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Preparing Paleontological Datasets for Phylogenetic Comparative Methods

  • Chapter
Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Abstract

The fossil record holds considerable promise for furthering our understanding of macroevolutionary patterns, particularly allowing us to analyze hypotheses which cannot be tested with phylogenies of extant taxa alone. However, although there is a growing number of paleontological studies that use phylogenetic comparative methods to address questions of trait evolution, there is little documentation on obtaining the timescaled phylogenies of fossil taxa required for such analyses. This chapter is an attempt to introduce interested readers to the issues involved with that process, including the uncertainties and biases involved with fossil data, which some might inadvertently overlook. In addition, I illustrate how the fossil records of different groups can be very different in terms of the datasets available, including the issues of that data, and stress that there is no ‘one size fits all’ solution. Instead, for several hypothetical examples, I recommend several approaches that explicitly consider potential uncertainties, unavailable data, and biasing factors.

The original version of this chapter was revised: Online Practical Material website has been updated. The erratum to this chapter is available at https://doi.org/10.1007/978-3-662-43550-2_23

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References

  • Alexandrou MA, Swartz BA, Matzke NJ, Oakley TH (2013) Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae. Mol Phylogenet Evol 69(3):514–523. doi:http://dx.doi.org/10.1016/j.ympev.2013.07.026

    CAS  PubMed  Google Scholar 

  • Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ (2009) Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci 106(32):13410–13414

    CAS  Google Scholar 

  • Alroy J (1998) Cope’s rule and the dynamics of body mass evolution in North American fossil mammals. Science 280(5364):731–734

    CAS  PubMed  Google Scholar 

  • Alroy J (2000) Understanding the dynamics of trends within evolving lineages. Paleobiology 26(3):319–329

    Google Scholar 

  • Aze T, Ezard THG, Purvis A, Coxall HK, Stewart DRM, Wade BS, Pearson PN (2011) A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol Rev 86(4):900–927. doi:10.1111/j.1469-185X.2011.00178.x

    Article  PubMed  Google Scholar 

  • Bapst DW (2012) paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods Ecol Evol 3(5):803–807. doi:10.1111/j.2041-210X.2012.00223.x

    Article  Google Scholar 

  • Bapst DW (2013a) A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods Ecol Evol 4(8):724–733. doi:10.1111/2041-210x.12081

    Article  Google Scholar 

  • Bapst DW (2013b) When can clades be potentially resolved with morphology? PLoS ONE 8(4):e62312. doi:10.1371/journal.pone.0062312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bapst DW (2014) Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Paleobiology 40(3):331–351

    Google Scholar 

  • Bapst DW, Bullock PC, Melchin MJ, Sheets HD, Mitchell CE (2012) Graptoloid diversity and disparity became decoupled during the Ordovician mass extinction. Proc Natl Acad Sci 109(9):3428–3433

    CAS  Google Scholar 

  • Bates DEB, Kozlowska A, Lenz AC (2005) Silurian retiolitid graptolites: morphology and evolution. Acta Palaeontol Pol 50(4):705–720

    Google Scholar 

  • Bell MA, Braddy SJ (2012) Cope’s rule in the Ordovician trilobite family Asaphidae (order Asaphida): patterns across multiple most parsimonious trees. Hist Biol 24(3):223–230. doi:10.1080/08912963.2011.616201

    Article  Google Scholar 

  • Benson RBJ, Choiniere JN (2013) Rates of dinosaur limb evolution provide evidence for exceptional radiation in Mesozoic birds. Proceedings of the Royal Society B: Biological Sciences 280(1768)

    PubMed  PubMed Central  Google Scholar 

  • Benson RBJ, Evans M, Druckenmiller PS (2012) High diversity, low disparity and small body size in Plesiosaurs (Reptilia, Sauropterygia) from the Triassic-Jurassic boundary. PLoS ONE 7(3):e31838. doi:10.1371/journal.pone.0031838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Benton MJ, Donoghue PCJ (2007) Paleontological evidence to date the tree of life. Mol Biol Evol 24(1):26–53

    CAS  PubMed  Google Scholar 

  • Benton MJ, Hitchin R (1997) Congruence between phylogenetic and stratigraphic data on the history of life. Proc R Soc Lond B: Biol Sci 264(1383):885–890

