Hostname: page-component-cd9895bd7-hc48f Total loading time: 0 Render date: 2024-12-26T19:11:22.744Z Has data issue: false hasContentIssue false
  • English
  • Français

Inferring temporal patterns of preservation, origination, and extinction from taxonomic survivorship analysis

Published online by Cambridge University Press:  20 May 2016

Michael Foote
Michael Foote*
Affiliation:
Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637. [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Apparent variation in rates of origination and extinction reflects the true temporal pattern of taxonomic rates as well as the distorting effects of incomplete and variable preservation, effects that are themselves exacerbated by true variation in taxonomic rates. Here I present an approach that can undo these distortions and thus permit estimates of true taxonomic rates, while providing estimates of preservation in the process. Standard survivorship probabilities are modified to incorporate variable taxonomic rates and rates of fossil recovery. Time series of these rates are explored by numerical optimization until the set of rates that best explains the observed data is found. If internal occurrences within stratigraphic ranges are available, or if temporal patterns of fossil recovery can otherwise be assumed, these constraints can be exploited, but they are by no means necessary. In its most general form, the approach requires no data other than first and last appearances. When tested against simulated data, the method is able to recover temporal patterns in rates of origination, extinction, and preservation. With empirical data, it yields estimates of preservation rate that agree with those obtained independently by tabulating internal occurrences within stratigraphic ranges. Moreover, when empirical occurrence data are artificially degraded, the method detects the resulting gaps in sampling and corrects taxonomic rates. Preliminary application to data on Paleozoic marine animals suggests that some features of the apparent record, such as the forward smearing of true origination events and the backward smearing of true extinction events, can be detected and corrected. Other features, such as the end-Ordovician extinction, may be fairly accurate at face value.

Type
Articles
Information
Paleobiology , Volume 27 , Issue 4 , Fall 2001 , pp. 602 - 630
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

Adrain, J. M.Westrop, S. R. 2000. An empirical assessment of taxic paleobiology. Science 289:110–112.Google Scholar
Alroy, J. 1996. Constant extinction, constrained diversification, and uncoordinated stasis in North American mammals. Palaeogeography, Palaeoclimatology, Palaeoecology 127:285–311.Google Scholar
Alroy, J. 1999. Equilibrial diversity dynamics in North American mammals. Pp. 233–287in McKinney and Drake 1998.Google Scholar
Alroy, J.Koch, P. L.Zachos, J. C. 2000. Global climate change and North American mammalian evolution. In Erwin, D. H.Wing, S. L., eds. Deep time: Paleobiology‘s perspective. Paleobiology 26(Suppl. to No. 4):259–288.Google Scholar
Alroy, J.Marshall, C. R.Bambach, R. K.Bezusko, K.Foote, M.Fürsich, F. T.Hansen, T. A.Holland, S. M.Ivany, L. C.Jablonski, D.Jacobs, D. K.Jones, D. C.Kosnik, M. A.Lidgard, S.Low, S.Miller, A. I.Novack, P. M.-Gottshall, Olszewski, T. D.Patzkowsky, M. E.Raup, D. M.Roy, K.Sepkoski, J. J. Jr.Sommers, M. G.Wagner, P. J.Webber, A. 2001. Effects of sampling standardization on estimates of Phanerozoic marine diversification. Proceedings of the National Academy of Sciences USA 98:6261–6266.Google Scholar
Baumiller, T. K. 1993. Survivorship analysis of Paleozoic Crinoidea: effect of filter morphology on evolutionary rates. Paleobiology 19:304–322.Google Scholar
