Problems due to missing data in phylogenetic analyses including fossils: a critical review

LITERATURE CITED

• Adams , E. N. 1972 . Consensus techniques and the comparison of taxonomic trees . Systematic Zoology , 1 : 390 – 397 .
   Google Scholar
• Anderson , J. S. 2001 . The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda) . Systematic Biology , 50 : 170 – 193 .
   PubMed Web of Science ®Google Scholar
• Ax , P. 1987 . The phylogenetic system: the systematization of organisms on the basis of their phylogenesis 340 New York : Wiley .
   Google Scholar
• Benton , M. J. 1990 . The species of Rhynchosaurus, a rhynchosaur (Reptilia, Diapsida) from the middle Triassic of England . Philosophical Transactions of the Royal Society of London , 328 : 213 – 306 .
   Web of Science ®Google Scholar
• Bremer , K. 1988 . The limits of amino acid sequence data in angiosperm phylogenetic reconstruction . Evolution , 42 : 795 – 803 .
   PubMed Web of Science ®Google Scholar
• Bremer , K. 1990 . Combinable component consensus . Cladistics , 6 : 369 – 372 .
   PubMed Web of Science ®Google Scholar
• Camin , J. H. and Sokal , R. R. 1965 . A method for deducing branching sequences in phylogeny . Evolution , 19 : 311 – 327 .
   Web of Science ®Google Scholar
• Carpenter , J. M. 1987 . Phylogenetic relationships and classification of the Vespinae (Hymenoptera: Vespidae) . Systematic Entomology , 12 : 413 – 431 .
   Web of Science ®Google Scholar
• Coddington , J. and Scharff , N. 1994 . Problems with zero-length branches . Cladistics , 10 : 415 – 424 .
   Web of Science ®Google Scholar
• de Pinna , M. C. C. 1991 . Concepts and tests of homology in the cladistic paradigm . Cladistics , 7 : 367 – 394 .
   Web of Science ®Google Scholar
• Donoghue , M. J. , Doyle , J. A. , Gauthier , J. , Kluge , A. G. and Rowe , T. 1989 . The importance of fossils in phylogeny reconstruction . Annual Review of Ecology and Systematics , 20 : 431 – 460 .
   Google Scholar
• Doyle , J. A. and Donoghue , M. J. 1987 . The importance of fossils in elucidating seed plant phylogeny and macroevolution . Review of Paleobotany and Palynology , 50 : 63 – 95 .
   Web of Science ®Google Scholar
• Ebach , M. C. and Ahyong , S. T. 2001 . Phylogeny of the trilobite sub-genus Acanthopyge (Lobopyge) . Cladistics , 17 : 1 – 10 .
   Web of Science ®Google Scholar
• Estes , R. , de Queiroz , K. and Gauthier , J. 1988 . “ Phylogenetic relationships within Squamata; ” . In Phylogenetic Relationships of the Lizard Families. Essays Commemorating Charles L. Camp. Edited by: Estes , R. and Pregili , G. K. 119 – 282 . Stanford, California : Stanford University Press .
   Google Scholar
• Farris , J. S. 1970 . Methods for computing Wagner Trees . Systematic Biology , 19 : 83 – 92 .
   Google Scholar
• Farris , J. S. 1983 . “ The logical basis of phylogenetic analysis; ” . In Advances in Cladistics Edited by: Platnick , N. I. and Funk , V. A. Vol. 2 , 7 – 36 . New York : Columbia University Press .
   Google Scholar
• Farris , J. S. 1988 . HENNIG86, version 1.5. Program and documentation New York : Port Jefferson Station .
   Google Scholar
• Farris , J. S. , Kluge , A. and Eckhardt , M. J. 1970 . A numerical approach to phylogenetic systematics . Systematic Zoology , 19 : 172 – 191 .
   Google Scholar
• Fitch , W. M. 1971 . Toward defining the course of evolution: minimum change for a specific tree topology . Systematic Zoology , 20 : 406 – 416 .
   Google Scholar
• Fraser , N. C. and Benton , M. 1989 . The Triassic reptiles Brachyrhinodon Polysphenodon and the relationships of the sphenodontids . Zoological Journal of the Linnean Society , 96 : 413 – 445 .
   Web of Science ®Google Scholar
• Gao , K. and Norell , M. A. 1998 . Taxonomic review of Carusia (Reptilia: Squamata) from the late Cretaceous of the Gobi Desert and phylogenetic relationships of anguimorphan lizards . American Museum Novitates , 3230 : 1 – 51 .
   Google Scholar
• Gatesy , J. , O'Grady , P. and Baker , R. H. 1999 . Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa . Cladistics , 15 : 271 – 314 .
   PubMed Web of Science ®Google Scholar
• Gauthier , J. 1986 . Saurischian monophyly and the origin of birds . Memoirs of the California Academy of Sciences , 8 : 1 – 56 .
   Google Scholar
• Gauthier , J. , Kluge , A. G. and Rowe , T. 1988 . Amniote phylogeny and the importance of fossils . Cladistics , 4 : 105 – 208 .
