washington, DC, 272
    • Huelsenbeck, J. P. and Rannala, B. 2000. Using stratigraphic information in phylogenetics. 165-191. ln Weins, J. J. (ed.). Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, DC, 272 pp.
    • (2000) Phylogenetic analysis of morphological data , pp. 165-191
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 23
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • Kluge, A. G. and Farris, J. S. 1969. Quantitative phyletics and the evolution of anurans. Systematic Zoology, 18, 1-32.
    • (1969) Systematic Zoology , vol.18 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 24
    • 84855473785 scopus 로고    scopus 로고
    • Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves
    • Ksepka, D. T. and Boyd, C. A. 2012. Quantifying historical trends in the completeness of the fossil record and the contributing factors: an example using Aves. Paleobiology, 38, 112-125.
    • (2012) Paleobiology , vol.38 , pp. 112-125
    • Ksepka, D.T.1    Boyd, C.A.2
  • 25
    • 84898933840 scopus 로고    scopus 로고
    • Morphological clocks in palaeontology, and a mid-Cretaceous origin of crown Aves
    • Lee, M. S. Y., Cau, A., Naish, D. and Dyke, G. J. 2014a. Morphological clocks in palaeontology, and a mid-Cretaceous origin of crown Aves. Systematic Biology, 63, 442-449.
    • (2014) Systematic Biology , vol.63 , pp. 442-449
    • Lee, M.S.Y.1    Cau, A.2    Naish, D.3    Dyke, G.J.4
  • 26
    • 84905907971 scopus 로고    scopus 로고
    • Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds
    • Lee, M. S. Y., Cau, A., Naish, D. and Dyke, G. J. 2014b. Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds. Science, 345, 562-566.
    • (2014) Science , vol.345 , pp. 562-566
    • Lee, M.S.Y.1    Cau, A.2    Naish, D.3    Dyke, G.J.4
  • 28
    • 84856238797 scopus 로고    scopus 로고
    • Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi)
    • Lloyd, G. T., Wang, S. C. and Brusatte, S. L. 2012. Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi). Evolution, 66, 330-348.
    • (2012) Evolution , vol.66 , pp. 330-348
    • Lloyd, G.T.1    Wang, S.C.2    Brusatte, S.L.3
  • 29
    • 3042649996 scopus 로고    scopus 로고
    • Mesquite: a modular system for evolutionary analysis
    • Version 2.75. Available at
    • Maddison, W. P. and Maddison, D. R. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75. Available at http://mesquiteproject.org.
    • (2011)
    • Maddison, W.P.1    Maddison, D.R.2
  • 30
    • 0002618993 scopus 로고
    • Taxic origin and temporal diversity: the effect of phylogeny
    • In Novacek, M J and Wheeler, Q D (eds) Columbia University Press, New York, 253
    • Norell, M. A. 1992. Taxic origin and temporal diversity: the effect of phylogeny. 89-118. In Novacek, M. J. and Wheeler, Q. D. (eds). Extinction and phylogeny. Columbia University Press, New York, 253 pp.
    • (1992) Extinction and phylogeny , pp. 89-118
    • Norell, M.A.1
  • 31
    • 0027101576 scopus 로고
    • Congruence between superpositional and phylogenetic patterns: comparing cladistic patterns with fossil records
    • Norell, M. A. and Novacek, M. J. 1992. Congruence between superpositional and phylogenetic patterns: comparing cladistic patterns with fossil records. Cladistics, 8, 319-337.
    • (1992) Cladistics , vol.8 , pp. 319-337
    • Norell, M.A.1    Novacek, M.J.2
  • 32
    • 84055217499 scopus 로고    scopus 로고
    • Variation in stratigraphic congruence (GER) through the Phanerozoic and across higher taxa is partially determined by sources of bias
    • In McGowan, A J and Smith, A B (eds) Geological Society, London, Special Publications, 358, 310
    • O'Connor, A., Moncrieff, C. and Wills, M. A. 2011. Variation in stratigraphic congruence (GER) through the Phanerozoic and across higher taxa is partially determined by sources of bias. 31-52. In McGowan, A. J. and Smith, A. B. (eds). Comparing the geological and fossil records: implications for biodiversity studies. Geological Society, London, Special Publications, 358, 310 pp.
    • (2011) Comparing the geological and fossil records: implications for biodiversity studies , pp. 31-52
    • O'Connor, A.1    Moncrieff, C.2    Wills, M.A.3
  • 33
    • 0032445972 scopus 로고    scopus 로고
    • Speciation and extinction asymmetries in paleontological phylogenies: evidence for evolutionary progress?
    • Pearson, P. N. 1998. Speciation and extinction asymmetries in paleontological phylogenies: evidence for evolutionary progress? Paleobiology, 24, 305-335.
    • (1998) Paleobiology , vol.24 , pp. 305-335
    • Pearson, P.N.1
  • 34
    • 0035720593 scopus 로고    scopus 로고
    • Comments on the Manhattan Stratigraphic Measure
    • Pol, D. and Norell, M. A. 2001. Comments on the Manhattan Stratigraphic Measure. Cladistics, 17, 285-289.