Benton, M. J.Wills, M. A.Hitchin, R. 2000. The quality of the fossil record through time. Nature 403:534–537.Google Scholar
Bodenbender, B. E.Fisher, D. C. 2001. Stratocladistic analysis of blastoid phylogeny. Journal of Paleontology 75:351–369.Google Scholar
Bowring, S. A.Erwin, D. H. 1998. A new look at evolutionary rates in deep time: uniting paleontology and high-precision geochronology. GSA Today 8(9):1–8.Google Scholar
Brett, C. E. 1998. Sequence stratigraphy, paleoecology, and evolution: biotic clues and responses to sea-level fluctuation. Palaios 13:241–262.Google Scholar
Budd, A. F.Johnson, K. G. 1999. Origination preceding extinction during late Cenozoic turnover of Caribbean reefs. Paleobiology 25:188–200.Google Scholar
Carter, J. G.Barrera, E.Tevesz, M. J. S. 1998. Thermal potentiation and mineralogical evolution in the Bivalvia (Mollusca). Journal of Paleontology 72:991–1010.Google Scholar
Cheetham, A. H.Jackson, J. B. C. 1998. The fossil record of cheilostome Bryozoa in the Neogene and Quaternary of tropical America: adequacy for phylogenetic and evolutionary studies. Pp. 227–242in Donovan, S. K.Paul, R. C., eds. The adequacy of the fossil record. Wiley, Chichester, England.Google Scholar
Clyde, W. C.Fisher, D. C. 1997. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology 23:1–19.Google Scholar
Connolly, S. R.Miller, A. I. 2001. Global Ordovician faunal transitions in the marine benthos. I. Proximal causes. Paleobiology 27:779–795 (this volume).Google Scholar
Conroy, M. J.Nichols, J. D. 1984. Testing for variation in taxonomic extinction probabilities: a suggested methodology and some results. Paleobiology 10:328–337.Google Scholar
Culver, S. J.Buzas, M. A.Collins, L. S. 1987. On the value of taxonomic standardization in evolutionary studies. Paleobiology 13:169–176.Google Scholar
Edwards, A. W. F. 1992. Likelihood, expanded ed. Johns Hopkins University Press, Baltimore.Google Scholar
Fisher, D. C. 1994. Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. Pp. 133–171in Grande, L.Rieppel, O., eds. Interpreting the hierarchy of nature. Academic Press, San Diego.Google Scholar
Foote, M. 1988. Survivorship analysis of Cambrian and Ordovician trilobites. Paleobiology 14:258–271.Google Scholar
Foote, M. 1996. On the probability of ancestors in the fossil record. Paleobiology 22:141–151.Google Scholar
Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23:278–300.Google Scholar
Foote, M. 1999. Morphological diversity in the evolutionary radiation of Paleozoic and post-Paleozoic crinoids. Paleobiology Memoirs No. 1. Paleobiology 25(Suppl. to No. 2):1–115.Google Scholar
Foote, M. 200a. Origination and extinction components of taxonomic diversity: general problems. In Erwin, D. H.Wing, S. L., eds. Deep time: Paleobiology‘s perspective. Paleobiology 26(Suppl. to No. 4):74–102.Google Scholar
Foote, M. 2000b. Origination and extinction components of taxonomic diversity: Paleozoic and post-Paleozoic dynamics. Paleobiology 26:578–605.Google Scholar
Foote, M. 2001a. Evolutionary rates and the age distributions of living and extinct taxa. Pp. 245–294in Jackson, J. B. C.Lidgard, S.McKinney, F. K., eds. Evolutionary patterns: growth, form, and tempo in the fossil record. University of Chicago Press, Chicago.Google Scholar
Foote, M. 2001b. Estimating completeness of the fossil record. Pp. 504–508in Briggs, D. E. G.Crowther, P. R., eds. Palaeobiology II. Blackwell Scientific, Oxford.Google Scholar
Foote, M.Raup, D. M. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121–140.Google Scholar
Foote, M.Sepkoski, J. J. Jr. 1999. Absolute measures of the completeness of the fossil record. Nature 398:415–417.Google Scholar
Fortey, R. A. 1983. Cambrian-Ordovician trilobites from the boundary beds in western Newfoundland and their phylogenetic significance. Special Papers in Palaeontology 30:179–211.Google Scholar
