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Phylogenetic analyses and the fossil record: Tests and inferences, hypotheses and models

Published online by Cambridge University Press:  26 February 2019

Peter J. Wagner
Department of Geology, Field Museum of Natural History, 1400 Lake Shore Drive, Chicago, Illinois 60605. E-mail:
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Tree-based paleobiological studies use inferred phylogenies as models to test hypotheses about macroevolution and the quality of the fossil record. Such studies raise two concerns. The first is how model trees might bias results. The second is testing hypotheses about parameters that affect tree inference.

Bias introduced by model trees is explored for tree-based assessments of the quality of the fossil record. Several nuisance parameters affect tree-based metrics, including consistency of sampling probability, rates of speciation / extinction, patterns of speciation, applied taxonomic philosophy, and assumed taxonomy. The first two factors affect probabilistic assessments of sampling, but also can be tested and accommodated in sophisticated probability tests. However, the final three parameters (and the assumption of a correct phylogeny) do not affect probabilistic assessments.

Often paleobiologists wish to test hypotheses such as rates of character change or rates of preservation. Assumptions about such parameters are necessary in simple phylogenetic methods, even if the assumptions are that rates are homogeneous or that sampling is irrelevant. Likelihood tests that evaluate phylogenies in light of stratigraphic data and / or alternative hypotheses of character evolution can reduce assumptions about unknowns by testing numerous unknowns simultaneously. Such tests have received numerous criticisms, largely based in philosophy. However, such criticisms are based on incorrect depictions of the logical structures of parsimony and likelihood, misunderstandings about when arguments are probabilistic (as opposed to Boolean), overly restrictive concepts of when data can test a hypothesis, and simply incorrect definitions of some terms.

Likelihood methods can test multiparameter hypotheses about phylogeny and character evolution (i.e., rates, independence, etc.). The best hypothesis positing a single rate of independent character change (with no variation among character states) is determined for each topology. Hypotheses about rate variation among characters or across phylogeny, character independence, and different patterns of state evolution then are examined until one finds the simplest (i.e., fewest varying parameters) hypothesis that cannot be rejected given knowledge of a more complicated hypothesis. This is repeated for alternative topologies. An example is presented using hyaenids. Two trees are contrasted, one of which requires the minimum necessary steps and the other of which requires at least seven additional steps. Given either tree, likelihood rejects fewer than three general rates of character change and also rejects the hypothesis of independence among the characters. However, hypotheses of changes in rates across the tree do not add substantially to the tree likelihood. The likelihoods of the trees given stratigraphic data also are determined. Both morphologic and stratigraphic data suggest that the multiparameter hypothesis including the parsimony tree is significantly less likely than the multiparameter hypothesis including a different tree.

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Copyright © 2000 by The Paleontological Society 

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Alroy, J. 1994. Four permutation tests for the presence of phylogenetic structure. Systematic Biology 43:430437.CrossRefGoogle Scholar
Archie, J. W. 1989. A randomization test for phylogenetic information in systematic data. Systematic Zoology 38:239252.CrossRefGoogle Scholar
Atchley, W. R., and Fitch, W. M. 1992. Gene trees and the origins of inbred strains of mice. Science 254:554558.CrossRefGoogle Scholar
Barnard, G. A., Jenkins, G. M., and Winston, C. B. 1962. Likelihood inference and time series. Journal of the Royal Statistics Society A 125:321372.CrossRefGoogle Scholar
