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Testing Character Evolution Models in Phylogenetic Paleobiology

A case study with Cambrian echinoderms

Published online by Cambridge University Press:  01 July 2021

April Wright
Affiliation:
Southeastern Louisiana University
Peter J. Wagner
Affiliation:
University of Nebraska, Lincoln
David F. Wright
Affiliation:
National Museum of Natural History (Smithsonian Institution)

Summary

Macroevolutionary inference has historically been treated as a two-step process, involving the inference of a tree, and then inference of a macroevolutionary model using that tree. Newer models blend the two steps. These methods make more complete use of fossils than the previous generation of Bayesian phylogenetic models. They also involve many more parameters than prior models, including parameters about which empiricists may have little intuition. In this Element, we set forth a framework for fitting complex, hierarchical models. The authors ultimately fit and use a joint tree and diversification model to estimate a dated phylogeny of the Cincta (Echinodermata), a morphologically distinct group of Cambrian echinoderms that lack the fivefold radial symmetrycharacteristic of extant members of the phylum. Although the phylogeny of cinctans remains poorly supported in places, this Element shows how models of character change and diversification contribute to understanding patterns of phylogenetic relatedness and testing macroevolutionary hypotheses.
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Online ISBN: 9781009049016
Publisher: Cambridge University Press
Print publication: 26 August 2021

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References

Allman, E. S., and Rhodes, J. A. 2008. Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites. Mathematical Biosciences, 211:1833.Google Scholar
Alroy, J. 2015. A more precise speciation and extinction rate estimator. Paleobiology, 41(4):633639. doi: https://doi.org/10.1017/pab.2015.26.Google Scholar
Alvaro, J. J., Lefebvre, B., Shergold, J. H., and Vizcaïno, D. 2001. The Middle–Upper Cambrian of the southern Montagne Noire. Annales de la Société Géologique du Nord (2e série), 8:205211.Google Scholar
Alvaro, J. J., Ferretti, A., González-Gómez, C., Serpagli, E., Tortello, M. F., Vecoli, M., and Vizcaïno, D. 2007. A review of the Late Cambrian (Furongian) palaeogeography in the western Mediterranean region, NW Gondwana. Earth-Science Reviews, 85(1):4781. doi: https://doi.org/10.1016/j.earscirev.2007.06.006.Google Scholar
Aris-Brosou, S., and Yang, Z. 2002. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18s ribosomal RNA phylogeny. Systematic Biology, 51(5):703714.Google Scholar
Baele, G., and Lemey, P. 2013. Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. Bioinformatics, 29(16):19701979.Google Scholar
Bapst, D. W. 2013. A stochastic rate-calibrated method for time-scaling phylogenies of fossil taxa. Methods in Ecology and Evolution, 4(8):724733. ISSN 2041-210X. doi: https://doi.org/10.1111/2041-210X.12081.Google Scholar
Barido-Sottani, J., Aguirre-Fernández, G., Hopkins, M. J., Stadler, T., and Warnock, R. 2019. Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth–death process. Proceedings of the Royal Society B, 286(1902): 20190685.Google Scholar
Barido-Sottani, J., Justison, J. A., Wright, A. M., Warnock, R. C. M., Pett, W., and Heath, T. A. 2020a. Estimating a time-calibrated phylogeny of fossil and extant taxa using RevBayes. In Scornavacca, Céline, Delsuc, Frédéric, and Galtier, Nicolas, editors, Phylogenetics in the Genomic Era, pages 5.2:1–5.2:23. No commercial publisher — Authors’ open access book. https://hal.archives-ouvertes.fr/hal-02536394.Google Scholar
