Hostname: page-component-586b7cd67f-rcrh6 Total loading time: 0 Render date: 2024-11-23T21:41:01.085Z Has data issue: false hasContentIssue false
  • English
  • Français

Accurate and precise estimates of origination and extinction rates

Published online by Cambridge University Press:  08 April 2016

John Alroy
John Alroy*
Affiliation:
Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia. E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Paleobiologists have used many different methods for estimating rates of origination and extinction. Unfortunately, all equations that consider entire age ranges are distorted by the Pull of the Recent, the Signor-Lipps effect, and simple edge effects. Attention has been paid recently to an equation of Foote's that considers counts of taxa either crossing the bottom and top of an interval or crossing one boundary but not the other. This generalized boundary-crosser (BC) method has important advantages but is still potentially subject to the major biases. The only published equation that circumvents all of them is the three-timer (3T) log ratio, which does so by focusing on a four-interval moving window. Although it is highly accurate it is noisy when turnover rates are very high or sampling is very poor. More precise values are yielded by a newly derived equation that uses the same counts. However, it also considers taxa sampled in a window's first and fourth intervals but missing from the third (i.e., gap-fillers). Simulations show that the 3T, gap-filler (GF), and BC equations yield identical values when sampling and turnover are uniform through time. When applied to Phanerozoic-scale marine animal data, 3T and GF agree well but the BC rates are systematically lower. The apparent reason is that (1) long-ranging but infrequently sampled genera are less likely to be split up by taxonomists and (2) the BC equation overweights taxa with long ranges. Thus, BC rates pertain more to rare genera that are likely to represent large clades whereas GF rates pertain more to actual species-level patterns. Given these results, all published turnover rates based either on genus-level data or on age ranges must be reconsidered because they may reflect taxonomic practices more strongly than the species-level dynamics of interest to biologists.

