in press
Developmental biology of Spiralicellula and the Ediacaran origin of crown metazoans
Sun W, Yin Z, Liu P, Zhu Z, Donoghue PCJ (2024) Proceedings of the Royal Society B
2024
Cryogenian origins of multicellularity in Archaeplastida
Bowles AMC, Williams TA, Williamson CJ, Donoghue PCJ (2024) Genome Biology & Evolution 16: evae026 | PDF
Resolving incongruences in insect phylogenomics: a reply to Boudinot et al. (2023)
Cai CY, Tihelka E, Pisani D, Donoghue PCJ (2024) Palaeoentomology 7: 176-183 | PDF
Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land
Donoghue PCJ, Clark JW (2024) Current Biology 34: R86-R89 | PDF
Testing hypotheses of pteraspid heterostracan feeding using computational fluid dynamics
Groghanz M, Ferron HG, Johanson Z, Donoghue PCJ (2024) Journal of Vertebrate Paleontology 43: e2272974 | PDF
The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes
Dearden R, Jones A, Giles S, Lanzetti A, Grohganz M, Johanson Z, Lautenschlager S, Randle E, Donoghue PCJ, Sansom IJ (in press) Proceedings of the Royal Society B 291: 20232258 | PDF
Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences
Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni WA, D’Aniello S, Bertolucci C, Irie N, Alev C, Sheng, G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE Pascual-Anaya J (2024) Nature Ecology & Evolution 8: 519-535 | PDF
2023
The origin and early evolution of plants
Bowles AM, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ (2023) Trends in Plant Sciences 28: 312-329 | PDF
A timescale for placental mammal diversification based on Bayesian modelling of the fossil record
Carlisle E, Janis CM, Pisani D, Donoghue PCJ, Silvestro D (2023) Current Biology 33: 3073-3082 | PDF
Constraining whole genome duplication events in geological time
Clark JW, Donoghue PCJ (2023) Pp. 139-154. In: Van der Peer (ed) Polyploidy: methods and protocols. Humana Press, New York | PDF
Evolution of phenotypic disparity in the plant kingdom
Clark JW, Hetherington AJ, Morris JL, Pressel S, Duckett JG, Puttick MN, Schneider H, Kenrick P, Wellman CH, Donoghue PCJ (2023) Nature Plants 9: 1618-1626 | PDF
Defining eukaryotes to dissect eukaryogenesis
Donoghue PCJ, Kay C, Spang A, Szollosi G, Nenarokova A, Moody ERR, Pisani D, Williams TA (2023) Current Biology 33: R919-929 | PDF
Getting inside the oldest known vertebrate skull
Gai ZK, Donoghue PCJ (2023) Nature 621: 696-698 | PDF
Postcranial disparity in galeaspids and the evolution of swimming speeds in stem-gnathostomes
Gai ZK, Lin X, Shan X, Ferrón HG, Donoghue PCJ (2023) National Science Review 10: nwad050 | PDF
Exceptionally preserved conodont natural assemblages from the Middle Triassic Luoping Biota, Yunnan Province, China: implications for architecture of conodont feeding apparatus
Huang J, Martínez-Pérez C, Zhang Q, Zhang K, Luo M, Wen W, Zhou C, Min X, Ma Z, Xie T, Benton MJ, and Donoghue PCJ (2023) Journal of Earth Science 34: 1762-1776 | PDF
ATP synthase evolution on a cross-braced dated tree of life
Mahendrarajah T, Moody ERR, Schrempf D, Szánthó L, Dombrowski N, Davín A, Pisani D, Donoghue PCJ, Szöllősi G, Williams TA, Spang A (2023) Nature Communications 14: 7456 | PDF
Three-dimensional reconstruction, taphonomic and petrological data suggest the oldest record of bioturbation is a body fossil coquina
Psarras C, Donoghue PCJ, Garwood RJ, Grazhdankin DV, Parry LA, Rogov VI, Liu AG (2023) Papers in Palaeontology 9: e1531 | PDF
Fossilisation can mislead analyses of phenotypic disparity
Smith TJ, Sansom RS, Pisani D, Donoghue PCJ (in press) Proceedings of the Royal Society B 290: 20230522 | PDF
The unbearable uncertainty of panarthropod relationships
Wu R, Pisani D, Donoghue PCJ (2023) Biology Letters 2022.0497 | PDF
2022
A species-level timeline of mammal evolution integrating phylogenomic data
Álvarez-Carretero S, Tamuri AU, Battini M, Nascimento FF, Carlisle E, Asher RJ, Yang Z, Donoghue PCJ, dos Reis M (2022) Nature 602: 263-267 | PDF
Integrated phylogenomics and fossil data illuminate the evolution of beetles
Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Huang D, Pisani D, Donoghue PCJ (2022) Royal Society Open Science 9: 211771 | PDF
Increasing morphological disparity and decreasing optiality for jaw speed and strength during the radiation of jawed vertebrates
Deakin WJ, Anderson PSL, den Boer W, Smith WJ, Hill JJ, Rücklin M, Donoghue PCJ, Rayfield EJ (2022) Science Advances 8: eabl3644 | PDF
Internal anatomy of a fossilized embryonic stage of the Cambrian-Ordovician scalidophoran Markuelia
Dong XP, Duan BC, Liu JB, Donoghue PCJ (2022) Royal Society Open Science 9: 220115 | PDF
Galeaspid anatomy and origin of vertebrate paired appendages
Gai ZK, Li Q, Ferrón HG, Keating JN, Wang JQ, Donoghue PCJ, Zhu M (2022) Nature 609: 959-963 | PDF
The evolution of the spiracular region from jawless fishes to tetrapods
Gai ZK, Zhu M, Ahlberg PE, Donoghue PCJ (2022) Frontiers in Ecology and Evolution 10: 887172 | PDF
Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants
Harris BJ, Clark JW, Schrempf D, Szöllösi GJ, Donoghue PCJ, Hetherington AM, Williams TA (2022) Nature Ecology & Evolution 6: 1634-1643 | PDF
Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data
Howard RJ, Giacomelli, M, Lozano-Fernandez J, Edgecombe GE, Fleming JF, Kristensen RM, Ma X, Olesen J, Sørensen MV, Thomsen PF, Wills MA, Donoghue PCJ, Pisani D (2022) Journal of the Geological Society 179: jgs2021-107 | PDF
Evolutionary analysis of swimming speed in early vertebrates challenges the ‘New Head Hypothesis’
Ferrón HG and Donoghue PCJ (2022) Communications Biology 5: 863 | PDF
Integrative phylogenetics: tools for palaeontologists to explore the tree of life
López-Antoñanzas R, Mitchell J, Simões TR, Condamine FL, Aguilée R, Peláez-Campomanes P, Renaud S, Rolland J, Donoghue PCJ (2022) Biology 11: 11081185 | PDF
Saccorhytus is an early ecdysozoan and not the earliest deuterostome
