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Detecting diversification rates in relation to preservation and tectonic history from simulated fossil records

  • Tara M. Smiley (a1)

For mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record toward the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per capita, three-timer, and capture–mark–recapture (CMR) metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and CMR metrics produced more accurate rate estimates, per capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

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Alroy J. 1996. Constant extinction, constrained diversification, and uncoordinated stasis in North American mammals. Palaeogeography, Palaeoclimatology, Palaeoecology 127:285311.
Alroy J. 2008. Dynamics of origination and extinction in the marine fossil record. Proceedings of the National Academy of Sciences USA 105:1153611542.
Alroy J. 2009. Speciation and extinction in the fossil record of North American mammals. Pp. 301323 in R. K. Butlin, J. R. Bridle, and D. Schuler, eds. Speciation and patterns of diversity. Cambridge University Press, Cambridge.
Alroy J. 2010. Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates. In J. Alroy and G. Hunt, eds. Quantitative methods in paleobiology. Paleontological Society Papers 16:5580.
Alroy J. 2014. Accurate and precise estimates of origination and extinction rates. Paleobiology 40:374397.
Alroy J., Koch P. L., and Zachos J. C.. 2000. Global climate change and North American mammalian evolution. Paleobiology 26:259288.
Alroy J., Marshall C. R., Bambach R. K., Bezusko K., Foote M., Fursich 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-Gottshall P. M., Olszewski T. D., Patzkowsky M. E., Raup D. M., Roy K., Sepkoski J. J., Sommers M. G., Wagner P. J., and Webber A.. 2001. Effects of sampling standardization on estimates of Phanerozoic marine diversification. Proceedings of the National Academy of Sciences USA 98:62616266.
Alroy J. M. Aberhan, 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., Willier 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., Tomašovych A., and Visaggi C. C.. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321:97100.
Atwater T., and Stock J.. 1998. Pacific-North America Plate tectonics of the Neogene southwestern United States: an update. International Geology Review 40:375402.
Badgley C. 2010. Tectonics, topography, and mammalian diversity. Ecography 33:220231.
Badgley C., and Finarelli J. A.. 2013. Diversity dynamics of mammals in relation to tectonic and climatic history: comparison of three Neogene records from North America. Paleobiology 39:373399.
Badgley C., and Fox D. L.. 2000. Ecological biogeography of North American mammals: species density and ecological structure in relation to environmental gradients. Journal of Biogeography 27:14371467.
Badgley C., Downs W., and Flynn L. J.. 1998. Taphonomy of small-mammal fossil assemblages from the middle Miocene Chinji formation, Siwalik group, Pakistan. National Science Museum Monographs 14:145166.
Badgley C., Smiley T. M., and Finarelli J. A.. 2014. Great Basin mammal diversity in relation to landscape history. Journal of Mammalogy 95:10901106.
Badgley C., Smiley T. M., and Loughney K.. 2015. Miocene mammal diversity of the Mojave region in the context of Great Basin mammal history. Pp. 3443 in Mojave Miocene, Desert Symposium Field Guide and Proceedings. California State University, Desert Studies Center, Fullerton, Calif.
Badgley C., Smiley T. M., Terry R. C., Davis E. B., DeSantis L. R. G., Fox D. L., Hopkins S. S. B., Jezkova T., Matocq M. D., Matzke N., McGuire J. L., Mulch A., Riddle B. R., Roth V. L., Samuels J. X., Strömberg C. A. E., and Yanites B. J.. 2017. Biodiversity and topographic complexity: modern and geohistorical perspectives. Trends in Ecology and Evolution 32:211226.
Barnosky A. D. 2001. Distinguishing the effects of the Red Queen and Court Jester on Miocene mammal evolution in the northern Rocky Mountains. Journal of Vertebrate Paleontology 21:172185.
Barnosky A. D., and Carrasco M. A.. 2002. Effects of Oligo-Miocene global climate changes on mammalian species richness in the northwestern quarter of the USA. Evolutionary Ecology Research 4:811841.