    PubMed Central  Google Scholar 

  • Benton MJ, Storrs GW (1994) Testing the quality of the fossil record: Paleontological knowledge is improving. Geology 22(2):111–114

    Google Scholar 

  • Bininda-Emonds ORP, Cardillo M, Jones KE, MacPhee RDE, Beck RMD, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A (2007) The delayed rise of present-day mammals. Nature 446(7135):507–512

    CAS  PubMed  Google Scholar 

  • Boettiger C, Coop G, Ralph P (2012) Is your phylogeny informative? Measuring the power of comparative methods. Evolution 66(7):2240–2251. doi:10.1111/j.1558-5646.2011.01574.x

    Article  PubMed  PubMed Central  Google Scholar 

  • Boyd CA, Cleland TP, Marrero NL, Clarke JA (2011) Exploring the effects of phylogenetic uncertainty and consensus trees on stratigraphic consistency scores: a new program and a standardized method. Cladistics 27(1):52–60. doi:10.1111/j.1096-0031.2010.00320.x

    Article  PubMed  Google Scholar 

  • Brocklehurst N, Kammerer CF, Fröbisch J (2013) The early evolution of synapsids, and the influence of sampling on their fossil record. Paleobiology 39:470–490. doi:10.1666/12049

    Article  Google Scholar 

  • Bronzati M, Montefeltro FC, Langer MC (2012) A species-level supertree of Crocodyliformes. Hist Biol 24(6):598–606. doi:10.1080/08912963.2012.662680

    Article  Google Scholar 

  • Brusatte SL, Benton MJ, Ruta M, Lloyd GT (2008) Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321(5895):1485–1488

    CAS  PubMed  Google Scholar 

  • Bulman OMB (1970) Treatise in invertebrate paleontology, Pt. V: Graptolithina, vol Part V. Treatise on invertebrate paleontology. University of Kansas Press and the Geological Society of America, Lawrence, KS

    Google Scholar 

  • Chan KMA, Moore BR (2002) Whole-tree methods for detecting differential diversification rates. Syst Biol 51(6):855–865

    PubMed  Google Scholar 

  • Core Team R (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria

    Google Scholar 

  • Davies TJ, Kraft NJB, Salamin N, Wolkovich EM (2011) Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism. Ecology 93(2):242–247. doi:10.1890/11-1360.1

    Article  Google Scholar 

  • Didier G, Royer-Carenzi M, Laurin M (2012) The reconstructed evolutionary process with the fossil record. J Theor Biol 315:26–37. doi:10.1016/j.jtbi.2012.08.046

    Article  PubMed  Google Scholar 

  • Eldredge N (1971) The allopatric model and phylogeny in Paleozoic invertebrates. Evolution 25(1):156–167

    PubMed  Google Scholar 

  • Eldredge N, Thompson JN, Brakefield PM, Gavrilets S, Jablonski D, Jackson JBC, Lenski RE, Lieberman BS, McPeek MA, Miller W (2005) The dynamics of evolutionary stasis. Paleobiology 31(sp5):133–145. doi:10.1666/0094-8373(2005)031[0133:TDOES]2.0.CO;2

    Google Scholar 

  • Evans AR, Jones D, Boyer AG, Brown JH, Costa DP, Ernest SKM, Fitzgerald EMG, Fortelius M, Gittleman JL, Hamilton MJ, Harding LE, Lintulaakso K, Lyons SK, Okie JG, Saarinen JJ, Sibly RM, Smith FA, Stephens PR, Theodor JM, Uhen MD (2012) The maximum rate of mammal evolution. Proc Natl Acad Sci 109(11):4187–4190

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ezard THG, Aze T, Pearson PN, Purvis A (2011) Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science 332(6027):349–351

    CAS  PubMed  Google Scholar 

  • Felsenstein J (1988) Phylogenies and Quantitative Characters. Annu Rev Ecol Syst 19(1):445

    Google Scholar 

  • Finarelli JA, Flynn JJ (2006) Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Syst Biol 55(2):301–313

    PubMed  Google Scholar 

  • Fisher DC (1991) Phylogenetic analysis and its implication in evolutionary paleobiology. In: Gilinsky NL, Signor PW (eds) Analytical paleobiology. Paleontological Society, Knoxville, Tennessee, pp 103–122

    Google Scholar 

  • Fisher DC (1994) Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. In: Grande L, Rieppel O (eds) Interpreting the hierarchy of nature. Academic Press, San Diego, pp 133–171

