1932

Abstract

With proliferation of molecular phylogenies and advances in statistical modeling, phylogeneticists can now address macroevolutionary questions that had traditionally been the purview of paleontology. Interest has focused on three areas at the intersection of phylogenetic and paleontological research: time-scaling phylogenies, understanding trait evolution, and modeling species diversification. Fossil calibrations have long been crucial for scaling phylogenies to absolute time, but recent advances allow more equal integration of extinct taxa. Simulation and empirical studies have shown that fossil data can markedly improve inferences about trait evolution, especially for models with heterogeneous temporal dynamics and in clades for which the living forms are unrepresentative remnants of their larger clade. Recent years have also seen a productive cross-disciplinary conversation about the nature and uncertainties of inferring diversification dynamics. Challenges remain, but the present time represents a flowering of interest in integrating these two views on the history of life.

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2016-11-01
2024-04-19
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Literature Cited

  1. Albert JS, Johnson DM, Knouft JH. 2009. Fossils provide better estimates of ancestral body size than do extant taxa in fishes. Acta Zool 90:357–84 [Google Scholar]
  2. Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A. et al. 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. PNAS 106:13410–14 [Google Scholar]
  3. Alroy J. 1998a. Cope's rule and the dynamics of body mass evolution in North American fossil mammals. Science 280:731–34 [Google Scholar]
  4. Alroy J. 1998b. Equilibrial diversity dynamics in North American mammals. Biodiversity Dynamics: Turnover of Populations, Taxa and Communities ML McKinney, JA Drake 232–87 New York: Columbia Univ. Press [Google Scholar]
  5. Alroy J. 2010. Fair sampling of taxonomic richness and unbiased estimation of origination and extinction rates. Quantitative Methods in Paleobiology J Alroy, G Hunt 55–80 New Haven, CT: Paleontol. Soc. [Google Scholar]
  6. Alroy J. 2014. Accurate and precise estimates of origination and extinction rates. Paleobiology 40:374–97 [Google Scholar]
  7. Arcila D, Pyron RA, Tyler JC, Ortí G, Betancur-R R. 2015. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae). Mol. Phylogenet. Evol. 82:131–45 [Google Scholar]
  8. Aze T, Ezard THG, Purvis A, Coxall HK, Stewart DRM. et al. 2011. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biol. Rev. 86:900–27 [Google Scholar]
  9. Baker J, Meade A, Pagel M, Venditti C. 2015. Adaptive evolution toward larger size in mammals. PNAS 112:5093–98 [Google Scholar]
  10. Bapst DW. 2012. paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods Ecol. Evol. 3:803–7 [Google Scholar]
  11. Bapst DW. 2013. A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods Ecol. Evol. 4:724–33 [Google Scholar]
  12. Bapst DW. 2014a. Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record. Paleobiology 40:331–51 [Google Scholar]
  13. Bapst DW. 2014b. Preparing paleontological datasets for phylogenetic comparative methods. Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology LZ Garamszegi 515–44 Berlin: Springer-Verlag [Google Scholar]
  14. Beaulieu JM, O'Meara BC. 2015. Extinction can be estimated from moderately sized molecular phylogenies. Evolution 69:1036–43 [Google Scholar]
  15. Benton MJ. 2015. Exploring macroevolution using modern and fossil data. Proc. R. Soc. B 282:20150569 [Google Scholar]
  16. Betancur-R R, Orti G, Pyron RA. 2015. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes. Ecol. Lett. 18:441–50 [Google Scholar]
