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The role of phylogeny in quantitative paleobiological data analysis

Published online by Cambridge University Press:  08 February 2016

Norman MacLeod
Norman MacLeod*
Affiliation:
Department of Palaeontology, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom. E-mail: [email protected]
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Abstract

Phylogenies provide a rich source of information that should be exploited in designing quantitative hypothesis tests in paleobiological contexts. Viewing such data analysis problems through the prism of phylogenetically structured comparisons can help add realism and depth to paleobiological data-analysis strategies. Two examples of the importance of adopting a phylogenetic perspective are discussed. In the first example, a phylogenetic-comparative approach is used to test correlations between ecological, morphological, and biological characteristics of planktonic foraminifera. Results suggest that the presence of spines and photosynthetic symbionts in Neogene-Recent species are not adaptations to living in shallow-intermediate planktonic depth habitats. In the second, a phylogenetic-comparative approach is used to reveal the presence of morphological correlations with locomotor function in a mammalian carnivore data set. Paleontologists can play an active role in improving comparative data analyses by (1) helping to develop improved phylogenies, especially those that provide better estimates of branch lengths, and (2) helping to resolve a number of outstanding issues surround the question of ancestral character-state specification.

Type
Articles
Information
Paleobiology , Volume 27 , Issue 2 , Spring 2001 , pp. 226 - 240
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Bakker, R. T. 1986. The dinosaur heresies. William Morrow, New York.Google Scholar
Bé, A. W. H. 1977. An ecological, zoographic, and taxonomic review of Recent planktonic foraminifera. Pp. 1–100in Ramsay, A. T. S., ed. Oceanic micropalaeontology. Academic Press, London.Google Scholar
Bé, A. W. H. 1982. Biology of planktonic foraminifera. Pp. 51–89in Buzas, M. A., Gupta, B. K. Sen, and Broadhead, T. W., eds. Foraminifera: notes for a short course. University of Tennessee, Knoxville.Google Scholar
Berger, W. H. 1969. Ecologic patterns of living planktonic foraminifera. Deep-Sea Research 16:1–24.Google Scholar
Boltovskoy, E., and Wright, R. 1976. Recent foraminifera. W. Junk, The Hague.CrossRefGoogle Scholar
Cooper, A., and Fortey, R. 1998. Evolutionary explosions and the phylogenetic fuse. Trends in Ecology and Evolution 13:151–156.CrossRefGoogle ScholarPubMed
de Vargas, C., Zaininetti, L., Hilbrecht, H., and Pawlowski, J. 1997. Phylogeny and rates of molecular evolution of planktonic foraminifera SSU rDNA sequences compared to the fossil record. Molecular Evolution 45:285–294.CrossRefGoogle ScholarPubMed
D'Hondt, S., and Zachos, J. C. 1993. On stable isotopic variation and earliest Paleocene planktonic foraminifera. Paleoceanography 8:527–547.CrossRefGoogle Scholar
D'Hondt, S., Zachos, J. C., and Schultz, G. 1994. Stable isotopic signals and photosymbiosis in planktic foraminifera. Paleobiology 20:391–406.CrossRefGoogle Scholar
Dobzhansky, T. 1974. Nothing in biology makes sense except in the light of evolution. American Biology Teacher 35:125–129.CrossRefGoogle Scholar
Eldredge, N., and Cracraft, J. 1980. Phylogenetic patterns and the evolutionary process. Columbia University Press, New York.Google Scholar
Fairbanks, R. G., Wiebe, P. H., and Bé, A. W. H. 1980. Vertical distribution and isotopic composition of living foraminifera in the western Atlantic. Science 207:61–63.CrossRefGoogle Scholar
Fairbanks, R. G., Sverdlove, M., Free, R., Wiebe, P. H., and Bé, A. W. H. 1982. Vertical distribution and isotopic fractionation of living planktonic foraminifera from the Panama Basin. Nature 298:841–844.CrossRefGoogle Scholar
Feduccia, A. 1996. The origin and evolution of birds. Yale University Press, New Haven, Conn.Google Scholar
