in press



The early Cambrian fossil embryo
Pseudooides is a direct developing cnidarian, not an early ecdysozoan
Duan, B., Dong, X.-P., Porras, L., Vargas, K., Cunningham, J. E.., Donoghue, P.C.J. (in press) Proceedings of the Royal Society B: Biological Sciences

The efficacy of consensus tree methods for summarising phylogenetic relationships from a posterior samples of tree estimated from morphological data
O’Reilly, J.E., Donoghue, P.C.J. (in press) Systematic Biology
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Ediacaran developmental biology
Dunn, F.S., Liu, A.G., Donoghue, P.C.J. (in press) Biological Reviews
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Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data
O’Reilly, J.E., Puttick, M.N., Pisani, D., Donoghue, P.C.J. (in press) Palaeontology
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2017


Constraining the timing of whole genome duplication in plant evolutionary history
Clark, J.W. and Donoghue, P.C.J (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20170912
PDF | Data

The origin of animals: can evidence from molecular clocks and the fossil record be reconciled?
Cunningham, J.E., Liu, A., Bengtson, S., Donoghue, P.C.J (2017) Bioessays 39: 1600120
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The Weng’an Biota (Doushantuo Formation): an Ediacaran window on soft bodied and multicellular microorganisms
Cunningham, J.A., Vargas, K., Yin, Z., Bengtson, S., Donoghue, P.C.J (2017) Journal of the Geological Society
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Open data and digital morphology
Davies, T.G., Rahman, I.A., Lautenschlager, S., Cunningham, J.A.,Asher, R.J., Barrett, P.M., Bates, K.T., Bengtson, S., Benson, R.B.J., Boyer, D.M., Braga, J., Bright, J.A., Claessens, L.P.A.M., Cox, P.G., Dong, X.P., Evans, A.R., Falkingham, P.L., Friedman, M., Garwood, R.J., Goswami, A., Hutchinson, J.R., Jeffery, N.S., Johanson, Z., Lebrun, R., Martínez-Pérez, C., Marugán-Lobón, J., O’Higgins, P.M., Metscher, B., Orliac, M., Rowe, T.B., Rücklin, M., Sánchez-Villagra, M.R., Shubin, N.H., Smith, S.Y., Starck, J.M., Stringer, C., Summers, A.P., Sutton, M.D., Walsh, S.A., Weisbecker, V., Witmer, L.M., Wroe, S., Yin, Z., Rayfield, E.J., Donoghue, P.C.J (2017) Proceedings of the Royal Society B: Biological Sciences 284: 2017.0194
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Divining the nature of the ancestral vertebrate

Donoghue, P.C.J (2017) Current Biology 27: R277-279
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RelTime rates collapse to a strict clock when estimating the timeline of animal diversification
Lozano-Fernandez, J., dos Reis, M., Donoghue, P.C.J. and Pisani, D. (2017) Genome Biology & Evolution
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Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data
Puttick, M.N., O’Reilly, J.E., Tanner, A.R., Fleming, J., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L., Tarver, J.E., Pisani, D. and Donoghue, P.C.J. (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20162290
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Parsimony and Maximum Likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history
Puttick, M.N., O’Reilly, J.E., Oakley, D., Tanner, A.R., Fleming, J., Clark, J., Holloway, L., Lozano-Fernandez, J., Parry, L., Tarver, J.E., Pisani, D. and Donoghue, P.C.J. (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20171636
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microRNA annotation in draft plant genomes - do it right or not at all
Taylor, R.S., Tarver, J.E., Foroozani, A., Donoghue, P.C.J (2017) Bioessays 39: 1600113

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Testing the molecular clock using mechanistic models of both fossil preservation and molecular evolution
Warnock, R.C.M., Yang, Z., Donoghue, P.C.J (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20170277
PDF | Code | Data

Nuclei and nucleoli in embryo-like fossils from the Ediacaran Weng’an Biota
Yin, Z., Cunningham, J.A., Vargas, K., Bengtson, S., Zhu, M., Donoghue, P.C.J. (2017) Precambrian Research 301: 145-151
PDF | Data



2016


A multicellular organism with embedded cellular clusters from the Ediacaran Weng’an Biota
Cunningham, J.E., Vargas, K., Marone, F., Bengtson, S.E. and Donoghue, P.C.J (2016) Evolution & Development 18: 308-316
PDF | Tomo Data

Tectonic blocks and molecular clocks
de Baets, K., Antonelli, A. and Donoghue, P.C.J (2016) Philosophical Transactions of the Royal Society, Series B-Biological Sciences 371: 20160098
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Developmental biology of the early Cambrian cnidarian Olivooides
Dong, X.-P-., Vargas, K., Cunningham, J.A., Zhang, H.-Q., Liu, T., Chen, F., Liu, J.-B., Bengtson, S., Donoghue, P.C.J. (2016) Palaeontology DOI: 10.1111/pala.12231
PDF | Dryad_button_v1 | Tomo Data