  17. Blomberg SP, Garland T, Ives AR. 2003. Testing for phylogenetic signal in comparative data: behavioural traits are more labile. Evolution 57:717–45 [Google Scholar]
  18. Bokma F. 2002. Detection of punctuated equilibrium from molecular phylogenies. J. Evol. Biol. 15:1048–56 [Google Scholar]
  19. Bokma F. 2008. Detection of “punctuated equilibrium” by Bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny. Evolution 62:2718–26 [Google Scholar]
  20. Bokma F, Godinot M, Maridet O, Ladevèze S, Costeur L. et al. 2015. Testing for Depéret's rule (body size increase) in mammals using combined extinct and extant data. Syst. Biol. 65:98–108 [Google Scholar]
  21. Brusatte SL, Benton MJ, Ruta M, Lloyd GT. 2008. Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs. Science 321:1485–88 [Google Scholar]
  22. Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL, Wadell PJ. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42:384–97 [Google Scholar]
  23. Cantalapiedra JL, FitzJohn RG, Kuhn TS, Fernandez MH, DeMiguel D. et al. 2014. Dietary innovations spurred the diversification of ruminants during the Caenozoic. Proc. R. Soc. B 281:20132746 [Google Scholar]
  24. Charlesworth B, Lande R, Slatkin M. 1982. A neo-Darwinian commentary on macroevolution. Evolution 36:474–98 [Google Scholar]
  25. Cheetham AH. 1986. Tempo of evolution in a Neogene bryozoan: rates of morphological change within and across species boundaries. Paleobiology 12:190–202 [Google Scholar]
  26. Clarke JA, Middleton KM. 2008. Mosaicism, modules, and the evolution of birds: results from a Bayesian approach to the study of morphological evolution using discrete character data. Syst. Biol. 57:185–201 [Google Scholar]
  27. Close RA, Friedman M, Lloyd GT, Benson RBJ. 2015. Evidence for a mid-Jurassic adaptive radiation in mammals. Curr. Biol. 25:2137–42 [Google Scholar]
  28. Clyde WC, Fisher DC. 1997. Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis. Paleobiology 23:1–19 [Google Scholar]
  29. Condamine FL, Rolland J, Morlon H. 2013. Macroevolutionary perspectives to environmental change. Ecol. Lett. 16:72–85 [Google Scholar]
  30. Cooper N, Purvis A. 2010. Body size evolution in mammals: complexity in tempo and mode. Am. Nat. 175:727–38 [Google Scholar]
  31. Cooper N, Thomas GH, Venditti C, Meade A, Freckleton RP. 2016. A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies. Biol. J. Linn. Soc. 118:64–77 [Google Scholar]
  32. Crampton JS, Cooper RA, Sadler PM, Foote M. 2016. Greenhouse-icehouse transition in the Late Ordovician marks a step change in extinction regime in the marine plankton. PNAS 113:1498–503 [Google Scholar]
  33. Donoghue PCJ, Benton MJ. 2007. Rocks and clocks: calibrating the tree of life using fossils and molecules. Trends Ecol. Evol. 22:424–31 [Google Scholar]
  34. Eastman JM, Alfaro ME, Joyce P, Hipp AL, Harmon LJ. 2011. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution 65:3578–89 [Google Scholar]
  35. Eldredge N, Gould SJ. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Models in Paleobiology TJM Schopf 82–115 San Francisco: Freeman, Cooper [Google Scholar]
  36. Etienne RS, Apol MEF. 2009. Estimating speciation and extinction rates from diversity data and the fossil record. Evolution 63:244–55 [Google Scholar]
  37. Etienne RS, Haegeman B, Stadler T, Aze T, Pearson PN. et al. 2012. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record. Proc. R. Soc. B 279:1300–9 [Google Scholar]
  38. Ezard THG, Aze T, Pearson PN, Purvis A. 2011. Interplay between changing climate and species' ecology drives macroevolutionary dynamics. Science 332:349–51 [Google Scholar]