Liu YH, Carlisle E, Zhang HQ, Yang B, Steiner M, Shao TQ, Duan BC, Marone F, Xiao SH, Donoghue PCJ (2022) Nature 609: 541-546 | PDF
Eukaryogenesis and oxygen in Earth history
Mills DB, Boyle RA, Daines SJ, Sperling EA, Pisani D, Donoghue PCJ, Lenton TM (2022) Nature Ecology & Evolution 6: 520-532 | PDF
Evolution of fungal phenotypic disparity
Smith TJ, Donoghue PCJ (2022) Nature Ecology & Evolution 6: 1489-1500 | PDF
Dietary inference from dental topographic analysis of feeding tools in diverse animals
Stockey C, Adams NF, Harvey THP, Donoghue PCJ, Purnell MA (2022) Methods in Ecology and Evolution 13: 1464-1474 | PDF
2021
X-Ray nanotomography and Electron Backscatter Diffraction demonstrate the crystalline, heterogeneous and impermeable nature of conodont white matter
Atakul-Özdemir A, Warren X, Martin, PG, Guizar-Sicairos M, Holler M, Marone F, Martínez-Pérez, Donoghue PCJ (2021) Royal Society Open Science | PDF
Diversification dynamics of total-, stem- and crown-groups are compatible with molecular clock estimates of divergence times
Beavan AJS, Pisani D, Donoghue PCJ (2021) Science Advances 7: eabf2257 | PDF
Experimental taphonomy of organelles and the fossil record of early eukaryote evolution
Carlisle EM, Jobbins M, Pankhania V, Cunningham JA, Donoghue PCJ (2021) Science Advances 7: eabe9487 | PDF
The evolutionary emergence of land plants
Donoghue PCJ, Harrison CJ, Paps J, Schneider H (2021) Current Biology 31: R1281-R1298 | PDF
The developmental biology of Charnia and the eumetazoan affinity of Ediacaran rangeomorphs
Dunn FS, Liu AG, Grazhdankin DV, Vixseboxse P, Flannery-Sutherland J, Green E, Harris S, Wilby PR, Donoghue PCJ (2021) Science Advances 7: eabe0291 | PDF
Functional assessment of morphological homoplasy in stem-gnathostomes
Ferrón HG, Martínez-Pérez C, Rahman IA, Selles de Lucas V, Botella H, Donoghue PCJ (2021) Proceedings of the Royal Society B 288: 20202719 | PDF
Coevolution of enamel, ganoin, enameloid, and their matrix SCPP genes in osteichthyans
Kawasaki K, Keating JN, Nakatomi M, Welten M, Mikami M, Sasagawa I, Puttick MN, Donoghue PCJ, Ishiyama M (2020) iScience 24: 102023 | PDF
Empirical distributions of homology in morphological data
Murphy JL, Puttick MN, O’Reilly JE, Pisani D, Donoghue PCJ (2021) Palaeontology 64: 505-518 PDF
Fossilization processes have little impact on tip-calibrated divergence time analyses
O’Reilly JE and Donoghue PCJ (2021) Palaeontology | PDF
Acanthodian dental development and the origin of gnathostome dentitions
Rücklin M, King B, Cunningham JA, Johanson Z, Marone F, Donoghue PCJ (2021) Nature Ecology & Evolution 5: 919-926 | PDF
Fossil data support a pre-Cretaceous origin of flowering plants
Silvestro D, Bacon CD, Ding W, Zhang Q, Donoghue PCJ, Antonelli A, Xing Y (2021) Nature Ecology & Evolution 5: 449-457 | PDF
Unbiased clade age estimation using a Bayesian Brownian Bridge
Silvestro D, Bacon CD, Ding W, Zhang Q, Donoghue PCJ, Antonelli A, Xing Y (2021) BioRxiv | PDF
Phylogenetic sampling affects evolutionary patterns of morphological disparity
Smith TJ, Puttick MN, O’Reilly JE, Pisani D, Donoghue PCJ (2021) Palaeontology 64: 765-787 | PDF
Exceptionally preserved early Cambrian bilaterian developmental stages from Mongolia
Steiner M, Yang B, Hohl S, Li D, Donoghue PCJ (2021) Nature Communications 12: 1037 | PDF
Ultrastructure and in-situ characterization of intracellular granules of embryo-like fossils from the early Ediacaran Weng’an Biota
Sun W-C, Yin Z-J, Liu P-J, Donoghue PCJ, Li J-H, Zhu M-Y (2021) PalZ | PDF
The evolution of insect biodiversity
Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D (2021) Current Biology 31: R1299-R1311 | PDF
2020
Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation
Beavan AJS, Donoghue PCJ, Beaumont MA, Pisani D (2020) Genome Biol Evol 12: 1087-1098 | PDF
Data curation and modeling of compositional heterogeneity in insect phylogenomics: a case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga)
Cai C, Tihelka E, Pisani D, Donoghue PCJ (2020) Molecular Phylogenetics and Evolution: 106782 | PDF
Plant Evolution: Assembling land plants
Donoghue PCJ, Paps J (2020) Current Biology 30: R81-R83 | PDF
Fossil cells
Donoghue PCJ (2020) Current Biology 30: R485-R490 | PDF
Categorical versus geometric morphometric approaches to characterizing the evolution of morphological disparity in Osteostraci (Vertebrata, stem Gnathostomata)
Ferrón HG, Greenwood JM, Deline B, Martínez‐Pérez C, Botella H, Sansom RS, Ruta M, Donoghue PCJ (2020) Palaeontology 63: 717-732 | PDF
Computational fluid dynamics suggests ecological diversification among stem-gnathostomes
Ferrón HG, Martínez-Pérez C, Rahman IA, Selles de Lucas V, Botella H, Donoghue PCJ (2020) Current Biology 30: 4808-4813 | PDF
Disparities in the analysis of morphological disparity
Guillerme T, Cooper N, Brusatte SL, Davis KE, Jackson AL, Gerber S, Goswami A, Healy K, Hopkins MJ, Jones MEH, Lloyd GT, O’Reilly JE, Pate A, Puttick MN, Rayfield EJ, Saupe EE, Sherratt E, Slater GJ, Weisbecker V, Thomas GH, Donoghue PCJ (2020) Biology Letters 16: 20200199 | PDF
The effect of fossil sampling on the estimation of divergence times with the fossilized birth death process
O’Reilly JE, Donoghue, PCJ (2019) Systematic Biology 69: 124-138 | PDF
The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates
Püschel, HP, O’Reilly, JE, Pisani, D, Donoghue, PCJ, and Rahman, I (2020) Palaeontology 63: 67-83 | PDF
Nucleus preservation in early Ediacaran Weng’an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record
Sun W, Yin Z, Cunningham JA, Liu P, Zhu M, Donoghue PCJ (2020) Interface Focus 10: 20200015 | PDF
Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera)
Tihelka E, Cai C, Pisani D, Donoghue PCJ (2020) Scientific Reports 10: 14515 | PDF
Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmodea) reveal a Permian-Triassic co-origination with insectivores
Tihelka E, Cai C, Giacomelli M, Pisani D, Donoghue PCJ (2020) Royal Society Open Science 7: 201689 | PDF