    • (2001) Cladistics , vol.17 , pp. 285-289
    • Pol, D.1    Norell, M.A.2
  • 35
    • 33747370710 scopus 로고    scopus 로고
    • Uncertainty in the age of fossils and stratigraphic fit to phylogenies
    • Pol, D. and Norell, M. A. 2006. Uncertainty in the age of fossils and stratigraphic fit to phylogenies. Systematic Biology, 55, 512-521.
    • (2006) Systematic Biology , vol.55 , pp. 512-521
    • Pol, D.1    Norell, M.A.2
  • 36
    • 79959381301 scopus 로고    scopus 로고
    • Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia
    • Pyron, R. A. 2011. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Systematic Biology, 60, 466-481.
    • (2011) Systematic Biology , vol.60 , pp. 466-481
    • Pyron, R.A.1
  • 37
    • 70649095407 scopus 로고    scopus 로고
    • Evaluating phylogenetic hypotheses of carpoids using stratigraphic congruence indices
    • Rahman, I. A., Sutton, M. D. and Bell, M. A. 2009. Evaluating phylogenetic hypotheses of carpoids using stratigraphic congruence indices. Lethaia, 42, 424-437.
    • (2009) Lethaia , vol.42 , pp. 424-437
    • Rahman, I.A.1    Sutton, M.D.2    Bell, M.A.3
  • 39
    • 33748275455 scopus 로고    scopus 로고
    • Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change
    • Ruta, M., Wagner, P. J. and Coates, M. I. 2006. Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change. Proceedings of the Royal Society of London, Series B: Biological Sciences, 273, 2107-2111.
    • (2006) Proceedings of the Royal Society of London, Series B: Biological Sciences , vol.273 , pp. 2107-2111
    • Ruta, M.1    Wagner, P.J.2    Coates, M.I.3
  • 40
    • 0031788712 scopus 로고    scopus 로고
    • Stratigraphic fit to phylogenies: a proposed solution
    • Siddall, M. E. 1998. Stratigraphic fit to phylogenies: a proposed solution. Cladistics, 14, 201-208.
    • (1998) Cladistics , vol.14 , pp. 201-208
    • Siddall, M.E.1
  • 42
    • 84924049415 scopus 로고    scopus 로고
    • PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
    • Swofford, D. L. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
    • (2003)
    • Swofford, D.L.1
  • 43
    • 0032408552 scopus 로고    scopus 로고
    • A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa
    • Wagner, P. J. 1998. A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology, 24, 430-449.
    • (1998) Paleobiology , vol.24 , pp. 430-449
    • Wagner, P.J.1
  • 44
    • 0033789368 scopus 로고    scopus 로고
    • Likelihood tests of hypothesized durations: determining and accommodating biasing factors
    • Wagner, P. J. 2000. Likelihood tests of hypothesized durations: determining and accommodating biasing factors. Paleobiology, 26, 431-449.
    • (2000) Paleobiology , vol.26 , pp. 431-449
    • Wagner, P.J.1
  • 45
    • 0030306128 scopus 로고    scopus 로고
    • Fossils, phylogeny and discovery: a cladistic study of the history of tree topologies and ghost lineage durations
    • Weishampel, D. B. 1996. Fossils, phylogeny and discovery: a cladistic study of the history of tree topologies and ghost lineage durations. Journal of Vertebrate Paleontology, 16, 191-197.
    • (1996) Journal of Vertebrate Paleontology , vol.16 , pp. 191-197
    • Weishampel, D.B.1
  • 47
    • 0033457184 scopus 로고    scopus 로고
    • Congruence between phylogeny and stratigraphy: randomization tests and the Gap Excess Ratio
    • Wills, M. A. 1999a. Congruence between phylogeny and stratigraphy: randomization tests and the Gap Excess Ratio. Systematic Biology, 48, 559-580.
    • (1999) Systematic Biology , vol.48 , pp. 559-580
    • Wills, M.A.1
  • 48
    • 84924059120 scopus 로고    scopus 로고
    • Significant tests for RCI, SCI and GER values by randomization. Basic code for chipmunk basic 3.5.3.
    • Wills, M. A. 1999b. Significant tests for RCI, SCI and GER values by randomization. Basic code for chipmunk basic 3.5.3.
    • (1999)
    • Wills, M.A.1
  • 50
    • 58149267587 scopus 로고    scopus 로고
    • The modified Gap Excess Ratio (GER*) and the stratigraphic congruence of dinosaur phylogenies
    • Wills, M. A., Barrett, P. M. and Heathcote, J. F. 2008. The modified Gap Excess Ratio (GER*) and the stratigraphic congruence of dinosaur phylogenies. Systematic Biology, 57, 891-904.
    • (2008) Systematic Biology , vol.57 , pp. 891-904
    • Wills, M.A.1    Barrett, P.M.2    Heathcote, J.F.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.