The evolution of methods for establishing evolutionary timescales
Donoghue, P.C.J and Yang, Z. (2016) Philosophical Transactions of the Royal Society, Series B-Biological Sciences 371: 20160020
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Bayesian molecular clock dating of species divergences in the genomic era
dos Reis, M., Yang, Z., Donoghue, P.C.J. (2016) Nature Reviews Genetics 17: 71-80
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Pigmented anatomy in Carboniferous cyclostomes, and the evolution of the vertebrate eye
Gabbott, S.E., Donoghue, P.C.J. Sansom, R.S., Vintner, J., Dolman, A., Purnell, M.A. (2016) Proceedings of the Royal Society B: Biological Sciences 283: 20161151
PDF | Dryad_button_v1

Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton
Keating, J. N. and Donoghue, P.C.J. (2016) Proceedings of the Royal Society B: Biological Sciences 283:20152917
PDF | Dryad_button_v1 | Tomo Data |

Evolution of the calcium-based intracellular signalling system
Marchadier, E., Oates, M. E., Fang, H., Donoghue, P.C.J., Hetherington, A. M., Gough, J. (2016) Genome Biology and Evolution 8:2118-2132
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Translating taxonomy into the evolution of conodont feeding ecology
Martínez-Perez, C., Rayfield, E. J., Botella, H., Donoghue, P.C.J. (2016) Geology 44: 247-250
PDF | Tomo Data

Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks
O’Reilly, J. E. and Donoghue, P.C.J (2016) Biology Letters 12: 20150975
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Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data
O’Reilly, J.E., Puttick, M.N., Parry, L., Tanner, A.R., Tarver, J.E., Fleming, J., Pisani, D. and Donoghue, P.C.J. (2016) Biology Letters 12: 20160081
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Response to “Placoderms and the evolutionary origin of teeth”: Burrow et al. (2016)
Rücklin, M., Donoghue, P.C.J (2016) Biology Letters 12: 20160526
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The interrelationships of placental mammals and the limits of phylogenetic inference
Tarver, J. E., dos Reis, M., King, B. L., Mirarab, S., O’Connell, M. J., Moran, R. J., Asher, R. J., Parker, S., Warnow, T., Peterson, K. J., Donoghue, P.C.J., Pisani, D. (2016) Genome Biology and Evolution 8: 330-344
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Dating species divergences using rocks and clocks
Yang, Z. and Donoghue, P.C.J. (2016) Philosophical Transactions of the Royal Society, Series B-Biological Sciences 371: 20150126
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2015


Constraints on the timescale of animal evolutionary history
Benton, M. J., Donoghue, P. C. J., Asher, R. J., Friedman, M., Near, T. J., Vinther, J. (2015) Paleontologica Electronica 18.1.1FC
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Experimental taphonomy of
Artemia reveals the role of endogenous microbes in mediating decay and fossilization
Butler, A. D., Cunningham, J. A., Budd, G. E. and Donoghue, P. C. J. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20150476
PDF | Dryad_button_v1

Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng’an Doushantuo biota
Cunningham, J. A., Vargas, K., Liu, Pengju, Belivanova, V., Marone, F., Martínez-Pérez, C., Guizar-Sicairos, M., Holler, M., Bengtson, S., Donoghue, P. C. J. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20151169
PDF | Data

Constraining the deep origin of parasitic flatworms and host interactions with fossil evidence
de Baets, K., Dentzien-Dias, P., Upeniece, I., Verneau, O., Donoghue, P. C. J. (2015) Advances in Parasitology 90:
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Embryology in deep time
Donoghue, P. C. J., Cunningham, J. E., Dong, X.-P. and Bengtson, S. (2015). pp. 45-63. In Wanninger, A. (ed.) Evolutionary developmental biology of invertebrates !: Introduction, non-Bilateria, Acoelomorpha, Xenoturbellida, Chaetognatha. Springer Verlag, Vienna.
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The ins and outs of the evolutionary origin of teeth
Donoghue, P. C. J. and Rücklin, M. (2015) Evolution & Development doi:10.1111/ede.12099
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Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales
dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, M.J., Donoghue, P.C.J., Yang, Z. (2015) Current Biology 25: 2939-2950
PDF | Dispatch

Ptychographic nanotomography at the Swiss Light Source
Guizar-Sicairos, M., Holler, M., Diaz, A., da Silva, J.C., Tsai, E.H.R., Bunk, O., Martinez-Perez, C., Donoghue, P.C.J., Wellman, C.H., Menze, A. (2015). In. Lai, B (ed) X-Ray Nanoimaging: Instruments and Methods II. SPIE Proceedings 9592: 95920A-1
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Do cladistic and morphometric data capture common patterns of morphological disparity?
Hetherington, A. J., Sherratt, E., Ruta, M., Wilkinson, M., Deline, B. and Donoghue, P. C. J. (2015) Palaeontology 58: 393-399
PDF | Dryad_button_v1

