Publications

in press

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta, Schimp.)
Sousa, F, Foster, P, Donoghue, PCJ, Schneider, H, Cox, C (in press) New Phytologist

2018

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution
Barba-Mantoya J, dos Reis M, Schneider H, Donoghue PCJ, Yang Z. (2018) New Phytologist 218: 819-834.
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Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin
Betts HC, Puttick MN, Clark JW, Williams TA, Donoghue PCJ, Pisani D. (2018) Nature Ecology & Evolution 2: 1556-1562.
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Unicellular origin of the animal microRNA machinery
Bråte J, Neumann RS, Fromm B, Haraldsen AAB, Tarver JE, Suga H, Donoghue PCJ, Peterson KJ, Ruiz-Trillo I, Grini PE, Shalchian-Tabrizi K. (2018) Current Biology
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Whole genome duplication and plant macroevolution
Clark JW and Donoghue PCJ. (2018) Trends in Plant Sciences 23: 933-945.
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Evolution of metazoan morphological disparity
Deline B, Greenwood JE, Clark JW, Puttick MN, Peterson KJ, Donoghue PCJ (2018) Proceedings of the National Academy of Sciences, USA 115: E8909-E8918
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Ediacaran developmental biology
Dunn FS, Liu AG, Donoghue PCJ. (2018) Biological Reviews 93: 914-932.
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Anatomy of the Ediacaran rangeomorph Charnia masoni
Dunn F, Wilby P, Kenchington C, Grazhdankin D, Donoghue PCJ, Liu, A. (2018) Papers in Palaeontology
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Evolution of jaw disparity in fishes
Hill JJ, Puttick MN, Stubbs TL, Rayfield EJ, Donoghue PCJ. (2018) Palaeontology 61: 847-854.
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Gondolelloid multielement apparatus (Nicoraella) from the Middle Triassic of Yunnan Province, southwest China
Huang J, Hu, S, Zhang Q, Donoghue PCJ, Benton MJ, Zhou C, Martínez-Pérez C, Wen W, Xie T, Chen Z-Q, Mao L, Yao H, Zhang K. (2018) Palaeogeography, Palaeoclimatology, Palaeoecology.
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Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography
Huang J, Martínez-Pérez C, Hu S, Donoghue PCJ, Zhang Q, Zhou C, Wen W, Benton MJ, Mao L, Yao H, Zhang K. (2018) Palaeoworld
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The nature of aspidin and the evolutionary origin of bone
Keating JN, Marquart CL, Donoghue PCJ. (2018) Nature Ecology & Evolution 2: 1501-1506.
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Vascular structure of the earliest shark teeth
Martínez-Pérez C, Marton-Lazaro A, Ferrón HG, Kirstein M, Donoghue PCJ, Botella H. (2018) Acta Geologica Polonica 68: 457-465
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The timescale of early land plant evolution
Morris JL, Puttick MN, Donoghue PCJ, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. (2018) Proceedings of the National Academy of Sciences, USA 115: E2274-E2283.
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Accurate timetrees do indeed require accurate calibrations. Response to comment by Hedges et al.
Morris JL, Puttick MN, Donoghue PCJ, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ. (2018) Proceedings of the National Academy of Sciences, USA
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The efficacy of consensus tree methods for summarising phylogenetic relationships from a posterior samples of tree estimated from morphological data
O’Reilly JE and Donoghue PCJ. (2018) Systematic Biology 67: 354-362.
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Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data
O’Reilly JE, Puttick MN, Pisani D, Donoghue PCJ. (2018) Palaeontology 61:105-118.
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Empirical realism of simulated data is more important than the model used to generate it. A reply to Goloboff et al.
O’Reilly JE, Puttick MN, Pisani D, Donoghue PCJ. (2018) Palaeontology 61: 631-635.
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Experimental analysis of soft tissue preservation – opening the black box
Purnell MA, Donoghue PCJ, Gabbott SE, McNamara M, Murdock DJE, Sansom RS. (2018) Palaeontology 61: 317-323.
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The interrelationships of land plants and the nature of the ancestral embryophyte
Puttick MN, Morris JL, Williams TA, Cox CJ, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Schneider H. Pisani D, Donoghue PCJ. (2018) Current Biology 28: 733-745.
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Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model
Puttick MN, O’Reilly JE, Pisani D, Donoghue PCJ. (2018) Palaeontology
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Well-annotated microRNAomes do not evidence pervasive miRNA loss
Tarver JE, Taylor R, Puttick MN, Lloyd G, Pett W, Fromm B, Schirrmeister B, Pisani D, Peterson KJ, Donoghue PCJ. (2018) Genome Biology and Evolution 10: 1457-1470.
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2017