Barnosky A. D., Bibi F., Hopkins S. S. B, and Nichols R.. 2007. Biostratigraphy and magnetostratigraphy of the mid-Miocene Railroad Canyon Sequence, Montana and Idaho, and age of the mid-Tertiary unconformity west of the Continental Divide. Journal of Vertebrate Paleontology 27:204224.
Barthlott W., Mutke J., Rafiqpoor D., Kier G., and Kreft H.. 2005. Global centers of vascular plant diversity. Nova Acta Leopoldina NF 92:6183.
Blois J. L., and Hadly E. A.. 2009. Mammalian response to Cenozoic climatic change. Annual Reviews in Earth and Planetary Sciences 37:181208.
Bivand R. S., and Lewin-Koh N.. 2017. maptools: tools for reading and handling spatial objects. R package, Version 0.9-2.
Bivand R. S., and Rundel C.. 2017. rgeos: interface to Geometry Engine—Open Source (GEOS). R package, Version 0.3-23.
Bivand R. S., Pebesma E., and Gomez-Rubio V.. 2013. Applied spatial data analysis with R, 2 nd ed. Springer, NY.
Carrasco M. A., Barnosky A. D., Kraatz B. P., and Davis E. B.. 2007. The Miocene Mammal Mapping Project (MIOMAP): an online database of Arikareean through Hemphillian fossil mammals. Bulletin of Carnegie Museum of Natural History 15.
Clark M. K. 2007. The significance of paleotopography. Reviews in Mineralogy and Geochemistry 66:121.
Coblentz D. D., and Riitters K. H.. 2004. Topographic controls on the regional-scale biodiversity of the south-western USA. Journal of Biogeography 31:11251138.
Connolly S. R., and Miller A. I.. 2001. Joint estimation of sampling and turnover rates from fossil databases: capture-mark-recapture methods revisited. Paleobiology 27:751767.
Connolly S. R., and Miller A. I.. 2002. Global Ordovician faunal transitions in the marine benthos: proximate causes. Paleobiology 27:779795.
Conroy M. J., and Nichols J. D.. 1984. Testing for variation in taxonomic extinction probabilities: a suggested methodology and some results. Paleobiology 10:328337.
Cooch E., and White G. C.. 2006. Program MARK: a gentle introduction.
Cracraft J. 1985. Biological diversification and its causes. Annals of the Missouri Botanical Garden 72:794822.
Davis E. B. 2005. Mammalian beta diversity in the Great Basin, western USA: palaeontological data suggest deep origin of modern macroecological structure. Global Ecology and Biogeography 14:479490.
DeSantis L. R. G., Beavins Tracy R. A., Koontz C. S., Roseberry J. C., and Velasco M. C.. 2012. Mammalian niche conservation through deep time. PLoS ONE 7:e35624.
Dickinson W. R. 2006. Geotectonic evolution of the Great Basin. Geosphere 2:353368.
Eronen J. T., Janis C. M., Chamberlain C. P., and Mulch A.. 2015. Mountain uplift explains differences in Palaeogene patterns of mammalian evolution and extinction between North America and Europe. Proceedings of the Royal Society of London B 282:20150136.
Fabre P.-H., Hautier L., Dimitrov D., and Douzery E. J. P.. 2012. A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evolutionary Biology 12:88.
Finarelli J. A., and Badgley C.. 2010. Diversity dynamics of Miocene mammals in relation to the history of tectonism and climate. Proceedings of the Royal Society of London B 277:27212726.
Foote M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology 23:278300.
Foote M. 2000. Origination and extinction components of taxonomic diversity: general problems. Paleobiology 26:74102.
Foote M., and Raup D. M.. 1996. Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22:121140.
Foote M., Hunter J. P., Janis C. M., and Sepkoski J. J.. 1999. Evolutionary and preservational constraints on origins of biologic groups: divergence times of eutherian mammals. Science 283:13101314.
