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Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

  • David F. Wright (a1)

Knowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth–death (FBD) process provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, the FBD tree prior allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.

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J. Alroy , 2010, Geographical, environmental and intrinsic biotic controls on Phanerozoic marine diversification: Palaeontology, v. 53, p. 12111235.

W.I. Ausich , and T.W. Kammer , 2001, The study of crinoids during the 20th century and the challenges of the 21st century: Journal of Paleontology, v. 75, p. 11611173.

W.I. Ausich , T.W. Kammer , and T.K. Baumiller , 1994, Demise of the middle Paleozoic crinoid fauna: A single extinction event or rapid faunal turnover?: Paleobiology, v. 20, p. 345361.

W.I. Ausich , T.W. Kammer , E.C. Rhenberg , and D.F. Wright , 2015, Early phylogeny of crinoids within the Pelmatozoan clade: Palaeontology, v. 58, p. 937952.

D.W. Bapst , 2012, When can clades be potentially resolved with morphology?: PLoS One, v. 8, e62312 doi: 10.1371/journal.pone.0062312.

D.W. Bapst , 2013, A stochastic rate‐calibrated method for time‐scaling phylogenies of fossil taxa: Methods in Ecology and Evolution, v. 4, p. 724733.

D.W. Bapst , A.M. Wright , N.J. Matzke , and G.T. Lloyd , 2016, Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria): Biology Letters, v. 12, 20160237, doi: 10.1098/rsbl.2016.0237.

M.A. Bell , and G.T. Lloyd , 2015, strap: An R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence: Palaeontology, v. 58, p. 379389.

J. Bergsten , A.N. Nilsson , and F. Ronquist , 2013, Bayesian tests of topology hypotheses with an example from diving beetles: Systematic Biology, v. 62, p. 660673.

F. Bokma , 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, v. 62, p. 27182726.

J.C. Brower , 1995, Dendrocrinid crinoids from the Ordovician of northern Iowa and southern Minnesota: Journal of Paleontology, v. 69, p. 939960.

S.L. Brusatte , 2010, Representing supraspecific taxa in higher‐level phylogenetic analyses: Guidelines for palaeontologists: Palaeontology, v. 53, p. 19.

S.L. Brusatte , M.J. Benton , M. Ruta , and G.T. Lloyd , 2008, Superiority, competition, and opportunism in the evolutionary radiation of dinosaurs: Science, v. 321, p. 14851488.

S.J. Carlson , and P.C. Fitzgerald , 2007, Sampling taxa, estimating phylogeny and inferring macroevolution: An example from Devonian terebratulide brachiopods: Earth and Environmental Science Transactions of the Royal Society of Edinburgh, v. 98, p. 311325.

J.A. Clarke , and K.M. Middleton , 2008, Mosaicism, modules, and the evolution of birds: Results from a Bayesian approach to the study of morphological evolution using discrete character data: Systematic Biology, v. 57, p. 185201.

S.R. Cole , 2017, Phylogeny and morphologic evolution of the Ordovician Camerata (Class Crinoidea, Phylum Echinodermata): Journal of Paleontology, doi:10.1017/jpa.2016.137.

R.A. Close , M. Friedman , G.T. Lloyd , and R.B. Benson , 2015, Evidence for a mid-Jurassic adaptive radiation in mammals: Current Biology, v. 25, p. 21372142.

B. Deline , and W.I. Ausich , 2011, Testing the plateau: A reexamination of disparity and morphologic constraints in early Paleozoic crinoids: Paleobiology, v. 37, p. 214236.

G. Didier , M. Royer-Carenzi , and M. Laurin , 2012, The reconstructed evolutionary process with the fossil record: Journal of Theoretical Biology, v. 315, p. 2637.

P.C.J. Donoghue , and M.J. Benton , 2007, Rocks and clocks: Calibrating the Tree of Life using fossils and molecules: Trends in Ecology and Evolution, v. 22, p. 424431.

M. dos Reis , P.C. Donoghue , and Z. Yang , 2016, Bayesian molecular clock dating of species divergences in the genomics era: Nature Reviews Genetics, v. 17, p. 7180.

A.J. Drummond , and A. Rambaut , 2007, BEAST: Bayesian evolutionary analysis by sampling trees: BMC Evolutionary Biology, v. 7, doi: 10.1186/1471-2148-7-214.

M. Foote , 1994, Morphological disparity in Ordovician-Devonian crinoids and the early saturation of morphological space: Paleobiology, v. 20, p. 320344.