  39. Ezard THG, Thomas GH, Purvis A. 2013. Inclusion of a near-complete fossil record reveals speciation-related molecular evolution. Methods Ecol. Evol. 4:745–53 [Google Scholar]
  40. Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Biol. 27:401–10 [Google Scholar]
  41. 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. 55:301–13 [Google Scholar]
  42. Finarelli JA, Goswami A. 2013. Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the Canidae (Mammalia, Carnivora). Evolution 67:3678–85 [Google Scholar]
  43. Finnegan S, Heim NA, Peters SE, Fischer WW. 2012. Climate change and the selective signature of the Late Ordovician mass extinction. PNAS 109:6829–34 [Google Scholar]
  44. Fisher DC. 2008. Stratocladistics: integrating temporal data and character data in phylogenetic inference. Annu. Rev. Ecol. Evol. Syst. 39:365–85 [Google Scholar]
  45. FitzJohn RG. 2012. Diversitree: comparative phylogenetic analyses of diversification in R. Methods Ecol. Evol. 3:1084–92 [Google Scholar]
  46. Foote M. 1990. Nearest-neighbor analysis of trilobite morphospace. Syst. Zool. 39:371–82 [Google Scholar]
  47. Foote M. 1991. Morphological and taxonomic diversity in a clade's history: the blastoid record and stochastic simulations. Contrib. Mus. Paleontol. (Univ. Mich. 28:101–40 [Google Scholar]
  48. Foote M. 1996a. Models of morphological diversification. Evolutionary Paleobiology D Jablonski, DH Erwin, JH Lipps 62–86 Chicago: Univ. Chicago Press [Google Scholar]
  49. Foote M. 1996b. On the probability of ancestors in the fossil record. Paleobiology 22:141–51 [Google Scholar]
  50. Foote M. 1997a. Estimating taxonomic durations and preservation probability. Paleobiology 23:278–300 [Google Scholar]
  51. Foote M. 1997b. The evolution of morphological diversity. Annu. Rev. Ecol. Syst. 28:129–52 [Google Scholar]
  52. Foote M. 2000. Origination and extinction components of taxonomic diversity: general problems. Paleobiology 26:74–102 [Google Scholar]
  53. Foote M. 2003. Origination and extinction through the Phanerozoic: a new approach. J. Geol. 111:125–48 [Google Scholar]
  54. Foote M. 2011. Evolutionary dynamics of taxonomic structure. Biol. Lett. 8:135–38 [Google Scholar]
  55. Fritz SA, Schnitzler J, Eronen JT, Hof C, Bohning-Gaese K, Graham CH. 2013. Diversity in time and space: wanted dead and alive. Trends Ecol. Evol. 28:509–16 [Google Scholar]
  56. Garamszegi LZ, Moller AP. 2011. Nonrandom variation in within-species sample size and missing data in phylogenetic comparative studies. Syst. Biol. 60:876–80 [Google Scholar]
  57. Gauthier J, Kluge AG, Rowe T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4:105–209 [Google Scholar]
  58. Gavryushkina A, Heath TA, Ksepka DT, Stadler T, Welch D, Drummond AJ. 2015. Bayesian total evidence dating reveals the recent crown radiation of penguins. arXiv:1506.04797 [q-bio.PE]
  59. Gavryushkina A, Welch D, Stadler T, Drummond AJ. 2014. Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLOS Comput. Biol. 10:e1003919 [Google Scholar]
  60. Gingerich PD. 1985. Species in the fossil record: concepts, trends, and transitions. Paleobiology 11:27–41 [Google Scholar]
  61. Goldberg EE, Igic B. 2012. Tempo and mode in plant breeding system evolution. Evolution 66:3701–9 [Google Scholar]
  62. Grimm GW, Kapli P, Bomfleur B, McLoughlin S, Renner SS. 2014. Using more than the oldest fossils: dating Osmundaceae with three Bayesian clock approaches. Syst. Biol. 64:396–405 [Google Scholar]
  63. Guillerme T, Cooper N. 2015. Assessment of cladistic data availability for living mammals. bioRxiv022970
  64. Guillerme T, Cooper N. 2016. Effects of missing data on topological inference using a Total Evidence approach. Mol. Phylogenet. Evol. 94:146–58 [Google Scholar]
  65. Hansen TA. 1982. Modes of larval development in Early Tertiary neogastropods. Paleobiology 8:367–77 [Google Scholar]
