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Comparing the stratigraphic record to estimates of phylogeny

Published online by Cambridge University Press:  08 February 2016

John P. Huelsenbeck
John P. Huelsenbeck*
Affiliation:
Department of Zoology, University of Texas, Austin, Texas 78712
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Abstract

The age of first occurrence of taxa remains an underutilized source of information in phylogenetic analysis. In this paper I develop a method whereby one can measure the fit of the stratigraphic record to an estimated phylogenetic tree. The method works as follows: (1) each of the internal nodes excluding the root node of a phylogenetic tree is visited, (2) the oldest age of first occurrence for the taxa above the node is compared to the oldest age of first occurrence for the sister node, and (3) if the age above the node is the same age or younger than the age below the node, then the node is stratigraphically consistent. A measure of the total fit of the stratigraphic record to the tree is the proportion of nodes that are stratigraphically consistent (expressed as the stratigraphic consistency index, SCI). This measure of stratigraphic fit is sensitive to errors in phylogenetic estimation as well as to missing lineages (or parts of lineages). The significance of the fit of the stratigraphic record to the tree can be determined through a permutation approach that generates the null distribution for SCI under the hypothesis that the stratigraphic fit is no better than would be expected at random. The method is applied to several studies taken from the literature. Almost all published trees had significant SCI values, meaning the trees fit the stratigraphic record quite well. Applications of stratigraphic consistency for determining the confidence that should be placed in a phylogenetic estimate, for determining the root of a tree, and as a modified optimality criterion for estimating phylogenetic trees are discussed.