    Google Scholar 

  • Fisher DC (2008) Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference. Annu Rev Ecol Evol Syst 39(1):365–385

    Google Scholar 

  • Foote M (1996) On the probability of ancestors in the fossil record. Paleobiology 22(2):141–151

    Google Scholar 

  • Foote M (1997) Estimating taxonomic durations and preservation probability. Paleobiology 23(3):278–300

    Google Scholar 

  • Foote M (2000) Origination and extinction components of taxonomic diversity: general problems. In: Erwin DH, Wing SL (eds) Deep time: paleobiology’s perspective. The Paleontological Society, Lawrence, Kansas, pp 74–102

    Google Scholar 

  • Foote M, Raup DM (1996) Fossil preservation and the stratigraphic ranges of taxa. Paleobiology 22(2):121–140

    CAS  PubMed  Google Scholar 

  • Fortey RA, Cooper RA (1986) A phylogenetic classification of the graptoloids. Palaeontology 29(4):631–654

    Google Scholar 

  • Friedman M (2009) Ecomorphological selectivity among marine teleost fishes during the end-Cretaceous extinction. Proc Natl Acad Sci 106(13):5218–5223

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fusco G, Garland JT, Hunt G, Hughes NC (2012) Developmental trait evolution in trilobites. Evolution 66(2):314–329. doi:10.1111/j.1558-5646.2011.01447.x

    Article  PubMed  Google Scholar 

  • Garland T Jr, Harvey PH, Ives AR (1992) Procedures for the analysis of comparative data using phylogenetically independent contrasts. Syst Biol 41(1):18–32

    Google Scholar 

  • Gates TA, Prieto-Márquez A, Zanno LE (2012) Mountain building triggered late cretaceous North American megaherbivore dinosaur radiation. PLoS ONE 7(8):e42135. doi:10.1371/journal.pone.0042135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gingerich PD (1979) The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. Phylogenet Anal Paleontol 1:41–77

    Google Scholar 

  • Green WA, Hunt G, Wing SL, DiMichele WA (2011) Does extinction wield an axe or pruning shears? How interactions between phylogeny and ecology affect patterns of extinction. Paleobiology 37(1):72–91. doi:10.1666/09078.1

    Article  Google Scholar 

  • Guinot G, Adnet S, Cappetta H (2012) An analytical approach for estimating fossil record and diversification events in sharks, skates and rays. PLoS ONE 7(9):e44632. doi:10.1371/journal.pone.0044632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hannisdal B (2006) Phenotypic evolution in the fossil record: numerical experiments. J Geol 114(2):133–153. doi:10.1086/499569

    Article  Google Scholar 

  • Hannisdal B (2009) Inferring phenotypic evolution in the fossil record by Bayesian inversion. Paleobiology 33(1):98–115. doi:10.1666/06038.1

    Article  Google Scholar 

  • Heath TA (2012) A hierarchical Bayesian model for calibrating estimates of species divergence times. Syst Biol 61(5):793–809

    PubMed  PubMed Central  Google Scholar 

  • Holland SM (2003) Confidence limits on fossil ranges that account for facies changes. Paleobiology 29(4):468–479

    Google Scholar 

  • Hopkins MJ (2011) How species longevity, intraspecific morphological variation, and geographic range size are related: a comparison using late Cambrian trilobites. Evolution 65(11):3253–3273. doi:10.1111/j.1558-5646.2011.01379.x

    Article  PubMed  Google Scholar 

  • Hopkins MJ (2013) Decoupling of taxonomic diversity and morphological disparity during decline of the Cambrian trilobite family Pterocephaliidae. J Evol Biol 26(8):1665–1676. doi:10.1111/jeb.12164

    Article  CAS  PubMed  Google Scholar 

  • Huelsenbeck JP (1994) Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20(4):470–483

    Google Scholar 

  • Huelsenbeck JP, Rannala B (1997) Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology 23(2):174–180

    Google Scholar 

  • Hunt G (2013) Testing the link between phenotypic evolution and speciation: an integrated palaeontological and phylogenetic analysis. Methods Ecol Evol 4(8):714–723. doi:10.1111/2041-210x.12085