Fritz S. A., Schnitzler J., Eronen J. T., Hof C., Böhning-Gaese K., and Graham C. H.. 2013. Diversity in time and space: wanted dead and alive. Trends in Ecology and Evolution 28:509516.
Hafner J. C., Light J. E., Hafner D. J., Hafner M. S., Reddington E., Rogers D. S., and Riddle B. R.. 2007. Basal clades and molecular systematics of heteromyid rodents. Journal of Mammalogy 88:11291145.
Hibbard C. W. 1941. New mammals from the Rexroad fauna, upper Pliocene of Kansas. American Midland Naturalist 26:337368.
Holland S. M. 2000. The quality of the fossil record: a sequence stratigraphic perspective. Paleobiology 26:148168.
Holland S. M. 2016. The non-uniformity of fossil preservation. Philosophical Transactions of the Royal Society of London B 371:20150130.
Holland S. M., and Patzkowsky M. E.. 1999. Models for simulating the fossil record. Geology 27:491494.
Hoorn C., Wesselingh F. P., ter Steege H., Bermudez M. A., Mora A., Sevink J., Sanmartin I., Sanchez-Meseguer A., Anderson C. L., Figueiredo J. P., Jaramillo C., Riff D., Negri F. R., Hooghiemstra H., Lundberg J., Stadler T., Sarkinen T., and Antonelli A.. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330:927931.
Horton T. W., and Chamberlain C. P.. 2006. Stable isotopic evidence for Neogene surface downdrop in the central Basin and Range Province. Geological Society of America Bulletin 118:475490.
Jablonski D., Roy K., and Valentine J. W.. 2006. Out of the tropics: evolutionary dynamics of the latitudinal diversity gradient. Science 314:102106.
Kidwell S. M., and Holland S. M.. 2002. The quality of the fossil record: implications for evolutionary analyses. Annual Review Ecology and Systematics 33:561588.
Kohn M. J., and Fremd T. J.. 2008. Miocene tectonics and climate forcing of biodiversity, western United States. Geology 36:783786.
Laake J. L. 2013. RMark: an R interface for analysis of capture-recapture data with MARK. AFSC Processed Rep 2013-01. Alaska Fisheries Science Center, NOAA, National Marine Fisheries Service, Seattle, Wash.
Lindsay E. H. 1972. Small mammal fossils from the Barstow Formation. California. University of California Publications in Geological Sciences 93:1104.
Liow L. H., and Finarelli J. A.. 2014. A dynamic global equilibrium in carnivoran diversification over 20 million years. Proceedings of the Royal Society of London B 281:20132312.
Liow L. H., and Finarelli J. A.. 2017. Correction to “CarnivoreCode.R in supplement of A dynamic global equilibrium in carnivoran diversification over 20 million years.” Proceedings of the Royal Society of London B 281:20132312.
Liow L. H., and Nichols J. D.. 2010. Estimating rates and probabilities of origination and extinction using taxonomic occurrence data: capture-mark-recapture (CMR) approaches. In J. Alroy and G. Hunt, eds. Quantitative methods in paleobiology. Paleontological Society Papers 16:8194.
Liow L. H., Quental T. B., and Marshall C. R.. 2010. When can decreasing diversification rates be detected with molecular phylogenies and the fossil record? Systematic Biology 59:646659.
Maguire K. C., and Stigall A. L.. 2008. Paleobiogeography of Miocene Equinae of North America: a phylogenetic biogeographic analysis of the relative roles of climate, vicariance, and dispersal. Palaeogeography, Palaeoclimatology, Palaeoecology 267:175184.
Martin R. A., Peláez-Campomanes P., Honey J. G., Fox D. L., Zakrzewski R. J., Albright L. B., Lindsay E. H., Opdyke N. D., and Goodwin H. T.. 2008. Rodent community change at the Pliocene–Pleistocene transition in southwestern Kansas and identification of the Microtus immigration event on the Central Great Plains. Palaeogeography, Palaeoclimatology, Palaeoecology 267:196207.