Type
Articles
Information
Paleobiology , Volume 40 , Issue 3 , Summer 2014 , pp. 374 - 397
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. 1996. Constant extinction, constrained diversification, and uncoordinated stasis in North American mammals. Palaeogeography, Palaeoclimatology, Palaeoecology 127:285–311.Google Scholar
Alroy, J. 2008. Dynamics of origination and extinction in the marine fossil record. Proceedings of the National Academy of Sciences USA 105:11,536–11,542.Google Scholar
Alroy, J. 2009. Speciation and extinction in the fossil record of North American mammals. Pp. 301–323inButlin, R., Bridle, J., and Schluter, D., eds. Speciation and patterns of diversity. Cambridge University Press, Cambridge.Google Scholar
Alroy, J. 2010a. The shifting balance of diversity among major marine animal groups. Science 329:1191–1194.Google Scholar
Alroy, J. 2010b. Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates. InAlroy, J. and Hunt, G., eds. Quantitative methods in paleobiology. Paleontological Society Papers 16:55–80.CrossRefGoogle Scholar
Alroy, J. 2010c. Geographical, environmental, and biotic controls on Phanerozoic marine diversification. Palaeontology 53:1211–1235.Google Scholar
Alroy, J., Aberhan, M., Bottjer, D. J., Foote, M., Fürsich, F. T., Harries, P. J., Hendy, A. J. W., Holland, S. M., Ivany, L. C., Kiessling, W., Kosnik, M. A., Marshall, C. R., McGowan, A. J., Miller, A. I., Olszewski, T. D., Patzkowsky, M. E., Peters, S. E., Villier, L., Wagner, P. J., Bonuso, N., Borkow, P. S., Brenneis, B., Clapham, M. E., Fall, L. M., Ferguson, C. A., Hanson, V. L., Krug, A. Z., Layou, K. M., Leckey, E. H., Nürnberg, S., Powers, C. M., Sessa, J. A., Simpson, C., Tomašových, A., and Visaggi, C. C. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321:97–100.Google Scholar
Bonelli, J. R. Jr., and Patzkowsky, M. E. 2011. Taxonomic and ecologic persistence across the onset of the late Paleozoic ice age: evidence from the Upper Mississippian (Chesterian Series), Illinois basin, United States. Palaios 26:5–17.Google Scholar
Cascales-Miñana, C.Ceal, J., and Diez, J. B. 2013. What is the best way to measure extinction? A reflection from the palaeobotanical record. Earth-Science Reviews 124:126–147.Google Scholar
Cermeño, P. 2012. Marine planktonic microbes survived climatic instabilities in the past. Proceedings of the Royal Society of London B 279:474–479.Google Scholar
Connolly, S. R., and Miller, A. I. 2002. Joint estimation of sampling and turnover rates from fossil databases: capture-mark-recapture methods revisited. Paleobiology 27:751–767.Google Scholar
Ernst, A. 2013. Diversity dynamics and evolutionary patterns of Devonian Bryozoa. Palaeobiodiversity and Palaeoenvironments 93:45–63.Google Scholar
Flessa, K. W., and Jablonski, D. 1985. Declining Phanerozoic background extinction rates: effect of taxonomic structure? Nature 313:216–218.CrossRefGoogle Scholar
Foote, M. 1994. Temporal variation in extinction risk and temporal scaling of extinction metrics. Paleobiology 20:424–444.CrossRefGoogle 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).Google Scholar
Foote, M. 2000. Origination and extinction components of taxonomic diversity: general problems. InErwin, D. H. and Wing, S. L., eds. Deep time: Paleobiology's perspective. Paleobiology 26(Suppl. to No. 4):74–102.Google Scholar
Foote, M. 2005. Pulsed origination and extinction in the marine realm. Paleobiology 31:6–20.Google Scholar
Foote, M. 2007. Extinction and quiescence in marine animal genera. Paleobiology 33:261–272.CrossRefGoogle Scholar
Foote, M., and Raup, D. M. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121–140.Google Scholar
Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264.Google Scholar
Groves, J. R., and Wang, Y. 2013. Timing and size selectivity of the Guadalupian (Middle Permian) fusulinoidean extinction. Journal of Paleontology 87:183–196.Google Scholar
Harnik, P. G., Lotze, H. K., Anderson, S. C., Finkel, Z. V., Finnegan, S., Lindberg, D. R., Liow, L. H., Lockwood, R., McClain, C. R., McGuire, J. L., O'Dea, A., Pandolfi, J. M., Simpson, C., and Tittensor, D. P. 2012. Extinctions in ancient and modern seas. Trends in Ecology and Evolution 27:608–617.Google Scholar
Heim, N. A., and Peters, S. E. 2011. Regional environmental breadth predicts geographic range and longevity in fossil marine genera. PLoS ONE 6 (5):e18946.Google Scholar
Jaramillo, C., Rueda, M. J., and Mora, G. 2006. Cenozoic plant diversity in the Neotropics. Science 311:1893–1896.CrossRefGoogle ScholarPubMed
Kaminski, M. A., Setoyama, E., and Cetean, C. G. 2010. The Phanerozoic diversity of agglutinated foraminifera: origination and extinction rates. Acta Palaeontologica Polonica 55:529–539.CrossRefGoogle Scholar
Kiessling, W., and Aberhan, M. 2007. Geographical distribution and extinction risk: lessons from Triassic-Jurassic marine benthic organisms. Journal of Biogeography 34:1473–1489.Google Scholar
Kiessling, W., and Simpson, C. 2011. On the potential for ocean acidification to be a general cause of ancient reef crises. Global Change Biology 17:56–67.CrossRefGoogle Scholar
Kiessling, W., Clapham, M. E., Hendy, A. J. W., Miller, A. I., Alroy, J., Aberhan, M., Wagner, P. J., Foote, M., Fürsich, F., and Patzkowsky, M. E. 2013. Taxonomic occurrences of Phanerozoic Metazoa recorded in Fossilworks and the Paleobiology Database. http://fossilworks.org.Google Scholar
Krug, A. Z., and Patzkowsky, M. E. 2007. Geographic variation in turnover and recovery from the Late Ordovician mass extinction. Paleobiology 33:435–454.Google Scholar
Leslie, P. H., and Chitty, D. 1951. The estimation of population parameters from data obtained by means of the capture-recapture method. I. The maximum likelihood equations for estimating the death-rate. Biometrika 38:269–292.Google Scholar
Mayhew, P. J., Jenkins, G. B., and Benton, T. G. 2008. A long-term association between global temperature and biodiversity, origination and extinction in the fossil record. Proceedings of the Royal Society of London B 275:47–53.Google Scholar
McKinney, M. L. 1997. Extinction vulnerability and selectivity: combining ecological and paleontological views. Annual Review of Ecology and Systematics 28:495–516.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
Miller, A. I., and Foote, M. 2009. Epicontinental seas versus open-ocean settings: the kinetics of mass extinction and origination. Science 326:1106–1109.Google Scholar
Morrow, J., Harries, P. J., and Krivanek, J. G. 2011. Reef recovery following the Frasnian-Famennian (Late Devonian) mass extinction: evidence from the Dugway Range, west-central Utah. Palaios 26:607–622.CrossRefGoogle Scholar
Nichols, J. D, and 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
Payne, J. L., Truebe, S., Nützel, A., and Chang, E. T. 2011. Local and global abundance associated with extinction risk in late Paleozoic and early Mesozoic gastropods. Paleobiology 37:616–632.Google Scholar
Peters, S. E. 2008. Environmental determinants of extinction selectivity in the fossil record. Nature 454:626–629.CrossRefGoogle ScholarPubMed
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. 1991. A kill curve for Phanerozoic marine species. Paleobiology 17:37–48.Google Scholar
Raup, D. M., and Sepkoski, J. J. Jr. 1982. Mass extinctions in the marine fossil record. Science 215:1501–1503.Google Scholar
Raup, D. M., and 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., and Simberloff, D. 1973. Stochastic models of phylogeny and the evolution of diversity. Journal of Geology 81:525–542.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. 1978. A kinetic model of Phanerozoic taxonomic diversity. I. Analysis of marine orders. Paleobiology 4:223–251.Google Scholar
Signor, P. W., and Lipps, J. H. 1982. Sampling bias, gradual extinction patterns, and catastrophes in the fossil record. Geological Society of American Special Publication 190:291–296.Google Scholar
Simpson, C., and Harnik, P. G. 2009. Assessing the role of abundance in marine bivalve extinction over the post-Paleozoic. Paleobiology 35:631–647.Google Scholar
Simpson, C., and Kiessling, W. 2009. The role of extinction in large-scale diversity-stability relationships. Proceedings of the Royal Society of London B 277:1451–1456.Google Scholar
Simpson, C., Kiessling, W., Mewis, H., Baron-Szabo, R. C., and Müller, J. 2011. Evolutionary diversification of reef corals: a comparison of the molecular and fossil records. Evolution 65:3274–3284.Google Scholar
Van Valen, L. M. 1984. A resetting of Phanerozoic community evolution. Nature 307:50–52.CrossRefGoogle Scholar
Xiong, C., Wang, D., Wang, Q., Benton, M. J., Xue, J., Meng, M., Zhao, Q., and Zhang, J. 2013. Diversity dynamics of Silurian-Early Carboniferous land plants in South China. PLoS ONE 8:e75706.Google Scholar