Barido-Sottani, J., van Tiel, N., Hopkins, M. J., Wright, D. F., Stadler, T., and Warnock, R. C. M. 2020b. Ignoring fossil age uncertainty leads to inaccurate topology and divergence time estimates using time calibrated tree inference. Frontiers in Ecology and Evolution, 8:123. doi: https://doi.org/10.3389/fevo.2020.00183.Google Scholar
Bergström, S. M., Chen, X., Gutiérrez-Marco, J. C., and Dronov, A. 2009. The new chronostratigraphic classification of the ordovician system and its relations to major regional series and stages and to δ13 C chemostratigraphy. Lethaia, 42(1):97107. doi: https://doi.org/10.1111/j.1502-3931.2008.00136.x.CrossRefGoogle Scholar
Blomberg, S. P., Garland, T. Jr, and Ives, A. R. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57(4):717745. doi: https://doi.org/10.1111/j.0014-3820.2003.tb00285.x.Google Scholar
Bottjer, D. J., and Jablonski, D. 1988. Paleoenvironmental patterns in the evolution of post-Paleozoic benthic marine invertebrates. Palaios, 3:540560. doi: https://doi.org/10.2307/3514444.Google Scholar
Bottjer, D. J., Davidson, E. H., Peterson, K. J., and Cameron, R. A. 2006. Paleogenomics of echinoderms. Science, 314(5801):956960.Google Scholar
Bromham, L., Rambaut, A., and Harvey, P. H. 1996. Determinants of rate variation in mammalian DNA sequence evolution. Journal of Molecular Evolution, 43(6):610621.Google Scholar
Bromham, L., Woolfit, M., Lee, M. S. Y., and Rambaut, A. 2002. Testing the relationship between morphological and molecular rates of change along phylogenies. Evolution, 56(10):19211930. doi: https://doi.org/10.1111/j.0014-3820.2002.tb00118.x.Google ScholarPubMed
Bromham, L., Hua, X., Lanfear, R., and Cowman, P. F. 2015. Exploring the relationships between mutation rates, life history, genome size, environment, and species richness in flowering plants. The American Naturalist, 185(4):507524.Google Scholar
Brusca, R. C., and Brusca, G. J. 2003. Invertebrates. Number QL 362. B78 2003. Basingstoke. Sinauer Associates, Sunderland, Massachusetts.Google Scholar
Chlupac, I., Havlicek, V., Kríž, J., Kukal, Z., and Storch, P. 1998. Palaeozoic of the Barrandian (Cambrian to Devonian). Czech Geological Survey, Prague.Google Scholar
Ciampaglio, C. N. 2002. Determining the role that ecological and developmental constraints play in controlling disparity: examples from the crinoid and blastozoan fossil record. Evolution and Development, 4(3):170188. doi: https://doi.org/10.1046/j.1525-142X.2002.02001.x.Google Scholar
Cramer, B. D., Brett, C. E., Melchin, M. J., Männik, P., Kleffner, M. A., McLaughlin, P. I., Loydell, D. K., Munnecke, A., Jeppsson, L., Corradini, C., Brunton, F. R., and Saltzman, M. R. 2011. Revised correlation of Silurian provincial series of North America with global and regional chronostratigraphic units and δ13Ccarb chemostratigraphy. Lethaia, 44(2):185202. doi: https://doi.org/10.1111/j.1502-3931.2010.00234.x.Google Scholar
David, B., Lefebvre, B., Mooi, R., and Parsley, R. 2000. Are homalozoans echinoderms? An answer from the extraxial-axial theory. Paleobiology, 26(4): 529555.Google Scholar
Drummond, A. J., and Rambaut, A. 2007. BEAST: Bayesian evolutionary analysis sampling trees. BMC Evolutionary Biology, 7:214.Google Scholar
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., and Rambaut, A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology, 4(5):e88.CrossRefGoogle ScholarPubMed
Drummond, A. J., and Stadler, T. 2016. Bayesian phylogenetic estimation of fossil ages. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1699):20150129.Google Scholar
Duchêne, D. A., Duchêne, S., Holmes, E. C., and Ho, S. Y. W. 2015. Evaluating the adequacy of molecular clock models using posterior predictive simulations. Molecular Biology and Evolution, 32(11):29862995.Google Scholar
