This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.
J. Alroy , 2010, Geographical, environmental and intrinsic biotic controls on Phanerozoic marine diversification: Palaeontology, v. 53, p. 1211–1235.
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. 1161–1173.
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. 345–361.
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. 937–952.
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. 724–733.
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. 379–389.
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. 660–673.
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. 2718–2726.
J.C. Brower , 1995, Dendrocrinid crinoids from the Ordovician of northern Iowa and southern Minnesota: Journal of Paleontology, v. 69, p. 939–960.
S.L. Brusatte , 2010, Representing supraspecific taxa in higher‐level phylogenetic analyses: Guidelines for palaeontologists: Palaeontology, v. 53, p. 1–9.
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. 1485–1488.
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. 311–325.
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. 185–201.
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. 2137–2142.
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. 214–236.
G. Didier , M. Royer-Carenzi , and M. Laurin , 2012, The reconstructed evolutionary process with the fossil record: Journal of Theoretical Biology, v. 315, p. 26–37.
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. 424–431.
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. 71–80.
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. 320–344.
M. Foote , 1996, On the probability of ancestors in the fossil record: Paleobiology, v. 22, p. 141–151.
M. Foote , 1997, Estimating taxonomic durations and preservation probability: Paleobiology, v. 23, p. 278–300.
M. Foote , 2000, Origination and extinction components of taxonomic diversity: General problems: Paleobiology, v. 26, p. 74–102.
M. Foote , and D.M. Raup , 1996, Fossil preservation and the stratigraphic ranges of taxa: Paleobiology, v. 22, p. 121–140.
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. 123–133.
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. 457–472.
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. 1209–1216.
T.E. Guensburg , 2012, Phylogenetic implications of the oldest crinoids: Journal of Paleontology, v. 86, p. 455–461.
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. 350–364.
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. 146–158.
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. 307–324.
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. E2957–E2966.
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. 360–377.
G. Hunt , and G. Slater , 2016, Integrating paleontological and phylogenetic approaches to macroevolution: Annual Review of Ecology, Evolution, and Systematics, v. 47, p. 189–213.
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. 700–710.
D. Jablonski , 2008, Biotic interactions and macroevolution: Extensions and mismatches across scales and levels: Evolution, v. 62, p. 715–739.
T.W. Kammer , 2001, Phenotypic bradytely in the Costalocrinus-Barycrinus lineage of Paleozoic cladid crinoids: Journal of Paleontology, v. 75, p. 383–389.
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. 461–480.
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. 835–866.
R.E. Kass , and A.E. Raftery , 1995, Bayes factors: Journal of the American Statistical Association, v. 90, p. 773–795.
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. 853–859.
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. 86–106.
M.S.Y. Lee , and A. Palci , 2015, Morphological phylogenetics in the genomic age: Current Biology, v. 25, p. R922–R929.
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. 442–449.
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. 2669–2680.
P.O. Lewis , 2001, A likelihood approach to estimating phylogeny from discrete morphological character data: Systematic Biology, v. 50, p. 913–925.
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. 330–348.
D.R. Maddison , 1991, The discovery and importance of multiple islands of most-parsimonious trees: Systematic Zoology, v. 40, p. 315–328.
N.J. Matzke , 2015, The evolution of antievolution policies after Kitzmiller v. Dover: Science, v. 351, p. 28–30, 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. 783–807.
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. 922–933.
, M.N. Puttick
, L. Parry
, A.R. Tanner
, J.E. Tarver
, J. Fleming
, D. Pisani
, and P.C.J. Donoghue
, Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data
: Biology Letters
, v. 12
E. Paradis , J. Claude , and K. Strimmer , 2004, APE: Analyses of phylogenetics and evolution in R language: Bioinformatics, v. 20, p. 289–290.
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. 23–32.
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. 225–241.
R.A. Pyron , 2011, Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia: Systematic Biology, v. 60, p. 466–481.
R.A. Pyron , 2015, Post-molecular systematics and the future of phylogenetics: Trends in Ecology and Evolution, v. 30, p. 384–389.
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. 735–743.
D.L. Rabosky , and A.R. McCune , 2009, Reinventing species selection with molecular phylogenies: Trends in Ecology and Evolution, v. 25, p. 68–74.
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. 304–311.
D.M. Raup , 1985, Mathematical models of cladogenesis: Paleobiology, v. 11, p. 42–52.
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. 525–542.
D.F. Robinson , and L.R. Foulds , 1981, Comparison of phylogenetic trees: Mathematical Biosciences, v. 53, p. 131–147.
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. 973–999.
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. 161–181.
J.J. Sepkoski Jr., 1981, A factor analytic description of the Phanerozoic marine fossil record: Paleobiology, v. 7, p. 36–53.
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. 734–744.
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. 4897–4902.
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. 699–702.
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. 365–382.
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. 525–553.
M.R. Spencer , and E.W. Wilberg , 2013, Efficacy or convenience? Model‐based approaches to phylogeny estimation using morphological data: Cladistics, v. 29, p. 663–671.
T. Stadler , 2010, Sampling-through-time in birth-death trees: Journal of Theoretical Biology, v. vol. 267, p. 396–404.
T. Stadler , and Z. Yang , 2013, Dating phylogenies with sequentially sampled tips: Systematic Biology, v. 62, p. 674–688.
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. 347–357.
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. 319–339.
PJ. Wagner , 1998, A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa: Paleobiology, v. 24, p. 430–449.
P.J. Wagner , 2000a, Phylogenetic analyses and the fossil record: Tests and inferences, hypotheses, and models: Paleobiology, v. 26, p. 341–371.
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. 65–86.
P.J. Wagner , 2000c, Exhaustion of morphologic character states among fossil taxa: Evolution, v. 54, p. 365–386.
P.J. Wagner , 2012, Modelling rate distributions using character compatibility: Implications for morphological evolution among fossil invertebrates: Biology Letters, v. 8, p. 143–146.
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. 703–713.
G.D. Webster , and C.G. Maples , 2006, Cladid crinoid (Echinodermata) anal conditions: A terminology problem and proposed solution: Palaeontology, v. 49, p. 187–212.
S. Weller , and A.D. Davidson , 1896,
Petalocrinus mirabilis (n. sp.) and a new American fauna: Journal of Geology, v. 4, p. 166–173.
W.C. Wheeler , and K.M. Pickett , 2007, Topology-Bayes versus Clade-Bayes in phylogenetic analysis: Molecular Biology and Evolution, v. 25, p. 447–453.
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. 570–591.
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. 1107–1128.
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. 150–160.
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. 228–249.