Histology of the heterostracan dermal skeleton: insight into the origin of the vertebrate mineralized skeleton
Keating, J. N., Marquart, C. L. and Donoghue, P. C. J. (2015) Journal of Morphology 276: 657-680
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The fossil calibration database, a new resource for divergence dating
Kspeka, D., Parham, J. D., Allman, J., Benton, M. J., Carrano, M, Cranston, K., Donoghue, P. C. J. Head, J., Hermsen, E., Irmis, R., Joyce, W., Kohli, M., Lamm, K., Leehr, D., Patane, J., Polly, P. D., Phillips, M., Smith, N., van Tuinen, M., Ware, J., Warnock, R. C. M. (2015) Systematic Biology 64: 853-859.
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Dating tips for divergence time estimation
O’Reilly, J., dos Reis, M., Donoghue, P.C.J. (2015) Trends in Genetics 31: 637-650.
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Size isn’t everything: rates of genome size evolution, not C value, correlate with speciation in angiosperms
Puttick, M., Clark, J., Donoghue, P.C.J. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20152289
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Romundina and the evolutionary origin of teeth
Rücklin, M. and Donoghue, P. C. J. (2015) Biology Letters 8: 833-837
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Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history
Sansom, R. S., Randle, E. and Donoghue, P. C. J. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20142245
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Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils
Schirrmeister, B. E., and Donoghue, P. C. J. (2015) Palaeontology doi:10.1111/pala.12178
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Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
Warnock, R. C. M., Parham, J. F., Joyce, W. G., Lyson, T. R. and Donoghue, P. C. J. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20141013
PDF | Dryad_button_v1



2014


A virtual world of palaeontology
Cunningham, J. A., Rahman, I. A., Lautenschlager, S., Rayfield, E. J. and Donoghue, P. C. J. (2014) Trends in Ecology & Evolution 29: 347-357
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Distinguishing biology from geology in soft tissue preservation
Cunningham, J. E., Donoghue, P. C. J. and Bengtson, S. (2014) Paleontological Society Special Publication 20: 275-288.
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Early vertebrate evolution
Donoghue, P. C. J. and Keating, J. N. (2014) Palaeontology 57: 879-893.
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Neither phylogenomic nor paleontological data support a Palaeogene origin of placental mammals
dos Reis, M., Donoghue, P. C. J. and Yang, Z. (2014) Biology Letters 10: 20131003
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There is no general model for occlusal kinematics in conodonts
Martínez-Pérez, C., Plasencia, P., Jones, D. O., Kolar-Jurkovsek, T., Sha, J., Botella, H. and Donoghue, P. C. J. (2014) Lethaia 47: 547-555.
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Finite element, occlusal, microwear and microstructural analyses indicate that conodont microstructure is adapted to dental function
Martínez-Peréz, C., Rayfield, E. J., Purnell, M. A. and Donoghue, P. C. J. (2014) Palaeontology 57: 1059-1066.
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Evaluating scenarios on the evolutionary assembly of brachiopod body plan
Murdock, D. J. E., Bengtson, S., Marone, F., Greenwood, J. M. and Donoghue, P. C. J. (2014) Evolution & Development 16: 13-24.
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Functional adaptation underpinned the evolutionary assembly of the earliest vertebrate skeleton
Murdock, D. J. E., Rayfield, E. J. and Donoghue, P. C. J. (2014) Evolution & Development 16: 354-361.
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Developmental paleobiology of the vertebrate skeleton
Rücklin, M., Donoghue, P. C. J., Cunningham, J. A., Marone, F. and Stampanoni, M. (2014) Journal of Paleontology 88: 676-683
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Evolutionary history of plant microRNAs
Taylor, R. S., Tarver, J. E., Hiscock, S. J. and Donoghue, P. C. J. (2014) Trends in Plant Sciences 19: 175-182.
PDF | hairpins | matures/stars | homology


2013


Embryos, polyps and medusa of the early Cambrian scyphozoan Olivooides
Dong, X.-P., Cunningham, J. A., Bengtson, S., Thomas, C.-W., Liu, J.-B., Stampanoni, M. and Donoghue, P. C. J. (2013) Proceedings of the Royal Society B: Biological Sciences 280, 20130071.
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The fascinating little whatzits
Donoghue, P. C. J. (2013) Science, 340: 813.
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A daily-updated tree of (sequenced) life as a reference for genome research
Fang, H., Oates, M., Pethica, R., Greenwood, J., Sardar, A., Rackham, O., Donoghue, P. C. J., Stamatakis, A., de Lima Morais, D. A., Gough, J. (2013) Nature Scientific Reports 3: 2015, 1-10.
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The histology of ‘placoderm’ dermal skeletons: implications for the nature of the ancestral gnathostome
Giles, S., Rücklin, M., Donoghue, P. C. J. (2013) Journal of Morphology, 274: 627-644.
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A divergence dating analysis of turtles using fossil calibrations: an example of best practise
Joyce, W. G., Parham, J. F., Lyson, T. R., Warnock, R. C. M. and Donoghue, P. C. J. (2013) Journal of Paleontology, 87: 612-634.
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The origin of conodonts and of vertebrate mineralized skeletons
Murdock, D. J. E., Dong, X.-P., Repetski, J. E., Marone, F., Stampanoni, M. and Donoghue, P. C. J. (2013) Nature 502: 546-549.
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Cutting the first ‘teeth’ - a new approach to functional analysis of conodont elements
Murdock, D. J., Sansom, I. J., Donoghue, P. C. J. (2013) Proceedings of the Royal Society B: Biological Sciences 280: 20131524.
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miRNAs: small genes with big potential in metazoan phylogenetics
Tarver, J. E., Sperling, E. A., Nailor, A., Heimberg, A. M., Robinson, J. M., King, B. L., Pisani, D., Donoghue, P. C. J., Peterson, K. J. (2013) Molecular Biology & Evolution 30: 2369-2382.
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2012