Eldredge, N. 1971. The allopatric model and phylogeny in paleozoic invertebrates. Evolution, 25(1):156167. doi: https://doi.org/10.2307/2406508.Google Scholar
Eldredge, N., and Gould, S. J. 1972. Punctuated equilibria: an alternative to phyletic gradualism, book section 82, pages 82115. Freeman, San Francisco.Google Scholar
Felsenstein, J. 1978. The number of evolutionary trees. Systematic Zoology, 27(1):2733. ISSN 00397989.Google Scholar
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6): 368376.CrossRefGoogle ScholarPubMed
Foote, M. 1992. Paleozoic record of morphological diversity in blastozoan echinoderms. Proceedings of the National Academy of Sciences, USA, 89(16):73257329. doi: https://doi.org/10.1073/pnas.89.16.7325.Google Scholar
Foote, M. 1993. Discordance and concordance between morphological and taxonomic diversity. Paleobiology, 19(2):185204. doi: https://doi.org/10.2307/2400876.Google Scholar
Foote, M. 1994. Morphological disparity in Ordovician–Devonian crinoids and the early saturation of morphological space. Paleobiology, 20(3):320344. doi: https://doi.org/10.2307/2401006.Google Scholar
Foote, M. 1996a. Ecological controls on the evolutionary recovery of post–paleozoic crinoids. Science, 274(5292):14921495. doi: https://doi.org/10.1126/science.274.5292.1492.Google Scholar
Foote, M. 1996b. Models of morphologic diversification, book section 62, pages 6286. University of Chicago Press, Chicago.Google Scholar
Foote, M. 1996c. On the probability of ancestors in the fossil record. Paleobiology, 22(2):141151. doi: https://doi.org/10.1666/0094-8373-22.2.141.CrossRefGoogle Scholar
Foote, M. 2016. On the measurement of occupancy in ecology and paleontology. Paleobiology, 42:707729. doi: https://doi.org/10.1017/pab.2016.24.Google Scholar
Foote, M., and Sepkoski, J. J. Jr. 1999. Absolute measures of the completeness of the fossil record. Nature, 398:415417. doi: https://doi.org/10.1038/18872.Google Scholar
Foote, M. 1997. Estimating taxonomic durations and preservation probability. Paleobiology, 23(3):278300.Google Scholar
Friedrich, W. P. 1993. Systematik und Funktionsmorphologie mittelkambrischer Cincta (Carpoidea, Echinodermata). Beringeria, 7.Google Scholar
Gaut, B. S., Muse, S. V., Clark, W. D., and Clegg, M. T. 1992. Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants. Journal of Molecular Evolution, 35(4):292303.CrossRefGoogle ScholarPubMed
Gavryushkina, A., Heath, T. A., Ksepka, D. T., Stadler, T., Welch, D., and Drummond, A. J. 2017. Bayesian total-evidence dating reveals the recent crown radiation of penguins. Systematic Biology, 66(1):5773.Google Scholar
Geyer, G. 2019. A comprehensive Cambrian correlation chart. International Union of Geological Sciences, 42(4):321332. doi: https://doi.org/10.18814/epiiugs/2019/019026.Google Scholar
Geyer, G., and Landing, E. 2006. Ediacaran–Cambrian depositional environments and stratigraphy of the western atlas regions. Beringeria Special Issue, 6: 47120.Google Scholar
Geyer, G., and Shergold, J. 2000. The quest for internationally recognized divisions of Cambrian time. Episodes, 23(3):188195.Google Scholar
Gradstein, F. M., Ogg, J. G., and Schmitz, M. 2012. The geologic time scale 2012, Volume 2. Elsevier, Amsterdam.Google Scholar
Gradstein, F. M., Ogg, J. G., Schmitz, M. D., and Ogg, G. M. 2020. Geologic time scale 2020. Elsevier, Amsterdam. ISBN 978-0-12-824360-2. doi: https://doi.org/10.1016/C2020-1-02369-3.Google Scholar
Harvey, P. H., and Pagel, M. D. 1991. The comparative method in evolutionary biology, Volume 239. Oxford University Press, Oxford.Google Scholar
Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating of the human–ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22(2):160174.Google Scholar