Benton, M. J. 1995. Testing the time axis of phylogenies. Philosophical Transactions of the Royal Society of London B 349:510.Google Scholar
Benton, M. J. 1998. Molecular and morphological phylogenies of mammals: congruence with stratigraphic data. Molecular Phylogenetics and Evolution 9:398407.CrossRefGoogle ScholarPubMed
Benton, M. J., and Hitchin, R. 1997. Congruence between phylogenetic and stratigraphic data on the history of life. Proceedings of the Royal Society of London B 264:885890.CrossRefGoogle Scholar
Benton, M. J., and Storrs, G. W. 1994. Testing the quality of the fossil record: paleontological knowledge is improving. Geology 22:111114.2.3.CO;2>CrossRefGoogle Scholar
Benton, M. J., Wills, M. A., and Hitchin, R. 2000. Quality of the fossil record through time. Nature 403:534537.CrossRefGoogle ScholarPubMed
Bottjer, D. J., and Jablonski, D. 1988. Paleoenvironmental patterns in the evolution of post-Paleozoic benthic marine invertebrates. Palaios 3:540560.CrossRefGoogle Scholar
Brady, R. H. 1985. On the independence of systematics. Cladistics 1:113126.CrossRefGoogle Scholar
Brochu, C. 1997. Morphology, fossils, divergence timing, and the phylogenetic relationships of Gavialis. Systematic Biology 46:479522.Google Scholar
Camin, J. H., and Sokal, R. R. 1965. A method for deducing branching sequences in phylogeny. Evolution 19:311326.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. 184207 in Erwin, D. H. and Anstey, R. L., eds. New approaches for studying speciation in the fossil record. Columbia University Press, New York.Google Scholar
Cloutier, R. 1991. Patterns, trends, and rates of evolution with the Actinistia. Environmental Biology of Fishes 32:2358.CrossRefGoogle Scholar
Clyde, W. C., and Fisher, D. C. 1997. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology 23:119.CrossRefGoogle Scholar
de Queiroz, K., and Gauthier, J. 1990. Phylogeny as a central principle in taxonomy: phylogenetic definitions of taxon names. Systematic Zoology 39:307332.CrossRefGoogle Scholar
de Queiroz, K., and Gauthier, J. 1992. Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23:449480.CrossRefGoogle Scholar
Edwards, A. W. F. 1992. Likelihood—expanded edition. Johns Hopkins University Press, Baltimore.Google Scholar
Edwards, A. W. F. 1996. The origin and early development of the method of minimum evolution for the reconstruction of phylogenetic trees. Systematic Biology 45:7991.CrossRefGoogle Scholar
Edwards, A. W. F., and Cavalli-Sforza, L. L. 1964. Reconstruction of evolutionary trees. Pp. 6776 in Heywood, J. H. and McNeil, J., eds. Phenetic and phylogenetic classification. Systematic Association, London.Google Scholar
Eldredge, N. 1971. The allopatric model and phylogeny in Paleozoic invertebrates. Evolution 25:156167.CrossRefGoogle ScholarPubMed
Eldredge, N., and Gould, S. J. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Pp. 82115 in Schopf, T. J. M., ed. Models in paleobiology. Freeman, Cooper, San Francisco.Google Scholar
Estabrook, G. F., Johnson, C. S. Jr., and McMorris, F. R. 1975. An idealized concept of the true cladistic character. Mathematical Biosciences 23:263272.CrossRefGoogle Scholar
Farris, J. S. 1973. A probability model for inferring evolutionary trees. Systematic Zoology 22:250256.CrossRefGoogle Scholar
Farris, J. S. 1977. Phylogenetic analysis under Dollo's Law. Systematic Biology 26:7788.CrossRefGoogle Scholar
Felsenstein, J. 1973. Maximum-likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology 22:240249.CrossRefGoogle Scholar
Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27:401410.CrossRefGoogle Scholar
Felsenstein, J. 1981a. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17:368376.CrossRefGoogle Scholar
Felsenstein, J. 1981b. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnean Society 16:183196.CrossRefGoogle Scholar
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:115.CrossRefGoogle Scholar
Felsenstein, J. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19:445471.CrossRefGoogle Scholar