    Article  Google Scholar 

  • Hunt G, Carrano MT (2010) Models and methods for analyzing phenotypic evolution in lineages and clades. In: Alroy J, Hunt G (eds) Short course on quantitative methods in paleobiology, vol 16., Paleontological SocietyNew Haven, Conneticut, pp 245–269

    Google Scholar 

  • Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO (2012) The global diversity of birds in space and time. Nature 491(7424):444–448. http://www.nature.com/nature/journal/v491/n7424/abs/nature11631.html#supplementary-information

    CAS  PubMed  Google Scholar 

  • Kendall DG (1948) On the generalized “birth-and-death” process. Ann Math Stat 19(1):1–15

    Google Scholar 

  • Lane A, Janis CM, Sepkoski JJ (2005) Estimating paleodiversity: a test of the taxic and phylogenetic methods. Paleobiology 31(1):21–34

    Google Scholar 

  • Laurin M (2004) The evolution of body size, Cope’s rule and the origin of amniotes. Syst Biol 53(4):594–622

    PubMed  Google Scholar 

  • Laurin M (2011) Use of paleontological and phylogenetic data in comparative and paleobiological analyses: a few recent developments. In: Pontarotti P (ed) Evolutionary biology: concepts, biodiversity, macroevolution and genome evolution. Springer, Berlin, pp 121–138. doi:10.1007/978-3-642-20763-1_8

    Google Scholar 

  • Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol 50(6):913–925

    CAS  PubMed  Google Scholar 

  • Liow LH, Quental TB, Marshall CR (2010) When can decreasing diversification rates be detected with molecular phylogenies and the fossil record? Syst Biol 59(6):646–659

    PubMed  Google Scholar 

  • Lloyd GT (2012) A refined modelling approach to assess the influence of sampling on palaeobiodiversity curves: new support for declining Cretaceous dinosaur richness. Biol Lett 8(1):123–126

    PubMed  Google Scholar 

  • Lloyd GT, Davis KE, Pisani D, Tarver JE, Ruta M, Sakamoto M, Hone DWE, Jennings R, Benton MJ (2008) Dinosaurs and the Cretaceous terrestrial revolution. Proc Roy Soc B: Biol Sci 275(1650):2483–2490

    Google Scholar 

  • Lloyd GT, Wang SC, Brusatte SL (2012) Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of Lungfish (Sarcopterygii, Dipnoi). Evolution 66(2):330–348. doi:10.1111/j.1558-5646.2011.01460.x

    Article  PubMed  Google Scholar 

  • Losos Jonathan B (2010) Adaptive radiation, ecological opportunity, and evolutionary determinism. Am Nat 175(6):623–639. doi:10.1086/652433

    Article  CAS  PubMed  Google Scholar 

  • Marcot JD, Fox DL (2008) StrataPhy: a new computer program for stratocladistics analysis. Palaeo-Electronica 11(1):5a

    Google Scholar 

  • Mooers AØ, Heard SB (1997) Inferring evolutionary processes from phylogenetic tree shape. Q Rev Biol 72(1):31–54

    Google Scholar 

  • Nee S, Mooers AO, Harvey PH (1992) Tempo and mode of evolution revealed from molecular phylogenies. Proc Natl Acad Sci USA 89(17):8322–8326

    CAS  Google Scholar 

  • Neige P, Brayard A, Gerber S, Rouget I (2009) Les Ammonoïdes (Mollusca, Cephalopoda): avancées et contributions récentes à la paléobiologie évolutive. CR Palevol 8(2–3):167–178

    Google Scholar 

  • Norell MA (1992) Taxic origin and temporal diversity: the effect of phylogeny. In: Novacek MJ, Wheeler QD (eds) Extinction and phylogeny. Columbia University Press, New York, pp 89–118

    Google Scholar 

  • Norell MA (1996) Ghost taxa, ancestors, and assumptions: a comment on Wagner. Paleobiology 22(3):453–455

    Google Scholar 

  • Norell MA, Novacek MJ (1992) The fossil record and evolution: comparing cladistic and paleontologic evidence for vertebrate history. Science 255(5052):1690–1693

    CAS  PubMed  Google Scholar 

  • Nowak MD, Smith AB, Simpson C, Zwickl DJ (2013) A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLoS ONE 8(6):e66245. doi:10.1371/journal.pone.0066245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oakley TH, Cunningham CW (2000) Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny. Evolution 54(2):397–405

