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Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis

Published online by Cambridge University Press:  08 February 2016

William C. Clyde  and
Daniel C. Fisher
William C. Clyde
Affiliation:
Museum of Paleontology, University of Michigan, Ann Arbor, Michigan 48109. E-mail: wclyde@umich.edu
Daniel C. Fisher
Affiliation:
Museum of Paleontology, University of Michigan, Ann Arbor, Michigan 48109. E-mail: dcfisher@umich.edu
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Abstract

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

Type
Articles
Information
Paleobiology , Volume 23 , Issue 1 , Winter 1997 , pp. 1 - 19
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Andrews, P. 1988. A phylogenetic analysis of the primates. pp. 143–175in Benton, M. J., ed. The phylogeny and classification of the tetrapods, Vol. 2, Mammals. Clarendon, Oxford.Google Scholar
Beard, K. C. 1993. Phylogenetic systematics of the Primatomorpha, with special reference to Dermoptera. pp. 129–150in Szalay, Novacek, and McKenna 1993b.Google Scholar
Benton, M. J., and Storrs, G. W. 1994. Testing the quality of the fossil record: paleontological knowledge is improving. Geology 22:111–114.2.3.CO;2>CrossRefGoogle Scholar
Bodenbender, B. E. 1994. Skeletal crystallography in cladistic and stratocladistic investigations of blastoid phylogeny. Ph.D. dissertation, University of Michigan, Ann Arbor.Google Scholar
Cifelli, R. L. 1993a. The phylogeny of the native South American ungulates. pp. 195–216in Szalay, Novacek, and McKenna 1993b.Google Scholar
Cifelli, R. L. 1993b. Theria of metatherian-eutherian grade and the origin of marsupials. pp. 205–215in Szalay, Novacek, and McKenna 1993a.Google Scholar
Conover, W. J. 1971. Practical nonparametric statistics. Wiley, New York.Google Scholar
Coombs, M. C. 1989. Interrelationships and diversity of Chalicotheriidae. pp. 438–457In Prothero, D. R. and Schoch, R. M., eds. The evolution of perissodactyls. Clarendon, New York.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.CrossRefGoogle Scholar
Eernisse, D. J., Albert, J. S., and Anderson, F. E. 1992. Annelida and Arthropoda are not sister taxa: a phylogenetic analysis of spiralian metazoan morphology. Systematic Biology 41:305–330.CrossRefGoogle Scholar
Eldredge, N. 1979. Cladism and common sense. Pp.165–198In Cracraft, J. and Eldredge, N., eds. Phylogenetic analysis and paleontology. Columbia University Press, New York.CrossRefGoogle Scholar
Eldredge, N., and Cracraft, J. 1980. Phylogenetic patterns and the evolutionary process. Columbia University Press, New York.Google Scholar
Engelmann, G. F., and Wiley, E. O. 1977. The place of ancestor-descendant relationships in phylogeny reconstruction. Systematic Zoology 26:1–11.CrossRefGoogle Scholar
Estes, R., de Queiroz, K., and Gauthier, J. 1988. Phylogenetic relationships within Squamata. pp. 119–281In Estes, R. and Pregill, G., eds. Phylogenetic relationships of the lizard families. Stanford University Press, Stanford, Calif.Google Scholar
Evans, S. E. 1988. The early history and relationships of the Diapsida. pp. 221–260in Benton, M. J., ed. The phylogeny and classification of the tetrapods, Vol. 1, Amphibians, reptiles, birds. Clarendon, Oxford.Google Scholar
Farris, J. S. 1983. The logical basis of phylogenetic analysis. pp. 7–36In Platnick, N. I. and Funk, V. A., eds. Advances in cladistics, Vol. 2. Proceedings of the Second Meeting of the Willi Hennig Society. Columbia University Press, New York.Google Scholar
Farris, J. S. 1989. The retention index and the rescaled consistency index. Cladistics 5:417–419.CrossRefGoogle ScholarPubMed
Fischer, M. S., and Tassy, P. 1993. Interrelation between Proboscidea, Sirenia, Hyracoidea and Mesaxonia: the morphological evidence. pp. 217–234in Szalay, Novacek, and McKenna 1993b.Google Scholar
Fisher, D. C. 1982. Phylogenetic and macroevolutionary patterns within the Xiphosurida. Proceedings of the Third North American Paleontological Convention 1:175–180.Google Scholar
Fisher, D. C. 1988. Stratocladistics: integrating stratigraphic and morphologic data in phylogenetic inference. Geological Society of America Abstracts with Programs 20:A186.Google Scholar