Fisher, D. C. 1982. Phylogenetic and macroevolutionary patterns within the Xiphosurida. Pp. 175180 in Mamet, B. and Copeland, M. J., eds. Proceedings of the third North American paleontological convention. Geological Survey of Canada, Montreal.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 Course in Paleontology 4:103122. Paleontological Society, Knoxville, Tenn.Google Scholar
Fisher, D. C. 1994. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. Pp. 133171 in Grande, L. and Rieppel, O., eds. Interpreting the hierarchy of nature—from systematic patterns to evolutionary process theories. Academic Press, Orlando.Google Scholar
Flynn, J. J. 1996. Carnivoran phylogeny and rates of evolution: morphological, taxic, and molecular. Pp. 542581 in Gittleman, J., ed. Carnivoran behavior, ecology and evolution, Vol. 2. Comstock, Ithaca, N.Y. Google Scholar
Foote, M. 1996. On the probability of ancestors in the fossil record. Paleobiology 22:141151.CrossRefGoogle Scholar
Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23:278300.CrossRefGoogle Scholar
Foote, M., Hunter, J. P., Janis, C. M., and Sepkoski, J. J. Jr. 1999. Evolutionary and preservational constraints on the origins of major biologic groups: limiting divergence times of eutherian mammals. Science 283:13101314.CrossRefGoogle Scholar
Foote, M., and Raup, D. M. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121140.CrossRefGoogle ScholarPubMed
Foote, M., and Sepkoski, J. J. Jr. 1999. Absolute measures of the completeness of the fossil record. Nature 398:415417.CrossRefGoogle ScholarPubMed
Fortey, R. A., and Jefferies, R. P. S. 1982. Fossils and phylogeny—a compromise approach. Pp. 197234 in Joysey and Friday 1982.Google Scholar
Gauthier, J., Kluge, A. G., and Rowe, T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105209.CrossRefGoogle Scholar
Gayon, J. 1990. Critics and criticisms of the modern synthesis—the viewpoint of a philosopher. Evolutionary Biology 24:149.Google Scholar
Goldman, N. 1993. Statistical tests of models of DNA substitution. Journal of Molecular Evolution 36:182198.CrossRefGoogle ScholarPubMed
Gould, S. J., and Lewontin, R. C. 1979. The spandrels of San Marco and the Panglossian Paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society of London B 205:581598.Google Scholar
Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? A simulation study. Systematic Biology 47:917.CrossRefGoogle ScholarPubMed
Grimaldi, R. P. 1994. Discrete and combinatorial mathematics, 3d ed. Addison-Wesley, New York.Google Scholar
Harvey, P. H., and Pagel, M. D. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford.Google Scholar
Hasagawa, M., Kishino, H., and Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160174.CrossRefGoogle Scholar
Heyning, J. E., and Thacker, C. 1999. Phylogenies, temporal data, and negative evidence. Science 285:1179.CrossRefGoogle Scholar
Hillis, D. M., and Huelsenbeck, J. P. 1992. Signal, noise, and reliability in molecular phylogenetic analysis. Journal of Heredity 83:189195.CrossRefGoogle Scholar
Hitchin, R., and Benton, M. J. 1997. Stratigraphic indices and tree balance. Systematic Biology 46:563569.CrossRefGoogle Scholar
Hoffmann, R., Minkin, V. I., and Carpenter, B. K. 1997. Ockham's Razor and chemistry. HYLE—An International Journal for the Philosophy of Chemistry 3:328.Google Scholar
Holland, S. M. 2000. The quality of the fossil record: a sequence stratigraphic perspective. In Erwin, D. H. and Wing, S. L., eds. Deep time: Paleobiology's perspective. Paleobiology 26(Suppl. to No.4):148168.CrossRefGoogle Scholar
Huelsenbeck, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis? Systematic Zoology 40:458469.CrossRefGoogle Scholar
Huelsenbeck, J. P. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20:470483.CrossRefGoogle Scholar
Huelsenbeck, J. P., and Crandall, K. A. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics 28:437466.CrossRefGoogle Scholar
Huelsenbeck, J. P., and Kirkpatrick, M. 1996. Do phylogenetic methods produce trees with biased shapes? Evolution 50:14181424.CrossRefGoogle ScholarPubMed
Huelsenbeck, J. P., and Nielsen, R. 1999. Effects of nonindependent substitution on phylogenetic accuracy. Systematic Biology 48:317328.CrossRefGoogle Scholar
Huelsenbeck, J. P., and Rannala, B. 1997. Maximum likelihood estimation of topology and node times using stratigraphic data. Paleobiology 23:174180.CrossRefGoogle Scholar
