MEASURING OCCUPANCY
——. 2015b. R code for JADE (Joint species-rank Abundance Distribution/Estimation) based on individual-based (abundance) and sampling-unit-based (incidence) data. Ecological Archives E096–107-S1.
Chen, Z.-Q., K. Kaiho, and A. D. George. 2005. Early Triassic recovery of the brachiopod faunas from the end-Permian mass extinction: a global review. Palaeogeography, Palaeo- climatology, Palaeoecology 224:270–290. Clapham, M. E., S. Shen, and D. J. Bottjer. 2009. The double mass extinction revisited: reassessing the severity, selectivity, and causes of the end-Guadalupian biotic crisis (Late Permian). Paleobiology 35:32–50. Colwell, R. K., A. Chao, N. J. Gotelli, S.-Y. Lin, C. X. Mao, R. L. Chazdon, and J. T. Longino. 2012. Models and estimators linking individual-based and sample-based rarefaction, extra- polation and comparison of assemblages. Journal of Plant Ecology 5:3–21.
Coull, B. A., and A. Agresti. 1999. The use ofmixed logit models to reflect heterogeneity in capture-recapture studies. Biometrics 55:294–301. Darroch, S. A. F., and P. J.Wagner. 2015. Responses of beta diver- sity to pulses of Ordovician–Silurian mass extinction. Ecology 96:532–549. Dorazio, R. M., J. A. Royle, B. Söderström, and A. Glimskär. 2006. Estimating species richness and accumulation by modeling species occurrence and detectability. Ecology 87:842–854. Edwards, A. W. F. 1991. Likelihood, expanded ed. Johns Hopkins University Press, Baltimore, Md.
Efron, B., and R. J. Tibshirani. 1993. An introduction to the bootstrap. Chapman and Hall, New York.
Erwin, D. H. 2001. Lessons from the past: biotic recoveries from mass extinctions. Proceedings of the National Academy of Sciences USA 98:5399–5403.
Feller, W. 1971. An introduction to probability theory and its applications, Vol. 2, 2nd ed.Wiley, New York. Ferguson, P. F. B.,M. J. Conroy, and J.Hepinstall-Cymerman. 2015. Occupancy models for datawith false positive and false negative errors and heterogeneity across sites and surveys. Methods in Ecology and Evolution 6:1395–1406. Finnegan, S., J. L. Payne, and S. C. Wang. 2008. The Red Queen revisited: reevaluating the age selectivity of Phanerozoic marine genus extinctions. Paleobiology 34:318–341.
Finney, D. J. 1949. The truncated binomial distribution. Annals of Eugenics 14:319–328.
Fisher, R. A. 1936. The effect of methods of ascertainment upon the estimation of frequencies. Annals of Eugenics 6:13–25.
Fisher, R. A., A. S. Corbet, and C. B. Williams. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. Journal of Animal Ecology 12:42–58.
Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23:278–300.
——. 2007. Symmetric waxing and waning of marine invertebrate genera. Paleobiology 33:517–529.
——. 2014. Environmental controls on geographic range size in marine animal genera. Paleobiology 40:440–458.
Foote, M., and A. I. Miller. 2013. Determinants of early survival in marine animal genera. Paleobiology 39:171–192.
Foote, M., and D. M. Raup. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121–140.
Foote, M., J. S. Crampton, A. G. Beu, B. A. Marshall, R. A. Cooper, P. A. Maxwell, and I. Matcham. 2007. Rise and fall of species occupancy in Cenozoic fossil mollusks. Science 318:1131–1134.
Foote, M., K. A. Ritterbush, and A. I. Miller. 2016. Geographic ranges of genera and their constituent species: structure, evolu- tionary dynamics, and extinction resistance. Paleobiology 42: 269–288.
725
Good, I. J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40:237–264.
Gradstein, F. M., J. Ogg, M. Schmitz, and G. Ogg. 2012. The geo- logic time scale 2012. Elsevier, Amsterdam.
Haldane, J. B. S. 1932. A method for investigating recessive characters in man. Journal of Genetics 26:251–255.
——. 1938. The estimation of the frequencies of recessive conditions in man. Annals of Eugenics 8:255–262.
Hallam, A., and P. B. Wignall. 1997. Mass extinctions and their aftermath. Oxford University Press, Oxford.
Jablonski, D., K. Roy, and J.W. Valentine. 2006. Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 314:102–106.
Jablonski, D., C. L. Belanger, S. K. Berke, S. Huang, A. Z. Krug, K. Roy, A. Tomasovych, and J. W. Valentine. 2013. Out of the tro- pics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient. Proceed- ings of the National Academy of Sciences USA 110:10487–10494.
Liow, L. H., and N. C. Stenseth. 2007. The rise and fall of species: implications formacroevolutionary and macroecological studies. Proceedings of the Royal Society of London B 274:2745–2752.
Liow, L. H., H. J. Skaug, T. Ergon, and T. Schweder. 2010. Global occurrence trajectories of microfossils: environmental volatility and the rise and fall of individual species. Paleobiology 36: 224–252.
MacKenzie, D. I., J. D. Nichols, G. B. Lachman, S. Droege, J. A. Royle, and C. A. Langtimm. 2002. Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248–2255.
MacKenzie, D. I., J. D. Nichols, J. E. Hines, M. G. Knutson, and A. B. Franklin. 2003. Estimating site occupancy, colonization, and local extinction when a species is detected imperfectly. Ecology 84:2200–2207.
MacKenzie, D. I., J. D. Nichols, J. A. Royle, K. H. Pollock, L. L. Bailey, and J. E. Hines. 2006. Occupancy estimation and modeling: inferring patterns and dynamics of species occurrence. Academic Press, Amsterdam.
McGill, B. J. 2003. DoesMother Nature really prefer rare species or are log-left-skewed SADs a sampling artefact? Ecology Letters 6:766–773.
Miller, A. I. 1997. A new look at age and area: the geographic and environmental expansion of genera during the Ordovician Radiation. Paleobiology 23:410–419.
Miller, A. I., and M. Foote. 2003. Increased longevities of post- Paleozoic marine genera after mass extinctions. Science 302:1030–1032.
Payne, J. L., and S. Finnegan. 2007. The effect of geographic range on extinction risk during background and mass extinction. Proceedings of the National Academy of Sciences USA 104: 10506–10511.
Preston, F. W. 1948. The commonness, and rarity, of species. Ecology 29:254–283.
R Development Core Team 2011. R: a language and environment for statistical computing. R Foundation for Statistical Comput- ing, Vienna, Austria.
http://www.R-project.org. Rabinowitz, D. 1981. Seven forms of rarity. Pp. 205–217 in H. Synge, ed. The biological aspects of rare plant conservation. Wiley, Chichester, U.K.
Rider, P. R. 1955. Truncated binomial and negative binomial distributions. Journal of the American Statistical Association 50:877–883.
Royle, J. A., and J. D. Nichols. 2003. Estimating abundance from repeatedpresence-absence data orpoint counts. Ecology 84:777–790.
Schubert, J. K., and D. J. Bottjer. 1995. Aftermath of the Permian– Triassic mass extinction event: paleoecology of Lower Triassic carbonates in the western USA. Palaeogeography, Palaeo- climatology, Palaeoecology 116:1–39.
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