Computer-Intensive randomization in systematics

Cladistics

Volumn 17, Issue 1 II, 2001, Pages

  Siddall, Mark E ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0035003434     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1006/clad.2000.0157     Document Type: Conference Paper

References (87)

1. M.W. Allard J.M. Carpenter On weighting and congruence Cladistics 12 1996 183 198
2. M.W. Allard J.S. Farris J.M. Carpenter Congruence among mammalian mitochondrial genes Cladistics 15 1999 75 85
3. J.W. Archie A randomization test for phylogenetic information in systematic data Syst. Zool. 38 1989 239 252
4. J.W.O. Ballard Combining data in phylogenetic analysis Trends Ecol. Evol. 11 1996 334 334
5. D.R. Brooks Parsimony analysis in historical biogeography and coevolution: Methodological and theoretical update Syst. Zool. 39 1990 14 30
6. J.J. Bull J.P. Huelsenbeck C.W. Cunningham D.L. Swofford P.J. Waddell Partitioning and combining data in phylogenetic analysis Syst. Biol. 42 1993 384 397
7. D.G. Buth The application of electrophoretic data in systematic studies Annu. Rev. Ecol. Syst. 15 1984 501 522
8. J.M. Carpenter P.A. Goloboff J.S. Farris PTP is meaningless, T-PTP is contradictory: A reply to Trueman Cladistics 14 1998 105 116
9. J.M. Carpenter J.E. Strassmann S. Turillazzi C.R. Hughes C.R. Solis R. Cervo Phylogenetic relationships among paper wasp social parasites and their hosts (Hymenoptera: Vespidae; Polistinae) Cladistics 9 1993 129 146
10. P.T. Chippindale J.J. Wiens Weighting, partitioning, and combining characters in phylogenetic analysis Syst. Biol. 43 1994 278 287
11. W.C. Clyde D.C. Fisher Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis Paloebiology 23 1997 1 19
12. J. Cracraft Deep-history biogeography: Retrieving the historical pattern of evolving continental biotas Syst. Zool. 37 1988 221 236
13. B.I. Crother Is some better than none or do allele frequencies contain phylogenetically useful information? Cladistics 6 1990 277 282
14. A. De Queiroz M.J. Donoghue J. Kim Separate versus combined analysis of phylogenetic evidence Annu. Rev. Ecol. Syst. 26 1995 657 681
15. A.W.F. Edwards Likelihood 1972 Cambridge Univ. Press Cambridge
16. A.W.F. Edwards Assessing molecular phylogenies Science 267 1995 253
17. D.J. Eernisse A.G. Kluge Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology Mol. Biol. Evol. 10 1993 1170 1195
18. D.P. Faith J.W.O. Ballard Length differences topology-dependent tests—A response Cladistics 10 1994 57 64
19. D.P. Faith P.S. Cranston Could a cladogram this short have arisen by change alone?: On permutation tests for cladistic structure Cladistics 7 1991 1 28
20. J.S. Farris Distance data in phylogenetic analysis V.A. Funk D.R. Brooks Advances in Cladistics I 1981 N.Y. Bot. Garden New York 3 23
21. J.S. Farris The logical basis of phylogenetic analysis N.I. Platnick V.A. Funk Advances in Cladistics 2 1983 Columbia Univ. Press New York 7 36
22. J.S. Farris On the boundaries of phylogenetic systematics Cladistics 2 1986 14 27
23. J.S. Farris Conjectures and refutations Cladistics 11 1995 105 118
24. J.S. Farris M. Källersjö A.G. Kluge C. Bult Permutations Cladistics 10 1994 65 76
25. J.S. Farris M. Källersjö A.G. Kluge C. Bult Testing significance of incongruence Cladistics 10 1994 315 319
26. J.S. Farris M. Källersjö A.G. Kluge C. Bult Constructing a significance test for incongruence Syst. Biol. 44 1995 570 572
27. J.S. Farris V.A. Albert M. Källersjö D. Lipscomb A.G. Kluge Parsimony jackknifing outperforms neighbor-joining Cladistics 12 1996 99 124
28. J. Felsenstein Confidence limits on phylogeneties: An approach using the bootstrap Evolution 39 1985 783 791
