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Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

Published online by Cambridge University Press:  08 April 2016

David W. Bapst
David W. Bapst*
Affiliation:
Department of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, Illinois 60637, U.S.A.
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Abstract

Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic “cal3” time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. The cal3 method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.

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Paleobiology , Volume 40 , Issue 3 , Summer 2014 , pp. 331 - 351
Copyright
Copyright © The Paleontological Society 

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References

Literature Cited

Akaike, H. 1973. Information theory and an extension of the maximum likelihood principle. Pp. 267–281inPetrov, B. N. and Csaki, F., eds. Second international symposium on information theory. Akademiai Kiado, Budapest.Google Scholar
Bapst, D. W. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution 3:803–807.Google Scholar
Bapst, D. W. 2013a. When can clades be potentially resolved with morphology? PLoS ONE 8 (4):e62312.Google Scholar
Bapst, D. W. 2013b. A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods in Ecology and Evolution 4:724–733.Google Scholar
Bell, M. A., and Braddy, S. J. 2012. Cope's rule in the Ordovician trilobite family Asaphidae (order Asaphida): patterns across multiple most parsimonious trees. Historical Biology 24:223–230.Google Scholar
Benson, R. B. J., Evans, M., and Druckenmiller, P. S. 2012. High diversity, low disparity and small body size in plesiosaurs (Reptilia, Sauropterygia) from the Triassic–Jurassic boundary. PLoS ONE 7 (3):e31838.CrossRefGoogle ScholarPubMed
Blomberg, S. P., Lefevre, J. G., Wells, J. A., and Waterhouse, M. 2012. Independent contrasts and PGLS regression estimators are equivalent. Systematic Biology 61:382–391.CrossRefGoogle ScholarPubMed
Boettiger, C., Coop, G., and Ralph, P. 2012. Is your phylogeny informative? Measuring the power of comparative methods. Evolution 66:2240–2251.Google Scholar
Brocklehurst, N., Kammerer, C. F., and Fröbisch, J. 2013. The early evolution of synapsids, and the influence of sampling on their fossil record. Paleobiology 39:470–490.Google Scholar
Brusatte, S. L., Benton, M. J., Ruta, M., and Lloyd, G. T. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321 (5895):1485–1488.Google Scholar
Burnham, K. P., and Anderson, D. R. 2002. Model selection and multimodel inference: a practical information-theoretic approach. Springer, New York.Google Scholar
Butler, M. A., and King, A. A. 2004. Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164:683–695.Google Scholar
Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1–15.Google Scholar
Finarelli, J. A., and Flynn, J. J. 2006. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Systematic Biology 55:301–313.Google Scholar
Fisher, D. C. 2008. Stratocladistics: integrating temporal data and character data in phylogenetic inference. Annual Review of Ecology, Evolution, and Systematics 39:365–385.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., and Sepkoski, J. J. Jr. 1999. Absolute measures of the completeness of the fossil record. Nature 398:415–417.Google Scholar
Friedman, M. 2012. Parallel evolutionary trajectories underlie the origin of giant suspension-feeding whales and bony fishes. Proceedings of the Royal Society of London B 279:944–951.Google Scholar
Fusco, G., Garland, J. T., Hunt, G., and Hughes, N. C. 2012. Developmental trait evolution in trilobites. Evolution 66:314–329.Google Scholar
Garland, T. Jr., Harvey, P. H., and Ives, A. R. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41:18–32.Google Scholar
Guinot, G., Adnet, S., and Cappetta, H. 2012. An analytical approach for estimating fossil record and diversification events in sharks, skates and rays. PLoS ONE 7 (9):e44632.Google Scholar
Hansen, T. F. 1997. Stabilizing selection and the comparative analysis of adaptation. Evolution 51:1341–1351.Google Scholar
Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E., and Challenger, W. 2008. GEIGER: investigating evolutionary radiations. Bioinformatics 24:129–131.Google Scholar
Hopkins, M. J. 2011. How species longevity, intraspecific morphological variation, and geographic range size are related: a comparison using Late Cambrian trilobites. Evolution 65:3253–3273.Google Scholar
Hopkins, M. J. 2013. Decoupling of taxonomic diversity and morphological disparity during decline of the Cambrian trilobite family Pterocephaliidae. Journal of Evolutionary Biology 26:1665–1676.CrossRefGoogle ScholarPubMed
Huelsenbeck, J. P., Nielsen, R., and Bollback, J. P. 2003. Stochastic mapping of morphological characters. Systematic Biology 52:131–158.Google Scholar
Hunt, G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578–601.CrossRefGoogle Scholar
Hunt, G. 2013. Testing the link between phenotypic evolution and speciation: an integrated palaeontological and phylogenetic analysis. Methods in Ecology and Evolution 4:714–723.Google Scholar