M. Foote , 1996, On the probability of ancestors in the fossil record: Paleobiology, v. 22, p. 141151.

M. Foote , 1997, Estimating taxonomic durations and preservation probability: Paleobiology, v. 23, p. 278300.

M. Foote , 2000, Origination and extinction components of taxonomic diversity: General problems: Paleobiology, v. 26, p. 74102.

M. Foote , and D.M. Raup , 1996, Fossil preservation and the stratigraphic ranges of taxa: Paleobiology, v. 22, p. 121140.

F.J. Gahn , and T.W. Kammer , 2002, The cladid crinoid Barycrinus from the Burlington Limestone (early Osagean) and the phylogenetics of Mississippian botryocrinids: Journal of Paleontology, v. 76, p. 123133.

A. Gavryshkina , D. Welch , T. Stadler , and A. J. Drummond , 2014, Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration: PLoS Computational Biology, v. 10, e1003919.

A. Gelman , and D.B. Rubin , 1992, Inference from iterative simulation using multiple sequences: Statistical Science, v. 7, p. 457472.

E. Gorscak , and P.M. O’Connor , 2016, Time-calibrated models support congruency between Cretaceous continental rifting and titanosaurian evolutionary history: Biology Letters, v. 12, 20151047.

T.E. Guensburg , 2010, Alphacrinus new genus and origin of the disparid clade: Journal of Paleontology, v. 84, p. 12091216.

T.E. Guensburg , 2012, Phylogenetic implications of the oldest crinoids: Journal of Paleontology, v. 86, p. 455461.

T.E. Guensburg , and J. Sprinkle , 2009, Solving the mystery of crinoid ancestry: New fossil evidence of arm origin and development: Journal of Paleontology, v. 83, p. 350364.

T. Guillerme , and N. Cooper , 2016, Effects of missing data on topological inference using a total evidence approach: Molecular Phylogenetics and Evolution, v. 94, p. 146158.

L.B. Harrison , and H.C.E. Larsson , 2015, Among-character rate variation distributions in phylogenetic analysis of discrete morphologic characters: Systematic Biology, v. 64, p. 307324.

T.A. Heath , J.P. Huelsenbeck , and T. Stadler , 2014, The fossilized birth–death process for coherent calibration of divergence-time estimates: Proceedings of the National Academy of Sciences, v. 111, p. E2957E2966.

J. Heled , and R.R. Bouckaert , 2013, Looking for trees in the forest: Summary tree from posterior samples: BMC Evolutionary Biology, v. 13, p. 221.

G. Hunt , 2008, Gradual or pulsed evolution: When should punctuational explanations be preferred?: Paleobiology, v. 34, p. 360377.

G. Hunt , and G. Slater , 2016, Integrating paleontological and phylogenetic approaches to macroevolution: Annual Review of Ecology, Evolution, and Systematics, v. 47, p. 189213.

G. Hunt , M.A. Bell , and M.P. Travis , 2008, Evolution toward a new adaptive optimum: Phenotypic evolution in a fossil stickleback lineage: Evolution, v. 62, p. 700710.

D. Jablonski , 2008, Biotic interactions and macroevolution: Extensions and mismatches across scales and levels: Evolution, v. 62, p. 715739.

T.W. Kammer , 2001, Phenotypic bradytely in the Costalocrinus-Barycrinus lineage of Paleozoic cladid crinoids: Journal of Paleontology, v. 75, p. 383389.

T.W. Kammer , and W.I. Ausich , 1992, Advanced cladid crinoids from the middle Mississippian of the east-central United States: Primitive-grade calyces: Journal of Paleontology, v. 66, p. 461480.

T.W. Kammer , and W.I. Ausich , 1996, Primitive cladid crinoids from upper Osagean-lower Meramecian (Mississippian) rocks of east-central United States: Journal of Paleontology, v. 70, p. 835866.

R.E. Kass , and A.E. Raftery , 1995, Bayes factors: Journal of the American Statistical Association, v. 90, p. 773795.

D.T. Ksepka , J.F. Parham , J.F. Allman , M.J. Benton , M.T. Carrano , K.A. Cranston , P.C. Donoghue , J.J. Head , E.J. Hermsen , R.B. Irmis , and W.G. Joyce , 2015, The Fossil Calibration Database—A new resource for divergence dating: Systematic Biology, v. 64, p. 853859.

C. Lakner , P. van der Mark , J.P. Huelsenbeck , B. Larget , and F. Ronquist , 2008, Efficiency of Markov chain Monte Carlo tree proposals in Bayesian phylogenetics: Systematic Biology, v. 57, p. 86106.

M.S.Y. Lee , and A. Palci , 2015, Morphological phylogenetics in the genomic age: Current Biology, v. 25, p. R922R929.