   PubMed Web of Science ®Google Scholar
• Goloboff , P. A. 1993 . Character optimization and calculation of tree lengths . Cladistics , 9 : 433 – 436 .
   PubMed Web of Science ®Google Scholar
• Goloboff , P. A. 1996 . Methods for faster parsimony analysis . Cladistics , 12 : 199 – 220 .
   PubMed Web of Science ®Google Scholar
• Goloboff , P. A. 1999 . Analyzing large data sets in reasonable times: solutions for composite optima . Cladistics , 15 : 415 – 428 .
   PubMed Web of Science ®Google Scholar
• Goloboff , P. A. 2000 . NONA, version 1.6. Program and documentation New York : American Museum of Natural History, Department of Entomology .
   Google Scholar
• Goloboff , P. , Farris , A. J. S. and Nixon , K. 2002 . T. N. T.: Tree Analysis Using New Technology Program available at www.cladistics.com
   Google Scholar
• Gordon , A. D. 1980 . “ On the assessment and comparison of classifications; ” . In Analyse de donnees et informatique Edited by: Tomassone , R. 149 – 160 . LeChesnay : INRIA .
   Google Scholar
• Grande , L. and Bemis , W. E. 1998 . A comprehensive phylogenetic study of amiid fishes (Amiidae) based on comparative skeletal anatomy. An empirical search for interconnected patterns of natural history. Society of Vertebrate Paleontology Memoir 4
   Google Scholar
• Huelsenbeck , J. 1991 . When are fossils better than extinct taxa in phylogenetic analysis? . Systematic Zoology , 40 : 458 – 469 .
   Google Scholar
• Kearney , M. 2002 . Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions . Systematic Biology , 51 : 369 – 381 .
   PubMed Web of Science ®Google Scholar
• Kitching , I. , Forey , P. , Humphries , C. and Williams , D. 1998 . Cladistics, The Theory and Practice of Parsimony Analysis. Systematics Association Special Publication 11 228 Oxford University Press .
   Google Scholar
• Kluge , A. G. 1989 . A concern for evidence and a phylogenetic hypothesis for relationships among Epicrates Boidae, Serpentes . Systematic Zoology , 38 : 1 – 25 .
   Google Scholar
• Maddison , W. P. and Maddison , D. R. 1992 . MacClade: Analysis of Phylogeny and Character Evolution, Version 3.04 Sunderland, Massachusetts : Sinauer .
   Google Scholar
• Margush , T. and McMorris , F. R. 1981 . Consensus n-trees . Bulletin of Mathematical Biology , 43 : 239 – 244 .
   Web of Science ®Google Scholar
• Matthee , C. A. , Burzlaff , J. D. and Bollback , J. R. 2001 . Mining the mammalian genome for artiodactyl systematics . Systematic Biology , 50 : 367 – 390 .
   PubMed Web of Science ®Google Scholar
• Messenger , S. L. and McGuire , J. A. 1998 . Morphology, molecules and the phylogenetics of cetaceans . Systematic Biology , 47 : 90 – 124 .
   PubMed Web of Science ®Google Scholar
• Nixon , K. C. 1996 . Paleobotany in cladistics and cladistics in paleobotany: enlightenment and uncertainty . Review of Paleobotany and Palynology , 90 : 361 – 373 .
   Google Scholar
• Nixon , K. C. 1999a . The parsimony ratchet, a new method for rapid parsimony analysis . Cladistics , 15 : 407 – 414 .
   PubMed Web of Science ®Google Scholar
• Nixon , K. C. 1999b . Winclada (BETA) Ver. 0.9.9 Ithaca, New York : published by the author .
   Google Scholar
• Nixon , K. C. and Carpenter , J. M. 1996a . On simultaneous analysis . Cladistics , 12 : 221 – 242 .
   PubMed Web of Science ®Google Scholar
• Nixon , K. C. and Carpenter , J. M. 1996b . On consensus, collapsibility, and clade concordance . Cladistics , 12 : 305 – 322 .
   PubMed Web of Science ®Google Scholar
• Nixon , K. C. and Wheeler , Q. D. 1992 . “ Extinction and the origin of species; ” . In Extinction and Phylogeny Edited by: Novacek , M. J. and Wheeler , Q. D. 119 – 143 . New York : Columbia University Press .
   Google Scholar
• Norell , M. A. and de Queiroz. , K. 1991 . The earliest iguanine lizard (Reptilia: Squamata) and its bearing on iguanine phylogeny . American Museum Novitates , 2997 : 1 – 16 .
   Google Scholar
• Norell , M. A. and Gao , K. 1997 . Braincase and phylogenetic relationships of Estesia mongoliensis from the Upper Cretaceous, Gobi Desert and the recognition of a new clade of lizards . American Museum Novitates , 3211 : 1 – 25 .
   Google Scholar
• Norell , M. A. and Wheeler , W. 2003 . Missing entry replacement data analysis: a replacement approach to dealing with missing data in paleontological and total evidence data sets . Journal of Vertebrate Paleontology , 23 : 275 – 283 .