Fleas are parasitic scorpionflies
Tihelka E, Giacomelli M, Huang D-Y, Pisani D, Donoghue PCJ (2020) Palaeoentomology 3: 641-653 | PDF
The origin and rise of complex life: progress requires interdisciplinary integration and hypothesis testing
Wood R, Donoghue PCJ, Lenton TM, Liu AG, Poulton SW (2020) Interface Focus 10: 20200024 | PDF
Developmental biology of Helicoforamina reveals holozoan affinity, cryptic diversity, and adaptation to heterogeneous environments in the early Ediacaran Weng’an biota (Doushantuo Formation, South China)
Yin Z, Sun W, Liu P, Zhu M, Donoghue PCJ (2020) Sciences Advances 6: eabb0083 | PDF
2019
Origin of horsetails and the role of whole-genome duplication in plant macroevolution
Clark JW, Puttick MN, Donoghue PCJ (2019) Proceedings of the Royal Society B 286: 20191662 | PDF
Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)
de Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ (2019) New Phytologist 222: 565-575 | PDF
The apparatus composition and architecture of Erismodus quadridactylus and the implications for element homology in prioniodinin conodonts
Dhanda R, Murdock DJE, Repetski JE, Donoghue PCJ, Smith MP (2019) Papers in Palaeontology 5: 657-677 | PDF
Tooth replacement in early sarcopterygians
Doeland M, Couzens AMC, Donoghue PCJ, Rücklin M (2019) Royal Society Open Science 6: 1-14 | PDF
Evolution: The flowering of land plant evolution
Donoghue PCJ (2019) Current Biology 29: R753-R756 | PDF
The circulatory system of Galeaspida (Vertebrata; stem-Gnathostomata) revealed by synchrotron X-ray tomographic microscopy
Gai Z-K, Zhu M, Donoghue PCJ (2019) Palaeoworld 28: 441-460 | PDF
Apparatus architecture of the conodont Nicoraella kockeli (Gondolelloidea, Prioniodinina) constrains functional interpretations
Huang J, Martínez‐Pérez C, Hu S, Zhang Q, Zhang K, Zhou C, Wen W, Xie T, Benton MJ, Chen ZQ, Luo M, Donoghue PCJ (2019) Palaeontology 62: 823-835 | PDF
Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography
Huang J-Y, Martínez-Pérez C, Hu S-X, Donoghue PCJ, Zhang Q-Y, Zhou C-Y, Wen W, Benton MJ, Luo M, Yao H-Z, Zhang K-X (2019) Palaeoworld 28: 429-440 | PDF
Cellular preservation of excysting developmental stages of new eukaryotes from the early Ediacaran Weng’an Biota
Landon ENU, Liu P-J, Yin Z-J, Sun W-C, Shang X-D, Donoghue PCJ (2019) Palaeoworld 28: 461-468 | PDF
The dermal skeleton of the jawless vertebrate Tremataspis mammillata (Osteostraci, stem-Gnathostomata)
O’Shea J, Keating JN, Donoghue PCJ (2019) Journal of Morphology 280: 999-1025 | PDF
Evolutionary origin of teeth
Rücklin M, and Donoghue PCJ (2019) in eLS, 1-7 | PDF
Tubular microfossils from the Ediacaran Weng’an Biota (Doushantuo Formation, South China) are not early animals
Sun W-C, Yin Z-J, Donoghue P, Liu P-J, Shang X-D, Zhu M-Y (2019) Palaeoworld 28: 469-477 | PDF
The early Ediacaran Caveasphaera foreshadows the evolutionary origin of animal-like embryology
Yin Z, Vargas K, Cunningham JA, Bengtson S, Zhu M, Marone F, Donoghue PCJ (2019) Current Biology 29: 4307-4314 | PDF
2018
Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution
Barba-Montoya J, Dos Reis M, Schneider H, Donoghue PCJ, Yang Z (2018) New Phytologist 218: 819-834 | PDF
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 | PDF
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 28:3288-3295 | PDF
Whole-genome duplication and plant macroevolution
Clark JW, Donoghue PCJ (2018) Trends in Plant Science 23: 933-945 | PDF
Evolution of metazoan morphological disparity
Deline B, Greenwood JM, Clark JW, Puttick MN, Peterson KJ, Donoghue PCJ (2018) Proceedings of the National Academy of Sciences 115: E8909-E8918 | PDF
Ediacaran developmental biology
Dunn FS, Liu AG, Donoghue PCJ (2018) Biological Revews 93: 914–932 | PDF
Anatomy of the Ediacaran rangeomorph Charnia masoni
Dunn FS, Wilby PR, Kenchington CG, Grazhdankin DV, Donoghue PCJ, Liu AG (2018) Papers in Palaeontology 5: 157-176 | PDF
Evolution of jaw disparity in fishes
Hill JJ, Puttick MN, Stubbs TL, Rayfield EJ, Donoghue PCJ (2018) Palaeontology 61: 847-854 | PDF
Gondolelloid multielement conodont apparatus (Nicoraella) from the Middle Triassic of Yunnan Province, southwestern China
Huang J, Hu S, Zhang Q, Donoghue PCJ, Benton MJ, Zhou C, Martínez-Pérez C, Wen W, Xie T, Chen Z-Q, Luo M, Yao H, Zhang K (2018) Palaeogeography, Palaeoclimatology, Palaeoecology 522: 98-110 | PDF
The nature of aspidin and the evolutionary origin of bone
Keating JN, Marquart CL, Marone F, Donoghue PCJ (2018) Nature Ecology & Evolution 2: 1501-1506 | PDF
Vascular structure of the earliest shark teeth
Martínez-Pérez C, Martín-Lazaro A, Ferrón HG, Kirstein M, Donoghue PCJ, Botella H (2018) Acta Geologica Polonica 68: 457-465 | PDF
The timescale of early land plant evolution
Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ (2018) Proceedings of the National Academy of Sciences 115: E2274-E2283 | PDF
Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations
Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH, Yang Z, Schneider H, Donoghue PCJ (2018) Proceedings of the National Academy of Sciences | PDF
Efficacy of consensus tree methods for summarizing phylogenetic relationships from a posterior sample of trees estimated from morphological data
O’Reilly JE, Donoghue PCJ (2018) Systematic Biology 67: 354-362 | PDF
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 | PDF
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 | PDF
Experimental analysis of soft-tissue fossilization: opening the black box
Purnell MA, Donoghue PCJ, Gabbott SE, McNamara ME, Murdock DJE, Sansom RS (2018) Palaeontology 61: 317-323 | PDF
The interrelationships of land plants and the nature of the ancestral embryophyte
Puttick MN, Morris JL, Williams TA, Cox CJ, Edwards D, Kenrick P, Pressel S, Wellman CH, Schneider H, Pisani D, Donoghue PCJ (2018) Current Biology 28: R210-R213 PDF
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 62: 1-17 | PDF
Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss
Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ (2018) Genome Biology & Evolution 10: 1457-1470 | PDF
2017
Constraining the timing of whole genome duplication in plant evolutionary history
Clark JW, Donoghue PCJ (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20170912 | PDF
The origin of animals: Can molecular clocks and the fossil record be reconciled?
Cunningham JA, Liu AG, Bengtson S, Donoghue PCJ (2017) Bioessays 39: e201600120 | PDF
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 | PDF
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 X-P, 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: 20170194 | PDF
Evolution: Divining the Nature of the Ancestral Vertebrate
Donoghue P (2017) Current Biology 27: R277-R279 | PDF
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 | PDF
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 | PDF
Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al
Puttick MN, O’Reilly JE, Oakley D, Tanner AR, Fleming JF, Clark J, Holloway L, Lozano-Fernandez J, Parry LA, Tarver JE, Pisani D, Donoghue PCJ (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20171636 | PDF
Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data
Puttick MN, O’Reilly JE, Tanner AR, Fleming JF, Clark J, Holloway L, Lozano-Fernandez J, Parry LA, Tarver JE, Pisani D, Donoghue PC (2017) Proceedings of the Royal Society B: Biological Sciences 284: | PDF
MicroRNA annotation of plant genomes – Do it right or not at all
Taylor RS, Tarver JE, Foroozani A, Donoghue PC (2017) Bioessays 39: 1600113 | PDF
Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution
Warnock RCM, Yang Z, Donoghue PCJ (2017) Proceedings of the Royal Society B: Biological Sciences 284: 20170227 | PDF
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 | PDF
2016
A multicellular organism with embedded cell clusters from the Ediacaran Weng’an biota (Doushantuo Formation, South China)
Cunningham JA, Vargas K, Marone F, Bengtson S, Donoghue PCJ (2016) Evolution & Development 18: 308-316 | PDF
Tectonic blocks and molecular clocks
De Baets K, Antonelli A, Donoghue PC (2016) Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20160098 | PDF
Developmental biology of the early Cambrian cnidarian Olivooides
Dong X-P, Vargas K, Cunningham JA, Zhang H, Liu T, Chen F, Liu J, Bengtson S, Donoghue PCJ (2016) Palaeontology 59: 387-407 | PDF
The ins and outs of the evolutionary origin of teeth
Donoghue PC, Rücklin M (2016) Evolution & Development 18: 19-30 | PDF
The evolution of methods for establishing evolutionary timescales
Donoghue PC, Yang Z (2016) Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20160020 | PDF
Bayesian molecular clock dating of species divergences in the genomics era
dos Reis M, Donoghue PCJ, Yang Z (2016) Nature Reviews Genetics 17: 71-80 | PDF
Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye
Gabbott SE, Donoghue PC, Sansom RS, Vinther J, Dolocan A, Purnell MA (2016) Proceedings of the Royal Society B: Biological Sciences 283: 20161151 | PDF
Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton
Keating JN, Donoghue PCJ (2016) Proceedings of the Royal Society B: Biological Sciences 283: 20152917 | PDF
Evolution of the Calcium-Based Intracellular Signaling System
Marchadier E, Oates ME, Fang H, Donoghue PC, Hetherington AM, Gough J (2016) Genome Biology & Evolution 8: 2118-2132 | PDF
Translating taxonomy into the evolution of conodont feeding ecology
Martinez-Perez C, Rayfield EJ, Botella H, Donoghue PCJ (2016) Geology 44: 247-250 | PDF
Tips and nodes are complementary not competing approaches to the calibration of molecular clocks
O’Reilly JE, Donoghue PCJ (2016) Biology Letters 12: 20150975 | PDF
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 LA, Tanner AR, Tarver JE, Fleming J, Pisani D, Donoghue PCJ (2016) Biology Letters 12: 20160081 | PDF
Reply to ‘placoderms and the evolutionary origin of teeth’: Burrow et al. (2016)
Rücklin M, Donoghue PCJ (2016) Biology Letters 12: 20160526 | PDF
The interrelationships of placental mammals and the limits of phylogenetic inference
Tarver JE, dos Reis M, Mirarab S, Moran RJ, Parker S, O’Reilly JE, King BL, O’Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D (2016) Genome Biology & Evolution 8: 330-344 | PDF
Dating species divergences using rocks and clocks
Yang Z, Donoghue PC (2016) Philosophical Transactions of the Royal Society B: Biological Sciences 371: 20150126 | PDF
2015
Constraints on the timescale of animal evolutionary history
Benton MJ, Donoghue PCJ, Asher RJ, Friedman M, Near TJ, Vinther J (2015) Palaeontologia Electronica 18: 1-106 | PDF
Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization
Butler AD, Cunningham JA, Budd GE, Donoghue PC (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20150476 | PDF
Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng’an Doushantuo biota
Cunningham JA, Vargas K, Pengju L, Belivanova V, Marone F, Martinez-Perez C, Guizar-Sicairos M, Holler M, Bengtson S, Donoghue PC (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20151169 | PDF
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) in DeBaets, K, and Littlewood, DTJ, eds. Fossil Parasites, 93-135 | PDF
Embryology in deep time
Donoghue PCJ, Cunningham JA, Dong X-P, Bengtson S (2015) in Wanninger, A, ed. Evolutionary developmental biology of invertebrates, Volume 1: Introduction, Non-Bilateria, Acoelomorpha, Xenoturbellida, Chaetognatha, Vienna: Springer, 45-63 | PDF
Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales
dos Reis M, Thawornwattana Y, Angelis K, Telford Maximilian J, Donoghue Philip CJ, Yang Z (2015) Current Biology 25: 2939-2950 | PDF
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, Menzel A, Lai B (2015) in X-Ray Nanoimaging: Instruments and Methods 9592: 95920A | PDF
Do cladistic and morphometric data capture common patterns of morphological disparity?