Matzke N. J. 2013. BioGeoBEARS: biogeography with Bayesian (and likelihood) evolutionary analysis in R scripts. R package, Version 0.2.
McQuarrie N., and Wernicke B. P.. 2005. An animated tectonic reconstruction of southwestern North America since 36 Ma. Geosphere 1:147172.
Mittelbach G. G., Schemske D. W., Cornell H. V., Allen A. P., Brown J. M., Bush M. B., Harrison S. P., Hurlbert A. H., Knowlton N., Lessios H. A., McCain C. M., McCune A. R., McDade L. A., McPeek M. A., Near T. J., Price T. D., Ricklefs R. E., Roy K., Sax D. F., Schluter D., Sobel J. M., and Turelli M.. 2007. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology Letters 10:315331.
Moen D., and Morlon H.. 2014. Why does diversification slow down? Trends in Ecology and Evolution 29:190197.
Mulch A. 2016. Stable isotope paleoaltimetry and the evolution of landscapes and life. Earth and Planetary Science Letters 433:180191.
Nichols J. D., and Pollock K. H.. 1983. Estimating taxonomic diversity, extinction rates, and speciation rates from fossil data using capture-recapture models. Paleobiology 9:150163.
Peters S. E. 2008. Macrostratigraphy and its promise for paleobiology. In P. H. Kelley and R.K. Bambach, eds. From evolution to geobiology: research questions driving paleontology at the start of a new century. Paleontological Society Papers 14:205232.
Peters S. E., and Foote M.. 2001. Biodiversity in the Phanerozoic: a reinterpretation. Paleobiology 27:583601.
Peters S. E., and Heim N. A.. 2010. The geological completeness of paleontological sampling in North America. Paleobiology 36:6179.
Pires M. M., Silvestro D., and Quental T. B.. 2015. Continental faunal exchange and the asymmetrical radiation of carnivores. Proceedings of the Royal Society of London B 282:20151952.
Pollock K. H., Nichols J. D., Brownie C., and Hines J. E.. 1990. Statistical inference for capture-recapture experiments. Wildlife Monographs 107:197.
Pradel R. 1996. Utilization of capture-mark-recapture for the study of recruitment and population growth rate. Biometrics 52:703709.
Purvis A., Orme C. D. L., Toomey N. H., and Pearson P. N.. 2009. Temporal patterns in diversification rates. Pp. 278300 in R. K. Butlin, J.R. Bridle, and D. Schuler, eds. Speciation and patterns of diversity. Cambridge University Press, Cambridge.
Quental T. B., and Marshall C. R.. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends in Ecology and Evolution 25:434441.
R Core Team. 2017. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Rabosky D. L. 2009. Extinction rates should not be estimated from molecular phylogenies. Evolution 64:18161824.
Rabosky D. L. 2013. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annual Reviews in Ecology and Evolution and Systematics 44:481502.
Rabosky D. L. 2014. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS ONE 9:e89543.
Rabosky D. L., and Hurlbert A. H.. 2015. Species richness at continental scales is dominated by ecological limits. American Naturalist 185:572583.
Raup D. M. 1975. Taxonomic diversity estimation using rarefaction. Paleobiology 1:333342.
Raup D. M. 1979. Biases in the fossil record of species and genera. Bulletin of the Carnegie Museum of Natural History 13:8591.
Renema W., Bellwood D. R., Braga J. C., and Bromfield K.. 2008. Hopping hotspots: global shifts in marine biodiversity. Science 321:654657.
Ricklefs R.E. 2007. Estimating diversification rates from phylogenetic information. Trends in Ecology and Evolution 22:601610.
Riddle B. R. 1996. The molecular phylogeographic bridge between deep and shallow history in continental biotas. Trends in Ecology and Evolution 11:207211.
