Hostname: page-component-cd9895bd7-jkksz Total loading time: 0 Render date: 2024-12-24T19:00:48.209Z Has data issue: false hasContentIssue false
  • English
  • Français

Global lability, regional resolution, and majority-rule consensus bias

Published online by Cambridge University Press:  08 February 2016

Colin. D. Sumrall ,
Christopher. A. Brochu  and
John W. Merck Jr.
Colin. D. Sumrall
Affiliation:
Frederick and Amey Geier Collections and Research Center, Cincinnati Museum Center, 1720 Gilbert Avenue, Cincinnati, Ohio 45202
Christopher. A. Brochu
Affiliation:
Department of Geology, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois 60605. E-mail: [email protected]
John W. Merck Jr.
Affiliation:
College Park Scholars, University of Maryland, College Park, Maryland 20742
Get access Rights & Permissions [Opens in a new window]

Abstract

Evolutionary interpretation of paleontological patterns requires a hypothesis of phylogeny, but our phylogenetic hypotheses may not perfectly mirror organismal phylogeny. Tree summary methods less conservative than strict consensus may increase resolution, but these methods may present a biased summary of the full set of most parsimonious trees. When we fail to acknowledge all equally optimal topologies, we risk disregarding trees that are closer to the correct phylogeny. We discuss a case where two subsets of trees were recovered in the set of most parsimonious trees, each with a profoundly different interpretation of character evolution near the root of Echinodermata. This was caused by the presence of a bimodally labile taxon in the matrix with two different topological subsets, each equally parsimonious but differing in the number of consistent trees. Majority-rule consensus favors the subset with the largest number of trees consistent with the placement of the rogue taxon. This bias favors clusters not because of the biological implications of the tree, but on the basis of great inequality in the sizes of the islands of parsimony. We thus recommend that majority-rule consensus trees not be used to summarize the results of a phylogenetic analysis.

Type
Articles
Information
Paleobiology , Volume 27 , Issue 2 , Spring 2001 , pp. 254 - 261
Copyright
Copyright © The Paleontological Society 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Literature Cited