Huelsenbeck, J. P., Hillis, D. M., and Jones, R. 1996. Parametric bootstrapping in molecular phylogenetics: applications and performance. Pp. 1945 in Ferraris, J. D. and Palumbi, S. R., eds. Molecular zoology: advances, strategies and protocols. Wiley-Liss, New York.Google Scholar
Hull, D. L. 1983. Karl Popper and Plato's metaphor. Pp. 177189 in Platnick, N. L. and Funk, V. A., eds. Advances in cladistics. Columbia University Press, New York.Google Scholar
Hume, D. 1748. An inquiry concerning human understanding. Bobbs Merrill, Indianapolis.Google Scholar
Hurlbert, S. H. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577586.CrossRefGoogle ScholarPubMed
Jackson, J. B. C., and Cheetham, A. H. 1994. Phylogeny reconstruction and the tempo of speciation in cheilostome Bryozoa. Paleobiology 20:407423.CrossRefGoogle Scholar
Jefferys, W. H., and Berger, J. O. 1992. Ockham's Razor and Bayesian analysis. American Scientist 80:6472.Google Scholar
Joysey, K. A., and Friday, A. E., eds. 1982. Problems of phylogenetic reconstruction. Academic Press, London.Google Scholar
Jukes, T. H., and Cantor, C. R. 1969. Evolution of protein molecules. Pp. 21132 in Munro, H. M., ed. Mammalian protein metabolism. Academic, New York.CrossRefGoogle Scholar
Kitching, I. J., Forey, P. L., Humphries, C., and Williams, D. M. 1998. Cladistics, 2d ed. The theory and practice of parsimony analysis. Oxford University Press, Oxford.Google Scholar
Kluge, A. G. 1997. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:8196.CrossRefGoogle Scholar
Kluge, A. G., and Farris, J. S. 1969. Quantitative phyletics and the evolution of anurans. Systematic Zoology 18:132.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 11:459468.Google ScholarPubMed
Lande, R. 1975. Natural selection and random genetic drift in phenotypic evolution. Evolution 30:314334.CrossRefGoogle Scholar
Le Quesne, W. J. 1969. A method of selection of characters in numerical taxonomy. Systematic Zoology 18:201205.CrossRefGoogle Scholar
Lipton, P. 1991. Inference to the best explanation. Routledge, London.CrossRefGoogle Scholar
Maddison, W. P., and Maddison, D. R. 1992. MacClade, analysis of phylogeny and character evolution. Sinauer, Sunderland, Mass.Google Scholar
Marshall, C. R. 1990. Confidence intervals on stratigraphic ranges. Paleobiology 16:110.CrossRefGoogle Scholar
Marshall, C. R. 1994. Confidence intervals on stratigraphic ranges: partial relaxation of the assumption of randomly distributed fossil horizons. Paleobiology 20:459469.CrossRefGoogle Scholar
Marshall, C. R. 1997. Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology 23:165173.CrossRefGoogle Scholar
Marshall, C. R., and Ward, P. D. 1996. Sudden and gradual molluscan extinctions in the latest Cretaceous of the western European Tethys. Science 274:13601363.CrossRefGoogle ScholarPubMed
Martin, R. M. 1997. Scientific thinking. Broadview, Toronto.Google Scholar
Mayr, E. 1942. Systematics and the origin of species. Columbia University Press, New York.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 48:17471763.CrossRefGoogle ScholarPubMed
Meacham, C. A. 1984. Evaluating characters by character compatibility analysis. Pp. 152165 in Duncan, T. and Stuessy, T. F., eds. Cladistics: perspectives on the reconstruction of evolutionary history. Columbia University Press, New York.Google Scholar
Mooers, A. Ø., and Schluter, D. 1999. Reconstructing ancestor states with maximum likelihood: support for one- and two-rate models. Systematic Biology 48:623633.CrossRefGoogle Scholar
Mooers, A. Ø., Page, R. D. M., Purvis, A., and Harvey, P. H. 1995. Phylogenetic noise leads to unbalanced cladistic tree reconstructions. Systematic Biology 44:332342.CrossRefGoogle Scholar
Newman, C. M., Cohen, J. E., and Kipnis, C. 1985. Neo-darwinian evolution implies punctuated equilibria. Nature 315:400401.CrossRefGoogle Scholar
Newton-Smith, W. H. 1981. The rationality of science. Routledge, London.CrossRefGoogle Scholar
Norell, M. A. 1992. Taxic origin and temporal diversity: the effect of phylogeny. Pp. 89118 in 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:407417.CrossRefGoogle Scholar
