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Evolutionary Patterns Within Fossil Lineages: Model-Based Assessment of Modes, Rates, Punctuations and Process

Published online by Cambridge University Press:  21 July 2017

Gene Hunt
Gene Hunt*
Affiliation:
Department of Paleobiology National Museum of Natural History, Smithsonian Institution NHB, MRC 121, P.O. Box 37012 Washington DC 20013-7012
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Abstract

Patterns of phenotypic change documented in the fossil record offer the only direct view scientists have of evolutionary transitions arrayed over significant durations of time. What lessons should be drawn from these data, however, has proven to be rather contentious. Although we as paleontologists have made great progress in documenting the geological record of phenotypic evolution with greater thoroughness and sophistication, these successes have been limited by the use of verbal models of how phenotypes change. Descriptive terms such as “gradual” have been understood differently by different authors, and this has led to completely incompatible summary statements about the fossil record of morphological evolution. Here I argue that the solution to this ambiguity lies in insisting that different evolutionary interpretations be represented as explicit, statistical models of evolution. With such an approach, the powerful machinery of likelihood-based inference can be help resolve long-standing paleontological questions.

Here I first review this approach and some aspects of its implementation. Then, I show how this approach leads to new traction on important issues in evolutionary paleobiology, including: understanding modes of evolution and determining their relative importance, separating evolutionary mode from tempo, assessing the evidence for hypotheses of punctuated change, and detecting adaptive evolution in the fossil record.

Type
Research Article
Information
The Paleontological Society Papers , Volume 14: From Evolution to Geobiology: Research Questions Driving Paleontology at the Start of a New Century , October 2008 , pp. 117 - 131
Copyright
Copyright © by the Paleontological Society 