Constraining the timing of whole genome duplication in plant evolutionary history
Clark JW and Donoghue PCJ. (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20170912
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The origin of animals: can evidence from molecular clocks and the fossil record be reconciled?
Cunningham JA, Liu AG, Bengtson S, Donoghue PCJ. (2017) Bioessays 39: 1600120
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The Weng’an Biota (Doushantuo Formation): an Ediacaran window on soft bodied and multicellular microorganisms
Cunningham JA, Vargas K, Yin Z, Bengtson S, Donoghue PCJ. (2017) Journal of the Geological Society 174: 793-802.
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Open data and digital morphology
Davies TG, Rahman IA, Lautenschlager S, Cunningham JA, Asher RJ, Barrett PM, Bates KT, Bengtson S, Benson RBJ, Boyer DM, Braga J, Bright JA, Claessens LPAM, Cox PG, Dong XP, Evans AR, Falkingham PL, Friedman M, Garwood RJ, Goswami A, Hutchinson JR, Jeffery NS, Johanson Z, Lebrun R, Martínez-Pérez C, Marugán-Lobón J, O’Higgins PM, Metscher B, Orliac M, Rowe TB, Rücklin M, Sánchez-Villagra MR, Shubin NH, Smith SY, Starck JM, Stringer C, Summers AP, Sutton MD, Walsh SA, Weisbecker V, Witmer LM, Wroe S, Yin Z, Rayfield EJ, Donoghue PCJ. (2017) Proceedings of the Royal Society B: Biological Sciences 284: 2017.0194
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Divining the nature of the ancestral vertebrate
Donoghue PCJ. (2017) Current Biology 27: R277-279
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The early Cambrian fossil embryo Pseudooides is a direct developing cnidarian, not an early ecdysozoan
Duan B, Dong XP, Porras L, Vargas K, Cunningham JA, Donoghue PCJ. (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20172188
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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 PCJ, Pisani D. (2017) Genome Biology & Evolution 9: 1320-1328.
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Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data
Puttick MN, O’Reilly JE, Tanner AR, Fleming J, Clark JW, Holloway L, Lozano-Fernandez J, Parry L, Tarver JE, Pisani D, Donoghue PCJ. (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 MN, O’Reilly JE, Oakley D, Tanner AR, Fleming J, Clark JW, Holloway L, Lozano-Fernandez J, Parry L, Tarver JE, Pisani D, Donoghue PCJ. (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 RS, Tarver JE, Foroozani A, Donoghue PCJ. (2017) Bioessays 39: 1600113
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Testing the molecular clock using mechanistic models of both fossil preservation and molecular evolution
Warnock RCM, Yang Z, Donoghue PCJ. (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20170277
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Nuclei and nucleoli in embryo-like fossils from the Ediacaran Weng’an Biota
Yin Z, Cunningham JA, Vargas K, Bengtson S, Zhu M, Donoghue PCJ. (2017) Precambrian Research 301: 145-151
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2016

A multicellular organism with embedded cellular clusters from the Ediacaran Weng’an Biota
Cunningham JE, Vargas K, Marone F, Bengtson SE, Donoghue PCJ. (2016) Evolution & Development 18: 308-316
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Tectonic blocks and molecular clocks
de Baets K, Antonelli A, Donoghue PCJ. (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 XP, Vargas K, Cunningham JA, Zhang HQ, Liu T, Chen F, Liu JB, Bengtson S, Donoghue PCJ. (2016) Palaeontology DOI: 10.1111/pala.12231
PDF | DRYAD | Tomo Data