29. J. Gauthier A.G. Kluge T. Rowe Amniote phylogeny and the importance of fossils Cladistics 4 1988 105 209
30. M.S. Hafner S.A. Nadler Phylogenetic trees support the coevolution of parasites and their hosts Nature 332 1988 258 259
31. J.P. Huelsenbeck Comparing the stratigraphic record to estimates of phylogeny Paleobiology 20 1994 470 483
32. J.P. Huelsenbeck Performance of phylogenetic methods in simulation Syst. Biol. 44 1995 17 48
33. J.P. Huelsenbeck D.M. Hillis Success of phylogenetic methods in the four-taxon case Syst. Biol. 42 1993 247 264
34. J.P. Huelsenbeck J.J. Bull C.W. Cunningham Combining data in phylogenetic analysis Trends Ecol. Evol. 11 1996 152 158
35. J.P. Huelsenbeck J.J. Bull C.W. Cunningham Combining data in phylogenetic analysis—Reply Trends Ecol. Evol. 11 1996 335 335
36. J.P. Huelsenbeck D.M. Hillis R. Jones Parametric bootstrapping in molecular phylogenetics: Applications and performance J.D. Ferraris S.R. Palumbi Molecular Zoology: Advances, Strategies, and Protocols 1996 Wiley-Liss New York 19 46
37. J.P. Huelsenbeck D.L. Swofford C.W. Cunningham J.J. Bull P.J. Waddell Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis Syst. Biol. 43 1994 288 329
38. M. Källersjö J.S. Farris A.G. Kluge C. Bult Skewness and permutation Cladistics 8 1992 275 287
39. G.J. Klassen R.D. Mooi A. Locke Consistency indexes and random data Syst. Zool. 40 1991 446 457
40. A.G. Kluge A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes) Syst. Zool. 38 1989 7 25
41. A.G. Kluge J.S. Farris Quantitative phyletics and the evolution of anurans Syst. Zool. 18 1969 1 32
42. A.G. Kluge A.J. Wolf Cladistics: What's in a word? Cladistics 9 1993 183 199
43. P.M. Mabee J. Humphries Coding polymorphic data: Examples from allozymes and ontogeny Syst. Biol. 42 1993 166 181
44. P. Mardulyn J.M. Pasteels Coding allozyme data using step matrices: Defining new original states for the ancestral taxa Syst. Biol. 43 1994 567 572
45. R.L. Mayden Vicariance biogeography, parsimony, and evolution in North American freshwater fishes Syst. Zool. 37 1988 329 355
46. R. Meier P. Kores S. Darwin Homoplasy slope ratio—A better measurement of observed homoplasy in cladistic analyses Syst. Zool. 40 1991 74 88
47. M.F. Mickevich J.S. Farris The implications of congruence in Menidia Syst. Zool. 30 1981 351 369
48. M.F. Mickevich M.S. Johnson Congruence between morphological and allozyme data in evolutionary inference and character evolution Syst. Zool. 25 1976 260 270
49. M.F. Mickevich C.M. Mitter Treating polymorphic characters in systematics: A phylogenetic treatment of electrophoretic data V.A. Funk D.R. Brooks Advances in Cladistics I 1981 N.Y. Bot. Garden New York 45 58
50. M.F. Mickevich C.M. Mitter Evolutionary patterns in allozyme data: A systematic approach N.I. Platnick V.A. Funk Advances in Cladistics II 1983 Columbia Univ. Press New York 169 176
51. D.P. Mindell J.W. Shultz P.W. Ewald The AIDS pandemic is new, but is HIV new? Syst. Biol. 44 1995 77 92
52. M.M. Miyamoto Consensus cladograms and general classifications Cladistics 1 1985 186 189
53. M.M. Miyamoto W.M. Fitch Testing species phylogenies and phylogenetic methods with congruence Syst. Biol. 44 1995 64 76
54. R.W. Murphy The phylogenetic analysis of allozyme data: Invalidity of coding alleles by presence/absence and recommended procedures Biochem. Syst. Ecol. 21 1993 25 38
55. K.C. Nixon J.M. Carpenter On simultaneous analysis Cladistics 12 1996 221 241
56. K.C. Nixon J.I. Davis Polymorphic taxa, missing values and cladistic analysis Cladistics 7 1991 233 241
57. E.W. Noreen Computer-Intensive Methods for Testing Hypotheses: An Introduction 1989 Wiley New York
