Skip to content Skip to navigation

Article: Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists

Publication: Palaeontology
Volume: 53
Part: 1
Publication Date: January 2010
Page(s): 1 – 9
Author(s): Stephen L. Brusatte
Addition Information

How to Cite

BRUSATTE, S. L. 2010. Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists. Palaeontology, 53, 1, 1–9.

Online Version Hosted By

Wiley Online Library
Get Article: Wiley Online Library [Pay-to-View Access] |

References

  • ANDERSON, J. S., REISZ, R. R., SCOTT, D., FRÖBISCH, N. B. and SUMIDA, S. S. 2008. A stem batrachian from the Early Permian of Texas and the origin of frogs and salamanders. Nature, 453, 515–518.
  • BENNETT, S. C. 1996. The phylogenetic position of the Pterosauria within the Archosauromorpha. Zoological Journal of the Linnean Society, 118, 261–308.
  • BENTON, M. J. 1999. Scleromochlus taylori and the origin of dinosaurs and pterosaurs. Philosophical Transactions of the Royal Society of London, Series B, 354, 1423–1446.
  • BENTON, M. J. 2004. Origin and relationships of Dinosauria. 7–19. In WEISHAMPEL, D. B., DODSON, P. and OSMOLSKA, H. (eds). The Dinosauria. Second edition. University of California Press, Berkelely, California, 861 pp.
  • BENTON, M. J. and WALKER, A. D. 2002. Erpetosuchus, a crocodile-like basal archosaur. From the Late Triassic of Elgin, Scotland. Zoological Journal of the Linnean Society, 136, 25–47.
  • BININDA-EMONDS, O. R. P. (ed.). 2004. Phylogenetic supertrees: combining information to reveal the Tree of Life., Computation Biology, Vol. 4. Kluwer Academic Publishers, Dordrecht, the Netherlands.
  • BININDA-EMONDS, O. R. P., BRYANT, H. N. and RUSSELL, A. P. 1998. Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods. Biological Journal of the Linnean Society, 64, 101–133.
  • BLOCH, J. I., SILCOX, M. T., BOYER, D. M. and SARGIS, E. J. 2007. New Paleocene skeletons and the relationship of plesiadapiforms to crown-clade primates. Proceedings of the National Academy of Sciences USA, 104, 1159–1164.
  • BRUSATTE, S. L. and SERENO, P. C. 2008. Phylogeny of Allosauroidea (Dinosauria: Theropoda): comparative analysis and resolution. Journal of Systematic Palaeontology, 6, 155–182.
  • CARROLL, R. L. 2007. The Palaeozoic ancestry of salamanders, frogs, and caecilians. Zoological Journal of the Linnean Society, 150, 1–140.
  • CLARK, J. M., NORELL, M. A. and MAKOVICKY, P. J. 2002. Cladistic approaches to the relationships of birds to other theropod dinosaurs. 31–60. In CHIAPPE, L. M. and WITMER, L. M. (eds). Mesozoic birds: above the heads of Dinosaurs. University of California Press, Berkeley, California.
  • DONOGHUE, P. C. J. and SMITH, M. P. 2001. The anatomy of Turinia pagei (Powrie), and the phylogenetic status of the Thelodonti. Transactions of the Royal Society of Edinburgh: Earth Sciences, 92, 15–37.
  • ESTES, R. K., DE QUIEROZ, K. and GAUTHIER, J. A. 1988. Phylogenetic relationships within Squamata. 119–281. In ESTES, R. and PREGILL, G. K. (eds). Phylogenetic relationships of the Lizard families. Stanford Univ. Press, Palo Alto, California.
  • GATESY, J., MATTHEE, C., DE SALLE, R. and HAYASHI, C. 2002. Resolution of supertree/supermatrix paradox. Systematic Biology, 51, 652–664.
  • GOLOBOFF, P. A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics, 15, 415–428.
  • GOLOBOFF, P. A., FARRIS, J. S. and NIXON, K. C. 2003. T.N.T.: Tree analysis using new technology. Version 1.0. Program and documentation available at http://www.zmuc.dk/public/Phylogeny/TNT.
  • HARRIS, S. R., PISANI, D., GOWER, D. J. and WILKINSON, M. 2007. Investigating stagnation in morphological phylogenies using consensus data. Systematic Biology, 56, 125–129.
  • JENNER, R.A. 2006. Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney. Development Genes and Evolution, 216, 385–394.
  • JUUL, L. 1994. The phylogeny of basal archosaurs. Palaeontologica Africana, 31, 1–38.
  • LANGER, M. C. and BENTON, M. J. 2006. Early dinosaurs: a phylogenetic study. Journal of Systematic Palaeontology, 4, 309–358.
  • MALIA, M. J., LIPSCOME, D. L. and ALLARD, M. W. 2003. The misleading effects of composite taxa in supermatrices. Molecular Phylogenetics and Evolution, 27, 522–527.
  • NESBITT, S. 2007. The anatomy of Effigia okeeffeae (Archosauria, Suchia), theropod-like convergence, and the distribution of related taxa. Bulletin of the American Museum of Natural History, 302, 1–84.
