in press
A divergence dating analysis of turtles using fossil calibrations: an example of best practiseJoyce, W. G., Parham, J. F., Lyson, T. R., Warnock, R. C. M. and Donoghue, P. C. J. (in press) Journal of Paleontology
Embryos, polyps and medusa of the early Cambrian scyphozoan OlivooidesDong, X.-P., Cunningham, J. A., Bengtson, S., Thomas, C.-W., Liu, J.-B., Stampanoni, M. and Donoghue, P. C. J. (in press) Proceedings of the Royal Society B: Biological Sciences.
The histology of ‘placoderm’ dermal skeletons: implications for the nature of the ancestral gnathostome
Giles, S., Rücklin, M., Donoghue, P. C. J. (in press) Journal of Morphology.
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.
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.
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.
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.
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.
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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.
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.
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.
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.
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.
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.
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:
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Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish)
Shimeld, S. M. and Donoghue, P. C. J. (2012). Developmental Biology 139: 2091-2099.
Do microRNAs have a deep evolutionary history?
Tarver, J. E., Peterson, K. J., Donoghue, P. C. J. (2012) BioEssays 34: 857-866.
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
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
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
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
Evolutionary origins of animal skeletal biomineralization
Murdock, D. J. E. and Donoghue, P. C. J. (2011) Cells, Tissues, Organs 194: 98-102
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
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
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.
2010
The anatomy, taphonomy, taxonomy and systematic affinity of Markuelia: Early Cambrian to Early Ordovician scalidophoransDong, 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.
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Origins of multicellularity
Donoghue, P. C. J. and Antcliffe, J. B. (2010). Nature 466: 41-42.
Are palaeoscolecids ancestral ecdysozoans?
Harvey, T. H. P., Dong, X.-P. and Donoghue, P. C. J. (2010). Evolution & Development 12: 177-200.
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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.
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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.
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.
2009
Calibrating and constraining the molecular clockBenton, 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
Enameloid microstructure in the oldest known chondrichthyan teeth
Botella, H., Donoghue, P. C. J. and Martínez-Pérez, C. 2009. Acta Zoologica 90: 103-108
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
Distinguishing heat from light in debate over controversial fossils
Donoghue, P. C. J. and Purnell, M. A. 2009. Bioessays 31: 178-189
The evolutionary emergence of vertebrates from their spineless relatives
Donoghue, P. C. J. and Purnell, M. A. 2009. Evolution: Education & Outreach 2: 204-212
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
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
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
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
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
2008
Exploring the links between development and evolutionDonoghue, P. C. J. 2008. In: Benton, M. J. (ed): Seventy great mysteries of the natural world, Thames & Hudson
The origin and evolution of the neural crest
Donoghue, P. C. J., Graham, A. and Kelsh, R. N. 2008. BioEssays 30: 530-541 (2008)
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
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
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
2007
Palaeontological evidence to date the Tree of LifeBenton, M. J. and Donoghue, P. C. J. 2007. Molecular Biology & Evolution 24: 26-53
Embryonic identity crisis
Donoghue, P. C. J. 2007. Nature 445:155-156
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
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
The homology and phylogeny of chondrichthyan tooth enameloid
Gillis, J. A. and Donoghue, P. C. J. 2007. Journal of Morphology 268: 33-49
The earliest fossil embryos begin to mature
Gostling, N. J., Donoghue, P. C. J. and Bengtson, S. 2007. Evolution & Development 9: 206-207
Molecular palaeobiology
Peterson, K. J., Summons, R. E. and Donoghue, P. C. J. 2007. Palaeontology 50: 775-809
2006
Synchrotron X-ray tomographic microscopy of fossilised embryosDonoghue, 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
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
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
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
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
2005
The anatomy, affinity and phylogenetic significance of MarkueliaDong, 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
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
Saving the stem-group - a contradiction in terms
Donoghue, P. C. J. 2005. Paleobiology 31: 553-558
Carl Gegenbaur and evolutionary morphology
Donoghue, P. C. J. 2005. Acta Zoologica 85: 265-266
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
Genome duplication, extinction and vertebrate evolution
Donoghue, P. C. J. and Purnell, M. A. 2005. Trends in Ecology & Evolution 20: 312-319
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
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
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
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
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 ChinaDong, 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 recordDonoghue, 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
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
2002
Evolution of development of vertebrate teeth and scales: unravelling concepts, regulatory theories and homologiesDonoghue, P. C. J. 2002. Paleobiology 28: 474-507
Origin and early evolution of vertebrate skeletonization
Donoghue, P. C. J. and Sansom, I. J. 2002. Microscopy Research & Technique 59: 352-372
2001
Microstructural variation in conodont enamel is a functional adaptationDonoghue, P. C. J. 2001. Proceedings of the Royal Society of London, Series B 268: 1691-1698
Conodonts meet cladistics: recovering relationships and assessing the completeness of the conodont fossil record
Donoghue, P. C. J. 2001. Palaeontology 44: 65-93
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
Conodonts: past, present and future
Sweet, W. C. and Donoghue, P. C. J. 2001. Journal of Paleontology 75: 1174-1184
2000
Orientation and anatomical notation in conodontsPurnell, M. A., Donoghue, P. C. J. and Aldridge, R. J. 2000. Journal of Paleontology 74: 113-122
Conodont affinity and chordate phylogeny
Donoghue, P. C. J., Forey, P. L. and Aldridge, R. J. 2000. Biological Reviews 75: 191-251
1999
Conchodontus, Mitrellataxis and Fungulodus: conodonts, fish, or both?Donoghue, P. C. J. and Chauffe, K. 1999. Lethaia 31: 283-292
Mammal-like occlusion in conodonts
Donoghue, P. C. J. and Purnell, M. A. 1999. Paleobiology 25: 58-74
Growth, function, and the fossil record of conodonts
Donoghue, P. C. J. and Purnell, M. A. 1999. Geology 27: 251-254
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
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
Conodont anatomy, chordate phylogeny and vertebrate classification
Donoghue, P. C. J., Purnell, M. A. and Aldridge, R. J. 1998. Lethaia 31: 211-219
Architecture and functional morphology of the skeletal apparatus of ozarkodinid conodonts
Purnell, M. A. and Donoghue, P. C. J. 1998. Palaeontology 41: 57-102
1997
A technique for conodont histologyDonoghue, P. C. J. 1997. Lethaia 30: 329-330
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
An Early Triassic conodont with periodic growth?
Zhang, S., Aldridge, R. J. and Donoghue, P. C. J. 1997. Journal of Micropalaeontology 16: 65-72
1995
Conodonts and the first vertebratesPurnell, M. A., Aldridge, R. J., Donoghue, P. C. J. and Gabbott, S. E. 1995. Endeavour 19: 20-27