Type
Research Article
Information
Paleobiology , Volume 20 , Issue 4 , Fall 1994 , pp. 470 - 483
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Bryant, H. 1991. The polarization of character transformations in phylogenetic systematics: role of axiomatic and auxiliary assumptions. Systematic Zoology 40:433–445.CrossRefGoogle Scholar
Carlson, S. J. 1991. A phylogenetic perspective on articulate brachiopod diversity and the Permo-Triassic extinctions. Pp. 119–142in Dudley, E. C., ed. The unity of evolutionary biology, Vol. I. Dioscorides Press, Ore.Google Scholar
Carter, J. 1990. Skeletal biomineralization: patterns, processes and evolutionary trends. Van Nostrand Reinhold, New York.Google Scholar
Cavalli-Sforza, L. L., and Edwards, A. W. F. 1967. Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19:233–257.Google ScholarPubMed
Coombs, M. C. 1989. Interrelationships and diversity in the Chalicotheriidae. Pp. 438–457in Prothero, and Schoch, 1989.Google Scholar
de Queiroz, K. 1985. The ontogenetic method for determining character polarity and its relevance to phylogenetic systematics. Systematic Zoology 34:280–299.CrossRefGoogle Scholar
Donoghue, M., Doyle, J., Gauthier, J., Kluge, A., and Rowe, T. 1989. The importance of fossils in phylogeny reconstruction. Annual Review of Ecology and Systematics 20:431–460.CrossRefGoogle 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.CrossRefGoogle Scholar
Evander, R. L. 1989. Phylogeny of the family equidae. Pp. 109–127in Prothero, and Schoch, 1989.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. I. Amphibians, reptiles, birds. Systematics Association Special Volume No. 35A. Clarendon, Oxford.Google Scholar
Faith, D. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40:366–375.CrossRefGoogle Scholar
Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27:401–410.CrossRefGoogle Scholar
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791.CrossRefGoogle ScholarPubMed
Fisher, D. C. 1982. Phylogenetic and macroevolutionary patterns within the Xiphosurida. North American Paleontological Convention III, Proceedings 1:175–180.Google Scholar
Fisher, D. C. 1988. Stratocladistics: integrating stratigraphic and morphologic data in phylogenetic inference. Geological Society of America, Abstracts with Program 20:A186.Google Scholar
Fisher, D. C. 1991. Phylogenetic analysis and its application in evolutionary paleobiology. Pp. 103–122in Gilinsky, N. L. and Signor, P. W., eds. Analytical paleobiology. Short courses in paleontology, No. 4. Paleontological Society, Lawrence, Kans.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. Sinauer, Sunderland, Mass.Google Scholar
Fitch, W. M., and Margoliash, E. 1967. Construction of phylogenetic trees. Science 155:279–284.CrossRefGoogle ScholarPubMed
Frost, D. R., and Hillis, D. M. 1990. Species in concept and practice: herpetological applications. Herpetologica 46:87–104.Google Scholar
Gauthier, J., Kluge, A., and Rowe, T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105–209.CrossRefGoogle ScholarPubMed
Gingerich, P. 1979. The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. Pp. 41–77in Cracraft, J. and Eldredge, N., eds. Phylogenetic analysis and paleontology. Columbia University Press, New York.CrossRefGoogle Scholar
Grande, L. 1990. Paddlefishes, paleontology, and the importance of a more complete data set. Journal of Vertebrate Paleontology, Abstracts of Papers, 10(supplement to number 3):25A.Google Scholar
Harper, C. 1976. Phylogenetic inference in paleontology. Journal of Paleontology 50:180–193.Google Scholar
Harry, H. 1985. Synopsis of the supraspecific classification of living oysters (Bivalvia: Gryphaeidae and Ostreidae). The Veliger 28:121–158.Google Scholar
Hillis, D. M., and Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42:182–192.CrossRefGoogle Scholar
Huelsenbeck, J. 1991. When are fossils better than extant taxa in phylogenetic analysis? Systematic Zoology 40:458–469.CrossRefGoogle Scholar
Huelsenbeck, J. 1992. Oyster phylogeny: fossils and confidence. Masters thesis. University of Texas, Austin.Google Scholar
Maden, B. J. 1989. The Brontotheriidae: a systematic revision and preliminary phylogeny of North American genera. Pp. 458–489in Prothero, and Schoch, 1989.Google Scholar
Marshall, C. R. 1991. Estimation of taxonomic ranges from the fossil record. Pp. 19–38in Gilinsky, N. L. and Signor, P. W., eds. Analytical paleobiology. Short courses in paleontology, No. 4. Paleontological Society, Lawrence, Kans.Google Scholar
Mitchell, C. E. 1987. Evolution and phylogenetic classification of the Diplograptacea. Paleontology 30:353–405.Google Scholar
Norell, M., and Novacek, M. 1992. The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255:1690–1693.CrossRefGoogle ScholarPubMed
Novacek, M. 1992a. Fossils, topologies, missing data and the higher level phylogeny of eutherian mammals. Systematic Biology 41:58–73.CrossRefGoogle Scholar
Novacek, M. 1992b. Fossils as critical data for phylogeny. Pp. 46–88 in Novacek, M. and Wheeler, Q., eds. Extinction and phylogeny. Columbia University Press, New York.Google Scholar
Paul, C. 1982. The adequacy of the fossil record. Pp. 75–117in Joysey, K. and Friday, A., eds. Systematics Association Special Volume No. 21, Problems of phylogenetic reconstruction. Academic Press, London.Google Scholar
Paul, C. 1985. The adequacy of the fossil record reconsidered. Special Papers in Paleontology 33:7–15.Google Scholar
Prothero, D. R., and Schoch, R. M., eds. 1989. The evolution of perissodactyls. Oxford University Press, New York.Google Scholar
Schoch, R. M. 1989. A review of the Taperioids. Pp. 298–320in Prothero, and Schoch, 1989.Google Scholar
Simpson, G. G. 1961. Principles of animal taxonomy. Columbia University Press, New York.CrossRefGoogle Scholar
Smith, A. B. 1988. Patterns of diversification and extinction in Early Paleozoic Echinoderms. Paleontology 31:799–828.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
Swofford, D. L. 1992. PAUP: phylogenetic analysis using parsimony, version 3.1. Illinois Natural History Survey, Champaign.Google Scholar
Thewissen, J. 1992. Temporal data in phylogenetic systematics: An example from the mammalian fossil record. Journal of Paleontology 66:1–8.CrossRefGoogle Scholar
Wiley, E. O. 1978. The evolutionary species concept reconsidered. Systematic Zoology 27:17–26.CrossRefGoogle Scholar
Wiley, E. O. 1980. Is the evolutionary species fiction?—a consideration of classes, individuals, and historical entities. Systematic Zoology 29:76–80.CrossRefGoogle Scholar
Wiley, E. O. 1981. Phylogenetics: the theory and practice of phylogenetic systematics. John Wiley & Sons, New York.Google Scholar
Wilson, M. 1990. Early fossil records of freshwater fishes and their role in phylogenetic analysis. Journal of Vertebrate Paleontology, Abstracts of Papers, 10(supplement to number 3):25A.Google Scholar
Wright, D. 1993. Evolution of sexually dimorphic characters in peccaries (Mammalia, Tayassuidae). Paleobiology 19:52–70.CrossRefGoogle Scholar