The evolution of methods for establishing evolutionary timescales
Donoghue PCJ 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 PCJ. (2016) Nature Reviews Genetics 17: 71-80
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Pigmented anatomy in Carboniferous cyclostomes, and the evolution of the vertebrate eye
Gabbott SE, Donoghue PCJ, Sansom RS, Vintner J, Dolman A, Purnell MA. (2016) Proceedings of the Royal Society B: Biological Sciences 283: 20161151
PDF | DRYAD

Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton
Keating JN and Donoghue PCJ. (2016) Proceedings of the Royal Society B: Biological Sciences 283:20152917
PDF | DRYAD | Tomo Data

Evolution of the calcium-based intracellular signalling system
Marchadier E, Oates ME, Fang H, Donoghue PCJ, Hetherington AM, 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 EJ, Botella H, Donoghue PCJ. (2016) Geology 44: 247-250
PDF | Tomo Data

Tips and nodes are complimentary not competing approaches to the calibration of molecular clocks
O’Reilly JE and Donoghue PCJ. (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 JE, Puttick MN, Parry L, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PCJ. (2016) Biology Letters 12: 20160081
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Response to “Placoderms and the evolutionary origin of teeth”: Burrow et al. (2016)
Rücklin M and Donoghue PCJ. (2016) Biology Letters 12: 20160526
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The interrelationships of placental mammals and the limits of phylogenetic inference
Tarver JE, dos Reis M, King BL, Mirarab S, O’Connell MJ, Moran RJ, Asher RJ, Parker S, Warnow T, Peterson KJ, Donoghue PCJ, 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 PCJ. (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 MJ, Donoghue PCJ, Asher RJ, Friedman M, Near TJ, 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 AD, Cunningham JA, Budd GE, Donoghue PCJ. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20150476
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Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng’an Doushantuo biota
Cunningham JA, Vargas K, Liu PJ, Belivanova V, Marone F, Martínez-Pérez C, Guizar-Sicairos M, Holler M, Bengtson S, Donoghue PCJ. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20151169
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Constraining the deep origin of parasitic flatworms and host interactions with fossil evidence
de Baets K, Dentzien-Dias P, Upeniece I, Verneau O, Donoghue PCJ. (2015) Advances in Parasitology 90: 93-135.
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Embryology in deep time
Donoghue PCJ, Cunningham JA, Dong XP, 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 PCJ and Rücklin M. (2015) Evolution & Development 18: 19-30.
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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 MJ, Donoghue PCJ, Yang Z. (2015) Current Biology 25: 2939-2950
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Ptychographic nanotomography at the Swiss Light Source
Guizar-Sicairos M, Holler M, Diaz A, da Silva JC, Tsai EHR, Bunk O, Martinez-Perez C, Donoghue PCJ, Wellman CH, 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 AJ, Sherratt E, Ruta M, Wilkinson M, Deline B, Donoghue PCJ. (2015) Palaeontology 58: 393-399
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Histology of the heterostracan dermal skeleton: insight into the origin of the vertebrate mineralized skeleton
Keating JN, Marquart CL, Donoghue PCJ. (2015) Journal of Morphology 276: 657-680
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The fossil calibration database, a new resource for divergence dating
Kspeka D, Parham JD, Allman J, Benton MJ, Carrano M, Cranston K, Donoghue PCJ, Head J, Hermsen E, Irmis R, Joyce W, Kohli M, Lamm K, Leehr D, Patane J, Polly PD, Phillips M, Smith N, van Tuinen M, Ware J, Warnock RCM. (2015) Systematic Biology 64: 853-859.
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Dating tips for divergence time estimation
O’Reilly J, dos Reis M, Donoghue PCJ. (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 MN, Clark JW, Donoghue PCJ. (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 PCJ. (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 RS, Randle E, Donoghue PCJ. (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 BE, Gugger M,  Donoghue PCJ. (2015) Palaeontology 58: 769-785.
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Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
Warnock RCM, Parham JF, Joyce WG, Lyson TR, Donoghue PCJ. (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20141013
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2014