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References

Literature Cited

Akaike, H. 1974. A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6):716–723.Google Scholar
Alroy, J. 2000. Understanding the dynamics of trends within evolving lineages. Paleobiology, 26(3):319–329.Google Scholar
Anderson, D. R., Burnham, K. P., and Thompson, W. L. 2000. Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management, 64(4):912–923.Google Scholar
Arnold, S. J., Pfrender, M. E., and Jones, A. G. 2001. The adaptive landscape as a conceptual bridge between micro- and macroevolution. Genetica, 112–113:9–32.Google Scholar
Bell, M. A., Aguirre, W. E., and Buck, N. J. 2004. Twelve years of contemporary armor evolution in a threespine stickleback population. Evolution, 58(4):814–824.Google Scholar
Bell, M. A., Travis, M. P., and Blouw, D. M. 2006. Inferring natural selection in a fossil threespine stickleback. Paleobiology, 32(4):562–577.Google Scholar
Bookstein, F. L. 1987. Random walk and the existence of evolutionary rates. Paleobiology, 13(4):446–464.CrossRefGoogle Scholar
Bookstein, F. L. 1988. Random walk and the biometrics of morphological characters. Evolutionary Biology, 9:369–398.Google Scholar
Butler, M. A., and King, A. A. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, 164(6):683–695.Google Scholar
Charlesworth, B. 1984. Some quantitative methods for studying evolutionary patterns in single characters. Paleobiology, 10(3):308–318.Google Scholar
Chiba, S. 1996. A 40,000-year record of discontinuous evolution of island snails. Paleobiology, 22(2):177–188.Google Scholar
Eldredge, N., and Gould, S. J. 1972. Punctuated equilibria: an alternative to phyletic gradualism, p. 82–115. In Schopf, T. J. M. (ed.), Models in Paleobiology. Freeman, Cooper & Company, San Francisco.Google Scholar
Eldredge, N., Thompson, J. N., Brakefield, P. M., Gavrilets, S., Jablonski, D., Jackson, J. B. C., Lenski, R. E., Lieberman, B. S., McPeek, M. A., and Miller, W. I. 2005. The dynamics of evolutionary stasis. Paleobiology, 31(Supplement to 2):133–145.Google Scholar
Erwin, D. H., and Anstey, R. L. 1995. Speciation in the fossil record, p. 11–38. In Erwin, D. H. and Anstey, R. L. (eds.), New Approaches to Speciation in the Fossil Record. Columbia University Press, New York.Google Scholar
Estes, S., and Arnold, S. J. 2007. Resolving the paradox of stasis: models with stabilizing selection explain evolutionary divergence on all timescales. American Naturalist, 169(2):227–244.Google Scholar
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist, 125(1):1–15.CrossRefGoogle Scholar
Finkel, Z. V., Sebbo, J., Feist-Burkhardt, S., Irwin, A. J., Katz, M. E., Schofield, O. M. E., Young, J. R., and Falkowski, P. G. 2007. A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic. Proceedings of the National Academy of Sciences USA, 104(51):20416–20420.Google Scholar
Foote, M. 1991. Analysis of morphological data, p. 59–86. In Gilinsky, N. L. and Signor, P. W. (eds.), Analytical Paleobiology. Volume 4. The Paleontological Society.Google Scholar
Fortey, R. A. 1988. Seeing is believing: gradualism and punctuated equilibria in the fossil record. Science Progress, 72:1–19.Google Scholar
Garland, T., and Ives, A. R. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist, 155(3):346–364.Google Scholar
Gingerich, P. D. 1985. Species in the fossil record: concepts, trends, and transitions. Paleobiology, 11(1):27–41.Google Scholar
Gingerich, P. D. 1993. Quantification and comparison of evolutionary rates. American Journal of Science, 293-A:453–478.Google Scholar
Gingerich, P. D. 2001. Rates of evolution on the time scale of evolutionary process. Genetica, 112–113:127–144.CrossRefGoogle Scholar
Gingerich, P. D., and Gunnell, G. F. 1995. Rates of evolution in Paleocene-Eocene mammals of the Clarks Fork Basin, Wyoming, and a comparison with Neogene Siwalik lineages of Pakistan. Palaeogeography, Palaeoclimatology, Palaeoecology, 115(1–4):227–247.Google Scholar
Gould, S. J. 2002. The Structure of Evolutionary Theory. Belknap Press, Cambridge, Massachusetts, 1433 p.Google Scholar
Gould, S. J., and Eldredge, N. 1977. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology, 3(2):115–151.Google Scholar
Haldane, J. B. S. 1949. Suggestions as to the quantitative measurement of rates of evolution. Evolution, 3:51–56.Google Scholar
Hannisdal, B. 2006. Phenotypic evolution in the fossil record: Numerical experiments. Journal of Geology, 114(2):133–153.Google Scholar
Hannisdal, B. 2007. Inferring phenotypic evolution in the fossil record by Bayesian inversion. Paleobiology, 33(1):98–115.Google Scholar
Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution, 51(5):1341–1351.Google Scholar