Hetherington AJ, Sherratt E, Ruta M, Wilkinson M, Deline B, Donoghue PCJ, Angielczyk K (2015) Palaeontology 58: 393-399 | PDF
Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton
Keating JN, Marquart CL, Donoghue PCJ (2015) Journal of Morphology 276: 657–680 | PDF
The Fossil Calibration Database, a new resource for divergence dating
Ksepka DT, Parham JF, Allman JF, Benton MJ, Carrano MT, Cranston KA, Donoghue PCJ, Head JJ, Hermsen EJ, Irmis RB, Joyce WG, Kohli M, Lamm KS, Leehr D, Patané JSL, Polly PD, Phillips MJ, Smith NA, Smith ND, van Tuinen M, Ware JL, Warnock RCM (2015) Systematic Biology 64: 853-859 | PDF
Dating tips for divergence-time estimation
O’Reilly JE, dos Reis M, Donoghue PCJ (2015) Trends in Genetics 31: 637-650 | PDF
Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms
Puttick MN, Clark J, Donoghue PC (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20152289 | PDF
Romundina and the evolutionary origin of teeth
Rucklin M, Donoghue PCJ (2015) Biology Letters 11: 20150326 | PDF
Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history
Sansom RS, Randle E, Donoghue PC (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20142245 | PDF
Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils
Schirrmeister BE, Gugger M, Donoghue PCJ (2015) Palaeontology 58: 769-785 | PDF
Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors
Warnock RC, Parham JF, Joyce WG, Lyson TR, Donoghue PC (2015) Proceedings of the Royal Society B: Biological Sciences 282: 20141013 | PDF
2014
A virtual world of paleontology
Cunningham JA, Rahman IA, Lautenschlager S, Rayfield EJ, Donoghue PC (2014) Trends in Ecology & Evolution 29: 347–357 | PDF
Distinguishing biology from geology in soft tissue preservation
Cunningham JE, Donoghue PCJ, Bengtson S (2014) Paleontological Society Special Publication 20: 275-288 | PDF
Early vertebrate evolution
Donoghue PCJ, Keating JN (2014) Palaeontology 57: 879-893 | PDF
Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals
dos Reis M, Donoghue PCJ, Yang Z (2014) Biology Letters 10: 20131003 | PDF
There is no general model for occlusal kinematics in conodonts
Martínez-Pérez C, Plasencia P, Jones D, Kolar-Jurkovšek T, Sha J, Botella H, Donoghue PCJ (2014) Lethaia 47: 547-555 | PDF
Finite element, occlusal, microwear and microstructural analyses indicate that conodont microstructure is adapated to dental function
Martinez-Perez C, Rayfield EJ, Purnell MA, Donoghue PCJ (2014) Palaeontology 57: 1059-1066 | PDF
Evaluating scenarios for the evolutionary assembly of the brachiopod body plan
Murdock DJE, Bengtson S, Marone F, Greenwood JM, Donoghue PCJ (2014) Evolution & Development 16: 13-24 | PDF
Functional adaptation underpinned the evolutionary assembly of the earliest vertebrate skeleton
Murdock DJE, Rayfield EJ, Donoghue PCJ (2014) Evolution & Development 16: 354-361 | PDF
Developmental paleobiology of the vertebrate skeleton
Rucklin M, Donoghue PCJ, Cunningham JA, Marone F, Stampanoni M (2014) Journal of Paleontology 88: 676-683 | PDF
Evolutionary history of plant microRNAs
Taylor RS, Tarver JE, Hiscock SJ, Donoghue PCJ (2014) Trends in Plant Science 19: 175-182 | PDF
2013
Embryos, polyps and medusae of the Early Cambrian scyphozoan Olivooides
Dong XP, Cunningham JA, Bengtson S, Thomas CW, Liu J, Stampanoni M, Donoghue PCJ (2013) Proceedings of the Royal Society B: Biological Sciences 280: 20130071 | PDF
The Great Fossil Enigma The Search for the Conodont Animal
Donoghue P (2013) Science 340: 813 | PDF
A daily-updated tree of (sequenced) life as a reference for genome research
Fang H, Oates ME, Pethica RB, Greenwood JM, Sardar AJ, Rackham OJL, Donoghue PCJ, Stamatakis A, Morais DAD, Gough J (2013) Scientific Reports 3: 02015 | PDF
Histology of “placoderm” dermal skeletons: Implications for the nature of the ancestral gnathostome
Giles S, Rucklin M, Donoghue PC (2013) Journal of Morphology 274: 627-644 | PDF
A divergence dating analysis of turtles using fossil calibrations: an example of best practices
Joyce WG, Parham JF, Lyson TR, Warnock RCM, Donoghue PCJ (2013) Journal of Paleontology 87: 612-634 | PDF
Cutting the first ‘teeth’: a new approach to functional analysis of conodont elements
Murdock DJ, Sansom IJ, Donoghue PC (2013) Proceedings of the Royal Society B: Biological Sciences 280: 20131524 | PDF
The origin of conodonts and of vertebrate mineralized skeletons
Murdock DJE, Dong X-P, Repetski JE, Marone F, Stampanoni M, Donoghue PCJ (2013) Nature 502: 546-549 | PDF
miRNAs: small genes with big potential in metazoan phylogenetics
Tarver JE, Sperling EA, Nailor A, Heimberg AM, Robinson JM, King BL, Pisani D, Donoghue PC, Peterson KJ (2013) Molecular Biology & Evolution 30: 2369-2382 | PDF
2012
A merciful death for the “earliest bilaterian,” Vernanimalcula
Bengtson S, Cunningham JA, Yin C, Donoghue PCJ (2012) Evolution & Development 14: 421-427 | PDF
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 | PDF
Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians
Cunningham JA, Thomas C-W, Bengtson S, Kearns SL, Xiao S, Marone F, Stampanoni M, Donoghue PCJ (2012) Proceedings of the Royal Society B: Biological Sciences 279: 2369-2376 | PDF
Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils
Cunningham JA, Thomas C-W, Bengtson S, Marone F, Stampanoni M, Turner FR, Bailey JV, Raff RA, Raff EC, Donoghue PCJ (2012) Proceedings of the Royal Society B: Biological Sciences 279: 1857-1864 | PDF
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 B: Biological Sciences 279: 3491-3500 | PDF
New palaeoscolecid worms from the Furongian (upper Cambrian) of Hunan, South China: is Markuelia an embryonic palaeoscolecid?
