Hostname: page-component-cd9895bd7-q99xh Total loading time: 0 Render date: 2024-12-27T10:40:39.508Z Has data issue: false hasContentIssue false
  • English
  • Français

Estimating paleodiversities: a test of the taxic and phylogenetic methods

Published online by Cambridge University Press:  08 April 2016

Abigail Lane ,
Christine M. Janis  and
J. John Sepkoski Jr.
Abigail Lane
Affiliation:
Department of Earth Sciences, Wills Memorial Building, Queens Road, Bristol, BS8 1RJ, United Kingdom
Christine M. Janis*
Affiliation:
Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912. E-mail: Christine-Janis@Brown.edu
*
∗Corresponding author
Get access Rights & Permissions [Opens in a new window]

Abstract

The traditional “taxon counting” method of estimating ancient biodiversity is open to many criticisms, not least of which are the problem of inconsistency in the preservation of fossil organisms and the associated error on first and last appearance times of taxa. Construction of phylogenetic trees provides a way of correcting the first appearance of a taxon based on the origination time of its sister group. Workers have suggested that biodiversity studies include such phylogenetically implied range extensions. Potential problems with this method, in particular the bias inherent in altering origination—but not extinction—times, and the potential for incorrect addition of ghost ranges if the ancestor of a taxon is defined as its sister, are investigated by using a new computer simulation. The program creates a phylogeny, samples it and then adds ghost lineages, with diversity counts being made at all three stages. Results show that under certain conditions, such as in the case of a taxonomic group with many extant representatives, the phylogenetic method is superior to the taxic at capturing diversity pattern. However, there are also important conditions where the taxic approach provides an equal or superior estimate of diversity, such as if the group is extinct or has few extant lineages. Use of the phylogenetic method has the effect of magnifying the Signor-Lipps sampling effect seen before mass extinction events, and if ancestral species within a phylogeny are misdiagnosed as the sister species of their descendants, the phylogenetic method also consistently overestimates diversity magnitudes.

Type
Articles
Information
Paleobiology , Volume 31 , Issue 1 , Winter 2005 , pp. 21 - 34
Copyright
Copyright © The Paleontological Society 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Literature Cited

