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A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa

Published online by Cambridge University Press:  08 February 2016

Peter J. Wagner
Peter J. Wagner*
Affiliation:
Department of Geology, Field Museum of Natural History, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605. E-mail: pwagner@fmnh.org
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Abstract

Estimates of phylogenetic relationships among fossil taxa implicitly provide hypotheses about the quality of the fossil record. Phylogenetic inferences also provide hypotheses about character evolution. The likelihood of any hypothesis that makes predictions about two data sets is simply the likelihood of the hypothesis given the first data set times the likelihood of the same hypothesis given the second data set. In this case, data set 1 represents stratigraphy and data set 2 represents morphology. Statistical methods exist for determining the likelihood of hypothesized levels of sampling. The likelihood of a hypothesized amount of character change yielding a particular most-parsimonious solution (i.e, L[hypothesized length | parsimony length] can be evaluated with simulations. A reanalysis of hyaenid phylogeny based on published character and stratigraphic data is presented here, using the maximum likelihood method. Two trees are found, depending on assumptions about ambiguous species, which are 11 and 10 steps longer than the most parsimonious tree (61 or 60 vs. 50 steps). However, the trees invoke far less stratigraphic debt (9 or 12 units vs. 47 units as measured in Mammal Zones). An important feature of the results is that the most likely tree length given hyaenid character data is estimated to be 56 to 62 steps (depending on the model of character evolution) rather than 50 steps. The likelihood tree suggests stronger trends toward bone-crushing specializations than does the parsimony tree and further suggests that high levels of homoplasy caused parsimony to underestimate the true extent of those trends. Simulations based on the character data and fossil record of hyaenids suggest that the maximum likelihood method is better able to estimate correct trees than is parsimony and somewhat better able to do so than previously proposed phylogenetic methods incorporating stratigraphy.