A merciful death for the “earliest bilaterlan”, Vernanimalcula
Bengtson, S., Cunningham, J. A., Yin, C., Donoghue, P. C. J. (2012) Evolution & Development 14: 421-427.
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Testing models of dental development in the earliest bony vertebrates, Andreolepis and Lophosteus
Cunningham, J. C., Rücklin, M., Blom, H., Botella, H., Donoghue, P. C. J. (2012) Biology Letters 8: 833-837.
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Experimental taphonomy of giant sulfur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils
Cunnigham, J. E., Thomas, C.-W., Bengtson, S., Marone, F., Stampanoni, M., Turner, F. R., Bailey, J. V., Raff, R. A., Raff, E. C., Donoghue, P. C. J. (2012) Proceedings of the Royal Society, London, Series B: Biological Sciences 279: 1857-1864.
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Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of origin of bilaterians
Cunningham, J. A., Thomas, C.-W., Bengtson, S., Kearns, S. L., Xiao, S., Marone, F., Stampanoni, M., and Donoghue, P. C. J. (2012) the Royal Society, London, Series B: Biological Sciences 279: 2369-2376.
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Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
dos Reis, M., Inoue, J., Hasegawa, M., Asher, R. J., Donoghue, P. C. J., Yang, Z. (2012). Proceedings of the Royal Society, London, Series B: Biological Sciences 279: 3491-3500.
PDF | F1000 | trees | 20.6M nt alignment | mt alignment | figure

New palaeoscolecid worms from the Furongian (late Cambrian) of Hunan, South China: is Markuelia an embryonic palaeoscolecid?
Duan Bai-chuan, Dong Xi-ping and Donoghue, P. C. J. (2012) Palaeontology 55: 613-622.
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Testing micro structural adaptation in the earliest dental tools
Jones, D. O., Evans, A. R., Rayfield, E. J., Siu, K. K. W., Donoghue, P. C. J. (2012) Biology Letters 8: 952-955.
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The sharpest tools in the box? Quantitative analysis of conodont element functional morphology
Jones, D. O., Evans, A. R., Siu, K., Rayfield, E. J., Donoghue, P. C. J. (2012) Proceedings of the Royal Society, London, Series B: Biological Sciences 275: 2849-2854.
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Response to comment on “Fossilized nuclei and germination structures identify Ediacaran ‘animal embryos’ as encysting protists”
Huldtgren, T. E. Cunnigham, J. E., Yin, C., Stampanoni, M., Marone, F., Donoghue, P. C. J., Bengtson, S. (2012) Science 335: 1169.
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Ontogeny and microstructure of the enigmatic Cambrian tommotiid Sunnaginia Missarzhevsky 1969
Murdock, D. J. E., Donoghue, P. C. J., Bengtson, S. and Marone, F. (2012) Palaeontology 55: 661-676.
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Best practices for applying paleontological data to molecular divergence dating
Parham, J. F., Donoghue, P. C. J., Bell, C. J., Calway, D. T., Head, J. J., Holroyd, P. A., Inoue, J. G., Irmis, R. B., Joyce, W. A., Ksepka, D. T., Patané, J. S. L., Smith, N. D., Tarver, J. E., van Tuinen, M., Yang, Z., Angielczyk, K. D., Greenwood, J., Nipsley, C. A., Jacobs, L., Makovicky, P. J., Müller, J., Smith, K. T., Theodor, J. M., Warnock, R. C. M., Benton, M. J. (2012) Systematic Biology 61:346-359.
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Development of teeth and jaws in the earliest jawed vertebrates
Rücklin, M., Donoghue, P. C. J., Johanson, Z., Trinajstic, K., Marone, F., Stampanoni, M. (2012) Nature 491:748-751.
PDF | Nature podcast

Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish)
Shimeld, S. M. and Donoghue, P. C. J. (2012). Developmental Biology 139: 2091-2099.
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Do microRNAs have a deep evolutionary history?
Tarver, J. E., Peterson, K. J., Donoghue, P. C. J. (2012) BioEssays 34: 857-866.
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Exploring uncertainty in the calibration of the molecular clock
Warnock, R. C. M., Yang, Z. and Donoghue, P. C. J. (2012) Biology Letters 8: 156-159
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2011