Hansen, T. F., and Martins, E. P. 1996. Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evolution, 50(4):1404–1417.Google Scholar
Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology, 32(4):578–601.Google Scholar
Hunt, G. 2007. The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages. Proceedings of the National Academy of Sciences USA, 104(47): 18404–18408.Google Scholar
Hunt, G. 2008. Gradual or pulsed evolution: when should punctuational explanations be preferred? Paleobiology, 34(3):360–377.Google Scholar
Hunt, G. 2008b. paleoTS: Modeling evolution in paleontological time-series. 0.3-1.Google Scholar
Hunt, G., Bell, M. A., and Travis, M. P. 2008. Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage. Evolution, 62(3):700–710.CrossRefGoogle Scholar
Hunt, G., and Roy, K. 2006. Climate change, body size evolution, and Cope's Rule in deep-sea ostracodes. Proceedings of the National Academy of Sciences USA, 103(5):1347–1352.Google Scholar
Jackson, J. B. C., and Cheetham, A. H. 1994. Phylogeny reconstruction and the tempo of speciation in cheilostome Bryozoa. Paleobiology, 20(4):407–423.Google Scholar
Jackson, J. B. C., and Cheetham, A. H. 1999. Tempo and mode of speciation in the sea. Trends in Ecology and Evolution, 14(2):72–77.Google Scholar
Kinnison, M. T., and Hendry, A. P. 2001. The pace of modern life II: from rates of contemporary microevolution to pattern and process. Genetica, 112–113:145–164.Google Scholar
Kitchell, J. A., Estabrook, G., and Macleod, N. 1987. Testing for equality of rates of evolution. Paleobiology, 13(3):272–285.Google Scholar
Lande, R. 1976. Natural selection and random genetic drift in phenotypic evolution. Evolution, 30:314–334.Google Scholar
Levinton, J. S. 2001. Genetics, Paleontology, and Macroevolution. Cambridge University Press, Cambridge.Google Scholar
Lynch, M. 1990. The rate of morphological evolution in mammals from the standpoint of the neutral expectation. American Naturalist, 136(6):727–741.CrossRefGoogle Scholar
Martins, E. P. 1994. Estimating the rate of phenotypic evolution from comparative data. American Naturalist, 144(2): 193–209.Google Scholar
Martins, E. P. 1999. Estimation of ancestral states of continuous characters: a computer simulation study. Systematic Biology, 48(3):642–650.Google Scholar
Novack-Gottshall, P. M. 2008. Ecosystemwide body-size trends in Cambrian-Devonian marine invertebrate lineages. Paleobiology, 34:210–228.CrossRefGoogle Scholar
O'Meara, B. C., Ané, C. C., Sanderson, M. J., and Wainwright, P. C. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution, 60(5):922–933.Google Scholar
Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature, 401:877–884.Google Scholar
Pagel, M. 2002. Modelling the evolution of continuously varying characters on phylogenetic trees: the case of hominid cranial capacity, p. 269–286. In MacLeod, N. and Forey, P. L. (eds.), Morphology, Shape and Phylogeny. Taylor & Francis, London.Google Scholar
Polly, P. D. 2004. On the simulation of the evolution of morphological shape: multivariate shape under selection and drift. Palaeontologia Electronica, 7(2):1–28.Google Scholar
R DEVELOPMENT CORE TEAM. 2008. R: A language and environment for statistical computing. 2.7.0. R Foundation for Statistical Computing. http://www.R-project.org.Google Scholar
Raup, D. M. 1977. Stochastic models in evolutionary paleobiology, p. 59–78. In Hallam, A. (ed.), Patterns of Evolution as Illustrated by the Fossil Record. Volume 5. Elsevier Scientific Publishing Company, Amsterdam.Google Scholar
Raup, D. M., and Crick, R. E. 1981. Evolution of single characters in the Jurassic ammonite Kosmoceras . Paleobiology, 7(2):200–215.Google Scholar
Roopnarine, P. D. 2001. The description and classification of evolutionary mode: a computational approach. Paleobiology, 27(3):446–465.Google Scholar
Roopnarine, P. D., Byars, G., and Fitzgerald, P. 1999. Anagenetic evolution, stratophenetic patterns, and random walk models. Paleobiology, 25(1):41–57.Google Scholar
Schmidt, D. N., Thierstein, H. R., Bollman, J., and Schiebel, R. 2004. Abiotic forcing of plankton evolution in the Cenozoic. Science, 303:207–210.Google Scholar
Sheets, H. D., and Mitchell, C. E. 2001. Why the null matters: statistical tests, random walks and evolution. Genetica, 112–113:105–125.Google Scholar
Simpson, G. G. 1944. Tempo and Mode in Evolution. Columbia University Press, New York, 237 p.Google Scholar
Sokal, R. R., and Rohlf, F. J. 1995. Biometry. W.H. Freeman and Company, New York, 887 p.Google Scholar
Turelli, M., Gillespie, J. H., and Lande, R. 1988. Rate tests for selection on quantitative characters during macroevolution and microevolution. Evolution, 42(5):1085–1089.Google Scholar