   Web of Science ®Google Scholar
• Novacek , M. J. 1992 . Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals . Systematic Biology , 41 : 58 – 73 .
   Web of Science ®Google Scholar
• O'Leary , M. A. 1999 . Parsimony analysis of total evidence from extinct and extant taxa, and the cetacean-artiodactyl question . Cladistics , 15 : 315 – 330 .
   PubMed Web of Science ®Google Scholar
• Patterson , C. 1981 . Significance of fossils in determining evolutionary relationships . Annual Review of Ecology and Systematics , 12 : 195 – 223 .
   Google Scholar
• Platnick , N. I. , Griswold , C. E. and Coddington , J. A. 1991 . On missing entries in cladistic analysis . Cladistics , 7 : 337 – 343 .
   Web of Science ®Google Scholar
• Remane , A. 1952 . Die Grundlagen des nat#252;rlichen Systems, der vergleichenden Anatomie und der Phylogenetic Leipzig : Akademische Verlagsgesellschaft .
   Google Scholar
• Rieppel , O. and Kearney , M. 2002 . Similarity . Biological Journal of the Linnean Society , 75 : 59 – 82 .
   Web of Science ®Google Scholar
• Rowe , T. 1988 . Definition, diagnosis and origin of Mammalia . Journal of Vertebrate Paleontology , 8 : 241 – 264 .
   Google Scholar
• Schuh , R. X. and Farris , J. S. 1981 . Methods for investigating taxonomic congruence and their application to the Leptopodomorpha . Systematic Zoology , 30 : 331 – 351 .
   Google Scholar
• Schuh , R. X. and Polhemus , J. X. 1981 . Analysis of taxonomic congruence among morphological, ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera) . Systematic Zoology , 29 : 1 – 26 .
   Google Scholar
• Sereno , P. 1999 . The evolution of dinosaurs . Science , 284 : 2 137–2, 147
   Web of Science ®Google Scholar
• Swofford , D. L. 1991 . “ When are phylogeny estimates from molecular and morphological data incongruent; ” . In Phylogenetic Analyses of DNA Sequences Edited by: Miyamoto , M. M. and Cracraft , J. 295 – 333 . New York : Oxford University Press .
   Google Scholar
• Swofford , D. L. 2001 . PAUP^*: Phylogenetic Analysis Using Parsimony^*, Version 4.0b8 Sunderland, Massachusetts : Sinauer .
   Google Scholar
• Swofford , D. L. and Begle , D. 1993 . PAUP, Phylogenetic Analysis Using Parsimony, Version 3.1.1 Champaign, Illinois : Illinois Natural History Survey .
   Google Scholar
• Swofford , D. L. and Maddison , D. 1987 . Reconstructing ancestral character states under Wagner parsimony . Mathematical Biosciences , 87 : 199 – 299 .
   Web of Science ®Google Scholar
• Wiens , J. J. 1998 . Does adding character with missing data increase of decrease phylogenetic accuracy? . Systematic Biology , 47 : 625 – 640 .
   PubMed Web of Science ®Google Scholar
• Wiens , J. J. and Reeder , T. 1995 . Combining data sets with different numbers of taxa for phylogenetic analysis . Systematic Biology , 44 : 548 – 558 .
   Web of Science ®Google Scholar
• Wilkinson , M. 1992 . TAXEQ2, software and documentation Bristol, , England : University of Bristol .
   Google Scholar
• Wilkinson , M. 1994 . Common cladistic information and its consensus representation: reduced Adams and reduced cladistic consensus trees and profiles . Systematic Biology , 43 : 343 – 368 .
   Web of Science ®Google Scholar
• Wilkinson , M. 1995a . Arbitrary resolutions, missing entries, and the problem of zero-length branches in parsimony analysis . Systematic Biology , 44 : 109 – 111 .
   Web of Science ®Google Scholar
• Wilkinson , M. 1995b . Coping with abundant missing entries in phylogenetic inference using parsimony . Systematic Biology , 44 : 501 – 514 .
   Web of Science ®Google Scholar
• Wilkinson , M. 1995c . More on reduced consensus methods . Systematic Biology , 44 : 436 – 440 .
   Web of Science ®Google Scholar
• Wilkinson , M. 2001 . TAXEQ3, software and documentation London : Department of Zoology, Natural History Museum .
   Google Scholar
• Wilkinson , M. and Benton , M. J. 1995 . Missing data and rhynchosaur phylogeny . Historical Biology , 10 : 137 – 150 .
   Google Scholar
• Wilkinson , M. , Thorley , J. L. and Upchurch , P. 2000 . A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses . Systematic Biology , 49 : 754 – 776 .
   PubMed Web of Science ®Google Scholar
• Wu , X.-C. , Brinkman , D. B. and Russell , A. P. 1996 . Sineoamphisbaena hexatabularis, an amphisbaenian (Diapsida: Squamata) from the Upper Cretaceous redbeds at Bayan Mandahu (Inner Mongolia, People's Republic of China), and comments on the phylogenetic relationships of the Amphisbaenia . Canadian Journal of Earth Sciences , 33 : 541 – 577 .
   Web of Science ®Google Scholar