  66. Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL. et al. 2010. Early bursts of body size and shape evolution are rare in comparative data. Evolution 64:2385–96 [Google Scholar]
  67. Harrison LB, Larsson HCE. 2015. Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters. Syst. Biol. 64:307–24 [Google Scholar]
  68. Heath TA, Huelsenbeck JP, Stadler T. 2014. The fossilized birth–death process for coherent calibration of divergence-time estimates. PNAS 111:E2957–66 [Google Scholar]
  69. Heim NA, Knope ML, Schaal EK, Wang SC, Payne JL. 2015. Cope's rule in the evolution of marine animals. Science 347:867–70 [Google Scholar]
  70. Hendricks JR, Saupe EE, Myers CE, Hermsen EJ, Allmon WD. 2014. The generification of the fossil record. Paleobiology 40:511–28 [Google Scholar]
  71. Hopkins MJ, Smith AB. 2015. Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution. PNAS 112:3758–63 [Google Scholar]
  72. Huang DW, Goldberg EE, Roy K. 2015. Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions. PNAS 112:4909–14 [Google Scholar]
  73. Huang S, Roy K, Jablonski D. 2014. Do past climate states influence diversity dynamics and the present-day latitudinal diversity gradient. Glob. Ecol. Biogeogr. 23:530–40 [Google Scholar]
  74. Huelsenbeck JP. 1991. When are fossils better than extant taxa in phylogenetic analysis. Syst. Biol. 40:458–69 [Google Scholar]
  75. Huelsenbeck JP. 1994. Comparing the stratigraphic record to estimates of phylogeny. Paleobiology 20:470–83 [Google Scholar]
  76. Huelsenbeck JP, Rannala B. 1997. Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology 23:174–80 [Google Scholar]
  77. Hughes M, Gerber S, Wills MA. 2013. Clades reach highest morphological disparity early in their evolution. PNAS 110:13875–79 [Google Scholar]
  78. Hunt G. 2006. Fitting and comparing models of phyletic evolution: random walks and beyond. Paleobiology 32:578–601 [Google Scholar]
  79. Hunt G. 2013. Testing the link between phenotypic evolution and speciation: an integrated palaeontological and phylogenetic analysis. Methods Ecol. Evol. 4:714–23 [Google Scholar]
  80. Hunt G, Hopkins MJ, Lidgard S. 2015. Simple versus complex models of trait evolution and stasis as a response to environmental change. PNAS 112:4885–90 [Google Scholar]
  81. Hunt G, Roy K. 2006. Climate change, body size evolution, and Cope's rule in deep-sea ostracodes. PNAS 103:1347–52 [Google Scholar]
  82. Jackson JBC, Cheetham AH. 1990. Evolutionary significance of morphospecies: a test with cheilostome Bryozoa. Science 248:579–82 [Google Scholar]
  83. Jepsen GL, Mayr E, Simpson GG. 1949. Genetics, Paleontology, and Evolution Princeton, NJ: Princeton Univ. Press
  84. Kidwell SM, Holland SM. 2002. The quality of the fossil record: implications for evolutionary analysis. Annu. Rev. Ecol. Syst. 33:561–88 [Google Scholar]
  85. Klopfstein S, Vilhelmsen L, Ronquist F. 2015. A nonstationary Markov model detects directional evolution in hymenopteran morphology. Syst. Biol. 64:1089–103 [Google Scholar]
  86. Ksepka DT, Benton MJ, Carrano MT, Gandolfo MA, Head JJ. et al. 2011. Synthesizing and databasing fossil calibrations: divergence dating and beyond. Biol. Lett. 7:801–3 [Google Scholar]
  87. Lane A, Janis CM, Sepkoski JJ. 2005. Estimating paleodiversities: a test of the taxic and phylogenetic methods. Paleobiology 31:21–34 [Google Scholar]
  88. Larson-Johnson K. 2016. Phylogenetic investigation of the complex evolutionary history of dispersal mode and diversification rates across living and fossil Fagales. N. Phytol. 209:418–35 [Google Scholar]
  89. Lewis PO. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50:913–25 [Google Scholar]