Alroy, J. 2000. New methods for quantifying macroevolutionary patterns and processes. Paleobiology 26:707–733.Google Scholar
Alroy, J. (and 25 others). 2001. Effects of sampling standardization on estimates of Phanerozoic marine diversification. Proceedings of the National Academy of Sciences USA 98:6261–6266.Google Scholar
Anderson, J., Anderson, H., Fatti, P., and Sichel, H. 1996. The Triassic Explosion(?): a statistical model for extrapolating biodiversity based on the terrestrial Molteno Formation. Paleobiology 22:318–328.Google Scholar
Bookstein, F. L. 1987. Random walk and the existence of evolutionary rates. Paleobiology 13:446–464.Google Scholar
Connor, E. F. 1986. Time series analysis in the fossil record. Pp. 119–147in Raup, D. M. and Jablonski, D., eds. Patterns and processes in the history of life. Springer, Berlin.Google Scholar
Doyle, J. A., and Donoghue, M. J. 1993. Phylogenies and angiosperm diversification. Paleobiology 19:141–167.CrossRefGoogle 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
Foote, M. 1996a. Perspective: evolutionary patterns in the fossil record. Evolution 50:1–11.Google Scholar
Foote, M. 1996b. On the probability of ancestors in the fossil record. Paleobiology 22:141–151.Google Scholar
Gould, S. J., Raup, D. M., Sepkoski, J. J. Jr., Schopf, T. J. M., and Simberloff, D. S. 1977. The shape of evolution: a comparison of real and random clades. Paleobiology 3:23–40.Google Scholar
Harvey, P. H., and Pagel, M. D. 1991. The comparative method in evolutionary biology. Oxford University Press, Oxford.Google Scholar
Hennig, W. 1965. Phylogenetic systematics. University of Illinois Press, Urbana.Google Scholar
Levinton, J. 1988. Genetics, paleontology, and macroevolution. Cambridge University Press, Cambridge.Google Scholar
Marshall, C. R. 1990. Confidence intervals on stratigraphic ranges. Paleobiology 16:1–10.Google Scholar
Marshall, C. R. 1991. Estimation of taxonomic ranges from the fossil record. In Gilinsky, N. L. and Signor, P. W., eds. Analytical paleobiology. Short Courses in Paleontology 4:19–38. Paleontological Society, Knoxville, Tenn.Google Scholar
Mayr, E. 1963. Animal species and evolution. Harvard University Press, Cambridge.Google Scholar
Miller, A. I., and Foote, M. 1996. Calibrating the Ordovician radiation of marine life: implications for Phanerozoic diversity trends. Paleobiology 22:304–309.Google 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
Norell, M. A., and Novacek, M. J. 1992a. Congruence between superpositional and phylogenetic patterns: comparing cladistic patterns with fossil evidence. Cladistics 8:319–337.Google Scholar
Norell, M. A., and Novacek, M. J. 1992b. The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255:1690–1693.Google Scholar
Novacek, M. J., and Norell, M. A. 1982. Fossils, phylogeny, and taxonomic rates of evolution. Systematic Zoology 31:266–275.Google Scholar
Omland, K. E. 1997. Examining two standard assumptions of ancestral state reconstruction: repeated loss of dichromatism in dabbling ducks (Anatini). Evolution 51:1636–1646.Google Scholar
Raup, D. M. 1972. Taxonomic diversity during the Phanerozoic. Science 231:177:1065–1071.Google Scholar
Raup, D. M. 1975. Taxonomic diversity estimation using rarefaction. Paleobiology 1:333–342.Google Scholar
Raup, D. M. 1979. Biases in the fossil record of species and genera. Bulletin of the Carnegie Museum of Natural History 13:85–91.Google Scholar
Robeck, H. E., Maley, C. C., and Donoghue, M. J. 2000. Taxonomy and temporal diversity patterns. Paleobiology 26:171–187.2.0.CO;2>CrossRefGoogle Scholar
Sepkoski, J. J. Jr. 1978. A kinetic model of Phanerozoic taxonomic diversity. I. Analysis of marine orders. Paleobiology 4:223–251.Google Scholar
Sepkoski, J. J. Jr. 1984. A kinetic model of Phanerozoic taxonomic diversity. III. Post-Paleozoic families and mass extinctions. Paleobiology 10:246–267.Google Scholar
Sepkoski, J. J. Jr., and Kendrick, D. C. 1993. Numerical experiments with model monophyletic and paraphyletic taxa. Paleobiology 19:168–184.Google Scholar
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.Google 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. Blackwell Science, Oxford.Google Scholar
Strauss, D., and Sadler, P. M. 1989. Confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21:411–427.Google Scholar
Valentine, J. W. 1969. Patterns of taxonomic and ecological structure of the shelf benthos during Phanerozoic times. Palaeontology 12:684–709.Google Scholar
Vrba, E. S. 1993. Turnover-pulses, the Red Queen, and related topics. American Journal of Science 293–A:418–452.Google Scholar
Wagner, P. J. 1995. Diversification among early Paleozoic gastropods—contrasting taxonomic and phylogenetic descriptions. Paleobiology 21:410–439.Google Scholar
Wagner, P. J. 2000a. Phylogenetic analyses and the fossil record: tests and inferences, hypotheses and models. In Erwin, D. H. and Wing, S. L., eds. Deep time: Paleobiology's perspective. Paleobiology Memoir 26(Suppl. to No. 4):341–371.Google Scholar
Wagner, P. J. 2000b. The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Systematic Biology 49:65–86.Google Scholar
Wagner, P. J., and Erwin, D. H. 1995. Phylogenetic tests of speciation hypotheses. Pp. 87–122in Erwin, D. H. and Anstey, R. L., eds. New approaches for studying speciation in the fossil record. Columbia University Press, New York.Google Scholar