    CAS  PubMed  Google Scholar 

  • Pagel M (1999) Inferring the historical patterns of biological evolution. Nature 401(6756):877–884

    CAS  PubMed  Google Scholar 

  • Patzkowsky ME, Holland SM (2012) Stratigraphic paleobiology: understanding the distribution of fossil taxa in time and space. University of Chicago Press, Chicago, IL

    Google Scholar 

  • Pearson PN (1998) Speciation and extinction asymmetries in paleontological phylogenies: evidence for evolutionary progress? Paleobiology 24(3):305–335

    Google Scholar 

  • Pennell MW, Harmon LJ, Uyeda JC (2014) Is there room for punctuated equilibrium in macroevolution? Trends Ecol Evol 29(1):23–32. http://dx.doi.org/10.1016/j.tree.2013.07.004

    Google Scholar 

  • Peters SE, Foote M (2001) Biodiversity in the Phanerozoic: a reinterpretation. Paleobiology 27(4):583–601

    Google Scholar 

  • Pfenninger M, Schwenk K (2007) Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evol Biol 7(1):121

    PubMed  PubMed Central  Google Scholar 

  • Pittman M, Gatesy SM, Upchurch P, Goswami A, Hutchinson JR (2013) Shake a tail feather: the evolution of the theropod tail into a stiff aerodynamic surface. PLoS ONE 8(5):e63115. doi:10.1371/journal.pone.0063115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pol D, Norell MA (2001) Comments on the Manhattan stratigraphic measure. Cladistics 17(3):285–289. doi:10.1111/j.1096-0031.2001.tb00125.x

    Article  PubMed  Google Scholar 

  • Pol D, Norell MA (2006) Uncertainty in the age of fossils and the stratigraphic fit to phylogenies. Syst Biol 55(3):512–521

    PubMed  Google Scholar 

  • Polly PD (1997) Ancestry and species definition in paleontology: a stratocladistic analysis of Paleocene-Eocene Viverravidae (Mammalia, Carnivora) from Wyoming, vol 30(1). Contributions from the Museum of Paleontology, University of Michigan, pp 1–53

    Google Scholar 

  • Pyenson N, Sponberg S (2011) Reconstructing body size in extinct crown Cetacea (Neoceti) using allometry, phylogenetic methods and tests from the fossil record. J Mamm Evol 18(4):269–288. doi:10.1007/s10914-011-9170-1

    Article  Google Scholar 

  • Pyron RA (2011) Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst Biol 60(4):466–481

    PubMed  Google Scholar 

  • Raia P, Carotenuto F, Passaro F, Piras P, Fulgione D, Werdelin L, Saarinen J, Fortelius M (2013) Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals. Proc Roy Soc B: Biol Sci 280(1750)

    Google Scholar 

  • Raup DM (1976) Species diversity in the Phanerozoic: an interpretation. Paleobiology 2(4):289–297

    Google Scholar 

  • Raup DM (1985) Mathematical models of cladogenesis. Paleobiology 11(1):42–52

    Google Scholar 

  • Raup DM, Gould SJ, Schopf TJM, Simberloff DS (1973) Stochastic models of phylogeny and the evolution of diversity. J Geol 81:525–542

    Google Scholar 

  • Rieppel O, Kearney M (2002) Similarity. Biol J Linnean Soc 75(1):59–82. doi:10.1046/j.1095-8312.2002.00006.x

    Article  Google Scholar 

  • Ronquist F, Klopfstein S, Vilhelmsen L, Schulmeister S, Murray DL, Rasnitsyn AP (2012) A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera. Syst Biol 61(6):973–999

    PubMed  PubMed Central  Google Scholar 

  • Roopnarine PD (2005) The likelihood of stratophenetic-based hypotheses of genealogical succession. Spec Pap Palaeontol 73:143–157

    Google Scholar 

  • Roy K, Hunt G, Jablonski D (2009) Phylogenetic conservatism of extinctions in marine bivalves. Science 325(5941):733–737

    CAS  PubMed  Google Scholar 

  • Ruta M, Cisneros JC, Liebrecht T, Tsuji LA, Muller J (2011) Amniotes through major biological crises: faunal turnover among Parareptiles and the end-Permian mass extinction. Palaeontology 54(5):1117–1137. doi:10.1111/j.1475-4983.2011.01051.x