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1–15.CrossRefGoogle Scholar
Felsenstein, J. 1988. Phylogenies and quantitative characters. Annual Review of Ecology and Systematics 19:445–471.CrossRefGoogle Scholar
Flynn, J. J. 1996. Carnivoran phylogeny and rates of evolution: morphological, taxic, and molecular. Pp. 542–581in Gittleman, J. L., ed. Carnivore behavior, ecology, and evolution. Cornell University Press, Ithaca, N.Y.Google Scholar
Foote, M. 1996. Perspective: evolutionary patterns in the fossil record. Evolution 50:1–11.CrossRefGoogle ScholarPubMed
Gittleman, J. L., ed. 1996. Carnivore behavior, ecology, and evolution. Cornell University Press, Ithaca, N.Y.CrossRefGoogle Scholar
Gittleman, J. L., and Kot, M. 1990. Adaptation: statistics and a null model for estimating phylogenetic effects. Systematic Zoology 39:227–241.CrossRefGoogle Scholar
Gittleman, J. L., and Luh, H.-K. 1994. Phylogeny, evolutionary models and comparative methods: a simulation study. Pp. 103–122in Eggleton, P. and Vane-Wright, R. I., eds. Phylogenetics and ecology. Academic Press, London.Google Scholar
Gittleman, J. L., Anderson, C. G., Kot, M., and Luh, H.-K. 1996. Comparative tests of evolutionary lability and rates using molecular phylogenies. Pp. 289–307in Harvey, P. H., Brown, A. J. Leigh, Smith, J. M., and Nee, S., eds. New uses for new phylogenies. Oxford University Press, Oxford.CrossRefGoogle Scholar
Gould, S. J., and Vrba, E. 1982. Exaptation—a missing term in the science of form. Paleobiology 8:4–15.CrossRefGoogle Scholar
Grafen, A. 1989. The phylogenetic regression. Philosophical Transactions of the Royal Society of London B 326:119–157.Google ScholarPubMed
Grafen, A., and Ridley, M. 1996. Statistical tests for discrete cross-species data. Journal of Theoretical Biology 183:255–267.CrossRefGoogle Scholar
Harvey, P. H., and Pagel, M. D. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford.CrossRefGoogle Scholar
Hemleben, C., Spindler, M., and Anderson, O. R. 1988. Modern planktonic foraminifera. Springer, New York.Google Scholar
Hutchinson, G. E. 1967. A treatise on limnology, Vol. 2. Introduction to lake biology and the limnology of plankton. Wiley, New York.Google Scholar
Lipps, J. H. 1979. Ecology and paleoecology of planktic foraminifera. Pp. 62–104in Lipps, J. H., Berger, W. H., Buzas, M. A., Douglas, R. G., and Ross, C. A., eds. Foraminiferal ecology and paleoecology. SEPM Short Course 6. Houston.CrossRefGoogle Scholar
Loeblich, A. R. Jr., and Tappan, H. 1988. Foraminiferal genera and their classification. Van Nostrand Reinhold, New York.CrossRefGoogle Scholar
Lohmann, G. P., and Schweitzer, P. N. 1990. On eigenshape analysis. In Rohlf, F. J., and Bookstein, F. L., eds. Proceedings of the Michigan morphometrics workshop. University of Michigan Museum of Zoology Special Publication 2:145–166.Google Scholar
MacLeod, N. 1993. The Maastrichtian-Danian radiation of triserial and biserial planktic foraminifera: testing phylogenetic and adaptational hypotheses in the (micro)fossil record. Marine Micropaleontology 21:47–100.CrossRefGoogle Scholar
MacLeod, N. 1999. Generalizing and extending the eigenshape method of shape visualization and analysis. Paleobiology 25:107–138.Google Scholar
MacLeod, N., and Rose, K. D. 1993. Inferring locomotor behavior in Paleogene mammals via eigenshape analysis. American Journal of Science 293-A:300–355.CrossRefGoogle Scholar
Maddison, D. R. 1994. Phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters. Annual Review of Entomology 39:267–292.CrossRefGoogle Scholar
Maddison, W. P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology 202:195–204.CrossRefGoogle ScholarPubMed
Martins, E. P. 1996. Phylogenies, spatial autoregression, and the comparative method: a computer simulation test. Evolution 50:1750–1765.CrossRefGoogle Scholar
Martins, E. P., and Hansen, T. F. 1996. The statistical analysis of interspecific data: a review and evaluation of comparative methods. Pp. 22–75in Martins, E. P., ed. Phylogenies and the comparative method in animal behavior. Oxford University Press, New York.CrossRefGoogle Scholar