A virtual world of palaeontology
Cunningham JA, Rahman IA, Lautenschlager S, Rayfield EJ, Donoghue PCJ. (2014) Trends in Ecology & Evolution 29: 347-357
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Distinguishing biology from geology in soft tissue preservation
Cunningham JE, Donoghue PCJ, Bengtson S. (2014) Paleontological Society Special Publication 20: 275-288.
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Early vertebrate evolution
Donoghue PCJ and Keating JN. (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 PCJ, 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 DO, Kolar-Jurkovsek T, Sha J, Botella H, Donoghue PCJ. (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 EJ, Purnell MA, Donoghue PCJ. (2014) Palaeontology 57: 1059-1066.
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Evaluating scenarios on the evolutionary assembly of brachiopod body plan
Murdock DJE, Bengtson S, Marone F, Greenwood JM, Donoghue PCJ. (2014) Evolution & Development 16: 13-24.
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Functional adaptation underpinned the evolutionary assembly of the earliest vertebrate skeleton
Murdock DJE, Rayfield EJ, Donoghue PCJ. (2014) Evolution & Development 16: 354-361.
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Developmental paleobiology of the vertebrate skeleton
Rücklin M, Donoghue PCJ, Cunningham JA, Marone F, Stampanoni M. (2014) Journal of Paleontology 88: 676-683
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Evolutionary history of plant microRNAs
Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ. (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 XP, Cunningham JA, Bengtson S, Thomas CW, Liu JB, Stampanoni M, Donoghue PCJ. (2013) Proceedings of the Royal Society B: Biological Sciences 280, 20130071.
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The fascinating little whatzits
Donoghue PCJ. (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 JE, Sardar A, Rackham O, Donoghue PCJ, Stamatakis A, de Lima Morais DA, Gough J. (2013) 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 PCJ. (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 WG, Parham JF, Lyson TR, Warnock RCM, Donoghue PCJ. (2013) Journal of Paleontology, 87: 612-634.
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The origin of conodonts and of vertebrate mineralized skeletons
Murdock DJE, Dong XP, Repetski JE, Marone F, Stampanoni M, Donoghue PCJ. (2013) Nature 502: 546-549.
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Cutting the first ‘teeth’ – a new approach to functional analysis of conodont elements
Murdock DJE, Sansom IJ, Donoghue PCJ. (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 JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PCJ, Peterson KJ. (2013) Molecular Biology & Evolution 30: 2369-2382.
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2012

A merciful death for the “earliest bilaterlan”, Vernanimalcula
Bengtson S, Cunningham JA, Yin C, Donoghue PCJ. (2012) Evolution & Development 14: 421-427.
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Testing models of dental development in the earliest bony vertebrates, Andreolepis and Lophosteus
Cunningham JA, Rücklin M, Blom H, Botella H, Donoghue PCJ. (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
Cunningham JA, Thomas CW, Bengtson S, Marone F, Stampanoni M, Turner FR, Bailey JV, Raff RA, Raff EC, Donoghue PCJ. (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 JA, Thomas CW, Bengtson S, Kearns SL, Xiao S, Marone F, Stampanoni M, Donoghue PCJ. (2012) Proceedings of 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 RJ, Donoghue PCJ, 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 BC, Dong XP, Donoghue, PCJ. (2012) Palaeontology 55: 613-622.
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Testing micro structural adaptation in the earliest dental tools
Jones DO, Evans AR, Rayfield EJ, Siu K, Donoghue PCJ. (2012) Biology Letters 8: 952-955.
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The sharpest tools in the box? Quantitative analysis of conodont element functional morphology
Jones DO, Evans AR, Siu K., Rayfield EJ, Donoghue PCJ. (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 TE, Cunnigham JA, Yin C, Stampanoni M, Marone F, Donoghue PCJ, Bengtson S. (2012) Science 335: 1169.
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Ontogeny and microstructure of the enigmatic Cambrian tommotiid Sunnaginia Missarzhevsky 1969
Murdock DJE, Donoghue PCJ, Bengtson S, Marone F. (2012) Palaeontology 55: 661-676.
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Best practices for applying paleontological data to molecular divergence dating
Parham JF, Donoghue PCJ, Bell CJ, Calway DT, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WA, Ksepka DT, Patané JSL, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood J, Hipsley CA, Jacobs L, Makovicky PJ, Müller J, Smith KT, Theodor JM, Warnock RCM, Benton MJ. (2012) Systematic Biology 61:346-359.
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Development of teeth and jaws in the earliest jawed vertebrates
Rücklin M, Donoghue PCJ, 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, SM and Donoghue PCJ. (2012) Developmental Biology 139: 2091-2099.
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Do microRNAs have a deep evolutionary history?
Tarver JE, Peterson KJ, Donoghue PCJ. (2012) BioEssays 34: 857-866.
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Exploring uncertainty in the calibration of the molecular clock
Warnock RCM, Yang Z, Donoghue PCJ. (2012) Biology Letters 8: 156-159
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2011