Duan BC, Dong XP, Donoghue PCJ (2012) Palaeontology 55: 613-622 | PDF
Response to Comment on “Fossilized Nuclei and Germination Structures Identify Ediacaran ‘Animal Embryos’ as Encysting Protists”
Huldtgren T, Cunningham JA, Yin C, Stampanoni M, Marone F, Donoghue PCJ, Bengtson S (2012) Science 335: 1169 | PDF
Testing microstructural adaptation in the earliest dental tools
Jones D, Evans AR, Rayfield EJ, Siu KKW, Donoghue PCJ (2012) Biology Letters 8: 952-955| PDF
The sharpest tools in the box? Quantitative analysis of conodont element functional morphology
Jones D, Evans AR, Siu KKW, Rayfield EJ, Donoghue PCJ (2012) Proceedings of the Royal Society B: Biological Sciences 279: 2849-2854 | PDF
Ontogeny and microstructure of the enigmatic Cambrian tommotiid Sunnaginia Missarzhevsky, 1969
Murdock DJE, Donoghue PCJ, Bengtson S, Marone F (2012) Palaeontology 55: 661-676 | PDF
Best practices for justifying fossil calibrations
Parham JF, Donoghue PC, Bell CJ, Calway TD, Head JJ, Holroyd PA, Inoue JG, Irmis RB, Joyce WG, Ksepka DT, Patane JS, Smith ND, Tarver JE, van Tuinen M, Yang Z, Angielczyk KD, Greenwood JM, Hipsley CA, Jacobs L, Makovicky PJ, Muller J, Smith KT, Theodor JM, Warnock RC, Benton MJ (2012) Systematic Biology 61: 346-359 | PDF
Development of teeth and jaws in the earliest jawed vertebrates
Rücklin M, Donoghue PC, Johanson Z, Trinajstic K, Marone F, Stampanoni M (2012) Nature 491: 748-751 | PDF
Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish)
Shimeld SM, Donoghue PCJ (2012) Development 139: 2091-2099 | PDF
Do miRNAs have a deep evolutionary history?
Tarver JE, Donoghue PCJ, Peterson KJ (2012) Bioessays 34: 857-866 | PDF
Exploring uncertainty in the calibration of the molecular clock
Warnock RCM, Yang Z, Donoghue PCJ (2012) Biology Letters 8: 156-159 | PDF
2011
Establishing a time-scale for plant evolution
Clarke JT, Warnock RC, Donoghue PC (2011) New Phytologist 192: 266-301 | PDF
Presentation of the 2010 Charles Schuchert Award of the Paleontological Society to Philip C. J. Donoghue – Response
Donoghue P (2011) Journal of Paleontology 85: 1016 | PDF
Fossil jawless fish from China foreshadows early jawed vertebrate anatomy
Gai Z, Donoghue PCJ, Zhu M, Janvier P, Stampanoni M (2011) Nature 476: 324-327 | PDF
Fossilized nuclei and germination structures identify Ediacaran “animal embryos” as encysting protists
Huldtgren T, Cunningham JA, Yin C, Stampanoni M, Marone F, Donoghue PCJ, Bengtson S (2011) Science 334: 1696-1699 | PDF
Evolutionary origins of animal skeletal biomineralization
Murdock DJE, Donoghue PCJ (2011) Cells Tissues Organs 104: 98-102 | PDF
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 | PDF
The trouble with topology: phylogenies without fossils provide a revisionist perspective of evolutionary history in topological analyses of diversity
Tarver JE, Donoghue PCJ (2011) Systematic Biology 60: 700-712 | PDF
Is evolutionary history repeatedly rewritten in light of new fossil discoveries?
Tarver JE, Donoghue PCJ, Benton MJ (2011) Proceedings of the Royal Society B: Biological Sciences 278: 599-604 | PDF
2010
The anatomy, taphonomy, taxonomy and systematic affinity of Markuelia: early Cambrian to early Ordovician scalidophorans
Dong X-P, 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
Origins of multicellularity
Donoghue PCJ, Antcliffe JB (2010) Nature 466: 41-42 | PDF
Are palaeoscolecids ancestral ecdysozoans?