Heath, T. A., Huelsenbeck, J. P., and Stadler, T. 2014. The fossilized birth–death process for coherent calibration of divergence-time estimates. Proceedings of the National Academy of Sciences, 111(29):E2957E2966.Google Scholar
Hopkins, M. J., and Smith, A. B. 2015. Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution. Proceedings of the National Academy of Sciences, 112(2):37583763. doi: https://doi.org/10.1073/pnas.1418153112.Google Scholar
Huelsenbeck, J. P., Larget, B., and Swofford, D. L. 2000. A compound Poisson process for relaxing the molecular clock. Genetics, 154:18791892.Google Scholar
Hughes, M., Gerber, S., and Wills, M. A. 2013. Clades reach highest morphological disparity early in their evolution. Proceedings of the National Academy of Sciences, 110(34):1387513879. doi: https://doi.org/10.1073/pnas.1302642110.Google Scholar
Jablonski, D. 2020. Macroevolutionary theory, book section 338, pages 338368. University of Chicago Press, Chicago.Google Scholar
Kass, R. E., and Raftery, A. E. 1995. Bayes factors. Journal of the American Statistical Association, 90:773795.Google Scholar
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2):111120.Google Scholar
King, B., and Beck, Robin. M. D. 2020. Tip dating supports novel resolutions of controversial relationships among early mammals. Proceedings of the Royal Society B: Biological Sciences, 287(1928):20200943. doi: https://doi.org/10.1098/rspb.2020.0943.Google Scholar
LaPolla, J. S., Dlussky, G. M., and Perrichot, V. 2013. Ants and the fossil record. Annual Review of Entomology, 58(1):609630. doi: https://doi.org/10.1146/annurev-ento-120710-100600.Google Scholar
Lefebvre, B., Guensburg, T. E., Martin, E. L., Rich, M., Elise, N., Nohejlová, M., Saleh, F., Kouraïss, K., Khadija, E. H., and David, B. 2019. Exceptionally preserved soft parts in fossils from the Lower Ordovician of Morocco clarify stylophoran affinities within basal deuterostomes. Geobios, 52:2736.Google Scholar
Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50(6):913925.Google Scholar
Liñán, E., Perejón, A., Gozalo, R., Moreno-Eiris, E., and de Oliveira, J. T. 2004. The Cambrian system in Iberia. Cuadernos del Museo Geominero, 3: 163.Google Scholar
Lewis, L. H. 2013. Simultaneous estimation of occupancy and detection probabilities: an illustration using Cincinnatian brachiopods. Paleobiology, 39(2):193213. ISSN 0094–8373. doi: https://doi.org/10.1666/12009.Google Scholar
Liow, L. H., Quental, T. B., and Marshall, C. R. 2010. When can decreasing diversification rates be detected with molecular phylogenies and the fossil record? Systematic Biology, 59(6):646.Google Scholar
Marshall, C. R. 2017. Five palaeobiological laws needed to understand the evolution of the living biota. Nature Ecology Evolution, 1(6):0165. doi: https://doi.org/10.1038/s41559-017-0165.Google Scholar
Nardin, E., Lefebvre, B., Fatka, O., Nohejlová, M., Kašička, L., Šinágl, M., and Szabad, M. 2017. Evolutionary implications of a new transitional blastozoan echinoderm from the Middle Cambrian of the Czech Republic. Journal of Paleontology, 91(4):672684. doi: https://doi.org/10.1017/jpa.2016.157.Google Scholar
Nichols, D. 1972. The water-vascular system in living and fossil echinoderms. Palaeontology, 15:519538.Google Scholar
Nowak, M. D., Smith, A. B., Simpson, C., and Zwickl, D. J. 2013. A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses. PLoS One, 8(6): e66245.Google Scholar
Nylander, J. A. A., Ronquist, F., Huelsenbeck, J. P., and Nieves-Aldrey, J. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology, 53(1):4767.Google Scholar
Poinar, G. O., and Mastalerz, M. 2000. Taphonomy of fossilized resins: determining the biostratinomy of amber. Acta Geologica Hispanica, 35(1): 171182.Google Scholar
Posada, D., and Crandall, K. A. 1998. Modeltest: testing the model of dna substitution. Bioinformatics (Oxford, England), 14(9): 817818.Google Scholar