Fortey, R. A. 1989. There are extinctions and extinctions: examples from the Lower Palaeozoic. Philosophical Transactions of the Royal Society of London B 325:327–355.Google Scholar
Fox, D. L.Fisher, D. C.Leighton, L. R. 1999. Reconstructing phylogeny with and without temporal data. Science 284:1816–1819.Google Scholar
Harper, E. M. 2000. Are calcitic layers an effective adaptation against shell dissolution in the Bivalvia? Journal of Zoology 251:179–186.Google Scholar
Harper, E. M.Palmer, T. J.Alphey, J. R. 1997. Evolutionary response by bivalves to changing Phanerozoic sea-water chemistry. Geological Magazine 134:403–407.Google Scholar
Holland, S. M. 1995. The stratigraphic distribution of fossils. Paleobiology 21:92–109.Google Scholar
Holland, S. M. 2000. The quality of the fossil record: a sequence-stratigraphic perspective. In Erwin, D. H.Wing, S. L., eds. Deep time: Paleobiology's perspective. Paleobiology 26(Suppl. to No. 4):148–168.Google Scholar
Holland, S. M.Patzkowsky, M. E. 1999. Models for simulating the fossil record. Geology 27:491–494.Google Scholar
Horowitz, A. S.Blakely, R. F.Macurda, D. B. Jr. 1985. Taxonomic survivorship within the Blastoidea (Echinodermata). Journal of Paleontology 59:543–550.Google Scholar
Johnson, K. G.McCormick, T. 1999. The quantitative description of biotic change using palaeontological databases. Pp. 227–247in Harper, D. A. T., ed. Numerical palaeobiology. Wiley, Chichester, England.Google Scholar
Jones, D. S.Nicol, D. 1986. Origination, survivorship, and extinction of rudist taxa. Journal of Paleontology 60:107–115.Google Scholar
Kendall, D. G. 1948. On the generalized “birth-and-death” process. Annals of Mathematical Statistics 19:1–15.Google Scholar
Kidwell, S. M.Brenchley, P. J. 1996. Evolution of the fossil record: thickness trends in marine skeletal accumulations and their implications. Pp. 290–336in Jablonski, D.Erwin, D. H.Lipps, J. H., eds. Evolutionary paleobiology. University of Chicago Press; Chicago.Google Scholar
Kirchner, J. W.Weil, A. 2000. Delayed biological recovery from extinctions throughout the fossil record. Nature 404:177–180.Google Scholar
Koch, C. F. 1991. Species extinctions across the Cretaceous-Tertiary boundary: observed patterns versus predicted sampling effects, stepwise or otherwise? Historical Biology 5:355–361.Google Scholar
Koch, C. F.Morgan, J. P. 1988. On the expected distribution of species’ ranges. Paleobiology 14:126–138.Google Scholar
Lane, N. G.Waters, J. A.Maples, C. G. 1997. Echinoderm faunas of the Hongguleleng Formation, Late Devonian (Famennian), Xinjiang-Uygur Autonomous Region, People's Republic of China. Paleontological Society Memoir 47. Journal of Paleontology 71(Suppl. to No. 2).Google Scholar
Markwick, P. J. 1998. Crocodilian diversity in space and time: the role of climate in paleoecology and its implications for understanding K/T extinctions. Paleobiology 24:470–497.Google Scholar
Marshall, C. R. 1997. Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons. Paleobiology 23:165–173.Google Scholar
McGhee, G. R. 1996. The Late Devonian mass extinction. Columbia University Press, New York.Google Scholar
McKinney, M. L.Drake, J. A., eds. 1998. Biodiversity dynamics: turnover of populations, taxa, and communities. Columbia University Press, New York.Google Scholar
Meldahl, K. H. 1990. Sampling, species abundance, and the stratigraphic signature of mass extinction: a test using Holocene tidal flat molluscs. Geology 18:890–893.Google Scholar
Miller, A. I. 1997a. Dissecting global diversity patterns: examples from the Ordovician Radiation. Annual Review of Ecology and Systematics 28:85–104.CrossRefGoogle ScholarPubMed