M.S. Lee , A. Cau , D. Naish , and G.J. Dyke , 2014, Morphological clocks in paleontology, and a mid-Cretaceous origin of crown Aves: Systematic Biology, v. 63, p. 442449.

T. Lepage , D. Bryant , H. Philippe , and N. Lartillot , 2007, A general comparison of relaxed molecular clock models: Molecular Biology and Evolution, v. 24, p. 26692680.

P.O. Lewis , 2001, A likelihood approach to estimating phylogeny from discrete morphological character data: Systematic Biology, v. 50, p. 913925.

G.T. Lloyd , S.C. Wang , and S.L. Brusatte , 2012, Identifying heterogeneity in rates of morphological evolution: Discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi): Evolution, v. 66, p. 330348.

D.R. Maddison , 1991, The discovery and importance of multiple islands of most-parsimonious trees: Systematic Zoology, v. 40, p. 315328.

N.J. Matzke , 2015, The evolution of antievolution policies after Kitzmiller v. Dover: Science, v. 351, p. 2830, doi: 10.1126/science.aad4057.

G.C. McIntosh , 2001, Devonian cladid crinoids: Families Glossocrinidae Goldring, 1923, and Rutkowskicrinidae new family: Journal of Paleontology, v. 75, p. 783807.

B.C. O’Meara , C. Ané , M.J. Sanderson , P.C. Wainwright , and T. Hansen , 2006, Testing for different rates of continuous trait evolution using likelihood: Evolution, v. 60, p. 922933.

J.E. O’Reilly , M.N. Puttick , L. Parry , A.R. Tanner , J.E. Tarver , J. Fleming , D. Pisani , and P.C.J. Donoghue , 2016, Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data: Biology Letters, v. 12, 20160081,

E. Paradis , J. Claude , and K. Strimmer , 2004, APE: Analyses of phylogenetics and evolution in R language: Bioinformatics, v. 20, p. 289290.

M.W. Pennell , L.J. Harmon , and J.C. Uyeda , 2014, Is there room for punctuated equilibrium in macroevolution?: Trends in Ecology and Evolution, v. 29, p. 2332.

J.R. Pollitt , R.A. Fortey , and M.A. Wills , 2005, Systematics of the trilobite families Lichidae Hawle and Corda, 1847 and Lichakephalidae Tripp, 1957: The application of Bayesian inference to morphological data: Journal of Systematic Palaeontology, v. 3, p. 225241.

R.A. Pyron , 2011, Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia: Systematic Biology, v. 60, p. 466481.

R.A. Pyron , 2015, Post-molecular systematics and the future of phylogenetics: Trends in Ecology and Evolution, v. 30, p. 384389.

D.L. Rabosky , 2009, Ecological limits and diversification rate: Alternative paradigms to explain the variation in species richness among clades and regions: Ecology Letters, v. 12, p. 735743.

D.L. Rabosky , and A.R. McCune , 2009, Reinventing species selection with molecular phylogenies: Trends in Ecology and Evolution, v. 25, p. 6874.

B. Rannala , and Z. Yang , 1996, Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference: Journal of Molecular Evolution, v. 43, p. 304311.

D.M. Raup , 1985, Mathematical models of cladogenesis: Paleobiology, v. 11, p. 4252.

D.M. Raup , S.J. Gould , T.J.M. Schopf , and D.S. Simberloff , 1973, Stochastic models of phylogeny and the evolution of diversity: Journal of Geology, v. 81, p. 525542.

D.F. Robinson , and L.R. Foulds , 1981, Comparison of phylogenetic trees: Mathematical Biosciences, v. 53, p. 131147.

F. Ronquist , S. Klopfstein , L. Vilhelmsen , S. Schulmeister , D.L. Murray , and A.P. Rasnitsyn , 2012, A total-evidence approach to dating with fossils, applied to the early radiation of the Hymenoptera: Systematic Biology, v. 61, p. 973999.

G.W. Rouse , L.S. Jermiin , N.G. Wilson , I. Eeckhaut , D. Lanterbecq , T. Oji , C.M. Young , T. Browning , P. Cisternas , L.E. Helgen , M. Stuckey , and C.G. Messing , 2013, Fixed, free, and fixed: The fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian–Triassic origin: Molecular Phylogenetics and Evolution, v. 66, p. 161181.

J.J. Sepkoski Jr., 1981, A factor analytic description of the Phanerozoic marine fossil record: Paleobiology, v. 7, p. 3653.

G.J. Slater , 2013, Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary: Methods in Ecology and Evolution, v. 4, p. 734744.

G.J. Slater , 2015, Iterative adaptive radiations of fossil canids show no evidence for diversity-dependent trait evolution: Proceedings of the National Academy of Sciences, v. 112, p. 48974902.