Quental, T. B., and Marshall, C. R. 2009. Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution, 63(12):31583167.Google Scholar
Quental, T. B., and Marshall, C. R. 2010. Diversity dynamics: molecular phylogenies need the fossil record. Trends in Ecology & Evolution, 25:434441.Google Scholar
Rahman, I. A., Zamora, S., Falkingham, P. L., and Phillips, J. C. 2015. Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome. Proceedings of the Royal Society B: Biological Sciences, 282(1818): 20151964.Google Scholar
Rahman, I. A. 2009. Making sense of carpoids. Geology Today, 25(1): 3438.Google Scholar
Rahman, I. A. 2016. Fossil focus: Cinctans. Palaeontology Online, 6(4): 17.Google Scholar
Rahman, I. A., O’Shea, J., Lautenschlager, S., and Zamora, S. 2020. Potential evolutionary trade-off between feeding and stability in Cambrian cinctan echinoderms. Palaeontology, 63(5):689701. ISSN 0031–0239. doi: https://doi.org/10.1111/pala.12495.Google Scholar
Rahman, I. A., Sutton, M. D., and Bell, M. A. 2009. Evaluating phylogenetic hypotheses of carpoids using stratigraphic congruence indices. Lethaia, 42(4):424437. doi: https://doi.org/10.1111/j.1502-3931.2009.00161.x.Google Scholar
Rahman, I. A., and Zamora, S. 2009. The oldest cinctan carpoid (stem-group echinodermata), and the evolution of the water vascular system. Zoological Journal of the Linnean Society, 157(2):420432. doi: https://doi.org/10.1111/j.1096-3642.2008.00517.x.Google Scholar
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., and Suchard, M. A. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67(5):901904. ISSN 1063–5157. doi: https://doi.org/10.1093/sysbio/syy032.Google Scholar
Rasmussen, C. M. Ø., Kröger, B., Nielsen, M. L., and Colmenar, J. 2019. Cascading trend of Early Paleozoic marine radiations paused by Late Ordovician extinctions. Proceedings of the National Academy of Sciences, 116(15):72077213. doi: https://doi.org/10.1073/pnas.1821123116.Google Scholar
Sánchez-Villagra, M. R., and Williams, B. A. 1998. Levels of homoplasy in the evolution of the mammalian skeleton. Journal of Mammalian Evolution, 5(2):113126. doi: https://doi.org/10.1023/A:1020549505177.Google Scholar
Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19(1):101109.Google Scholar
Sdzuy, K. 1993. Early cincta (carpoidea) from the Middle Cambrian of Spain. Beringia, 8:189207.Google Scholar
Sepkoski, J. J. Jr. 1981. A factor analytic description of the Phanerozoic marine fossil record. Paleobiology, 7(1):3653. doi: https://doi.org/10.1017/S0094837300003778.Google Scholar
Sheffield, S. L., and Sumrall, C. D. 2019. The phylogeny of the diploporita: a polyphyletic assemblage of blastozoan echinoderms. Journal of Paleontology, 93(4):740752.Google Scholar
Smith, A. B., and Zamora, S. 2009. Rooting phylogenies of problematic fossil taxa: a case study using cinctans (stem-group echinoderms). Palaeontology, 52(4):803821. doi: https://doi.org/10.1111/j.1475-4983.2009.00880.x.Google Scholar
Smith, A. B., and Zamora, S. 2013. Cambrian spiral-plated echinoderms from Gondwana reveal the earliest pentaradial body plan. Proceedings of the Royal Society B: Biological Sciences, 270(1765):20131197.Google Scholar
Smith, A. B., Zamora, S., and Álvaro, J. J. 2013. The oldest echinoderm faunas from Gondwana show that echinoderm body plan diversification was rapid. Nature Communications, 4(1):17.Google Scholar
Smith, A. B. 2005. The pre-radial history of echinoderms. Geological Journal, 40(3):255280.Google Scholar
Smith, A. B., and Swalla, B. J. 2009. Deciphering deuterostome phylogeny: molecular, morphological, and palaeontological perspectives. In Telford, M. J., and Littlewood, D. T. J., editors, Animal Evolution: Genomes, Fossils and Trees, pages 8092. Oxford University Press, Oxford.Google Scholar