Fisher, D. C. 1991. Phylogenetic analysis and its application in evolutionary paleobiology. In Gilinsky, N. L. and Signor, P. W., eds. Analytical paleobiology. Paleontological Society Short Courses in Paleontology No. 4:103–121. University of Tennessee, Knoxville.Google Scholar
Fisher, D. C. 1992. Stratigraphic Parsimony. pp. 124–129in Maddison, W. P. and Maddison, D. R.MacClade: analysis of phylogeny and character evolution, Version 3. Sinauer Associates, Sunderland, Mass.Google Scholar
Fisher, D. C. 1994a. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. pp. 133–171In Grande, L. and Rieppel, O., eds. Interpreting the hierarchy of nature. Academic Press, San Diego.Google Scholar
Fisher, D. C. 1994b. Measures of congruence between stratigraphic data and phylogenetic hypotheses. Geological Society of America Abstracts with Programs 26:A-123.Google Scholar
Foote, M. 1996. On the probability of ancestors in the fossil record. Paleobiology 22:141–151.CrossRefGoogle Scholar
Foote, M., and Raup, D. M. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121–140.CrossRefGoogle ScholarPubMed
Gaffney, E. S., Meylan, P. A., and Wyss, A. R. 1991. A computer assisted analysis of the relationships of the higher categories of turtles. Cladistics 7:313–335.CrossRefGoogle Scholar
Gauthier, J. A., Kluge, A. G., and Rowe, T. 1988a. Amniote phylogeny and the importance of fossils. Cladistics 4:105–209.CrossRefGoogle ScholarPubMed
Gauthier, J. A., Kluge, A. G., and Rowe, T. 1988b. The early evolution of the Amniota. Pp.103–155in Benton, M. J., ed. The phylogeny and classification of the tetrapods, Vol. 1, Amphibians, reptiles, birds. Clarendon, Oxford.Google Scholar
Gentry, A. W., and Hooker, J. J. 1988. The phylogeny of Artiodactyla. pp. 235–272in Benton, M. J., ed. The phylogeny and classification of the tetrapods, Vol. 2, Mammals. Clarendon, Oxford.Google Scholar
Gingerich, P. D. 1979. The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. pp. 41–77In Cracraft, and Eldredge, N., eds. Phylogenetic analysis and paleontology. Columbia University Press, New York.CrossRefGoogle Scholar
Huelsenbeck, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20:470–483CrossRefGoogle Scholar
Huelsenbeck, J. P., and Hillis, D. M. 1993. Success of phylogenetic methods in the four-taxon case. Systematic Biology 42:247–264CrossRefGoogle Scholar
Hulburt, R. C. 1989. Phylogenetic interrelationships and evolution of North American late Neogene Equidae. pp. 176–196In Prothero, R. and Schoch, R. M., eds. The evolution of perissodactyls. Clarendon, New York.Google Scholar
Kay, R. F., Thewissen, J. G. M., and Yoder, A. D. 1992. Cranial anatomy of Ignacius graybullianus and the affinities of Plesiadapiformes. American Journal of Physical Anthropology 89:477–498.CrossRefGoogle Scholar
Kluge, A. G. 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Systematic Zoology 38:7–25.CrossRefGoogle Scholar
Maddison, W. P., and Maddison, D. R. 1992. MacClade: analysis of phylogeny and character evolution, Version 3. Sinauer Associates, Sunderland, Mass.Google Scholar
Marshall, C. R. 1990. Confidence intervals on stratigraphic ranges. Paleobiology 16:1–10.CrossRefGoogle Scholar
Marshall, C. R. 1995. Stratigraphy, the true order of species’ originations and extinctions, and testing ancestor-descendant hypotheses among Caribbean bryozoans. pp. 208–236In Erwin, D. H. and Antsey, R. L., eds. New approaches to studying speciation in the fossil record. Columbia University Press, New York.Google Scholar
Miyamoto, M. M., and Fitch, W. M. 1995. Testing species phytogenies and phylogenetic methods with congruence. Systematic Biology 44:64–76.CrossRefGoogle Scholar
Naylor, G., and Kraus, F. 1995. The relationship between s and m and the retention index. Systematic Biology 44:559–562.CrossRefGoogle Scholar
Norell, M. A. 1993. Tree based approaches to understanding history: comments on ranks, rules, and the quality of the fossil record. American Journal of Science 293-A:407–417.CrossRefGoogle Scholar
Norell, M. A. 1996. Ghost taxa, ancestors, and assumptions: a comment on Wagner. Paleobiology 22:453–455CrossRefGoogle Scholar
Norell, M. A., and Novacek, M. J. 1992a. The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255:1690–1693.CrossRefGoogle ScholarPubMed