    Article  Google Scholar 

  • Ruta M, Pisani D, Lloyd GT, Benton MJ (2007) A supertree of Temnospondyli: cladogenetic patterns in the most species-rich group of early tetrapods. Proc Roy Soc B: Biol Sci 274(1629):3087–3095

    Google Scholar 

  • Ruta M, Wagner PJ, Coates MI (2006) Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change. Proc Roy Soc B: Biol Sci 273(1598):2107–2111

    PubMed  PubMed Central  Google Scholar 

  • Sadler PM (1981) Sediment accumulation rates and the completeness of stratigraphic sections. J Geol 89(5):569–584

    Google Scholar 

  • Sadler PM, Cooper RA, Melchin M (2009) High-resolution, early Paleozoic (Ordovician-Silurian) time scales. Geol Soc Am Bull 121(5–6):887–906

    Google Scholar 

  • Sallan LC, Friedman M (2012) Heads or tails: staged diversification in vertebrate evolutionary radiations. Proc Roy Soc B: Biol Sci 279(1735):2025–2032

    Google Scholar 

  • Sanderson MJ, Purvis A, Henze C (1998) Phylogenetic supertrees: assembling the trees of life. Trends Ecol Evol 13(3):105–109

    CAS  PubMed  Google Scholar 

  • Scotland RW, Olmstead RG, Bennett JR (2003) Phylogeny reconstruction: the role of morphology. Syst Biol 52(4):539–548

    PubMed  Google Scholar 

  • Siddall ME (1996) Stratigraphic consistency and the shape of things. Syst Biol 45(1):111–115

    Google Scholar 

  • Simpson C, Kiessling W, Mewis H, Baron-Szabo RC, Müller J (2011) Evolutionary diversification of reef corals: a comparison of the molecular and fossil records. Evolution 65(11):3274–3284. doi:10.1111/j.1558-5646.2011.01365.x

    Article  PubMed  Google Scholar 

  • Slater GJ (2013) Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods Ecol Evol 4(8):734–744. doi:10.1111/2041-210x.12084

    Article  Google Scholar 

  • Slater GJ, Harmon LJ, Alfaro ME (2012) Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66(12):3931–3944. doi:10.1111/j.1558-5646.2012.01723.x

    Article  PubMed  Google Scholar 

  • Smith AB (1994) Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific, Oxford

    Google Scholar 

  • Smith AB, McGowan AJ (2007) The shape of the Phanerozoic marine palaeodiversity curve: how much can be predicted from the sedimentary rock record of Western Europe? Palaeontology 50(4):765–774

    Google Scholar 

  • Smith ND (2012) Body mass and foraging ecology predict evolutionary patterns of skeletal pneumaticity in the diverse “waterbird” clade. Evolution 66(4):1059–1078. doi:10.1111/j.1558-5646.2011.01494.x

    Article  PubMed  Google Scholar 

  • Solow AR, Smith W (1997) On fossil preservation and the stratigraphic ranges of taxa. Paleobiology 23(3):271–277

    Google Scholar 

  • Stadler T (2010) Sampling-through-time in birth-death trees. J Theor Biol 267(3):396–404

    PubMed  Google Scholar 

  • Stanley SM (1979) Macroevolution: patterns and process. W. H Freeman & Co., San Francisco

    Google Scholar 

  • Strauss DJ, Sadler PM (1989) Classical confidence intervals and Bayesian probability estimates for ends of local taxon ranges. Math Geol 21:411–427

    Google Scholar 

  • Tarver JE, Donoghue PCJ (2011) The trouble with topology: phylogenies without fossils provide a revisionist perspective of evolutionary history in topological analyses of diversity. Syst Biol 60(5):700–712

    PubMed  Google Scholar 

  • Tomiya S (2013) Body size and extinction risk in terrestrial mammals above the species level. Am Nat 182(6):E196–E214. doi:10.1086/673489

    Article  PubMed  Google Scholar 

  • Trontelj P, Fiser C (2009) Cryptic species diversity should not be trivialised. Syst Biodivers 7(01):1–3

    Google Scholar 

  • Valentine JW, Jablonski D, Kidwell S, Roy K (2006) Assessing the fidelity of the fossil record by using marine bivalves. Proc Natl Acad Sci 103(17):6599–6604