Establishing a timescale for plant evolution
Clarke, J. T., Warnock, R. C. M. and Donoghue, P. C. J. (2011) New Phytologist 192: 266-301
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Fossil jawless fish from China foreshadows early jawed vertebrate anatomy
Gai, Z.-k., Donoghue, P. C. J., Zhu, M., Janvier, P. and Stampanoni, M. (2011) Nature 476: 324-327
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Fossilized nuclei and germination structures identify Ediacaran ‘animal embryos’ as encysting protists
Huldtgren, T. E. Cunnigham, J. E., Yin, C., Stampanoni, M., Marone, F., Donoghue, P. C. J., Bengtson, S. (2011) Science 334: 1696-1699
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Evolutionary origins of animal skeletal biomineralization
Murdock, D. J. E. and Donoghue, P. C. J. (2011) Cells, Tissues, Organs 194: 98-102
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Teeth before jaws? Comparative analysis of the structure and development of the external and internal scales in the extinct jawless vertebrate Loganellia scotica
Rücklin, M., Giles, S., Janvier, P. and Donoghue, P. C. J. (in press) Evolution & Development 13: 523-532
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The trouble with topology: phylogenies without fossils provide a revisionist perspective of evolutionary history in topological analyses of diversity
Tarver, J. E. and Donoghue, P. C. J. (2011) Systematic Biology 60: 700-712
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Is evolutionary history repeatedly rewritten in light of new fossil discoveries?
Tarver, J. E., Donoghue, P. C. J. and Benton, M. J. (2011) Proceedings of the Royal Society: Biological Sciences 278: 599-604.
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2010

The anatomy, taphonomy, taxonomy and systematic affinity of Markuelia: Early Cambrian to Early Ordovician scalidophorans
Dong, X.-P., Bengtson, S., Gostling, N. J., Cunningham, J. A., Harvey, T. H. P., Kouchinsky, A., Val'kov, A. K., Repetski, J. E., Stampanoni, M., Donoghue, P. C. J. (2010). Palaeontology 53: 1291-1314.
PDF | Data available at Dryad_button_v1

Origins of multicellularity
Donoghue, P. C. J. and Antcliffe, J. B. (2010). Nature 466: 41-42.
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Are palaeoscolecids ancestral ecdysozoans?

Harvey, T. H. P., Dong, X.-P. and Donoghue, P. C. J. (2010). Evolution & Development 12: 177-200.

PDF | Data available at Dryad_button_v1

microRNAs reveal the interrelationships of hagfishes, lampreys and gnathostomes, and the nature of the ancestral vertebrate
Heimberg, A. M., Cowper-Sal lari, R., Sémon, M., Donoghue, P. C. J., Peterson, K. J. (2010) Proceedings of the National Academy of Sciences 107: 19379-19383.
PDF | Data available at Dryad_button_v1

A formula for maximum possible steps in multistate characters: isolating matrix parameter effects on measures of evolutionary convergence
Hoyal Cuthill, J. F., Braddy, S. J. and Donoghue, P. C. J. 2010. Cladistics 26: 98-102.
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The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times
Inoue, J., Yang, Z. and Donoghue, P. C. J. 2010. Systematic Biology 59: 74-89.
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2009

Calibrating and constraining the molecular clock
Benton, M. J., Donoghue, P. C. J. and Asher, R. J. 2009. In: Hedges, B. and Kumar, S. (eds): Dating the Tree of Life. Pp. 35-86. Oxford University Press
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Enameloid microstructure in the oldest known chondrichthyan teeth
Botella, H., Donoghue, P. C. J. and Martínez-Pérez, C. 2009. Acta Zoologica 90: 103-108
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Origin of vertebrates
Donoghue, P. C. J. 2009. In: Wilson, E. O., Ruse, M. Travis, J. (eds): Evolution: the first four billion years. Pp. 788-792. Belknap Press, Cambridge, MA
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Distinguishing heat from light in debate over controversial fossils
Donoghue, P. C. J. and Purnell, M. A. 2009. Bioessays 31: 178-189
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The evolutionary emergence of vertebrates from their spineless relatives
Donoghue, P. C. J. and Purnell, M. A. 2009. Evolution: Education & Outreach 2: 204-212
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Skeletal histology of Bothriolepis canadensis (Placodermi, Antiarchi) and the evolution of the skeleton at the origin of jawed vertebrates
Downs, J. P. and Donoghue, P. C. J. 2009. Journal of Morphology 270: 1364-1380
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Ontogeny and taphonomy: An experimental taphonomy study of the development of the brine shrimp Artemia salina
Gostling, N. J., Dong, X.-P. and Donoghue, P. C. J. 2009. Palaeontology 52: 169-186
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A new species of Markuelia from the Middle Cambrian of Australia
Haug, J. T., Maas, A., Waloszek, D., Donoghue, P. C. J., Bengtson, S. 2009. Memoirs of the Association of Australasian Palaeontologists 37: 303-313
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Scanning electron microscopy and synchrotron radiation X-ray tomographic microscopy of 330 million year old charcoalified seed fern fertile organs
Scott, A. C., Galtier, J., Gostling, N. J., Smith, S. Y., Collinson, M. E., Stampanoni, M., Marone, F., Donoghue, P. C. J. and Bengtson, S. 2009. Microscopy & Microanalysis 15: 166-173
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Origin and evolution of the integumentary skeleton in non-tetrapod vertebrates
Sire, J.-Y., Donoghue, P. C. J. and Vickaryous, M. 2009. Journal of Anatomy 214: 409-440
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2008