Miller, A. I. 1997b. A new look at age and area: the geographic and environmental expansion of genera during the Ordovician Radiation. Paleobiology 23:410–419.Google Scholar
Miller, A. I. 1998. Biotic transitions in global marine diversity. Science 281:1157–1160.Google Scholar
Miller, A. I.Foote, M. 1996. Calibrating the Ordovician Radiation of marine life: implications for Phanerozoic diversity trends. Paleobiology 22:304–309.Google Scholar
Miller, A. I.Mao, S. G. 1995. Association of orogenic activity with the Ordovician Radiation of marine life. Geology 23:305–308.Google Scholar
Miller, A. I.Mao, S. G. 1998. Scales of diversification and the Ordovician Radiation. Pp. 288–310in McKinney and Drake 1998.Google Scholar
Newell, N. D. 1967. Revolutions in the history of life. Geological Society of America Special Paper 89:63–91.Google Scholar
Nichols, J. D.Pollock, K. H. 1983. Estimating taxonomic diversity, extinction rates, and speciation rates from fossil data using capture-recapture models. Paleobiology 9:150–163.Google Scholar
Nichols, J. D.Morris, R. W.Brownie, C.Pollock, K. H. 1986.Google Scholar
Sources of variation in extinction rates, turnover, and diversity of marine invertebrate families during the Paleozoic. Paleobiology 12:421–432.Google Scholar
Palmer, A. R.Geissman, J. 1999. 1999 geologic time scale. Geological Society of America, Boulder, Colo.Google Scholar
Paul, C. R. C. 1982. The adequacy of the fossil record. Pp. 75–117in Joysey, K. A.Friday, A. E., eds. Problems of phylogenetic reconstruction. Academic Press, London.Google Scholar
Paul, C. R. C. 1998. Adequacy, completeness and the fossil record. Pp. 1–22in Donovan, S. K.Paul, C. R. C., eds. The Adequacy of the fossil record. Wiley, Chichester, U.K.Google Scholar
Pearson, P. N. 1992. Survivorship analysis of fossil taxa when real-time extinction rates vary: the Paleogene planktonic foraminifera. Paleobiology 18:115–131.Google Scholar
Pease, C. M. 1985. Biases in the durations and diversities of fossil taxa. Paleobiology 11:272–292.Google Scholar
Peters, S. E.Foote, M. 2001. Biodiversity in the Phanerozoic: a reinterpretation. Paleobiology 27:583–601 (this volume).Google Scholar
Press, W. H.Teukolsky, S. A.Vetterling, W. T.Flannery, B. P. 1992. Numerical recipes in C, 2d ed.Cambridge University Press, Cambridge.Google Scholar
Rampino, M. R.Adler, A. C. 1998. Evidence for abrupt latest Permian mass extinction of foraminifera: Results of tests for the Signor-Lipps effect. Geology 26:415–418.Google Scholar
Raup, D. M. 1972. Taxonomic diversity during the Phanerozoic. Science 177:1065–1071.Google Scholar
Raup, D. M. 1976. Species diversity in the Phanerozoic: an interpretation. Paleobiology 2:289–297.Google Scholar
Raup, D. M. 1978. Cohort analysis of generic survivorship. Paleobiology 4:1–15.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
Raup, D. M. 1985. Mathematical models of cladogenesis. Paleobiology 11:42–52.Google Scholar
Raup, D. M. 1986. Biological extinction in Earth history. Science 231:1528–1533.Google Scholar
Raup, D. M.Boyajian, G. E. 1988. Patterns of generic extinction in the fossil record. Paleobiology 14:109–125.Google Scholar
Raup, D. M.Sepkoski, J. J. Jr. 1982. Mass extinctions in the marine fossil record. Science 215:1501–1503.CrossRefGoogle ScholarPubMed
Raup, D. M.Sepkoski, J. J. Jr. 1984. Periodicity of extinctions in the geologic past. Proceedings of the National Academy of Sciences USA 81:801–805.Google Scholar
Raup, D. M.Gould, S. J.Schopf, T. J. M.Simberloff, D. S. 1973. Stochastic models of phylogeny and the evolution of diversity. Journal of Geology 81:525–542.Google Scholar
Raymond, A.Metz, C. 1995. Laurussian land-plant diversity during the Silurian and Devonian: mass extinction, sampling bias, or both? Paleobiology 21:74–91.Google Scholar