Hunt, G., and Carrano, M. T. 2010. Models and methods for analyzing phenotypic evolution in lineages and clades. Pp. 245–269inAlroy, J. and Hunt, G., eds. Short course on quantitative methods in paleobiology. Paleontological Society, Denver.Google Scholar
Lane, A., Janis, C. M., and Sepkoski, J. J. 2005. Estimating paleodiversity: a test of the taxic and phylogenetic methods. Paleobiology 31:21–34.Google Scholar
Laurin, M. 2004. The evolution of body size, Cope's Rule and the origin of amniotes. Systematic Biology 53:594–622.Google Scholar
Losos, J. B. 2011. Seeing the forest for the trees: the limitations of phylogenies in comparative biology. American Naturalist 177:709–727.Google Scholar
Marjanovic, D., and Laurin, M. 2007. Fossils, molecules, divergence times, and the origin of lissamphibians. Systematic Biology 56:369–388.Google Scholar
Mooers, A. O., Vamosi, S. M., and Schluter, D. 1999. Using phylogenies to test macroevolutionary hypotheses of trait evolution in cranes (Gruinae). American Naturalist 154:249–259.Google Scholar
Nee, S. 2006. Birth-death models in macroevolution. Annual Review of Ecology, Evolution, and Systematics 37:1–17.Google Scholar
Norell, M. A. 1992. Taxic origin and temporal diversity: the effect of phylogeny. Pp. 89–118inNovacek, M. J. and Wheeler, Q. D., eds. Extinction and phylogeny. Columbia University Press, New York.Google Scholar
Norell, M. A. 1993. Tree-based approaches to understanding history; comments on ranks, rules and the quality of the fossil record. American Journal of Science 293 A:407–417.Google Scholar
Norell, M. A. 1996. Ghost taxa, ancestors, and assumptions: a comment on Wagner. Paleobiology 22:453–455.Google Scholar
O'Meara, B. C., Ane, C., Sanderson, M. J., Wainwright, P. C., and Hansen, T. 2006. Testing for different rates of continuous trait evolution using likelihood. Evolution 60:922–933.Google Scholar
Paradis, E., Claude, J., and Strimmer, K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290.CrossRefGoogle ScholarPubMed
Pennell, M. W., and Harmon, L. J. 2013. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Annals of the New York Academy of Sciences 1289:90–105.Google Scholar
Pol, D., and Norell, M. A. 2006. Uncertainty in the age of fossils and the stratigraphic fit to phylogenies. Systematic Biology 55:512–521.Google Scholar
R Core Team. 2013. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.Google Scholar
Rabosky, D. L. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64:1816–1824.Google Scholar
Raia, P., Carotenuto, F., Passaro, F., Piras, P., Fulgione, D., Werdelin, L., Saarinen, J., and Fortelius, M. 2013. Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals. Proceedings of the Royal Society of London B Sciences 280(1750). doi:20122244.Google Scholar
Ruta, M., Wagner, P. J., and Coates, M. I. 2006. Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change. Proceedings of the Royal Society of London B 273:2107–2111.Google Scholar
Sallan, L. C., and Friedman, M. 2012. Heads or tails: staged diversification in vertebrate evolutionary radiations. Proceedings of the Royal Society of London B 279:2025–2032.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
Slater, G. J. 2013. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods in Ecology and Evolution 4:734–744.Google Scholar
Slater, G. J., Harmon, L. J., and Alfaro, M. E. 2012. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66:3931–3944.Google Scholar
Smith, A. B. 1994. Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific, Oxford.Google Scholar
Smith, K. L., Harmon, L. J., Shoo, L. P., and Melville, J. 2011. Evidence of constrained phenotypic evolution in a cryptic species complex of agamid lizards. Evolution 65:976–992.Google Scholar
Sookias, R. B., Butler, R. J., and Benson, R. B. J. 2012. Rise of dinosaurs reveals major body-size transitions are driven by passive processes of trait evolution. Proceedings of the Royal Society of London B 279:2180–2187.Google ScholarPubMed
Stanley, S. M. 1979. Macroevolution: patterns and process. W. H. Freeman, San Francisco.Google Scholar
Wagner, P. J. 1995. Diversity patterns among early gastropods: contrasting taxonomic and phylogenetic descriptions. Paleobiology 21:410–439.Google Scholar
Wagner, P. J. 1996. Ghost taxa, ancestors, assumptions, and expectations: a reply to Norell. Paleobiology 22:456–460.Google Scholar
Wagner, P. J. 2000. 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., and Erwin, D. H. 1995. Phylogenetic patterns as tests of speciation models. Pp. 87–122inErwin, D. H. and Anstey, R. L., eds. New approaches to speciation in the fossil record. Columbia University Press, New York.Google Scholar
Young, M. T., Bell, M. A., and Brusatte, S. L. 2011. Craniofacial form and function in Metriorhynchidae (Crocodylomorpha: Thalattosuchia): modelling phenotypic evolution with maximum-likelihood methods. Biology Letters 7:913–916.Google Scholar
Zanno, L. E., and Makovicky, P. J. 2013. No evidence for directional evolution of body mass in herbivorous theropod dinosaurs. Proceedings of the Royal Society of London B 280(1751). doi:20122526.Google Scholar