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Extinct meets extant: simple models in paleontology and molecular phylogenetics

Published online by Cambridge University Press:  08 February 2016

Sean Nee
Sean Nee*
Affiliation:
Ashworth Laboratories, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom. E-mail: sean.nee@ed.ac.uk
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Extract

Paleontologists have a long tradition of the use of mathematical models to assist in describing and understanding patterns of diversification through time (e.g., Raup et al. 1973; Stanley 1975; Sepkoski 1978; Raup 1985; Foote 1988; Gilinsky and Good 1989). This is natural, as the information, phylogenetic and otherwise, that paleontologists work with comes equipped with a temporal dimension, albeit approximate, which endows these phylogenies with information about the tempo of evolution as well as the genealogical relationships among the lineages. Mathematical and statistical modeling are the tools for unlocking the quantitative information in the phylogenies.

Type
Matters of the Record
Information
Paleobiology , Volume 30 , Issue 2 , Spring 2004 , pp. 172 - 178
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Bailey, N. T. J. 1964. The elements of stochastic processes with applications to the natural sciences. Wiley, New York.Google Scholar
Baldwin, B. G., and Sanderson, M. J. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences USA 95:9402–9406.CrossRefGoogle ScholarPubMed
Caccone, A., Amato, G. D., and Powell, J. R. 1988. Rates and patters of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup. Genetics 118:671–683.CrossRefGoogle Scholar
Cotgreave, P., and Harvey, P. H. 1994. Associations among biogeography, phylogeny and bird species diversity. Biodiversity Letters 2:46–55.CrossRefGoogle Scholar
Cox, D. R., and Lewis, P. A. A. 1966. The statistical analysis of series of events. Methuen, London.CrossRefGoogle Scholar
Feller, W. 1957. An introduction to probability theory and its applications, Vol. 1. Wiley, New York.Google Scholar
Foote, M. 1988. Survivorship analysis of Cambrian and Ordovician trilobites. Paleobiology 14:258–271.CrossRefGoogle Scholar
Foote, M. 2001. Evolutionary rates and the age distributions of living and extinct taxa. Pp. 245–295in Jackson, J. B. C., Lidgard, S., and McKinney, F. K., eds. Evolutionary patterns: growth, form and tempo in the fossil record. University of Chicago Press, Chicago.Google Scholar
Gilinsky, N. L., and Good, I. J. 1989. Analysis of clade shape using queuing theory and the fast Fourier transform. Paleobiology 15:321–333.CrossRefGoogle Scholar
Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46:627–640.CrossRefGoogle ScholarPubMed
Hillis, D. M., Moritz, C., and Mable, B. K. 1996. Molecular systematics. Sinauer, Sunderland, Mass.Google Scholar
Hubbell, S. P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, NJ.Google Scholar
Hudson, R. R. 1990. Gene genealogies and the coalescent process. In Futuyma, D. and Antonovics, J., eds. Oxford Surveys in Evolutionary Biology 8:1–49.Oxford University Press, Oxford.Google Scholar
Kendall, D. G. 1948. On some modes of population growth leading to R. A. Fisher's logarithmic series distribution. Biometrika 35:6–15.CrossRefGoogle Scholar
Kendall, D. G. 1949. Stochastic processes and population growth. Journal of the Royal Statistical Society B 11:230–264.Google Scholar
Kitchell, J. K., and MacLeod, N. 1988. Macroevolutionary interpretations of symmetry and synchroneity in the fossil record. Science 240:1190–1193.CrossRefGoogle ScholarPubMed
Losos, J. B., and Adler, F. R. 1995. Stumped by trees? A generalized null model for patterns of organismal diversity. American Naturalist 145:329–342.CrossRefGoogle Scholar
Moran, P. A. P. 1958. Random processes in genetics. Proceedings of the Cambridge Philosophical Society 54:60–71.CrossRefGoogle Scholar
Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution 55:661–668.CrossRefGoogle ScholarPubMed
Nee, S., and May, R. M. 1994. The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London B 344:305–311.Google ScholarPubMed
Nee, S., Mooers, A. O., and Harvey, P. H. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proceedings of the National Academy of Sciences USA 89:8322–8326.CrossRefGoogle ScholarPubMed
Nee, S., Holmes, E. C., May, R. M., and Harvey, P. H. 1995. Estimating extinction from molecular phylogenies. Pp. 164–182in Lawton, J. L. and May, R. M., eds. Extinction rates. Oxford University Press, Oxford.CrossRefGoogle Scholar
Nee, S., Barraclough, T., and Harvey, P. H. 1996. Temporal changes in biodiversity: detecting patterns and identifying causes. Pp. 230–252in Gaston, K. J., ed. Biodiversity: an introduction. Blackwell Science, Oxford.Google Scholar
Paradis, E. 1997. Assessing temporal variation in diversification rates from phylogenies: estimation and hypothesis testing. Proceedings of the Royal Society of London B 264:1141–1147.CrossRefGoogle Scholar
Purvis, A., Nee, S., and Harvey, P. H. 1995. Macroevolutionary inferences from primate phylogeny. Proceedings of the Royal Society of London B 260:329–333.Google ScholarPubMed
Raup, D. M. 1975. Taxonomic survivorship curves and Van Valen's law. Paleobiology 1:82–96.CrossRefGoogle Scholar
Raup, D. M. 1985. Mathematical models of cladogenesis. Paleobiology 11:42–52.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 81:525–542.CrossRefGoogle Scholar
Sepkoski, J. J. Jr. 1978. A kinetic model of Phanerozoic taxonomic diversity. I. Analysis of marine orders. Paleobiology 4:223–251.CrossRefGoogle Scholar
Sepkoski, J. J. Jr., and Kendrick, D. C. 1993. Numerical experiments with model monophyletic and paraphyletic taxa. Paleobiology 19:168–184.CrossRefGoogle ScholarPubMed
Sibley, C. G., and Ahlquist, J. E. 1990. Phylogeny and classification of birds. Yale University Press, New Haven, Conn.Google Scholar
Stanley, S. M. 1975. A theory of evolution above the species level. Proceedings of the National Academy of Sciences USA 72:646–650.CrossRefGoogle ScholarPubMed
Stanley, S. M., and Newman, W. A. 1980. Competitive exclusion in evolutionary time: the case of the acorn barnacles. Paleobiology 6:173–183.CrossRefGoogle Scholar
Strathman, R. R., and Slatkin, M. 1983. The improbability of animal phyla with few species. Paleobiology 9:97–106.CrossRefGoogle Scholar
Uhen, M. D. 1996. An evaluation of clade-shape statistics using simulations and extinct families of mammals. Paleobiology 22:8–22.CrossRefGoogle Scholar
Yule, G. U. 1924. A mathematical theory of evolution based on the conclusions of Dr. J.C. Willis, FRS. Philosophical Transactions of the Royal Society of London B 213:21–87.Google Scholar