Hostname: page-component-78c5997874-fbnjt Total loading time: 0 Render date: 2024-11-17T13:13:07.685Z Has data issue: false hasContentIssue false

Signal or noise? A null model method for evaluating the significance of turnover pulses

Published online by Cambridge University Press:  31 July 2017

W. Andrew Barr*
Affiliation:
Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, D.C. 20052, U.S.A. E-mail: [email protected]

Abstract

Patterns of turnover in the mammalian fossil record have been interpreted as reflecting “pulses” of originations and extinctions hypothesized to be driven by climate change. However, criteria for determining what constitutes a meaningful pulse have been idiosyncratic, and investigations of turnover patterns in mammals have yielded mixed results.

This study presents simple simulations of fossil records in which origination and extinction probabilities for each lineage are held constant. Nonetheless, the total number of turnover events per time bin varies stochastically, producing statistical “noise.” Various simulation and analytical assumptions are examined to determine their impact on the type I error rate (i.e., how often “pulses” are detected in a purely stochastic process).

Results suggest that simple analytical parameters (length of time bins and turnover-pulse criterion) have predictable and straightforward effects on false-positive rates. Furthermore, “pulses” of turnover of a magnitude similar to that observed in the terrestrial mammalian fossil record may be quite common under realistic analytical conditions.

The null turnover model offers a practical way to evaluate the significance of observed turnover events in future empirical studies of the fossil record. In evaluating the significance of a “pulse” of fossil origination or extinction events, analytical parameters can be explored using this null model to determine the approximate type I error rate for a set of parameters. Because false-positive rates are shown to be quite high, functional trait-based approaches may offer more reliable indicators of the impact of climate change on turnover dynamics.

Type
Methods in Paleobiology
Copyright
Copyright © 2017 The Paleontological Society. All rights reserved 