Norell, M. A., and Novacek, M. J. 1992b. Congruence between superpositional and phylogenetic patterns: comparing cladistic patterns with fossil records. Cladistics 8:319–337.CrossRefGoogle ScholarPubMed
Novacek, M. J. 1992. Fossils, topologies, missing data, and the higher level phylogeny of eutherian mammals. Systematic Biology 41:58–73.CrossRefGoogle Scholar
Patterson, C. 1981. Significance of fossils in determining evolutionary relationships. Annual Review of Ecology and Systematics 12:195–223.CrossRefGoogle Scholar
Patterson, C. 1982. Morphological characters and homology. pp. 21–74In Joysey, K. A. and Friday, A. E., eds. Problems of phylogenetic reconstruction. Academic Press, London.Google Scholar
Paul, C. R. C. 1982. The adequacy of the fossil record. pp. 75–117In Joysey, K. A. and Friday, A. E., eds. Problems of phylogenetic reconstruction. Academic Press, London.Google Scholar
Paul, C. R. C. 1985. The adequacy of the fossil record reconsidered. Special Papers on Palaeontology 33:7–15.Google Scholar
Paul, C. R. C. 1992. The recognition of ancestors. Historical Biology 6:239–250.CrossRefGoogle Scholar
Rohlf, F. J., Chang, W. S., Sokal, R. R., and Kim, J. 1990. Accuracy of estimated phylogenies: effects of tree topology and evolutionary model. Evolution 44:1671–1684.CrossRefGoogle ScholarPubMed
Rowe, T. 1988. Definition, diagnosis, and origin of mammalia. Journal of Vertebrate Paleontology 8:241–264.CrossRefGoogle Scholar
Schaeffer, B., Hecht, M. K., and Eldredge, N. 1972. Phylogeny and paleontology. Evolutionary Biology 6:31–46.Google Scholar
Scott, K. M. and Janis, C. M. 1993. Relationships of the Ruminantia (Artiodactyla) and an analysis of the characters used in ruminant taxonomy. pp. 282–302in Szalay, Novacek, and McKenna 1993b.Google Scholar
Simmons, N. B. 1993. Phylogeny of Multituberculata. pp. 146–164in Szalay, Novacek, and McKenna 1993a.Google Scholar
Smith, A. B. 1994. Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific, London.CrossRefGoogle Scholar
Sober, E. 1988. Reconstructing the past: parsimony, evolution, and inference. MIT Press, London.Google Scholar
Strauss, D., and Sadler, P. M. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21:411–427.CrossRefGoogle Scholar
Suter, S. 1994. Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees. Biological Journal of the Linnean Society 53:31–72.CrossRefGoogle Scholar
Szalay, F. S. 1977. Ancestors, descendants, sister groups and testing of phylogenetic hypotheses. Systematic Zoology 26:12–18.CrossRefGoogle Scholar
Szalay, F. S., Novacek, M. J., and McKenna, M. C. 1993a. Mammal phylogeny: Mesozoic differentiation, multituberculates, monotremes, early therians, and marsupials. Springer, New York.Google Scholar
Szalay, F. S., Novacek, M. J., and McKenna, M. C. 1993b. Mammal phylogeny: placentals. Springer, New York.Google Scholar
Thewissen, J. G. M. 1992. Temporal data in phylogenetic systematics: an example from the mammalian fossil record. Journal of Paleontology 66:1–8.CrossRefGoogle Scholar
Wagner, P. J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21:153–178.CrossRefGoogle Scholar
Wagner, P. J. 1996. Ghost taxa, ancestors, assumptions, and expectations: a reply to Norell. Paleobiology 22:456–460.CrossRefGoogle Scholar
Wagner, P. J., and Erwin, D. H. 1995. Phylogenetic patterns as tests of speciation models. pp. 87–122In Erwin, D. H. and Antsey, R. L., eds. New approaches to studying speciation in the fossil record. Columbia University Press, New York.Google Scholar
Wei, K.-Y. 1994. Stratophenetic tracing of phylogeny using SIMCA pattern recognition technique: a case study of the late Neogene planktic foraminifera Globoconella clade. Paleobiology 20:52–65.CrossRefGoogle Scholar
Wheeler, W. C., Cartwright, P., and Hayashi, C. Y. 1993. Arthropod phylogeny: a combined approach. Cladistics 9:1–39.CrossRefGoogle ScholarPubMed
Wible, J. R., and Hopson, J. A. 1993. Basicranial evidence for early mammal phylogeny. pp. 45–62in Szalay, Novacek, and McKenna 1993a.CrossRefGoogle Scholar
Wyss, A. R., and Flynn, J. J. 1993. Phylogenetic analysis and definition of Carnivora. pp. 32–52in Szalay, Novacek, and McKenna 1993b.Google Scholar