Sprinkle, J., and Collins, D. 2006. New eocrinoids from the Burgess Shale, southern British Columbia, Canada, and the Spence Shale, northern Utah, USA. Canadian Journal of Earth Sciences, 43(3):303322. doi: https://doi.org/10.1139/e05-107.Google Scholar
Sprinkle, J. 1973. Morphology and evolution of blastozoan echinoderms. Harvard University, Museum of Comparative Zoology, Special Publication, Cambridge, MA, pages 1283.Google Scholar
Sprinkle, J., and Kier, P. M. 1987. Phylum Echinodermata, pages 550611. In Boardman, R. S., Cheetham, A. H., and Rowell, A. J. (eds.), Fossil Invertebrates. Blackwell Scientific Publications, Palo Alto, CaliforniaGoogle Scholar
Stadler, T. 2011. Mammalian phylogeny reveals recent diversification rate shifts. Proceedings of the National Academy of Sciences, 108(15): 61876192.Google Scholar
Stadler, T., Kühnert, D., Bonhoeffer, S., and Drummond, A. J. 2013. Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences, 110(1):228233.Google Scholar
Sumrall, C. D. 1997. The role of fossils in the phylogenetic reconstruction of echinodermata. The Paleontological Society Papers, 3:267288.Google Scholar
Sumrall, C. D., and Waters, J. A. 2012. Universal elemental homology in glyptocystitoids, hemicosmitoids, coronoids and blastoids: steps toward echinoderm phylogenetic reconstruction in derived blastozoa. Journal of Paleontology, 86:956927.Google Scholar
Tavaré, S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Some Mathematical Questions in Biology: DNA Sequence Analysis, 17:5786.Google Scholar
Termier, H., and Termier, G. 1973. Les echinodermes cincta du cambriende la Montagne Noire (France). Geobios, 6(4):243265. doi: https://doi.org/10.1016/S0016-6995(73)80019-1.Google Scholar
Thomas, J. A., Welch, J. J., Woolfit, M., and Bromham, L. 2006. There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proceedings of the National Academy of Sciences, 103(19):73667371.Google Scholar
Valentine, J. W. 1980. Determinants of diversity in higher taxonomic categories. Paleobiology, 6(4):444450.Google Scholar
Valentine, J. W. et al. 1969. Patterns of taxonomic and ecological structure of the shelf benthos during Phanerozoic time. Palaeontology, 12(4): 684709.Google Scholar
Wagner, P. 2021. PaleoDB for RevBayes Webinar: PBDB for RevBayes v01.0. January. doi: https://doi.org/10.5281/zenodo.4426555.Google Scholar
Wagner, P. J. 1995. Testing evolutionary constraint hypotheses with early paleozoic gastropods. Paleobiology, 21(3):248272. doi: https://doi.org/10.2307/2401166.Google Scholar
Wagner, P. J. 2019. On the probabilities of branch durations and stratigraphic gaps in phylogenies of fossil taxa when rates of diversification and sampling vary over time. Paleobiology, 28(1):3055. doi: https://doi.org/10.1017/pab.2018.35.Google Scholar
Wagner, P. J., and Erwin, D. H. 1995. Phylogenetic patterns as tests of speciation models, book section 87, pages 87122. Columbia University Press, New York.Google Scholar
Wagner, P. J., and Estabrook, G. F. 2015. The implications of stratigraphic compatibility for character integration among fossil taxa. Systematic Biology, 64(5):838852. doi: https://doi.org/10.1093/sysbio/syv040.Google Scholar
Wagner, P. J., and Marcot, J. D. 2010. Probabilistic phylogenetic inference in the fossil record: current and future applications, Volume 16, book section 195, pages 195217. Paleontological Society, New Haven, CT.Google Scholar
Wagner, P. J., and Marcot, J. D. 2013. Modelling distributions of fossil sampling rates over time, space and taxa: assessment and implications for macroevolutionary studies. Methods in Ecology and Evolution, 4 (8):703713. doi: https://doi.org/10.1111/2041-210X.12088.Google Scholar
Warnock, R. C., and Wright, A. M. (2021). Understanding the tripartite approach to Bayesian divergence time estimation. Cambridge University Press.Google Scholar