  • NIXON, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15, 407–414.
  • NOVAS, F. E. 1996. Dinosaur monophyly. Journal of Vertebrate Paleontology, 16, 723–741.
  • PARRISH, J. M. 1993. Phylogeny of the Crocodylotarsi, with reference to archosaurian and crurotarsan monophyly. Journal of Vertebrate Paleontology, 13, 287–308.
  • PRENDINI, L. 2000. Phylogeny and classification of the superfamily Scorpionoidea Latreille 1802 (Chelicerata, Scorpiones): an exemplar approach. Cladistics, 16, 1–78.
  • PRENDINI, L. 2001. Species or supraspecific taxa as terminals in cladistic analysis? Groundplans versus exemplars revisited. Systematic Biology, 50, 290–300.
  • PRENDINI, L. 2003. A new genus and species of bothriurid scorpion from the Brandberg Massif, Namibia, with a reanalysis of bothriurid phylogeny and a discussion of the phylogenetic position of Lisposoma Lawrence. Systematic Entomology, 28, 149–172.
  • PRENDINI, L., CROWE, T. M. and WHEELER, W. C. 2003. Systematics and biogeography of the Family Scorpionidae (Chelicerata: Scorpiones), with a discussion of phylogenetic methods. Invertebrate Systematics, 17, 185–259.
  • PRENDINI, L. and WHEELER, W. C. 2005. Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing. Cladistics, 21, 446–494.
  • O’LEARY, M. A. 1999. Parsimony analysis of total evidence from extinct and extant taxa and the cetacean-artiodactyl question (Mammalia, Ungulata). Cladistics, 15, 315–330.
  • QUICKE, D. L., TAYLOR, J. J. and PURVIS, A. 2001. Changing the landscape: a new strategy for estimating large phylogenies. Systematic Biology, 50, 60–66.
  • RICE, K. A., DONOGHUE, M. J. and OLMSTEAD, R. G. 1997. Analyzing large data sets: rbcL revisited. Systematic Biology, 46, 554–563.
  • ROSHAN, U. M., MORET, B. M. E., WILLIAMS, T. L. and WARROW, T. 2004. Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. Proceedings 3rd IEEE Computational Systems Bioinformatics Conference, CSB 2004, 98–109.
  • RUTA, M., COATES, M. I. and QUICKE, D. L. J. 2003. Early tetrapod relationships revisited. Biological Reviews, 78, 251–345.
  • RUTA, M. and COATES, M. I. 2007. Dates, nodes and character conflict: addressing the lissamphibian origin problem. Journal of Systematic Palaeontology, 5, 69–122.
  • SALISBURY, B. A. and KIM, J. 2001. Ancestral state estimation and taxon sampling density. Systematic Biology, 50, 557–564.
  • SANSOM, R. S. 2008. The origin and early evolution of the Osteostraci (Vertebrata): a phylogeny for the Thyestiida. Journal of Systematic Palaeontology, 6, 317–332.
  • SCHOCH, R. R. 2009. Evolution of life cycles in early amphibians. Annual Review of Earth and Planetary Sciences, 27, 15.1–15.28.
  • SCOTT, E. 2005. A phylogeny of ranid frogs (Anura: Ranoidea: Ranidae), based on a simultaneous analysis of morphological and molecular data. Cladistics, 21, 507–574.
  • SERENO, P. C. 1991. Basal archosaurs: phylogenetic relationships or functional implications. Society of Vertebrate Paleontology Memoir, 2, 1–53.
  • SERENO, P. C. and ARCUCCI, A. B. 1990. The monophyly of crurotarsal archosaurs and the origin of bird and crocodile ankle joints. Neues Jahrbuch für Geologie und Palontologie, Abhandlung, 180, 21–52.
  • SIMMONS, N. B. 2001. Misleading results from the use of ambiguity coding to score polymorphisms in higher-level taxa. Systematic Biology, 50, 613–620.
  • TRUEB, L. and CLOUTIER, R. 1991. A phylogenetic investigation of the inter- and intrarelationships of the Lissamphibia (Amphibia: Temnospondyli). 223–313. In SCHULTZE, H.-P. and TRUEB, L. (eds). Origins of the higher groups of tetrapods: controversy and consensus. Cornell Univ. Press, Ithaca, New York.
  • WIENS, J. J. 1998. The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study. Systematic Biolology, 47, 397–413.
  • WIENS, J. J. 2003. Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem? Journal of Vertebrate Paleontology, 23, 297–310.
  • WIENS, J. J. 2005. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction? Systematic Biology, 54, 731–742.
  • WIENS, J. J. 2006. Missing data and the design of phylogenetic analyses. Journal of Biomedical Informatics, 39, 34–42.
  • YEATES, D. K. 1995. Groundplans and exemplars: paths to the tree of life. Cladistics, 11, 343–357.
PalAss Go! URL: http://go.palass.org/5di | Twitter: Share on Twitter | Facebook: Share on Facebook | Google+: Share on Google+