Type
Articles
Information
Paleobiology , Volume 24 , Issue 4 , Fall 1998 , pp. 430 - 449
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Alroy, J. 1994. Four permutation tests for the presence of phylogenetic structure. Systematic Biology 43:430–437.CrossRefGoogle Scholar
Archie, J. W. 1996. Measures of homoplasy. Pp. 153–187in Sanderson, M. J. and Hufford, L., eds. Homoplasy—the recurrence of similarity in evolution. Academic Press, San Diego.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
Bull, J. J., Huelsenbeck, J. P., Cunningham, C. W., Swofford, D. L., and Waddell, P. J. 1993. Partitioning and combining data in phylogenetic analysis. Systematic Biology 42:384–397.CrossRefGoogle Scholar
Camin, J. H., and Sokal, R. R. 1965. A method for deducing branching sequences in phylogeny. Evolution 19:311–326.CrossRefGoogle Scholar
Cheetham, A. H., and Jackson, J. B. C. 1995. Process from pattern: tests for selection versus random change in punctuated bryozoan speciation. Pp. 184–207in Erwin, and Anstey, 1995.Google Scholar
Chippindale, P. T., and Wiens, J. J. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Systematic Biology 43:278–287.CrossRefGoogle Scholar
Clyde, W. C., and Fisher, D. C. 1997. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology 23:1–19.CrossRefGoogle Scholar
Edwards, A. W. F. 1992. Likelihood—expanded edition. Johns Hopkins University Press, Baltimore.Google Scholar
Eldredge, N., and Gould, S. J. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Pp. 82–115in Schopf, T. J. M., ed. Models in paleobiology. Freeman, Cooper, San Francisco.Google Scholar
Erwin, D. H., and Anstey, R. L. 1995. New approaches for studying speciation in the fossil record. Columbia University Press, New York.Google Scholar
Faith, D. P. 1991. Cladistic permutation tests for monophyly and nonmonophyly. Systematic Zoology 40:366–375.CrossRefGoogle Scholar
Faith, D. P., and Cranston, P. S. 1991. Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 7:1–28.CrossRefGoogle Scholar
Felsenstein, J. 1973. Maximum-likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22:240–249.CrossRefGoogle Scholar
Felsenstein, J. 1981a. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnean Society 16:183–196.CrossRefGoogle Scholar
Felsenstein, J. 1981b. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368–376.CrossRefGoogle ScholarPubMed
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 implication in evolutionary paleobiology. In Gilinsky, N. L. and Signor, P. W., eds. Analytical paleobiology. Short Courses in Paleontology 4: 103–122. Paleontological Society, Knoxville, Tenn.Google Scholar
Fisher, D. C. 1994. 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—from systematic patterns to evolutionary theories. Academic Press, Orlando, Fla.Google Scholar
Flynn, J. J. 1996. Carnivoran phylogeny and rates of evolution: morphological, taxic, and molecular. Pp. 542–581in Gittleman, J., ed. Carnivoran behavior, ecology and evolution, Vol. 2. Comstock Publishing, Ithaca, N.Y.Google Scholar
Foote, M. 1994. Morphological disparity in Ordovician-Devonian crinoids and the early saturation of morphological space. Paleobiology 20:320–344.CrossRefGoogle Scholar
Foote, M. 1996. On the probability of ancestors in the fossil record. Paleobiology 22:141–151.CrossRefGoogle Scholar
Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23:278–300.CrossRefGoogle Scholar
Foote, M., and Raup, D. M. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121–140.CrossRefGoogle ScholarPubMed
Goldman, N. 1993. Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36:182–198.CrossRefGoogle ScholarPubMed
Huelsenbeck, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20:470–483.CrossRefGoogle Scholar
Huelsenbeck, J. P., and Bull, J. J. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Systematic Biology 45:92–98.CrossRefGoogle Scholar
Huelsenbeck, J. P., and Kirkpatrick, M. 1996. Do phylogenetic methods produce trees with biased shapes? Evolution 50:1418–1424.CrossRefGoogle ScholarPubMed
Huelsenbeck, J. P., and Rannala, B. 1997. Maximum likelihood estimation of topology and node times using stratigraphic data. Paleobiology 23:174–180.CrossRefGoogle Scholar
Jackson, J. B. C., and Cheetham, A. H. 1994. Phylogeny reconstruction and the tempo of speciation in cheilostome Bryozoa. Paleobiology 20:407–423.CrossRefGoogle Scholar
Kuhner, M. K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11:459–468.Google ScholarPubMed
Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18:201–205.CrossRefGoogle Scholar
Maddison, W. P. 1990. A method for testing the correlated evolution of two binary characters: are gains or losses concentrated on certain branches of a phylogenetic tree? Evolution 44:539–557.CrossRefGoogle ScholarPubMed
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, and Anstey, 1995.Google Scholar
Mayr, E. 1963. Animal species and evolution. Harvard University Press, Cambridge.CrossRefGoogle Scholar
McShea, D. W. 1994. Mechanisms of large-scale evolutionary trends. Evolution 48:1747–1763.CrossRefGoogle ScholarPubMed
Mooers, A. Ø., Page, R. D. M., Purvis, A., and Harvey, P. H. 1995. Phylogenetic noise leads to unbalanced cladistic tree reconstructions. Systematic Biology 44:332–342.CrossRefGoogle Scholar
Norell, M. A. 1992. Taxic origin and temporal diversity: the effect of phylogeny. Pp. 89–118in Novacek, M. J. and Wheeler, Q. D., eds. Extinction and phylogeny. Columbia University Press, New York.Google 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.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
Penny, D., and Hendy, M. D. 1985. Testing methods of evolutionary tree construction. Cladistics 1:266–278.CrossRefGoogle ScholarPubMed
Schlosser, M. 1890. Die Affen, Lemuren, Chiropteren, Insectivoren, Marsupialier, Creodonten und Carnivoren des europäischen Tertiärs. III. Beiträge zur Paläontologie und Geologie Österreich-Ungarns und des Orients 8:1–107.Google Scholar
Schmidt-Kittler, N. 1976. Raubtiere aus dem Juntertiär Kleinasiens. Palaeontographica A 155:1–131.Google Scholar
Sepkoski, J. J. Jr. 1975. Stratigraphic biases in the analysis of taxonomic survivorship. Paleobiology 1:343–355.Google Scholar
Sharkey, M. J. 1989. A hypothesis-independent method of character weighting for cladistic analysis. Cladistics 5:63–86.Google ScholarPubMed
Signor, P. W., and Lipps, J. H. 1982. Sampling bias, gradual extinction patterns and catastrophes in the fossil record. Geological Society of America Special Paper 190:291–296.CrossRefGoogle Scholar
Simpson, G. G. 1953. The major features of evolution. Columbia University Press, New York.CrossRefGoogle Scholar
Smith, A. B. 1988. Patterns of diversification and extinction in early Palaeozoic echinoderms. Palaeontology 31:799–828.Google Scholar
Smith, A. B. 1994. Systematics and the fossil record—documenting evolutionary patterns. Blackwell Scientific, Oxford.Google Scholar
Smith, A. B., and Littlewood, D. T. J. 1994. Paleontological data and molecular phylogenetic analysis. Paleobiology 20:259–273.CrossRefGoogle Scholar
Sober, E. 1988. Reconstructing the past. MIT Press, Cambridge.Google Scholar
Sokal, R. R., and Rohlf, F. J. 1981. Biometry, 2d ed.W. H. Freeman, New York.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. 1996. PAUP*: Phylogenetic analysis using parsimony. Program distributed by Sinauer Associates, Sunderland, Mass.Google Scholar
Van Valen, L. 1973. A new evolutionary law. Evolutionary Theory 1:1–30.Google Scholar
Wagner, P. J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21:153–178.CrossRefGoogle Scholar
Wagner, P. J.In press. The quality of the fossil record and the accuracy of estimated phylogenies. Systematic Biology 47.Google Scholar
Wagner, P. J., and Erwin, D. H. 1995. Phylogenetic tests of speciation hypotheses. Pp. 87–122in Erwin, and Anstey, 1995.Google Scholar
Werdelin, L. 1989. Constraint and adaptation in the bone-cracking canid Osteoborus (Mammalia: Canidae). Paleobiology 15:387–401.CrossRefGoogle Scholar
Werdelin, L., and Solounias, N. 1991. The Hyaenidae: taxonomic systematics and evolution. Fossils and Strata 30:1–104.CrossRefGoogle Scholar
Werdelin, L. 1996. The evolutionary history of hyaenas in Europe and western Asia during the Miocene. Pp. 290–306in Bernor, R. L., Fahlbusch, V. and Mittmann, H.-W., eds. The evolution of western Eurasian Neogene mammal faunas. Colombia University Press, New York.Google Scholar
Werdelin, L., Tuner, A., and Solounias, N. 1994. Studies of fossil hyaenids: the genera Hyaenictis Gaudry and Chasmaporthetes Hay, with a reconsideration of the Hyaenidae of Langebannweg, South Africa. Zoological Journal of the Linnean Society 111:197–217.Google Scholar