    CAS  PubMed  PubMed Central  Google Scholar 

  • Van Valen L (1973) A new evolutionary law. Evol Theor 1:1–30

    Google Scholar 

  • Wagner PJ (1995) Diversity patterns among early gastropods: contrasting taxonomic and phylogenetic descriptions. Paleobiology 21(4):410–439

    Google Scholar 

  • Wagner PJ (1996) Ghost taxa, ancestors, assumptions, and expectations: a reply to Norell. Paleobiology 22(3):456–460

    Google Scholar 

  • Wagner PJ (1998) A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24(4):430–449

    Google Scholar 

  • Wagner PJ (2000) The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity. Syst Biol 49(1):65–86

    CAS  PubMed  Google Scholar 

  • Wagner PJ (2012) Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates. Biol Lett 8(1):143–146

    PubMed  Google Scholar 

  • Wagner PJ, Erwin DH (1995) Phylogenetic patterns as tests of speciation models. In: Erwin DH, Anstey RL (eds) New approaches to speciation in the fossil record. Columbia University Press, New York, pp 87–122

    Google Scholar 

  • Wagner PJ, Erwin DH (2006) Patterns of convergence in general shell form among Paleozoic gastropods. Paleobiology 32(2):316–337. doi:10.1666/04092.1

    Article  Google Scholar 

  • Wagner PJ, Marcot JD (2010) Probabilistic phylogenetic inference in the fossil record: current and future applications. In: Alroy J, Hunt G (eds) Short course on quantitative methods in paleobiology, vol 16., Paleontological SocietyNew Haven, Connecticut, pp 189–211

    Google Scholar 

  • Wagner PJ, Marcot JD (2013) Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies. Methods Ecol Evol 4(8):703–713. doi:10.1111/2041-210x.12088

    Article  Google Scholar 

  • Warnock RCM, Yang Z, Donoghue PCJ (2012) Exploring uncertainty in the calibration of the molecular clock. Biol Lett 8(1):156–159

    PubMed  Google Scholar 

  • Wayne RK (1986) Cranial morphology of domestic and wild canids: the influence of development on morphological change. Evolution 40(2):243–261. doi:10.2307/2408805

    Article  PubMed  Google Scholar 

  • Webb CO, Donoghue MJ (2005) Phylomatic: tree assembly for applied phylogenetics. Mol Ecol Notes 5(1):181–183. doi:10.1111/j.1471-8286.2004.00829.x

    Article  Google Scholar 

  • Wei K-Y (1994) Stratophenetic tracing of phylogeny using SIMCA pattern recognition technique: a case study of the late Neogene Planktic Foraminifera Globoconella clade. Paleobiology 20(1):52–65

    Google Scholar 

  • Wickström L, Donoghue PCJ (2005) Cladograms, phylogenies and the veracity of the conodont fossil record. Spec Pap Palaeontol 73:185–218

    Google Scholar 

  • Wills MA (1999) Congruence between phylogeny and stratigraphy: randomization tests and the gap excess ratio. Syst Biol 48(3):559–580

    Google Scholar 

  • Wills MA, Barrett PM, Heathcote JF (2008) The modified gap excess ratio (GER*) and the stratigraphic congruence of dinosaur phylogenies. Syst Biol 57(6):891–904

    PubMed  Google Scholar 

  • Wood HM, Matzke NJ, Gillespie RG, Griswold CE (2013) Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the Palpimanoid spiders. Syst Biol 62(2):264–284

    PubMed  Google Scholar 

  • Zanno LE, Makovicky PJ (2013) No evidence for directional evolution of body mass in herbivorous theropod dinosaurs. Proc Roy Soc B: Biol Sci 280(1751)

    Google Scholar 

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Acknowledgments

I’d like to thank D. Wright and P. Smits for their comments on an early draft of this manuscript. Suggestion from two anonymous reviewers and the editor greatly improved this chapter. Many of the ideas came from conversations with G. Lloyd, G. Slater, L. Soul, A. Wright, N. Matzke, J. Mitchell, K. Larson, M. Pennell, and E. King.

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  1. South Dakota School of Mines and Technology, Rapid City, SD, USA

    David W. Bapst

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Correspondence to David W. Bapst .

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  1. Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Sevilla, Spain

    László Zsolt Garamszegi

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Bapst, D.W. (2014). Preparing Paleontological Datasets for Phylogenetic Comparative Methods. In: Garamszegi, L. (eds) Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-43550-2_22

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