Rong, J.-Y.Harper, D. A. T. 1999. Brachiopod survival and recovery from the latest Ordovician mass extinctions in South China. Geological Journal 34:321–348.Google Scholar
Sepkoski, J. J. Jr. 1975. Stratigraphic biases in the analysis of taxonomic survivorship. Paleobiology 1:343–355.Google Scholar
Sepkoski, J. J. Jr. 1987. Environmental trends in extinction during the Paleozoic. Science 235:64–66.Google Scholar
Sepkoski, J. J. Jr. 1992. A compendium of fossil marine animal families, 2d ed.Milwaukee Public Museum Contributions in Biology and Geology 83:1–156.Google Scholar
Sepkoski, J. J. Jr. 1996. Patterns of Phanerozoic extinctions: a perspective from global databases. Pp. 35–52in Walliser, O. H., ed. Global events and event stratigraphy. Springer, Berlin.Google Scholar
Sepkoski, J. J. Jr. 1997. Biodiversity: past, present, and future. Journal of Paleontology 71:533–539.Google Scholar
Sepkoski, J. J. Jr. 1998. Rates of speciation in the fossil record. Philosophical Transactions of the Royal Society of London B 353:315–326.Google Scholar
Shaw, A. B. 1964. Time in stratigraphy. McGraw-Hill, NewYork.Google Scholar
Signor, P. W. IIILipps, 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. 2000. Stratigraphy in phylogeny reconstruction. Journal of Paleontology 74:763–766.Google Scholar
Smith, A. B. 2001. Large-scale heterogeneity of the fossil record: implications for Phanerozoic biodiversity studies. Philosophical Transactions of the Royal Society of London B 356:1–17.Google Scholar
Sokal, R. R.Rohlf, F. J. 1981. Biometry, 2d ed.W. H. Freeman, San Francisco.Google Scholar
Solow, A. R.Smith, W. 1997. On fossil preservation and the stratigraphic ranges of taxa. Paleobiology 23:271–278.Google Scholar
Stanley, S. M.Hardie, L. A. 1998. Secular oscillations in the carbonate mineralogy of reef-building and sediment-producing organisms driven by tectonically forced shifts in seawater chemistry. Palaeogeography, Palaeoclimatology, Palaeoecology 144:3–19.Google Scholar
Strauss, D.Sadler, P. M. 1989. Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Mathematical Geology 21:411–427.Google Scholar
Van Valen, L. M. 1973. A new evolutionary law. Evolutionary Theory 1:1–30.Google Scholar
Van Valen, L. M. 1984. A resetting of Phanerozoic community evolution. Nature 307:50–52.Google Scholar
Wagner, P. J. 1997. Patterns of morphologic diversification among the Rostroconchia. Paleobiology 23:115–150.Google Scholar
Wagner, P. J. 1998. A likelihood approach for evaluating estimates of phylogenetic relationship among fossil taxa. Paleobiology 24:430–449.Google Scholar
Wagner, P. J. 1999. 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. 2000. Likelihood tests of hypothesized durations: determining and accommodating biasing factors. Paleobiology 26:431–449.Google Scholar
Wagner, P. J.Sidor, C. A. 2000. Age rank/clade rank metrics—sampling, taxonomy, and the meaning of “stratigraphic consistency.” Systematic Biology 49:463–479.Google Scholar
Webster, G. D.Hafley, D. J.Blake, D. B.Glass, A. 1999. Crinoids and stelleroids (Echinodermata) from the Broken Rib Member, Dyer Formation (Late Devonian, Famennian) of the White River Plateau, Colorado. Journal of Paleontology 73:461–486.Google Scholar
Weiss, R. E.Marshall, C. R. 1999. The uncertainty in the true end point of a fossil's stratigraphic range when stratigraphic sections are sampled discretely. Mathematical Geology 31:435–453.Google Scholar
Whittington, H. B. 1954. Status of invertebrate paleontology, 1953, VI. Arthropoda: Trilobita. Bulletin of the Museum of Comparative Zoology, Harvard College 112:193–200.Google Scholar
Wilkinson, B. H. 1979. Biomineralization, paleoceanography, and the evolution of calcareous marine organisms. Geology 7:524–527.Google Scholar