Exploring the links between development and evolution
Donoghue, P. C. J. 2008. In: Benton, M. J. (ed): Seventy great mysteries of the natural world, Thames & Hudson
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The origin and evolution of the neural crest
Donoghue, P. C. J., Graham, A. and Kelsh, R. N. 2008. BioEssays 30: 530-541 (2008)
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The interrelationships of 'complex' conodonts (Vertebrata)
Donoghue, P. C. J., Purnell, M. A., Aldridge, R. J. and Zhang, S. 2008. Journal of Systematic Palaeontology 6: 119-153
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Deciphering the fossil record of bilaterian embryonic development in light of experimental taphonomy
Gostling, N. J., Thomas, C.-W., Greenwood, J. M., Dong, X.-P., Bengtson, S., Raff, E. C., Raff, R. A., Degnan, B. M., Stampanoni, M. and Donoghue, P. C. J. 2008. Evolution & Development 10: 339-349
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microRNAs and the advent of vertebrate morphological complexity
Heimberg, A., Sempere, L., Moy, V., Donoghue, P. C. J. and Peterson, K. J. 2008. Proceedings of the National Academy of Sciences, USA 105: 2946-2950
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Embryo fossilization is a biological process mediated by microbial biofilms
Raff, E. C., Schollaerrt, K. L., Nelson, D. E., Donoghue, P. C. J., Thomas, C.-W., Turner, F. R., Stein, B. D., Dong, X.-P., Bengtson, S., Huldtgren, T., Stampanoni, M., Yin, C.-y. and Raff, R. A. 2008. Proceedings of the National Academy of Sciences, USA 105: 19359-19364
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The anatomy and affinities of Ilemoraspis kirkinskyae from the Devonian of Siberia, Russia and its bearing on the evolution of the Osteostraci
Sansom, R. S., Rodygin, S. and Donoghue, P. C. J. 2008. Journal of Vertebrate Paleontology 20: 613-625
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2007

Palaeontological evidence to date the Tree of Life
Benton, M. J. and Donoghue, P. C. J. 2007. Molecular Biology & Evolution 24: 26-53
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Embryonic identity crisis
Donoghue, P. C. J. 2007. Nature 445:155-156
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Rocks and clocks: calibrating the Tree of Life using fossils and molecules
Donoghue, P. C. J. and Benton, M. J. 2007. Trends in Ecology and Evolution 22: 424-431
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Phase-contrast X-ray microtomography links Cretaceous seeds with Gnetales and Bennettitales
Friis, E.-M., Crane, P. R., Pedersen, K. R., Bengtson, S., Donoghue, P. C. J., Grimm, G. W. and Stampanoni, M. 2007. Nature 450: 549-552
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The homology and phylogeny of chondrichthyan tooth enameloid
Gillis, J. A. and Donoghue, P. C. J. 2007. Journal of Morphology 268: 33-49
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The earliest fossil embryos begin to mature
Gostling, N. J., Donoghue, P. C. J. and Bengtson, S. 2007. Evolution & Development 9: 206-207
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Molecular palaeobiology
Peterson, K. J., Summons, R. E. and Donoghue, P. C. J. 2007. Palaeontology 50: 775-809
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2006