Norell, M. A. 1996. Ghost taxa, ancestors and assumptions—a comment on Wagner. Paleobiology 22:454455.CrossRefGoogle Scholar
Norell, M. A., and Novacek, M. J. 1992a. Congruence between superpositional and phylogenetic patterns: comparing cladistic patterns with fossil records. Cladistics 8:319337.CrossRefGoogle Scholar
Norell, M. A., and Novacek, M. J. 1992b. The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255:16901693.CrossRefGoogle Scholar
O'Keefe, F. R., and Sander, P. M. 1999. Paleontological paradigms and inferences of phylogenetic pattern: a case study. Paleobiology 25:518533.CrossRefGoogle Scholar
O'Keefe, F. R., and Wagner, P. J. 1999. A compatibility-based method for assess the independence of cladistic characters. Geological Society of America Abstracts with Programs 32:A30.Google Scholar
Pagel, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London B 255:3745.Google Scholar
Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48:612622.CrossRefGoogle Scholar
Patterson, C. 1982. Morphological characters and homology. Pp. 2174 in Joysey and Friday 1982.Google Scholar
Paul, C. R. C. 1982. The adequacy of the fossil record. Pp. 75117 in Joysey and Friday 1982.Google Scholar
Paul, C. R. C. 1985. The adequacy of the fossil record revisited. Pp. 116 in Cope, J. C. W. and Skelton, P. W., eds. Evolutionary case histories from the fossil record. Palaeontological Society, London.Google Scholar
Paul, C. R. C. 1992. The recognition of ancestors. Historical Biology 6:239250.CrossRefGoogle Scholar
Peirce, C. S. 1878. Deduction, induction, and hypothesis. Popular Science Monthly 13:470482.Google Scholar
Platnick, N. I. 1977. Cladograms, phylogenetic trees, and hypothesis testing. Systematic Zoology 26:438442.CrossRefGoogle Scholar
Popper, K. R. 1959. The logic of scientific discovery. Routledge, London.Google Scholar
Raup, D. M., and Gould, S. J. 1974. Stochastic simulation and evolution of morphology—towards a nomothetic paleontology. Systematic Zoology 23:305322.CrossRefGoogle Scholar
Raup, D. M., Gould, S. J., Schopf, T. J. M., and Simberloff, D. S. 1973. Stochastic models of phylogeny and the evolution of diversity. Journal of Geology 81:525542.CrossRefGoogle Scholar
Rensch, B. 1960. Evolution above the species level. Columbia University Press, New York.Google Scholar
Rieppel, O. 1997. Falsificationist versus verificationist approaches to history. Journal of Vertebrate Paleontology 17A:71A.Google Scholar
Rieppel, O., and Grande, L. 1994. Summary and comments on systematic pattern and evolutionary process. Pp. 133171 in Grande, L. and Rieppel, O., eds. Interpreting the hierarchy of nature—from systematic patterns to evolutionary process theories. Academic Press, Orlando.Google 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 44:16711684.CrossRefGoogle ScholarPubMed
Sanderson, M. J. 1993. Reversibility in evolution: a maximum likelihood approach to character gain/loss bias in phylogenies. Evolution 47:236252.CrossRefGoogle ScholarPubMed
Sanderson, M. J., and Donoghue, M. J. 1989. Patterns of variation in levels of homoplasy. Evolution 43:17811795.CrossRefGoogle ScholarPubMed
Sanderson, M. J., and Donoghue, M. J. 1994. Shifts in diversification rate with the origin of angiosperms. Science 264:15901593.CrossRefGoogle ScholarPubMed
Sankoff, D., and Rousseau, P. 1975. Locating the vertices of a Steiner tree in arbitrary space. Mathematical Programming 9:240246.CrossRefGoogle Scholar
Schluter, D., Price, T., Mooers, A. Ø., and Ludwig, D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:16991711.CrossRefGoogle ScholarPubMed
Shaffer, H. B., Clark, J. M., and Kraus, F. 1991. When molecules and morphology clash: a phylogenetic analysis of the North American ambystomatid salamanders (Caudata: Ambystomatidae). Systematic Zoology 40:284303.CrossRefGoogle Scholar
Siddall, M. E., and Kluge, A. G. 1997. Probabilism and phylogenetic inference. Cladistics 13:313336.CrossRefGoogle Scholar
Sidor, C. A., and Hopson, J. A. 1998. Ghost lineages and “mammalness”: assessing the temporal pattern of character acquisition in the Synapsida. Paleobiology 24:254273.Google Scholar
Smith, A. B. 1988. Patterns of diversification and extinction in early Palaeozoic echinoderms. Palaeontology 31:799828.Google Scholar