  90. Liow LH, Finarelli JA. 2014. A dynamic global equilibrium in carnivoran diversification over 20 million years. Proc. R. Soc. B 281:20132312 [Google Scholar]
  91. Liow LH, Fortelius M, Bingham E, Lintulaakso K, Mannila H. et al. 2008. Higher origination and extinction rates in larger mammals. PNAS 105:6097–102 [Google Scholar]
  92. Liow LH, Nichols JD. 2010. Estimating rates and probabilities of origination and extinction using taxonomic occurrence data: capture-mark-recapture (CMR) approaches. Quantitative Methods in Paleobiology J Alroy, G Hunt 81–94 New Haven, CT: Paleontol. Soc. [Google Scholar]
  93. Liow LH, Quental TB, Marshall CR. 2010. When can decreasing diversification rates be detected with molecular phylogenies and the fossil record. Syst. Biol. 59:646–59 [Google Scholar]
  94. Maddison WP, FitzJohn RG. 2015. The unsolved challenge to phylogenetic correlation tests for categorical characters. Syst. Biol. 64:127–36 [Google Scholar]
  95. Maddison WP, Midford PE, Otto SP. 2007. Estimating a binary character's effect on speciation and extinction. Syst. Biol. 56:701–10 [Google Scholar]
  96. Magnuson-Ford K, Otto SP. 2012. Linking the investigations of character evolution and species diversification. Am. Nat. 180:225–45 [Google Scholar]
  97. Marcot JD, Fox DL. 2008. StrataPhy: a new computer program for stratocladistic analysis. Palaeontol. Electron. 11:1–16 [Google Scholar]
  98. McShea DW. 1994. Mechanisms of large-scale evolutionary trends. Evolution 48:1747–63 [Google Scholar]
  99. Moen D, Morlon H. 2014. Why does diversification slow down. Trends Ecol. Evol. 29:190–97 [Google Scholar]
  100. Monroe MJ, Bokma F. 2010. Little evidence for Cope's rule from Bayesian phylogenetic analysis of extant mammals. J. Evol. Biol. 23:2017–21 [Google Scholar]
  101. Morlon H. 2014. Phylogenetic approaches for studying diversification. Ecol. Lett. 17:508–25 [Google Scholar]
  102. Morlon H, Parsons TL, Plotkin JB. 2011. Reconciling molecular phylogenies with the fossil record. PNAS 108:16327–32 [Google Scholar]
  103. Nee S, May RM, Harvey PH. 1994. The reconstructed evolutionary process. Philos. Trans. R. Soc. B 344:305–11 [Google Scholar]
  104. Norell MA. 1992. Taxic origin and temporal diversity: the effect of phylogeny. Extinction and Phylogeny MJ Novacek, QD Wheeler 89–118 New York: Columbia Univ. Press [Google Scholar]
  105. Novack-Gottshall PM, Lanier MA. 2008. Scale-dependence of Cope's rule in body size evolution of Paleozoic brachiopods. PNAS 105:5430–34 [Google Scholar]
  106. O'Meara BC. 2012. Evolutionary inferences from phylogenies: a review of methods. Annu. Rev. Ecol. Evol. Syst. 43:267–85 [Google Scholar]
  107. O'Reilly JE, dos Reis M, Donoghue P. 2015. Dating tips for divergence-time estimation. Trends Genet 31:637–50 [Google Scholar]
  108. Pagel M, Venditti C, Meade A. 2006. Large punctuational contribution of speciation to evolutionary divergence at the molecular level. Science 314:119–21 [Google Scholar]
  109. Pattinson DJ, Thompson RS, Piotrowski AK, Asher RJ. 2014. Phylogeny, paleontology, and primates: Do incomplete fossils bias the tree of life. Syst. Biol. 64:169–86 [Google Scholar]
  110. Pennell MW, Harmon LJ. 2013. An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology. Ann. N.Y. Acad. Sci. 1289:90–105 [Google Scholar]
  111. Pennell MW, Harmon LJ, Uyeda JC. 2014. Is there room for punctuated equilibrium in macroevolution. Trends Ecol. Evol. 29:23–32 [Google Scholar]
  112. Peters SE, Ausich WI. 2008. A sampling-adjusted macroevolutionary history for Ordovician–Early Silurian crinoids. Paleobiology 34:104–16 [Google Scholar]
  113. Phillimore AB, Price TD. 2008. Density-dependent cladogenesis in birds. PLOS Biol 6:e71 [Google Scholar]