Establishing a timescale for plant evolution
Clarke JT, Warnock RCM, Donoghue PCJ. (2011) New Phytologist 192: 266-301
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Fossil jawless fish from China foreshadows early jawed vertebrate anatomy
Gai ZK, Donoghue PCJ, Zhu M, Janvier P, Stampanoni M. (2011) Nature 476: 324-327
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Fossilized nuclei and germination structures identify Ediacaran ‘animal embryos’ as encysting protists
Huldtgren TE, Cunnigham JE, Yin C, Stampanoni M, Marone F, Donoghue PCJ, Bengtson S. (2011) Science 334: 1696-1699
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Evolutionary origins of animal skeletal biomineralization
Murdock DJE and Donoghue PCJ. (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, Donoghue PCJ. (2011) 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 JE and Donoghue PCJ. (2011) Systematic Biology 60: 700-712
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Is evolutionary history repeatedly rewritten in light of new fossil discoveries?
Tarver JE, Donoghue PCJ, Benton MJ. (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 XP, Bengtson S, Gostling NJ, Cunningham JA, Harvey THP, Kouchinsky A, Val’kov AK, Repetski JE, Stampanoni M, Donoghue PCJ. (2010). Palaeontology 53: 1291-1314.
PDF | DRYAD

Origins of multicellularity
Donoghue PCJ and Antcliffe JB. (2010) Nature 466: 41-42.
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Are palaeoscolecids ancestral ecdysozoans?
Harvey THP, Dong XP, Donoghue PCJ. (2010) Evolution & Development 12: 177-200.
PDF | DRYAD

microRNAs reveal the interrelationships of hagfishes, lampreys and gnathostomes, and the nature of the ancestral vertebrate
Heimberg AM, Cowper-Sal lari R, Sémon M, Donoghue PCJ, Peterson KJ. (2010) Proceedings of the National Academy of Sciences 107: 19379-19383.
PDF | Data

A formula for maximum possible steps in multistate characters: isolating matrix parameter effects on measures of evolutionary convergence
Hoyal Cuthill JF, Braddy SJ, Donoghue PCJ. (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, Donoghue PCJ. (2010) Systematic Biology 59: 74-89.
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2009

Calibrating and constraining the molecular clock
Benton MJ, Donoghue PCJ Asher RJ. (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 PCJ, Martínez-Pérez C. (2009) Acta Zoologica 90: 103-108
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Origin of vertebrates
Donoghue PCJ. (2009) In: Wilson EO, 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 PCJ and Purnell MA. (2009) Bioessays 31: 178-189
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The evolutionary emergence of vertebrates from their spineless relatives
Donoghue PCJ and Purnell MA. (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 JP and Donoghue PCJ. (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 NJ, Dong XP, Donoghue PCJ. (2009) Palaeontology 52: 169-186
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A new species of Markuelia from the Middle Cambrian of Australia
Haug JT, Maas A, Waloszek D, Donoghue PCJ, 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 AC, Galtier J, Gostling NJ, Smith SY, Collinson ME, Stampanoni M, Marone F, Donoghue PCJ, Bengtson S. (2009) Microscopy & Microanalysis 15: 166-173
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Origin and evolution of the integumentary skeleton in non-tetrapod vertebrates
Sire JY, Donoghue PCJ, Vickaryous M. (2009) Journal of Anatomy 214: 409-440
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2008