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. Paleogeography Paleoclimatology Paleoecology 127:285311.CrossRefGoogle Scholar
Bapst, D. W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution 3:803807.CrossRefGoogle Scholar
Barnosky, A. D., Matzke, N., Tomiya, S., Wogan, G. O. U., Swartz, B., Quental, T. B., Marshall, C., McGuire, J. L., Lindsey, E. L., Maguire, K. C., et al. 2011. Has the Earth’s sixth mass extinction already arrived? Nature 471:5157.CrossRefGoogle ScholarPubMed
Barr, W. A. 2017. Bovid locomotor functional trait distributions reflect land cover and annual precipitation in sub-Saharan Africa. Evolutionary Ecology Research 18:253269.Google Scholar
Baumiller, T. K. 1996. Exploring the pattern of coordinated stasis: simulations and extinction scenarios. Palaeogeography, Palaeoclimatology, Palaeoecology 127:135145.CrossRefGoogle Scholar
Behrensmeyer, A. K., Todd, N. E., Potts, R., and McBrinn, G. E.. 1997. Late Pliocene faunal turnover in the Turkana Basin, Kenya and Ethiopia. Science 278:15891594.CrossRefGoogle ScholarPubMed
Bibi, F., and Kiessling, W.. 2015. Continuous evolutionary change in Plio-Pleistocene mammals of eastern Africa. Proceedings of the National Academy of Sciences USA 112:1062310628.CrossRefGoogle ScholarPubMed
Blaauw, M., Bennett, K. D., and Christen, J. A.. 2010. Random walk simulations of fossil proxy data. The Holocene 20:645649.CrossRefGoogle Scholar
Bobe, R., and Behrensmeyer, A. K.. 2004. The expansion of grassland ecosystems in Africa in relation to mammalian evolution and the origin of the genus Homo. Palaeogeography, Palaeoclimatology, Palaeoecology 207:399420.CrossRefGoogle Scholar
Bobe, R., Behrensmeyer, A., and Chapmam, R.. 2002. Faunal change, environmental variability and late Pliocene hominin evolution. Journal of Human Evolution 42:475497.CrossRefGoogle ScholarPubMed
Brett, C. E., and Baird, G.. 1995. Coordinated stasis and evolutionary ecology of Silurian to Middle Devonian faunas in the Appalachian Basin. Pp. 285315 in D. H. Erwin and R. L. Anstey, eds. New approaches to speciation in the fossil record. Columbia University Press, New York.Google Scholar
deMenocal, P. B. 1995. Plio-Pleistocene African climate. Science 270:53.CrossRefGoogle ScholarPubMed
Eronen, J. T., Polly, P. D., Fred, M., Damuth, J., Frank, D. C., Mosbrugger, V., Scheidegger, C., Stenseth, N. C., and Fortelius, M.. 2010a. Ecometrics: the traits that bind the past and present together. Integrative Zoology 5:88101.CrossRefGoogle Scholar
Eronen, J. T., Puolamäki, K., Liu, L., Lintulaakso, K., Damuth, J., Janis, C., and Fortelius, M.. 2010b. Precipitation and large herbivorous mammals II: application to fossil data. Evolutionary Ecology Research 12:235248.Google Scholar
Eronen, J. T., Puolamäki, K., Liu, L., Lintulaakso, K., Damuth, J., Janis, C. M., and Fortelius, M.. 2010c. Precipitation and large herbivorous mammals I: estimates from present-day communities. Evolutionary Ecology Research 12:217233.Google Scholar
Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23:278300.CrossRefGoogle Scholar
Foote, M. 2000. Origination and extinction components of taxonomic diversity: general problems. Paleobiology 26:74102.CrossRefGoogle Scholar
Foote, M., and Raup, D. M.. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121140.CrossRefGoogle ScholarPubMed
Fortelius, M., Eronen, J., Jernvall, J., Liu, L., Pushkina, D., Rinne, J., Tesakov, A., Vislobokova, I., Zhang, Z., and Zhou, L.. 2002. Fossil mammals resolve regional patterns of Eurasian climate change over 20 million years. Evolutionary Ecology Research 4:10051016.Google Scholar
Fortelius, M., Žliobaitė, I., Kaya, F., Bibi, F., Bobe, R., Leakey, L., Leakey, M., Patterson, D., Rannikko, J., and Werdelin, L.. 2016. An ecometric analysis of the fossil mammal record of the Turkana Basin. Philosophical Transactions of the Royal Society of London B 371:20150232.CrossRefGoogle ScholarPubMed
Gotelli, N. J., and Graves, G. R.. 1996. Null models in ecology. Smithsonian Institution Press, Washington, D.C.Google Scholar
Jablonski, D., and Chaloner, W. G.. 1994. Extinctions in the fossil record [and Discussion]. Philosophical Transactions of the Royal Society of London B 344:1117.Google Scholar
Kendall, D. G. 1948. On the generalized “birth-and-death” process. Annals of Mathematical Statistics 19:115.CrossRefGoogle Scholar
McKee, J. K. 1995. Turnover patterns and species longevity of large mammals from the late Pliocene and Pleistocene of southern Africa: a comparison of simulated and empirical data. Journal of Theoretical Biology 172:141147.CrossRefGoogle Scholar
McKee, J. K. 2001. Faunal turnover rates and mammalian biodiversity of the late Pliocene and Pleistocene of eastern Africa. Paleobiology 27:500511.2.0.CO;2>CrossRefGoogle Scholar