  114. Pires MM, Silvestro D, Quental TB. 2015. Continental faunal exchange and the asymmetrical radiation of carnivores. Proc. R. Soc. B 282:20151952 [Google Scholar]
  115. Plotnick RE, Wagner PJ. 2006. Round up the usual suspects: common genera in the fossil record and the nature of wastebasket taxa. Paleobiology 32:126–46 [Google Scholar]
  116. Polly PD. 2001. Paleontology and the comparative method: ancestral node reconstructions versus observed node values. Am. Nat. 157:596–609 [Google Scholar]
  117. Puttick MN, Thomas GH. 2015. Fossils and living taxa agree on patterns of body mass evolution: a case study with Afrotheria. Proc. R. Soc. B 282:20152023 [Google Scholar]
  118. Pybus OG, Harvey PH. 2000. Testing macro-evolutionary models using incomplete molecular phylogenies. Proc. R. Soc. B 267:2267–72 [Google Scholar]
  119. Pyron RA. 2011. Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia. Syst. Biol. 60:466–81 [Google Scholar]
  120. Pyron RA, Burbrink FT. 2012. Trait-dependent diversification and the impact of palaeontological data on evolutionary hypothesis testing in New World ratsnakes (tribe Lampropeltini). J. Evol. Biol. 25:497–508 [Google Scholar]
  121. Pyron RA, Burbrink FT. 2013. Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses. Trends Ecol. Evol. 28:729–36 [Google Scholar]
  122. Quental TB, Marshall CR. 2009. Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution 63:3158–67 [Google Scholar]
  123. Quental TB, Marshall CR. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol. Evol. 25:434–41 [Google Scholar]
  124. Rabosky DL. 2006. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60:1152–64 [Google Scholar]
  125. Rabosky DL. 2010. Extinction rates should not be estimated from molecular phylogenies. Evolution 64:1816–24 [Google Scholar]
  126. Rabosky DL. 2013. Diversity-dependence, ecological speciation, and the role of competition in macroevolution. Annu. Rev. Ecol. Evol. Syst. 44:481–502 [Google Scholar]
  127. Rabosky DL. 2014. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLOS ONE 9:e89543 [Google Scholar]
  128. Rabosky DL. 2015. No substitute for real data: a cautionary note on the use of phylogenies from birth–death polytomy resolvers for downstream comparative analyses. Evolution 69:3207–16 [Google Scholar]
  129. Rabosky DL, Goldberg EE. 2015. Model inadequacy and mistaken inferences of trait-dependent speciation. Syst. Biol. 64:340–55 [Google Scholar]
  130. Rabosky DL, Lovette IJ. 2008a. Density-dependent diversification in North American wood warblers. Proc. R. Soc. B 275:2363–71 [Google Scholar]
  131. Rabosky DL, Lovette IJ. 2008b. Explosive evolutionary radiations: Decreasing speciation or increasing extinction through time. Evolution 62:1866–75 [Google Scholar]
  132. Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B. et al. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 4:1958 [Google Scholar]
  133. 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. 61:973–99 [Google Scholar]
  134. Roy K, Hunt G, Jablonski D. 2009. Phylogenetic conservatism of extinctions in marine bivalves. Science 325:733–37 [Google Scholar]
  135. 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. R. Soc. B 273:2107–11 [Google Scholar]
  136. Sansom RS, Wills MA. 2013. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees. Sci. Rep. 3:2545 [Google Scholar]
  137. Schluter D, Price T, Mooers A, Ludwig D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699–711 [Google Scholar]
  138. Sepkoski JJ, Bambach RK, Raup DM, Valentine JW. 1981. Phanerozoic marine diversity and the fossil record. Nature 293:435–37 [Google Scholar]
  139. Sepkoski JJ, Kendrick DC. 1993. Numerical experiments with model monophyletic and paraphyletic taxa. Paleobiology 19:168–84 [Google Scholar]