Exploring the links between development and evolution
Donoghue PCJ. (2008) In: Benton MJ (ed): Seventy great mysteries of the natural world, Thames & Hudson
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The origin and evolution of the neural crest
Donoghue PCJ, Graham A, Kelsh RN. (2008) BioEssays 30: 530-541
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The interrelationships of ‘complex’ conodonts (Vertebrata)
Donoghue PCJ, Purnell MA, Aldridge RJ, 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, NJ, Thomas CW, Greenwood JM, Dong XP, Bengtson S, Raff EC, Raff RA, Degnan BM, Stampanoni M, Donoghue PCJ. (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 PCJ, Peterson KJ. (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 EC, Schollaerrt KL, Nelson DE, Donoghue PCJ, Thomas CW, Turner FR, Stein BD, Dong XP, Bengtson S, Huldtgren T, Stampanoni M, Yin C, Raff RA. (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 RS, Rodygin S, Donoghue PCJ. (2008) Journal of Vertebrate Paleontology 20: 613-625
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2007

Palaeontological evidence to date the Tree of Life
Benton MJ and Donoghue PCJ. (2007) Molecular Biology & Evolution 24: 26-53
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Embryonic identity crisis
Donoghue PCJ. (2007) Nature 445:155-156
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Rocks and clocks: calibrating the Tree of Life using fossils and molecules
Donoghue PCJ and Benton MJ. (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 EM, Crane PR, Pedersen KR, Bengtson S, Donoghue PCJ, Grimm GW, Stampanoni M. (2007) Nature 450: 549-552
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The homology and phylogeny of chondrichthyan tooth enameloid
Gillis JA and Donoghue PCJ. (2007) Journal of Morphology 268: 33-49
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The earliest fossil embryos begin to mature
Gostling NJ, Donoghue PCJ, Bengtson S. (2007) Evolution & Development 9: 206-207
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Molecular palaeobiology
Peterson KJ, Summons RE, Donoghue PCJ. (2007) Palaeontology 50: 775-809
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2006

Synchrotron X-ray tomographic microscopy of fossilised embryos
Donoghue PCJ, Bengtson S, Dong XP, Gostling NJ, Huldtgren T, Cunningham JA, Yin C, Yue Z, Fan P, 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 PCJ, Gostling NJ, Bengtson S, Huldtgren T, Dong XP, Peng F, 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 PCJ, Kouchinsky A, Waloszek D, Bengtson S., Dong XP, Val’kov AK, Cunningham JA, Repetski JE. (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 PCJ, Sansom IJ, Downs JP. (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 JW, Xiao S, Donoghue PCJ, Bengtson S, Gostling NJ, Pawlowska M, Raff EC, Raff RA, Turner FR, Yin C, Zhou C, Yuan X, McFeely MB, Stampanoni M, Nealson KH. (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 XP, Donoghue PCJ, Muller KJ, Olempska E, Repetski JE, Siveter DJ, Stein M, Waloszek D. (2006) Palaeoworld 15: 266-282
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Experimental taphonomy shows the feasibility of fossil embryos
Raff EC, Vilinski JT, Turner FR, Donoghue PCJ, Raff RA. (2006) Proceedings of the National Academy of Sciences, USA 103: 5846-5851
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2005