Harvey THP, Dong X, Donoghue PCJ (2010) Evolution & Development 12: 177-200 | PDF
microRNAs reveal the interrelationships of hagfish, 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
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 | PDF
The impact of the representation of fossil calibrations on bayesian estimation of species divergence times
Inoue J, Donoghue P, Yang Z (2010) Systematic Biology 59: 74-89 | PDF
2009
Calibrating and constraining molecular clocks
Benton MJ, Donoghue PCJ, Asher RJ (2009) in Hedges, SB, and Kumar, S, eds. The timetree of Life, Cambridge: Cambridge University Press, 35-86 | PDF
Enameloid microstructure in the oldest known chondrichthyan teeth
Botella H, Donoghue PCJ, MartÌnez-Pèrez C (2009) Acta Zoologica 90: 103-108 | PDF
Origin of vertebrates
Donoghue PCJ (2009) in Ruse, M, and Travis, J, eds. Evolution: the first four billion years, Cambridge, MA: Belknap, 788-792 | PDF
Distinguishing heat from light in debate over controversial fossils
Donoghue PCJ, Purnell MA (2009) Bioessays 31: 178-189 | PDF
The evolutionary emergence of vertebrates from among their spineless relatives
Donoghue PCJ, Purnell MA (2009) Evolution: Education and Outreach 2: 204-212 | PDF
Skeletal histology of Bothriolepis canadensis (Placodermi, Antiarchi) and evolution of the skeleton at the origin of jawed vertebrates
Downs JP, Donoghue PC (2009) Journal of Morphology 270: 1364-1380 | PDF
Ontogeny and taphonomy: an experimental taphonomy study of the development of the brine shrimp Artemia salina
Gostling NJ, Dong X, Donoghue PCJ (2009) Palaeontology 52: 169-186 | PDF
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 | PDF
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 and Microanalysis 15: 166-173 | PDF
Origin and evolution of the integumentary skeleton in non-tetrapod vertebrates
Sire J-Y, Donoghue PCJ, Vickaryous MK (2009) Journal of Anatomy 214: 409-440 | PDF
2008
Exploring the links between evolution and development
Donoghue PCJ (2008) in Benton, MJ, ed. The seventy great mysteries of the natural world, London: Thames & Hudson, 127-130 | PDF
The origin and evolution of the neural crest
Donoghue PCJ, Graham A, Kelsh RN (2008) Bioessays 30: 530-541 | PDF
The interrelationships of ‘complex’ conodonts (Vertebrata)
Donoghue PCJ, Purnell MA, Aldridge RJ, Zhang S (2008) Journal of Systematic Palaeontology 6: 119-153 | PDF
Deciphering the fossil record of early bilaterian embryonic development in light of experimental taphonomy
Gostling NJ, Thomas C-W, Greenwood JM, Dong X-P, Bengtson S, Raff EC, Raff RA, Degnan BM, Stampanoni M, Donoghue PCJ (2008) Evolution & Development 10: 339-349 | PDF
MicroRNAs and the advent of vertebrate morphological complexity
Heimberg AM, Sempere LF, Moy VN, Donoghue PCJ, Peterson KJ (2008) Proceedings of the National Academy of Sciences, USA 105: 2946-2950 | PDF
Embryo fossilization is a biological process mediated by microbial biofilms
Raff EC, Schollaert KL, Nelson DE, Donoghue PCJ, Thomas C-W, Turner FR, Stein BD, Dong X, Bengtson S, Huldtgren T, Stampanoni M, Chongyu Y, Raff RA (2008) Proceedings of the National Academy of Sciences, USA 105: 19359-19364 | PDF
The anatomy, affinity and phylogenetic significance of Ilemoraspis kirkinskyae (Osteostraci) from the Devonian of Siberia
Sansom RS, Rodygin SA, Donoghue PCJ (2008) Journal of Vertebrate Palaeontology 28: 613-625 | PDF
2007
Paleontological evidence to date the Tree of Life
Benton MJ, Donoghue PCJ (2007) Molecular Biology & Evolution 24: 26-53 | PDF
Embryonic identity crisis
Donoghue PCJ (2007) Nature 445: 155-156 | PDF
Rocks and clocks: calibrating the Tree of Life using fossils and molecules
Donoghue PCJ, Benton MJ (2007) Trends in Ecology & Evolution 22: 424-431 | PDF
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 | PDF
The homology and phylogeny of chondrichthyan tooth enameloid
Gillis JA, Donoghue PCJ (2007) Journal of Morphology 268: 33-49 | PDF
The earliest fossil embryos begin to mature
Gostling NJ, Donoghue PCJ, Bengtson S (2007) Evolution & Development 9: 206-207 | PDF
Molecular palaeobiology
Peterson KJ, Summons RE, Donoghue PCJ (2007) Palaeontology 50: 775-809 | PDF
2006
Synchrotron X-ray tomographic microscopy of fossil embryos
Donoghue PCJ, Bengtson S, Dong X-P, Gostling NJ, Huldtgren T, Cunningham JA, Yin C, Yue Z, Peng F, Stampanoni M (2006) Nature 442: 680-683 | PDF
Swiss light shed on the nature of fossilised embryos from the dawn of animal evolution
Donoghue PCJ, Gostling NJ, Bengtson S, Huldtgren T, Dong X-P, Peng F, Stampanoni M (2006) in PSI Scientific Report 2005. Volume 1: Condensed matter, photons, neutrons and charged particles, 10-11 | PDF
Fossilized embryos are widespread but the record is temporally and taxonomically biased
Donoghue PCJ, Kouchinsky A, Waloszek D, Bengtson S, Dong X-P, Val’kov AK, Cunningham JA, Repetski JE (2006) Evolution & Development 8: 232-238 | PDF
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 | PDF
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 | PDF
The `Orsten’–More than a Cambrian Konservat-Lagerstatte yielding exceptional preservation
Maas A, Braun A, Dong X-P, Donoghue PCJ, Muller KJ, Olempska E, Repetski JE, Siveter DJ, Stein M, Waloszek D (2006) Palaeoworld 15: 266-282 | PDF
Experimental taphonomy shows the feasibility of fossil embryos
Raff EC, Villinski JT, Turner FR, Donoghue PCJ, Raff RA (2006) Proceedings of the National Academy of Sciences, USA 103: 5846-5851 | PDF
2005
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 | PDF
The anatomy, affinity and phylogenetic significance of Markuelia
Dong XP, Donoghue PCJ, Cunningham J, Liu J, Cheng H (2005) Evolution & Development 7: 468-482 | PDF
The fossils of Orsten-type preservation from Middle and Upper Cambrian in Hunan, China
Dong XP, Donoghue PCJ, Liu Z, Liu J, Peng F (2005) Chinese Science Bulletin 50: 1352-1357 | PDF
Saving the stem-group – a contradiction in terms
Donoghue PCJ (2005) Paleobiology 31: 553-558 | PDF
Carl Gegenbaur and evolutionary morphology
Donoghue PCJ (2005) Acta Zoologica 85: 265-266 | PDF
Embryos and ancestors
Donoghue PCJ, Dong XP (2005) in Briggs, DEG, ed. Evolving form and function: fossils and development, New Haven, Connecticut: Yale University, 81-99 | PDF
Genome duplication, extinction and vertebrate evolution
Donoghue PCJ, Purnell MA (2005) Trends in Ecology & Evolution 20: 312-319 | PDF
Conodont biology and phylogeny – interpreting the fossil record
Purnell MA, Donoghue PCJ (2005) Special Papers in Palaeontology 73: 218.