  140. Silvestro D, Antonelli A, Salamin N, Quental TB. 2015. The role of clade competition in the diversification of North American canids. PNAS 112:8684–89 [Google Scholar]
  141. Silvestro D, Schnitzler J, Liow LH, Antonelli A, Salamin N. 2014. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Syst. Biol. 63:349–67 [Google Scholar]
  142. Simpson C, Kiessling W, Mewis H, Baron-Szabo RC, Muller J. 2011. Evolutionary diversification of reef corals: a comparison of the molecular and fossil records. Evolution 65:3274–84 [Google Scholar]
  143. Simpson GG. 1944. Tempo and Mode in Evolution New York: Columbia Univ. Press
  144. Slater GJ. 2013. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods Ecol. Evol. 4:734–44 [Google Scholar]
  145. Slater GJ. 2014. Correction to ‘Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous–Palaeogene boundary’, and a note on fitting macroevolutionary models to comparative paleontological data sets. Methods Ecol. Evol. 5:714–18 [Google Scholar]
  146. Slater GJ. 2015. Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution. PNAS 112:4897–902 [Google Scholar]
  147. Slater GJ, Harmon LJ, Alfaro ME. 2012a. Integrating fossils with molecular phylogenies improves inference of trait evolution. Evolution 66:3931–44 [Google Scholar]
  148. Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME. 2012b. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution 66:752–62 [Google Scholar]
  149. Slater GJ, Pennell MW. 2014. Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution. Syst. Biol. 63:293–308 [Google Scholar]
  150. Soul LC, Friedman M. 2015. Taxonomy and phylogeny can yield comparable results in comparative paleontological analyses. Syst. Biol. 64:608–20 [Google Scholar]
  151. Spencer MR, Wilberg EW. 2013. Efficacy or convenience? Model-based approaches to phylogeny estimation using morphological data. Cladistics 29:663–71 [Google Scholar]
  152. Stadler T. 2011. Mammalian phylogeny reveals recent diversification rate shifts. PNAS 108:6187–92 [Google Scholar]
  153. Stanley SM. 1973. An explanation for Cope's rule. Evolution 27:1–26 [Google Scholar]
  154. Stanley SM. 1979. Macroevolution: Pattern and Process Baltimore, MD: Johns Hopkins Univ. Press
  155. Stanley SM. 1990. The general correlation between rate of speciation and rate of extinction: fortuitous causal linkages. Causes of Evolution: A Paleontological Perspective RM Ross, WD Allmon103–27 Chicago: Univ. Chicago Press [Google Scholar]
  156. Valentine JW. 1980. Determinants of diversity in higher taxonomic categories. Paleobiology 6:444–50 [Google Scholar]
  157. Venditti C, Meade A, Pagel M. 2011. Multiple routes to mammalian diversity. Nature 479:393–96 [Google Scholar]
  158. Wagner PJ. 1995. Testing evolutionary constraint hypotheses with early Paleozoic gastropods. Paleobiology 21:248–72 [Google Scholar]
  159. Wagner PJ. 1998. A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24:430–49 [Google Scholar]
  160. Wagner PJ. 2012. Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates. Biol. Lett. 8:143–46 [Google Scholar]
  161. 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. 4:703–13 [Google Scholar]
  162. Webster AJ, Purvis A. 2002. Testing the accuracy of methods for reconstructing ancestral states of continuous characters. Proc. R. Soc. B 269:143–49 [Google Scholar]
  163. Wright AM, Hillis DM. 2014. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLOS ONE 9:e109210 [Google Scholar]
  164. Xing Y, Onstein RE, Carter RJ, Stadler T, Peter Linder H. 2014. Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected. Evolution 68:2821–32 [Google Scholar]
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