Smith, A. B. 1994. Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific, Oxford.CrossRefGoogle Scholar
Smith, A. B., and Littlewood, D. T. J. 1994. Paleontological data and molecular phylogenetic analysis. Paleobiology 20:259273.CrossRefGoogle Scholar
Smith, A. B., Lafay, B., and Christen, R. 1992. Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids. Philosophical Transactions of the Royal Society of London B 338:365382.Google ScholarPubMed
Sneath, P. H. A. 1995. Thirty years of numerical taxonomy. Systematic Biology 44:281298.CrossRefGoogle Scholar
Sober, E. 1988. The nature of selection: evolutionary theory in philosophical focus. MIT Press, Cambridge.Google Scholar
Sokal, R. R., and Rohlf, F. J. 1981. Biometry, 2d ed. W. H. Freeman, New York.Google Scholar
Solow, A. R. 1993. Inferring extinction in a declining population. Ecology 74:962963.CrossRefGoogle Scholar
Solow, A. R. 1996. Tests and confidence intervals for a common upper endpoint in fossil taxa. Paleobiology 22:406410.CrossRefGoogle Scholar
Solow, A. R., and Smith, W. 1997. On fossil preservation and the stratigraphic ranges of taxa. Paleobiology 23:271277.CrossRefGoogle Scholar
Springer, M. S., and Lilje, A. 1988. Biostratigraphy and gap analysis: the expected sequence of biostratigraphic events. Journal of Geology 96:228236.CrossRefGoogle Scholar
Strauss, D., and Sadler, P. M. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21:411427.CrossRefGoogle Scholar
Swofford, D. L., and Olsen, G. J. 1990. Phylogeny reconstruction. Pp. 411501 in Hillis, D. M. and Moritz, G., eds. Molecular Systematics. Sinauer, Sunderland, Mass.Google Scholar
Wagner, P. J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21:153178.CrossRefGoogle Scholar
Wagner, P. J. 1997. Patterns of morphologic diversification among the Rostroconchia. Paleobiology 23:115150.CrossRefGoogle Scholar
Wagner, P. J. 1998. A likelihood approach for estimating phylogenetic relationships among fossil taxa. Paleobiology 24:430449.CrossRefGoogle Scholar
Wagner, P. J. 1999. Phylogenetics of Ordovician-Silurian Lophospiridae (Gastropoda: Murchisoniina): the importance of stratigraphic data. American Malacological Bulletin 15:131.Google Scholar
Wagner, P. J. 2000a. The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Systematic Biology 49:6586.CrossRefGoogle Scholar
Wagner, P. J. 2000b. Exhaustion of morphologic character states among fossil taxa. Evolution 54:365386.CrossRefGoogle Scholar
Wagner, P. J. 2000c. Likelihood tests of hypothesized durations: determining and accommodating biasing factors. Paleobiology 26:431449.2.0.CO;2>CrossRefGoogle Scholar
Wagner, P. J., and Sidor, C. A. 2000. Age rank:clade rank metrics—sampling, taxonomy, and the meaning of “Stratigraphic Consistency.” Systematic Biology 49:463479.Google Scholar
Weiss, R. E., and Marshall, C. R. 1999. The uncertainty in the true end point of a fossil's stratigraphic ranges when stratigraphic sections are sampled discretely. Mathematical Geology 31:435453.CrossRefGoogle Scholar
Werdelin, L., and Solounias, N. 1991. The Hyaenidae: taxonomic systematics and evolution. Fossils and Strata 30:1104.Google Scholar
Wheeler, W. C. 1990. Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure. Cladistics 6:269275.CrossRefGoogle Scholar
Wiley, E. O. 1975. Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists. Systematic Zoology 24:233243.CrossRefGoogle Scholar
Wills, M. A. 1998. Crustacean disparity through the Phanerozoic: comparing morphological and stratigraphic data. Biological Journal of the Linnean Society 65:455500.CrossRefGoogle Scholar
Wills, M. A. 1999. The congruence between phylogeny and stratigraphy: randomization tests and the Gap Excess Ratio. Systematic Biology 48:559580.CrossRefGoogle Scholar
Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97159.Google ScholarPubMed
Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the Sixth International Congress of Genetics 1:356366.Google Scholar
Yang, Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39:306314.CrossRefGoogle ScholarPubMed
Zadeh, L. A. 1965. Fuzzy sets. Information Control 8:338353.CrossRefGoogle Scholar

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