Martins, E. P., and Hansen, T. F. 1997. Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data. American Naturalist 149:646–667.CrossRefGoogle Scholar
Mooers, A. Ø., and Schluter, D. 1999. Reconstructing ancestor states with maximum likelihood: support for one and two-rate models. Systematic Biology 48:623–633.CrossRefGoogle Scholar
Murray, J. W. 1991. Ecology and distribution of planktonic foraminifera. Pp. 255–284in Lee, J. J. and Anderson, O. R., eds. Biology of foraminifera. Academic Press, London.Google Scholar
Nelson, G. 1994. Homology and systematics. Pp. 101–149in Hall, B. K., ed. Homology: the hierarchical basis of comparative biology. Academic Press, London.Google Scholar
Norris, R. D. 1996. Symbiosis as an evolutionary innovation in the radiation of Paleocene planktic foraminifera. Paleobiology 22:461–480.CrossRefGoogle Scholar
Omland, K. E. 1999. The assumptions and challenges of ancestral state reconstructions. Systematic Biology 48:604–611.CrossRefGoogle Scholar
Ostrom, J. H. 1979. Bird flight: how did it begin? American Scientist 67:4656.Google ScholarPubMed
Padian, K., and Chiappe, L. 1998. The origin and early evolution of birds. Biological Reviews 73:1–42.CrossRefGoogle Scholar
Pagel, M. D. 1991. A method for the analysis of comparative data. Journal of Theoretical Biology 156:431–442.CrossRefGoogle Scholar
Pagel, M. D. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London B 255:37–45.Google Scholar
Pagel, M. D. 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta 26:331–348.CrossRefGoogle Scholar
Pagel, M. D. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48:612–622.CrossRefGoogle Scholar
Paul, G. S. 1988. Predatory dinosaurs of the world. Simon and Schuster, New York.Google Scholar
Perle, A. M., Norell, M. A., Chiappe, L. M., and Clark, J. M. 1994. Flightless bird from the Cretaceous of Mongolia. Nature 362:188.Google Scholar
Prothero, D. R., and Lazarus, D. B. 1980. Planktonic microfossils and the recognition of ancestors. Systematic Zoology 29:119–129.CrossRefGoogle Scholar
Purvis, A., Gittleman, J. L., and Luh, H.-K. 1994. Truth or consequences: effects of phylogenetic accuracy on two comparative methods. Journal of Theoretical Biology 167:293–300.CrossRefGoogle Scholar
Regal, P. J. 1975. The evolutionary origin of feathers. Quarterly Review of Biology 50:35–66.Google ScholarPubMed
Ridley, M. 1983. The explanation of organic diversity: the comparative method and adaptations for mating. Oxford University Press, Oxford.Google Scholar
Schluter, D. 1995. Uncertainty in ancient phylogenies. Nature 377:108–109.CrossRefGoogle ScholarPubMed
Schluter, D., Price, T., Mooers, A. Ø., and Ludwig, D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699–1711.CrossRefGoogle ScholarPubMed
Stanley, S. M., Wetmore, K. L., and Kennett, J. P. 1988. Macroevolutionary differences between two major clades of Neogene planktonic foraminifera. Paleobiology 14:235–249.CrossRefGoogle Scholar
Swofford, D. L., and Maddison, W. P. 1992. Parsimony, character-state reconstructions, and evolutionary inferences. Pp. in Mayden, R. C., ed. Systematics, historical ecology, and North American freshwater fishes. Stanford University Press, Palo Alto, Calif.Google Scholar
Theriot, E. 1992. Clusters, species concepts, and morphological evolution of diatoms. Systematic Biology 41:141–157.CrossRefGoogle Scholar
Wagner, P. J. 1998. Phylogenetic analysis and the quality of the fossil record. Pp. 165–187in Donovan, S. K., and Paul, C. R. C., eds. The adequacy of the fossil record. Wiley, New York.Google Scholar
Wayne, R. K., Benveniste, R. E., Janczewski, D. N., and O'Brien, S. J. 1996. Molecular and biochemical evolution of the Carnivora. Pp. 465–493in Gittleman, 1996.Google Scholar
Wozencraft, W. C. 1996. The phylogeny of recent Carnivora. Pp. 495–535in Gittleman, 1996.Google Scholar
Wyss, A., and Flynn, J. J. 1993. A phylogenetic analysis and definition of the Carnivora. Pp. 32–52in Szalay, F., Novacek, M., and McKenna, M., eds. Mammal phylogeny: placentals. Springer, New York.CrossRefGoogle Scholar