Nee, S., Holmes, E. C., May, R. M., and Harvey, P. H.. 1994a. Extinction rates can be estimated from molecular phylogenies. Philosophical Transactions of the Royal Society of London B 344:7782.Google ScholarPubMed
Nee, S., May, R. M., and Harvey, P. H.. 1994b. The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London B 344:305311.Google ScholarPubMed
Polly, P. 2010. Tiptoeing through the trophics: geographic variation in carnivoran locomotor ecomorphology in relation to environment. Pp. 347410 in A. Goswami and A. Friscia, eds. Carnivoran evolution: new views on phylogeny, form, and function. Cambridge University Press, Cambridge.Google Scholar
Polly, P. D., Lawing, A. M., Eronen, J. T., and Schnitzler, J.. 2015. Processes of ecometric patterning: modelling functional traits, environments, and clade dynamics in deep time. Biological Journal of the Linnean Society 118:3963.CrossRefGoogle Scholar
Potts, R. 2007. Environmental hypotheses of Pliocene human evolution. In: Bobe, R., Alemseged, Z. and Behrensmeyer, A. K., editor. Hominin Environments In The East African Pliocene: An Assessment Of The Faunal Evidence. Vertebrate Paleobiology and Paleoanthropology Series. Springer. p. 2549.CrossRefGoogle Scholar
R Development Core Team. 2015. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.Google Scholar
Raia, P., Piras, P., and Kotsakis, T.. 2005. Turnover pulse or Red Queen? Evidence from the large mammal communities during the Plio-Pleistocene of Italy. Palaeogeography, Palaeoclimatology, Palaeoecology 221:293312.CrossRefGoogle Scholar
Raup, D. M. 1991. Extinction: bad genes or bad luck? 1st paperback ed. Norton, New York.Google ScholarPubMed
Raup, D. M., Gould, S. J., Schopf, T. J. M., and Simberloff, D. S.. 1973. Stochastic models of phylogeny and the evolution of diversity. Journal of Geology 81:525542.CrossRefGoogle Scholar
Schulte, P., Alegret, L., Arenillas, I., Arz, J. A., Barton, P. J., Bown, P. R., Bralower, T. J., Christeson, G. L., Claeys, P., Cockell, C. S., et al. 2010. The Chicxulub asteroid impact and mass extinction at the Cretaceous-Paleogene boundary. Science 327:12141218.CrossRefGoogle ScholarPubMed
Sepkoski, J. J. 1998. Rates of speciation in the fossil record. Philosophical Transactions of the Royal Society of London B 353:315326.CrossRefGoogle ScholarPubMed
Thomas, C. D., Cameron, A., Green, R. E., Bakkenes, M., Beaumont, L. J., Collingham, Y. C., Erasmus, B. F. N., de Siqueira, M. F., Grainger, A., Hannah, L., et al. 2004. Extinction risk from climate change. Nature 427:145148.CrossRefGoogle ScholarPubMed
Villmoare, B., Kimbel, W., Seyoum, C., Campisano, C., DiMaggio, E., Rowan, J., Braun, D., Arrowsmith, J., and Reed, K.. 2015. Early Homo at 2.8Ma from Ledi-Geraru, Afar, Ethiopia. Science 347:13521355.CrossRefGoogle Scholar
Vrba, E. S. 1985. Ecological and adaptive changes associated with early hominid evolution. Pp. 6371 in E. Delson, ed. Ancestors: the hard evidence. Liss, New York.Google Scholar
Vrba, E. S. 1988. Late Pliocene climatic events and hominid evolution. Pp. 405426 in F. E. Grine, ed. Evolutionary history of the “Robust” Australopithecines. Aldine, New York.Google Scholar
Vrba, E. S. 1993. Turnover-pulses, the Red Queen, and related topics. American Journal of Science 293:418.CrossRefGoogle Scholar
Vrba, E. S. 1995. The fossil record of African antelopes (Mammalia, Bovidae) in relation to human evolution and paleoclimate. Pp. 383424 in E. S. Vrba, G. H. Denton, T. C. Partridge and L. H. Burckle, eds. Paleoclimate and evolution with emphasis on human origins. Yale University Press, New Haven, Conn.Google Scholar
Vrba, E. S. 1999. Habitat theory in relation to the evolution in African Neogene biota and hominids. Pp. 1934 in T. G. Bromage and F. Schrenk, eds. African biogeography, climate change, and human evolution. Oxford University Press, Oxford.CrossRefGoogle Scholar
Werdelin, L., and Lewis, M. E.. 2005. Plio-Pleistocene Carnivora of eastern Africa: species richness and turnover patterns. Zoological Journal of the Linnean Society 144:121144.CrossRefGoogle Scholar
Wesselman, H. B. 1995. Of mice and almost-men: regional paleoecology and human evolution in the Turkana Basin. Pp. 356368 in E. S. Vrba, G. H. Denton, T. C. Partridge, and L. H. Burckle, eds. Paleoclimate and evolution with emphasis on human origins. Yale University Press, New Haven, Conn.Google Scholar
White, T. 1995. African omnivores: global climatic change and Plio-Pleistocene hominids and suids. Pp. 369384 in E. S. Vrba, G. H. Denton, T. C. Partridge, and L. H. Burckle, eds. Paleoclimate and evolution with emphasis on human origins. Yale University Press, New Haven, Conn.Google Scholar
Žliobaitė, I., Rinne, J., Tóth, A. B., Mechenich, M., Liu, L., Behrensmeyer, A. K., and Fortelius, M.. 2016. Herbivore teeth predict climatic limits in Kenyan ecosystems. Proceedings of the National Academy of Sciences USA 113:1275112756.CrossRefGoogle ScholarPubMed