Adams, E. N. 1972. Consensus techniques and the comparison of taxonomic trees. Systematic Zoology 21:390–397.Google Scholar
Ausich, W. I. 1998. Early phylogeny and subclass division of the Crinoidea (Phylum Echinodermata). Journal of Paleontology 72:499–510.CrossRefGoogle Scholar
Barthélemy, J.-P., and Monjardet, B. 1981. The median procedure in cluster analysis and the social choice theory. Mathematical Social Sciences 1:235–267.CrossRefGoogle Scholar
Bremer, K. 1990. Combinable component consensus. Cladistics 6:369–372.CrossRefGoogle ScholarPubMed
Brochu, C. A. 1997. Fossils, morphology, divergence timing, and the phylogenetic relationships of Gavialis. Systematic Biology 46:479–522.CrossRefGoogle ScholarPubMed
Brochu, C. A. 1999. Phylogenetics, taxonomy, and historical biogeography of Alligatoroidea. Society of Vertebrate Paleontology Memoir 6:9–100.CrossRefGoogle Scholar
Caldwell, M. W. 1999a. Description and phylogenetic relationships of a new species of Coniasaurus Owen, 1850 (Squamata). Journal of Vertebrate Paleontology 19:438–455.CrossRefGoogle Scholar
Caldwell, M. W. 1999b. Squamate phylogeny and the relationships of snakes and mosasauroids. Zoological Journal of the Linnean Society 125:115–147.CrossRefGoogle Scholar
Colless, D. H. 1980. Congruence between morphometric and allozyme data for Menidia species: a reappraisal. Systematic Zoology 29:288–299.CrossRefGoogle Scholar
Edgecombe, G. D., and Ramsköld, L. 1999. Relationships of Cambrian Arachnata and the systematic position of Trilobita. Journal of Paleontology 73:263–287.CrossRefGoogle Scholar
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Gauthier, J., Kluge, A. G., and Rowe, T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105–209.CrossRefGoogle ScholarPubMed
Hillis, D. M., and Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 44:3–16.CrossRefGoogle Scholar
Jefferies, R. P. S. 1986. The ancestry of the vertebrates. British Museum (Natural History) and Cambridge University Press, London.Google Scholar
Livezey, B. C. 1997. A phylogenetic analysis of geese and swans (Anseriformes: Anserinae), including selected fossil species. Systematic Biology 45:415–450.CrossRefGoogle Scholar
Maddison, D. R. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Systematic Zoology 40:315–328.CrossRefGoogle Scholar
Margush, T., and McMorris, F. R. 1981. Consensus n-trees. Bulletin of Mathematical Biology 43:239–244.Google Scholar
Naylor, G. J. P., and Brown, W. M. 1998. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Systematic Biology 47:61–76.CrossRefGoogle ScholarPubMed
Nixon, K. C., and Carpenter, J. M. 1996. On consensus, collapsibility, and clade concordance. Cladistics 12:305–321.CrossRefGoogle ScholarPubMed
Nützel, A., Erwin, D. H., and Mapes, R. H. 2000. Identity and phylogeny of the late Paleozoic Subulitoidea (Gastropoda). Journal of Paleontology 74:575–598.2.0.CO;2>CrossRefGoogle Scholar
Parsley, R. L. 1997. The echinoderm classes Stylophora and Homoiostelea: non-Calcichordata. In Waters, J. A. and Maples, C. G., eds. Geobiology of echinoderms. Paleontological Society Papers 3:225–248. Paleontological Society, Pittsburgh.Google Scholar
Sanderson, M. J. 1995. Objections to bootstrapping phylogenies: a critique. Systematic Biology 44:299–320.CrossRefGoogle Scholar
Schram, F. R., Vonk, R., and Hof, C. H. J. 1997. Mazon Creek Cycloidea. Journal of Paleontology 71:261–284.CrossRefGoogle Scholar
Schuh, R. T., and Polhemus, J. T. 1981. Analysis of taxonomic congruence among morphological, ecological, and biogeographic data sets for the Leptopodomorpha (Hemiptera). Systematic Zoology 29:1–26.CrossRefGoogle Scholar
Shaffer, H. B., Meylan, P., and McKnight, M. L. 1997. Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. Systematic Biology 46:235–268.CrossRefGoogle ScholarPubMed
Simmons, N. B. 1993. Phylogeny of Multituberculata. Pp. 146–164in Szalay, F. S., Novacek, M. J., and McKenna, M. C., eds. Mammal phylogeny, Vol. 1. Mesozoic differentiation, multituberculates, monotremes, early therians, and marsupials. Springer, New York.CrossRefGoogle Scholar
Sokal, R. R., and Rohlf, F. J. 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Systematic Zoology 30:309–325.CrossRefGoogle Scholar
Sumrall, C. D. 1996. A phylogenetic analysis of Echinodermata based on primitive fossil taxa. Ph.D. dissertation. University of Texas, Austin.Google Scholar
Sumrall, C. D. 1997. The role of fossils in the phylogenetic reconstruction of Echinodermata. In Waters, J. A. and Maples, C. G., eds. Geobiology of echinoderms. Paleontological Society Papers 3:267–288. Paleontological Society, Pittsburgh.Google Scholar
Swofford, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pp. 295–333in Miyamoto, M. M. and Cracraft, J., eds. Phylogenetic analysis of DNA sequences. Oxford University Press, New York.CrossRefGoogle Scholar
Trueman, J. W. H. 1998. Reverse successive weighting. Systematic Biology 47:733–737.CrossRefGoogle ScholarPubMed
Wheeler, W. C. 1992. Extinction, sampling, and molecular phylogenetics. Pp. 205–215in Novacek, M. J. and Wheeler, Q. D., eds. Extinction and phylogeny. Columbia University Press, New York.Google Scholar
Wiens, J. J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology 47:625–640.CrossRefGoogle ScholarPubMed
Wiens, J. J., and Reeder, T. W. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Systematic Biology 44:548–558.CrossRefGoogle 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.CrossRefGoogle Scholar
Wilkinson, M. 1995a. Arbitrary resolutions, missing entries, and the problem of zero-length branches in parsimony analysis. Systematic Biology 44:108–111.CrossRefGoogle Scholar
Wilkinson, M. 1995b. More on reduced consensus methods. Systematic Biology 44:435–439.CrossRefGoogle Scholar
Wilkinson, M. 1995c. Coping with abundant missing entries in phylogenetic inference using parsimony. Systematic Biology 44:501–514.CrossRefGoogle Scholar
Wilkinson, M. 1996. Majority-rule reduced consensus trees and their use in bootstrapping. Molecular Biology and Evolution 13:437–444.CrossRefGoogle ScholarPubMed
Wilkinson, M., and Benton, M. J. 1995. Missing data and rhynchosaur phylogeny. Historical Biology 10:137–150.CrossRefGoogle Scholar
Wilkinson, M., and Benton, M. J. 1996. Sphenodontid phylogeny and the problems of multiple trees. Philosophical Transactions of the Royal Society of London B 351:1–16.Google Scholar
Williams, A., Popov, L. E., Holmer, L. E., and Cusac, M. 1998. The diversity and phylogeny of the paterinate brachiopods. Palaeontology 41:221–262.Google Scholar