Synchrotron X-ray tomographic microscopy of fossilised embryos
Donoghue, P. C. J., Bengtson, S., Dong, X., Gostling, N. J., Huldtgren, T., Cunningham, J. A., Yin, C., Yue, Z., Fan, P. and Stampanoni, M. 2006.
Nature 442:680-683
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Swiss light shed on the nature of fossilised embryos from the dawn of animal evolution
Donoghue, P. C. J., Gostling, N. J., Bengtson, S., Huldtgren, T., Dong, X., Peng, F. and Stampanoni, M. 2006. PSI Scientific Report 2005. Volume 1: Condensed matter, photons, neutrons and charged particles. pp. 10-11
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Fossilized embryos are widespread but the record is temporally and taxonomically biased
Donoghue, P. C. J., Kouchinsky, A., Waloszek, D., Bengtson, S., Dong, X., Val’kov, A. K., Cunningham, J. A. and Repetski, J. E. 2006. Evolution & Development 8: 232-238
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Early evolution of vertebrate skeletal tissues and cellular interactions, and the canalization of skeletal development
Donoghue, P. C. J., Sansom, I. J. and Downs, J. P. 2006. Journal of Experimental Zoology - Part B: Molecular and Developmental Evolution 306B: 278-294
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Cellular and subcellular structure of Neoproterozoic animal embryos
Hagadorn, J. W., Xiao, S., Donoghue, P. C. J., Bengtson, S., Gostling, N. J., Pawlowska, M., Raff, E. C., Raff, R. A., Turner, F. R., Yin, C., Zhou, C., Yuan, X., McFeely, M. B., Stampanoni, M. and Nealson, K. H. 2006. Science 314:291-294
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The 'Orsten'- More than a Cambrian Konservat-Lagerstatte yielding exceptional preservation
Maas, A., Braun, A., Dong, X.-P., Donoghue, P. C. J., Muller, K. J., Olempska, E., Repetski, J. E., Siveter, D. J., Stein, M. and Waloszek, D. 2006. Palaeoworld 15: 266-282
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Experimental taphonomy shows the feasibility of fossil embryos
Raff, E. C., Vilinski, J. T., Turner, F. R., Donoghue, P. C. J. and Raff, R. A. 2006. Proceedings of the National Academy of Sciences of the United States of America 103: 5846-5851
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2005

The anatomy, affinity and phylogenetic significance of Markuelia
Dong, X., Donoghue, P. C. J., Cunningham, J., Liu, J. and Cheng, H. 2005. Evolution & Development 7: 468-482
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Basal tissue structure in the earliest euconodonts: testing hypotheses of developmental plasticity in euconodont phylogeny
Dong, X., Donoghue, P. C. J. and Repetski, J. E. 2005. Palaeontology 48: 411-421
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The fossils of Orsten-type preservation from Middle and Upper Cambrian in Hunan, China
Dong, X.-P., Donoghue, P. C. J., Liu, Z., Liu, J. and Peng, F. 2005. Chinese Science Bulletin 50: 1352-1357
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Saving the stem-group - a contradiction in terms
Donoghue, P. C. J. 2005. Paleobiology 31: 553-558
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Carl Gegenbaur and evolutionary morphology
Donoghue, P. C. J. 2005. Acta Zoologica 85: 265-266
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Embryos and ancestors
Donoghue, P. C. J. and Dong, X. P. 2005. In D. E. G. Briggs (ed.) Evolving form and function: fossils and development. Yale Peabody Museum of Natural History, Yale University, New Haven. pp. 81-99
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Genome duplication, extinction and vertebrate evolution
Donoghue, P. C. J. and Purnell, M. A. 2005. Trends in Ecology & Evolution 20: 312-319
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Between death and data: biases in interpretation of the fossil record of conodonts
Purnell, M. A. and Donoghue, P. C. J. 2005. Special Papers in Palaeontology 73: 7-25
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Histology and affinity of the earliest armoured vertebrate
Sansom, I. J., Donoghue, P. C. J. and Albanesi, G. L. 2005. Biology Letters 2: 446-449
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The apparatus composition and architecture of Cordylodus Pander - concepts of homology in primitive conodonts
Smith, M. P., Donoghue, P. C. J. and Repetski, J. E. 2005. In. Barrick, J. E. and Lane, H. R. (eds) A standing ovation: papers in honor of Gilbert Klapper. Bulletins of American Paleontology 369: 19-33
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Histology of the galeaspid dermoskeleton and endoskeleton, and the origin and early evolution of the vertebrate cranial endoskeleton
Wang, N. Z., Donoghue, P. C. J., Smith, M. M. and Sansom, I. J. 2005. Journal of Vertebrate Paleontology 25: 745-756
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Cladograms, phylogenies and the veracity of the conodont fossil record
Wickström, L. M. and Donoghue, P. C. J. 2005. Special Papers in Palaeontology 73: 185-218
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2004

Fossil embryos from the Middle and Late Cambrian period of Hunan, south China
Dong, X., Donoghue, P. C. J., Cheng, H. and Liu, J. 2004. Nature 427: 237-240
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2003

Telling the evolutionary time: molecular clocks and the fossil record
Donoghue, P. C. J. and Smith, M. P. (eds)
CRC Press, London (2003)

Introduction: Molecular clocks and the fossil record - towards consilience?
Donoghue, P. C. J. and Smith, M. P. In P. C. J. Donoghue and M. P. Smith (eds)
Telling the evolutionary time: molecular clocks and the fossil record CRC Press, London. pp. 1-4 (2003)

The origin and early evolution of chordates: molecular clocks and the fossil record
Donoghue, P. C. J., Smith, M. P. and Sansom, I. J. 2003. In P. C. J. Donoghue and M. P. Smith (eds). Telling the evolutionary time: molecular clocks and the fossil record CRC Press, London. pp. 190-223
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The emergence of vertebrates
Donoghue, P. C. J., Smith, M. P. and Sansom, I. J.In McGraw-Hill Yearbook of Science. McHraw-Hill, New York. pp. 107-109 (2003)