The anatomy, affinity and phylogenetic significance of Markuelia
Dong XP, Donoghue PCJ, Cunningham JA, Liu JB, 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 XP, Donoghue PCJ, Repetski JE. (2005) Palaeontology 48: 411-421
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The fossils of Orsten-type preservation from Middle and Upper Cambrian in Hunan, China
Dong XP, Donoghue PCJ, Liu Z, Liu JB, Peng F. (2005) Chinese Science Bulletin 50: 1352-1357
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Saving the stem-group – a contradiction in terms
Donoghue PCJ. (2005) Paleobiology 31: 553-558
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Carl Gegenbaur and evolutionary morphology
Donoghue PCJ. (2005) Acta Zoologica 85: 265-266
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Embryos and ancestors
Donoghue PCJ and Dong XP. (2005) In: Briggs DEG (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 PCJ and Purnell MA. (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 MA and Donoghue PCJ. (2005) Special Papers in Palaeontology 73: 7-25
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Histology and affinity of the earliest armoured vertebrate
Sansom IJ, Donoghue PCJ, Albanesi GL. (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 MP, Donoghue PCJ, Repetski JE. (2005) In: Barrick JE and Lane HR. (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 NZ, Donoghue PCJ, Smith MM, Sansom IJ. (2005) Journal of Vertebrate Paleontology 25: 745-756
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Cladograms, phylogenies and the veracity of the conodont fossil record
Wickström LM and Donoghue PCJ. (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 XP, Donoghue PCJ, Cheng H, Liu JB. (2004). Nature 427: 237-240
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2003

Telling the evolutionary time: molecular clocks and the fossil record
Donoghue PCJ and Smith MP. (eds) CRC Press, London (2003)

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

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

The distribution of ostracoderms in the Mid-Ordovician of Laurentia and Gondwana
Sansom IJ, Smith MP, Donoghue PCJ. (2003) pp. 545-549 In: Albanesi GL Beresi MS, Peralta SH (eds). Ordovician from the Andes. Instituto Superior de Correlación Geológica, Tucumán, Argentina.

The spatial and temporal diversification of Early Palaeozoic vertebrates
Smith MP, Donoghue PCJ, Sansom IJ. (2003) pp. 69-83 In: Crame JA and Owen AWA (eds). Palaeobiogeography and biodiversity change: the Ordovician and Mesozoic-Cenozoic radiations. Geological Society Special Publication 194. The Geological Society, London.
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2002

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

Microstructural variation in conodont enamel is a functional adaptation
Donoghue PCJ. (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 PCJ. (2001) Palaeontology 44: 65-93
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Origin of a mineralised skeleton
Donoghue PCJ and Aldridge RJ. (2001) pp. 85-105 In: Ahlberg PE (ed.). Major events in early vertebrate evolution: palaeontology, phylogeny, genetics and development. Taylor & Francis, London.

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

Orientation and anatomical notation in conodonts
Purnell MA, Donoghue PCJ, Aldridge RJ. (2000) Journal of Paleontology 74: 113-122
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Conodont affinity and chordate phylogeny
Donoghue PCJ, Forey PL, Aldridge RJ. (2000) Biological Reviews 75: 191-251
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1999

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

1998

Conodonts: a sister group to hagfish?
Aldridge RJ and Donoghue PCJ. (1998) pp. 15-31 In: Jørgensen JM, Lomholt JP, Weber RE, Malte H. (ed.) The Biology of Hagfishes. Chapman and Hall, London.
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Growth and patterning in the conodont skeleton
Donoghue PCJ. (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 PCJ, Purnell MA, Aldridge RJ. (1998) Lethaia 31: 211-219
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Architecture and functional morphology of the skeletal apparatus of ozarkodinid conodonts
Purnell MA and Donoghue PCJ. (1998) Palaeontology 41: 57-102
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1997

A technique for conodont histology
Donoghue PCJ. (1997) Lethaia 30: 329-330
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Skeletal architecture and functional morphology of ozarkodinid conodonts
Purnell MA and Donoghue PCJ. (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 RJ, Donoghue PCJ. (1997) Journal of Micropalaeontology 16: 65-72
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1995

Conodonts and the first vertebrates
Purnell MA, Aldridge RJ, Donoghue PCJ, Gabbott SE (1995). Endeavour 19: 20-27
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