Wright, A. M., and Hillis, D. M. 2014. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLoS One, 9(10):e109210.Google Scholar
Wright, A. M., Lloyd, G. T., and Hillis, D. M. 2016. Modeling character change heterogeneity in phylogenetic analyses of morphology through the use of priors. Systematic Biology, 65(4):602611.Google Scholar
Wright, D. F. 2017a. Phenotypic innovation and adaptive constraints in the evolutionary radiation of Palaeozoic crinoids. Scientific Reports, 7(1):13745. doi: https://doi.org/10.1038/s41598-017-13979-9.Google Scholar
Wright, D. F. 2017b. Bayesian estimation of fossil phylogenies and the evolution of Early to Middle Paleozoic crinoids (echinodermata). Journal of Paleontology, 91(4):799814.Google Scholar
Wright, D. F., Ausich, W. I., Cole, S. R., Peter, M. E., and Rhenberg, E. C. 2017. Phylogenetic taxonomy and classification of the crinoidea (echinodermata). Journal of Paleontology, 91(4):829846.Google Scholar
Wright, D. F., and Toom, U. 2017. New crinoids from the Baltic region (Estonia): fossil tip-dating phylogenetics constrains the origin and Ordovician–Silurian diversification of the flexibilia (echinodermata). Palaeontology, 60(6):893910.Google Scholar
Xie, W., Lewis, P. O., Fan, Y., Kuo, L., and Chen, M. H. 2011. Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic Biology, 60(2):150160.Google Scholar
Zamora, S. 2009. Equinodermos del Cámbrico medio de las Cadenas Ibéricas y de la zona Cantábrica (Norte de España). Thesis.Google Scholar
Zamora, S., and Álvaro, J. J. 2010. Testing for a decline in diversity prior to extinction: Languedocian (latest mid-Cambrian) distribution of cinctans (echinodermata) in the Iberian Chains, NE Spain. Palaeontology, 56(6): 13491368.Google Scholar
Zamora, S., Lefebvre, B., Álvaro, J. J., Clausen, S., Elicki, O., Fatka, O., Jell, P., Kouchinsky, A., Lin, J. P., Nardin, E., and Parsley, R. 2013a. Cambrian echinoderm diversity and palaeobiogeography. Geological Society of London, Memoirs, 38(1):157171.Google Scholar
Zamora, S., Rahman, I. A., and Smith, A. B. 2012. Plated Cambrian bilaterians reveal the earliest stages of echinoderm evolution. PLoS One, 7(6):e38296.Google Scholar
Zamora, S., and Smith, A. B. 2008. A new Middle Cambrian stem-group echinoderm from Spain: Palaeobiological implications of a highly asymmetric cinctan. Acta Palaeontologica Polonica, 53(2):207220.Google Scholar
Zamora, S., and Rahman, I. A. 2014. Deciphering the early evolution of echinoderms with Cambrian fossils. Palaeontology, 57(6): 11051119.Google Scholar
Zamora, S., and Rahman, I. A. 2015. Palaeobiological implications of a mass-mortality assemblage of cinctans (echinodermata) from the Cambrian of Spain. In Zamora, S., and Rábano, I., editors, Progress in Echinoderm Paleobiology, pages 203206. Instituto Geológico y Minero de España.Google Scholar
Zamora, S., Rahman, I. A., and Smith, A. B. 2013b. The ontogeny of cinctans (stem-group echinodermata) as revealed by a new genus, graciacystis, from the Middle Cambrian of Spain. Palaeontology, 56(2): 399410. doi: https://doi.org/10.1111/j.1475-4983.2012.01207.x.Google Scholar
Zamora, S., Wright, D. F., Mooi, R., Lefebvre, B., Guensburg, T. E., Gorzelak, P., David, B., Sumrall, C. D., Cole, S. R., Hunter, A. W., Sprinkle, J., Thompson, J. R., Ewin, T. A. M., Fatka, O., Nardin, E., Reich, M., Nohejlová, M., and Rahman, I. 2020. Re-evaluating the phylogenetic position of the enigmatic Early Cambrian deuterostome yanjiahella. Nature Communications, 11(1): 1286.Google Scholar
Zwickl, D. J., and Holder, M. T. 2004. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Systematic Biology, 53(6):877888.Google Scholar

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