G.J. Slater , and L.J. Harmon , 2013, Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution: Methods in Ecology and Evolution, v. 4, p. 699702.

A.B. Smith , B. Lafay , and R. Christen , 1992, Comparative variation of morphological and molecular evolution through geologic time: 28S ribosomal RNA versus morphology in echinoids: Philosophical Transactions: Biological Sciences, v. 338, p. 365382.

E. Snively , A.P. Russell , and G.L. Powell , 2004, Evolutionary morphology of the coelurosaurian arctometatarsus: Descriptive, morphometric and phylogenetic approaches: Zoological Journal of the Linnean Society, v. 142, p. 525553.

M.R. Spencer , and E.W. Wilberg , 2013, Efficacy or convenience? Model‐based approaches to phylogeny estimation using morphological data: Cladistics, v. 29, p. 663671.

T. Stadler , 2010, Sampling-through-time in birth-death trees: Journal of Theoretical Biology, v. vol. 267, p. 396404.

T. Stadler , and Z. Yang , 2013, Dating phylogenies with sequentially sampled tips: Systematic Biology, v. 62, p. 674688.

T. Stadler , R. Kouyos , V. Wyl , S. von, Yerly , J. Böni , P. Bürgisser , T. Klimkait , B. Joos , P. Rieder , D. Xie , H.F. Günthard , A.J. Drummond , and S. Bonhoeffer , the Swiss HIV Cohort Study, 2012, Estimating the basic reproductive number from viral sequence data: Molecular Biology and Evolution, v. 29, p. 347357.

M.M. Summers , C.G. Messing , and G.W. Rouse , 2014, Phylogeny of Comatulidae (Echinodermata: Crinoidea: Comatulida): A new classification and an assessment of morphological characters for crinoid taxonomy: Molecular Phylogenetics and Evolution, v. 80, p. 319339.

PJ. Wagner , 1998, A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa: Paleobiology, v. 24, p. 430449.

P.J. Wagner , 2000a, Phylogenetic analyses and the fossil record: Tests and inferences, hypotheses, and models: Paleobiology, v. 26, p. 341371.

P.J. Wagner , 2000b, The quality of the fossil record and the accuracy of phylogenetic inferences about sampling and diversity: Systematic Biology, v. 49, p. 6586.

P.J. Wagner , 2000c, Exhaustion of morphologic character states among fossil taxa: Evolution, v. 54, p. 365386.

P.J. Wagner , 2012, Modelling rate distributions using character compatibility: Implications for morphological evolution among fossil invertebrates: Biology Letters, v. 8, p. 143146.

P.J. Wagner , and J.D. Marcot , 2013, Modelling distributions of fossil sampling rates over time, space and taxa: Assessment and implications for macroevolutionary studies: Methods in Ecology and Evolution, v. 4, p. 703713.

G.D. Webster , and C.G. Maples , 2006, Cladid crinoid (Echinodermata) anal conditions: A terminology problem and proposed solution: Palaeontology, v. 49, p. 187212.

S. Weller , and A.D. Davidson , 1896, Petalocrinus mirabilis (n. sp.) and a new American fauna: Journal of Geology, v. 4, p. 166173.

W.C. Wheeler , and K.M. Pickett , 2007, Topology-Bayes versus Clade-Bayes in phylogenetic analysis: Molecular Biology and Evolution, v. 25, p. 447453.

A.M. Wright , and D.M. Hillis , 2014, Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data: PloS One, v. 9, e109210.

D.F. Wright , 2015, Fossils, homology, and “Phylogenetic Paleo-ontogeny”: A reassessment of primary posterior plate homologies among fossil and living crinoids with insights from developmental biology: Paleobiology, v. 41, p. 570591.

D.F. Wright , and A.L. Stigall , 2013, Phylogenetic revision of the Late Ordovician orthid brachiopod genera Plaesiomys and Hebertella from Laurentia: Journal of Paleontology, v. 87, p. 11071128.

D.F. Wright , W.I. Ausich , S.R. Cole , M.E. Peter , and E.C. Rhenburg , 2017, Phylogenetic taxonomy and classification of the Crinoidea: Journal of Paleontology, doi:10.1017/jpa.2016.142.

W. Xie , P.O. Lewis , Y. Fan , L. Kuo , and M.–H. Chen , 2010, Improving marginal likelihood estimation for Bayesian phylogenetic model selection: Systematic Biology, v. 60, p. 150160.

C. Zhang , T. Stadler , S. Klopfstein , T.A. Heath , and F. Ronquist , 2016, Total-evidence dating under the fossilized birth–death process: Systematic Biology, v. 65, p. 228249.

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