The distribution of ostracoderms in the Mid-Ordovician of Laurentia and Gondwana
Sansom, I. J., Smith, M. P. and Donoghue, P. C. J. 2003. In G. L. Albanesi, M. S. Beresi and S. H. Peralta (eds). Ordovician from the Andes. Instituto Superior de Correlación Geológica, Tucumán, Argentina. pp. 545-549 (2003)

The spatial and temporal diversification of Early Palaeozoic vertebrates
Smith, M. P., Donoghue, P. C. J. and Sansom, I. J. 2003. In J. A. Crame and A. W. Owen (eds). Palaeobiogeography and biodiversity change: the Ordovician and Mesozoic-Cenozoic radiations. Geological Society Special Publication No. 194. The Geological Society, London. pp. 69-83
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2002

Evolution of development of vertebrate teeth and scales: unravelling concepts, regulatory theories and homologies
Donoghue, P. C. J. 2002. Paleobiology 28: 474-507
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Origin and early evolution of vertebrate skeletonization
Donoghue, P. C. J. and Sansom, I. J. 2002. Microscopy Research & Technique 59: 352-372
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2001

Microstructural variation in conodont enamel is a functional adaptation
Donoghue, P. C. J. 2001. Proceedings of the Royal Society of London, Series B 268: 1691-1698
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Conodonts meet cladistics: recovering relationships and assessing the completeness of the conodont fossil record
Donoghue, P. C. J. 2001. Palaeontology 44: 65-93
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Origin of a mineralised skeleton
Donoghue, P. C. J. and Aldridge, R. J. 2001. In P. E. Ahlberg (ed.). Major events in early vertebrate evolution: palaeontology, phylogeny, genetics and development. Taylor & Francis, London. pp. 85-105

The anatomy of Turinia pagei (Powrie) and the phylogenetic status of the Thelodonti
Donoghue, P. C. J. and Smith, M. P. 2001. Transactions of the Royal Society of Edinburgh (Earth Sciences) 92: 15-37
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Conodonts: past, present and future
Sweet, W. C. and Donoghue, P. C. J. 2001. Journal of Paleontology 75: 1174-1184
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2000

Orientation and anatomical notation in conodonts
Purnell, M. A., Donoghue, P. C. J. and Aldridge, R. J. 2000. Journal of Paleontology 74: 113-122
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Conodont affinity and chordate phylogeny
Donoghue, P. C. J., Forey, P. L. and Aldridge, R. J. 2000. Biological Reviews 75: 191-251
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1999

Conchodontus, Mitrellataxis and Fungulodus: conodonts, fish, or both?
Donoghue, P. C. J. and Chauffe, K. 1999. Lethaia 31: 283-292
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Mammal-like occlusion in conodonts
Donoghue, P. C. J. and Purnell, M. A. 1999. Paleobiology 25: 58-74
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Growth, function, and the fossil record of conodonts
Donoghue, P. C. J. and Purnell, M. A. 1999. Geology 27: 251-254
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Flattened fossils, physical modelling and the restoration of collapsed skeleton
Purnell, M. A. and Donoghue, P. C. J. 1999. In E. Savazzi (ed.). Functional morphology of the invertebrate skeleton. John Wiley & Sons Ltd., Chichester. pp. 91-99


1998

Conodonts: a sister group to hagfish?
Aldridge, R. J. and Donoghue, P. C. J. 1998. In J. M. Jørgensen, J. P. Lomholt, R. E. Weber and H. Malte (ed.). The Biology of Hagfishes. Chapman and Hall, London. pp. 15-31
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Growth and patterning in the conodont skeleton
Donoghue, P. C. J. 1998. Philosophical Transactions of the Royal Society of London, Series B 353: 633-666
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Conodont anatomy, chordate phylogeny and vertebrate classification
Donoghue, P. C. J., Purnell, M. A. and Aldridge, R. J. 1998. Lethaia 31: 211-219
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Architecture and functional morphology of the skeletal apparatus of ozarkodinid conodonts
Purnell, M. A. and Donoghue, P. C. J. 1998. Palaeontology 41: 57-102
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1997

A technique for conodont histology
Donoghue, P. C. J. 1997. Lethaia 30: 329-330
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Skeletal architecture and functional morphology of ozarkodinid conodonts
Purnell, M. A. and Donoghue, P. C. J. 1997. Philosophical Transactions of the Royal Society of London, Series B 352: 1545-1564
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An Early Triassic conodont with periodic growth?
Zhang, S., Aldridge, R. J. and Donoghue, P. C. J. 1997. Journal of Micropalaeontology 16: 65-72
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1995

Conodonts and the first vertebrates
Purnell, M. A., Aldridge, R. J., Donoghue, P. C. J. and Gabbott, S. E. 1995. Endeavour 19: 20-27
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