Between death and data: biases in interpretation of the fossil record of conodonts
Purnell MA, Donoghue PCJ (2005) Special Papers in Palaeontology 73: 7-25 | PDF
Histology and affinity of the earliest armoured vertebrate
Sansom IJ, Donoghue PCJ, Albanesi GL (2005) Biology Letters 2: 446-449 | PDF
The apparatus composition and architecture of Cordylodus Pander – concepts of homology in primitive conodonts
Smith MP, Donoghue PCJ, Repetski JE (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 | PDF
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 | PDF
Cladograms, phylogenies and the veracity of the conodont fossil record
Wickstrom LM, Donoghue PCJ (2005) in Purnell, MA, and Donoghue, PCJ, eds. Conodont Biology and Phylogeny: Interpreting the Fossil Record, Special Papers in Palaeontology 73: 185-218 | PDF
2004
Fossil embryos from the Middle and Late Cambrian period of Hunan, south China
Dong X-P, Donoghue PCJ, Cheng H, Liu J (2004) Nature 427: 237-240 | PDF | N&V
2003
Introduction – Molecular clocks and the fossil record – towards consilience?
Donoghue PCJ, Smith MP (2003) in Telling the evolutionary time: molecular clocks and the fossil record, 1-4.
Telling the evolutionary time: molecular clocks and the fossil record
Donoghue PCJ, Smith MP (2003) London: Systematics Association and Taylor & Francis, 288pp.
The emergence of vertebrates
Donoghue PCJ, Smith MP, Sansom IJ (2003) in McGraw-Hill yearbook of science, New York: McHraw-Hill, 107-109.
The origin and evolution of chordates: molecular clocks and the fossil record
Donoghue PCJ, Smith MP, Sansom IJ (2003) in Donoghue, PCJ, and Smith, MP, eds. Telling the evolutionary time: molecular clocks and the fossil record, London: Taylor & Francis, 190-223 | PDF
The distribution of ostracoderms in the Mid-Ordovician of Laurentia and Gondwana
Sansom IJ, Smith MP, Donoghue PCJ (2003) in Albanesi, GL, Beresi, MS, and Peralta, SH, eds. Ordovician from the Andes, Tucumán, Argentina: Instituto Superior de Correlación Geológica, 545-549.
2002
Evolution of development of vertebrate teeth and scales: unravelling concepts, regulatory theories and homologies
Donoghue PCJ (2002) Paleobiology 28: 474-507 PDF
Origin and early evolution of vertebrate skeletonization
Donoghue PCJ, Sansom IJ (2002) Microscopy Research & Technique 59: 352-372 PDF
The spatial and temporal diversification of Early Palaeozoic vertebrates
Smith MP, Donoghue PCJ, Sansom IJ (2002) in Crame, JA, and Owen, AW, eds. Palaeobiogeography and biodiversity change: the Ordovician and Mesozoic-Cenozoic radiations. Geological Society Special Publication No. 194, London: The Geological Society, 69-83 PDF
2001
Conodonts meet cladistics: recovering relationships and assessing the completeness of the conodont fossil record
Donoghue PCJ (2001) Palaeontology 44: 65-93 | PDF
Microstructural variation in conodont enamel is a functional adaptation
Donoghue PCJ (2001) Proceedings of the Royal Society of London B: Biological Sciences 268: 1691-1698 | PDF
Origin of a mineralised skeleton
Donoghue PCJ, Aldridge RJ (2001) in Ahlberg, PE, ed. Major events in early vertebrate evolution: palaeontology, phylogeny, genetics and development, London: Taylor & Francis, 85-105 | PDF
The anatomy of Turinia pagei (Powrie), and the phylogenetic status of the Thelodonti
Donoghue PCJ, Smith MP (2001) Transactions of the Royal Society of Edinburgh-Earth Sciences 92: 15-37 PDF
Conodonts: past, present and future
Sweet WC, Donoghue PCJ (2001) Journal of Paleontology 75: 1174-1184 PDF
2000
Conodont affinity and chordate phylogeny
Donoghue PCJ, Forey PL, Aldridge RJ (2000) Biological Reviews 75: 191-251 | PDF
Orientation and anatomical notation in conodonts
Purnell MA, Donoghue PCJ, Aldridge RJ (2000) Journal of Paleontology 74: 113-122 | PDF
1999
Conchodontus, Mitrellataxis and Fungulodus: conodonts, fish, or both?
Donoghue PCJ, Chauffe K (1999) Lethaia 31: 283-292 PDF
Growth, function, and the conodont fossil record
Donoghue PCJ, Purnell MA (1999) Geology 27: 251-254 | PDF
Mammal-like occlusion in conodonts
Donoghue PCJ, Purnell MA (1999) Paleobiology 25: 58-74 | PDF
Flattened fossils, physical modelling and the restoration of collapsed skeleton
Purnell MA, Donoghue PCJ (1999) in Savazzi, E, ed. Functional morphology of the invertebrate skeleton, Chichester: John Wiley & Sons Ltd., 91-99.
1998
Conodonts: a sister group to hagfish?
Aldridge RJ, Donoghue PCJ (1998) in Jørgensen, JM, Lomholt, JP, Weber, RE, and Malte, H, eds. The Biology of Hagfishes, London: Chapman and Hall, 15-31 | PDF
Growth and patterning in the conodont skeleton
Donoghue PCJ (1998) Philosophical Transactions of the Royal Society of London, Series B 353: 633-666 | PDF
Conodont anatomy, chordate phylogeny and vertebrate classification
Donoghue PCJ, Purnell MA, Aldridge RJ (1998) Lethaia 31: 211-219 | PDF
Skeletal architecture, homologies and taphonomy of ozarkodinid conodonts
Purnell MA, Donoghue PCJ (1998) Palaeontology 41: 57-102 | PDF
1997
A technique for conodont histology
Donoghue PCJ (1997) Lethaia 30: 329-330 | PDF
Skeletal architecture and functional morphology of ozarkodinid conodonts
Purnell MA, Donoghue PCJ (1997) Philosophical Transactions of the Royal Society of London, Series B 352: 1545-1564 | PDF
An Early Triassic conodont with periodic growth?
Zhang S-X, Aldridge RJ, Donoghue PCJ (1997) Journal of Micropalaeontology 16: 65-72 | PDF
1995
Conodonts and the first vertebrates
Purnell MA, Aldridge RJ, Donoghue PCJ, Gabbott SE (1995) Endeavour 19: 20-27 | PDF