Riddle B. R., Jezkova T., Hornsby A. D., and Matocq M. D.. 2014. Assembling the modern Great Basin mammal biota: insights from molecular biogeography and the fossil record. Journal of Mammalogy 95:11071127.
Rolland J., Condamine F. L., Jiguet F., and Morlon H.. 2014. Faster speciation and reduced extinction in the tropics contribute to the mammalian latitudinal diversity gradient. PLoS Biol 12:e1001775.
Rosenzweig M. L. 1995. Species diversity in space and time. Cambridge University Press, Cambridge.
Ruggiero A., and Hawkins B. A.. 2008. Why do mountains support so many species of birds? Ecography 31:306315.
Samuels J. X., and Hopkins S. S. B.. 2017. The impacts of Cenozoic climate and habitat changes on small mammal diversity of North America. Global and Planetary Change 149:3652.
Sepkoski J. J., Bambach R. K., Raup D. M., and Valentine J. W.. 1981. Phanerozoic marine diversity and the fossil record. Nature 293:435437.
Signor P. W., and Lipps J. H.. 1982. Sampling bias, gradual extinction patterns and catastrophes in the fossil record. Geological Society of America Special Papers 190:291296.
Silvestro D., Salamin N., and Schnitzler J.. 2014a. PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data. Methods in Ecology and Evolution 5:11261131.
Silvestro D., Schnitzler J., Liow L. H., Antonelli A., and Salamin N.. 2014b. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology 63:349367.
Silvestro D., Antonelli A., Salamin N., and Quental T. B.. 2015. The role of clade competition in the diversification of North American canids. Proceedings of the National Academy of Sciences USA 112:86848689.
Silvestro D., Zizka A., Bacon C. D., Cascales-Miñana B., Salamin N., and Antonelli A.. 2016. Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data. Philosophical Transactions of the Royal Society of London B 371:20150225.
Smith A. B., Lloyd G. T., and McGowan A. J.. 2012. Phanerozoic marine diversity: rock record modeling provides an independent test of large-scale trends. Proceedings of the Royal Society of London B 279:44894495.
Snow J. K., and Wernicke B. P.. 2000. Cenozoic tectonism, in the Central Basin and Range: magnitude, rate, and distribution of upper crustal strain. American Journal of Science 300:659719.
Sonder L. J., and Jones C. H.. 1999. Western United States extension: how the west was widened. Annual Reviews in Earth and Planetary Sciences 27:417462.
Stadler T. 2011. Mammalian phylogeny reveals recent diversification rate shifts. Proceedings of the National Academy of Sciences USA 108:61876192.
Stanley S. M. 1979. Macroevolution: pattern and process. Freeman, San Francisco.
Stigall A. L., and Lieberman B. S.. 2006. Quantitative palaeobiogeography: GIS, phylogenetic biogeographical analysis, and conservation insights. Journal of Biogeography 33:20512060.
Terry R. C. 2010. The dead do not lie: using skeletal remains for rapid assessment of historical small-mammal community baselines. Proceedings of the Royal Society of London B 277:11931201.
Terry R. C., Li C. L., and Hadly E. A.. 2011. Predicting small-mammal responses to climatic warming: autecology, geographic range, and the Holocene fossil record. Global Change Biology 17:30193034.
Vrba E. S. 1992. Mammals as a key to evolutionary theory. Journal of Mammalogy 73:128.
Weir J. T., and Schluter D.. 2007. The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315:15741576.
Wilson D. E., and Reeder D. M., eds. 2005. Mammal species of the world: a taxonomic and geographic reference, 3 rd ed. Johns Hopkins University Press, Baltimore, Md.
Zachos J. C., Dickens G. R., and Zeebe R. E.. 2008. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451:279283.
Zelditch M. L., Li J., Tran L. A. P., and Swiderski D. L.. 2015. Relationships of diversity, disparity, and their evolutionary rates in squirrels (Sciuridae). Evolution 69:12841300.
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