58. M. Norell M. Novacek The fossil record and evolution: Comparing cladistic and paleontologic evidence for vertebrate history Science 255 1992 1690 1693
59. R.D.M. Page Genes, organisms, and areas—the problem of multiple lineages Syst. Biol. 42 1993 77 84
60. R.D.M. Page Parallel phylogenies—Reconstructing the history of host-parasite assemblages Cladistics 10 1994 155 173
61. R.D.M. Page Maps between trees and cladistic-analysis of historical associations among genes, organisms, and areas Syst. Biol. 43 1994 58 77
62. Page, R. D. M. (, 1996, ), TreeMap. Software available from the author.
63. D. Pol M.E. Siddall Biases in maximum likelihood and parsimony: A simulation approach to a ten-taxon case Cladistics 2001
64. J.S. Rogers Deriving phylogenetic trees from allele frequencies Syst. Zool. 33 1984 52 63
65. J.S. Rogers Deriving phylogenetic trees from allele frequencies: A comparison of nine genetic distances Syst. Zool 35 1986 297 310
66. D. Sankoff P. Rousseau Locating the vertices of a Steiner tree in an arbitrary metric space Math. Prog. 9 1975 240 246
67. D. Sankoff R.J. Cedergren G. Lapalme Frequency of insertion—deletion, transversion, and transition in the evolution of 5S ribosomal RNA J. Mol. Evol. 7 1976 133 149
68. I. Scheffler Explanation, prediction and abstraction A. Danto S. Morgentaler Philosophy of Science 1957 The World Publishing Co New York 274 287
69. M.E. Siddall Phylogenetic covariance probability: Confidence and historical associations Syst. Biol. 45 1995 48 66
70. M.E. Siddall Stratigraphic consistency and the shape of things Syst. Biol. 45 1995 111 115
71. M.E. Siddall Random Cladistics 1996 University of TorontoDepartment of Biology Toronto
72. M.E. Siddall Stratigraphic indices in the balance: A reply to Hitchin and Benton Syst. Biol. 46 1997 569 573
73. M.E. Siddall Prior agreement: Arbitration or arbitrary Syst. Biol. 46 1997 766 770
74. M.E. Siddall Stratigraphic fit to phylogenies: A proposed solution Cladistics 14 1998 201 208
75. M.E. Siddall Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone Cladistics 14 1998 209 220
76. M.E. Siddall E.M. Burreson Phylogeny of leeches (Hirudinea) based on mitochondrial cytochrome c oxidase subunit I Mol. Phylogenet. Evol. 9 1998 156 162
77. M.E. Siddall A.G. Kluge Probabilism and phylogenetic inference Cladistics 13 1997 313 336
78. π software for determining the association of base compositions to tree structure 1997 University of MichiganMuseum of Zoology Ann Arbor
79. D.L. Swofford PAUP* 4.0: Phylogenetic Analysis Using Parsimony (*and Other Methods) 2000 Sinauer Sunderland
80. D.L. Swofford S.H. Berlocher Inferring evolutionary trees from gene frequency data under the principle of maximum parsimony Syst. Zool. 36 1987 293 325
81. D.L. Swofford R.B. Selander BIOSYS-1: A FORTRAN program for the comprehensive analysis of electrophoretic data in population genetics and systematics J. Hered. 72 1981 281 283
82. D.L. Swofford J.L. Thorne J. Felsenstein B.M. Wiegmann The topology-dependent permutation test for monophyly does not test for monophyly Syst. Biol. 45 1996 575 579
83. T.B. Thorston D.R. Brooks M.A. Mayes The evolution of freshwater adaptation in stingrays Nat. Geog. Soc. Res. Rep. 15 1983 663 694
84. J.J. Wenzel M.E. Siddall Noise Cladistics 15 1999 51 64
85. W.C. Wheeler P. Cartwright C.Y. Hayashi Arthropod phylogeny: A combined approach Cladistics 9 1993 1 39
86. J.J. Wiens Polymorphic characters in phylogenetic systematics Syst. Biol. 44 1995 482 500
87. M.L. Zelditch W.L. Fink D.L. Swiderski B.L. Lundrigan On applications of geometric morphometrics to studies of ontogeny and phylogeny: A reply to Rohlf Syst. Biol. 47 1998 159 167