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List of works by Philip C.J. Donoghue

"Fascinating Little Whatzits"

scientific article published in Science

A daily-updated tree of (sequenced) life as a reference for genome research.

scientific article

A divergence dating analysis of turtles using fossil calibrations: an example of best practices

article

A formula for maximum possible steps in multistate characters: isolating matrix parameter effects on measures of evolutionary convergence

article

A merciful death for the "earliest bilaterian," Vernanimalcula

scientific article

A multicellular organism with embedded cell clusters from the Ediacaran Weng'an biota (Doushantuo Formation, South China).

scientific article

A species-level timeline of mammal evolution integrating phylogenomic data

scientific article published on 22 December 2021

A virtual world of paleontology

scientific article published on 10 May 2014

An Early Triassic conodont with periodic growth?

Anatomy of the Ediacaran rangeomorph Charnia masoni.

scientific article

Apparatus architecture of the conodont Nicoraella kockeli (Gondolelloidea, Prioniodinina) constrains functional interpretations

scientific article published in 2019

Are palaeoscolecids ancestral ecdysozoans?

scientific article

Author Correction: Evolutionary analysis of swimming speed in early vertebrates challenges the ‘New Head Hypothesis’

scientific article published in 2023

BASAL TISSUE STRUCTURE IN THE EARLIEST EUCONODONTS: TESTING HYPOTHESES OF DEVELOPMENTAL PLASTICITY IN EUCONODONT PHYLOGENY

article

Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data

scientific article

Bayesian molecular clock dating of species divergences in the genomics era.

scientific article published on 21 December 2015

Best practices for justifying fossil calibrations

scientific article (publication date: March 2012)

Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

scientific article

Cellular and subcellular structure of neoproterozoic animal embryos

scientific article

Computational Fluid Dynamics Suggests Ecological Diversification among Stem-Gnathostomes

scientific article published on 26 September 2020

Conodont affinity and chordate phylogeny

scientific article

Conodont affinity and chordate phylogeny

scholarly article by Philip Donoghue et al published 11 January 2007 in Biological Reviews

Conodonts Meet Cladistics: Recovering Relationships and Assessing the Completeness of the Conodont Fossil Record

scientific article published in 2001

Conodonts and the first vertebrates

article by Mark Purnell et al published January 1995 in Endeavour

Conodonts: Past, Present, Future

scientific article published in November 2001

Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence

scientific article

Constraining the timing of whole genome duplication in plant evolutionary history

scientific article

Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution

scientific article

Critical appraisal of tubular putative eumetazoans from the Ediacaran Weng'an Doushantuo biota

scientific article

Cryogenian Origins of Multicellularity in Archaeplastida

scholarly article

Cutting the first 'teeth': a new approach to functional analysis of conodont elements

scientific article (publication date: 7 October 2013)

Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils

scientific article

Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils

article

Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga)

scientific article published on 05 March 2020

Dating Tips for Divergence-Time Estimation

scientific article published on 12 September 2015

Dating species divergences using rocks and clocks

scientific article

Deciphering the fossil record of early bilaterian embryonic development in light of experimental taphonomy.

scientific article

Development of teeth and jaws in the earliest jawed vertebrates.

scientific article published on 17 October 2012

Developmental Paleobiology of the Vertebrate Skeleton

scientific article

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)

scientific article published on 12 June 2020

Developmental biology of the early Cambrian cnidarianOlivooides

article

Discriminating signal from noise in the fossil record of early vertebrates reveals cryptic evolutionary history

scientific article

Disparities in the analysis of morphological disparity

scientific article published on 01 July 2020

Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians

scientific article (publication date: 22 June 2012)

Distinguishing heat from light in debate over controversial fossils

scientific article published on February 2009

Do cladistic and morphometric data capture common patterns of morphological disparity?

article by Alexander J. Hetherington et al published 31 March 2015 in Palaeontology

Do miRNAs have a deep evolutionary history?

scientific article published on 30 July 2012

Early evolution of vertebrate skeletal tissues and cellular interactions, and the canalization of skeletal development.

scientific article

Early life: Origins of multicellularity

scientific article published in July 2010

Early vertebrate evolution

article

Ediacaran developmental biology

scientific article

Embryo fossilization is a biological process mediated by microbial biofilms

scientific article (publication date: 9 December 2008)

Embryology in Deep Time

Embryos, polyps and medusae of the Early Cambrian scyphozoan Olivooides

scientific article (publication date: 22 April 2013)

Empirical realism of simulated data is more important than the model used to generate it: a reply to Goloboff et al

scientific article published in 2018

Establishing a time-scale for plant evolution

scientific article (publication date: October 2011)

Eukaryogenesis and oxygen in Earth history

scientific article published in 2022

Evaluating scenarios for the evolutionary assembly of the brachiopod body plan

scientific article published in January 2014

Evolution of development of the vertebrate dermal and oral skeletons: unraveling concepts, regulatory theories, and homologies

article

Evolution of fungal phenotypic disparity

scientific article published in 2022

Evolution of jaw disparity in fishes

scientific article published in 2018

Evolution of metazoan morphological disparity

article published in the Proceedings of the National Academy of Sciences of the United States of America

Evolution of phenotypic disparity in the plant kingdom

scientific article published in 2023

Evolution of the Calcium-Based Intracellular Signaling System

scientific article published on 29 June 2016

Evolution: Divining the Nature of the Ancestral Vertebrate

scientific article published in April 2017

Evolution: The Flowering of Land Plant Evolution

scientific article published on 01 August 2019

Evolutionary analysis of swimming speed in early vertebrates challenges the ‘New Head Hypothesis’

scientific article published in 2022

Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish).

scientific article published on June 2012

Evolutionary history of plant microRNAs

scientific article published on 07 January 2014

Evolutionary origins of animal skeletal biomineralization

scientific article

Exceptionally preserved early Cambrian bilaterian developmental stages from Mongolia

scientific article

Experimental analysis of soft-tissue fossilization: opening the black box

scientific article published in 2018

Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization

scientific article

Experimental taphonomy of organelles and the fossil record of early eukaryote evolution

scientific article

Experimental taphonomy shows the feasibility of fossil embryos

scientific article

Exploring uncertainty in the calibration of the molecular clock

scientific article (publication date: 23 February 2012)

Finite element, occlusal, microwear and microstructural analyses indicate that conodont microstructure is adapted to dental function

scientific article published in 2014

Fossil cells

scientific article published on 01 May 2020

Fossil data support a pre-Cretaceous origin of flowering plants

scientific article published in 2021

Fossil embryos from the Middle and Late Cambrian period of Hunan, south China

scientific article published in January 2004

Fossil jawless fish from China foreshadows early jawed vertebrate anatomy

scientific article

Fossilized embryos are widespread but the record is temporally and taxonomically biased

scientific article published in March 2006

Fossilized nuclei and germination structures identify Ediacaran "animal embryos" as encysting protists

scientific article

Functional adaptation underpinned the evolutionary assembly of the earliest vertebrate skeleton

scientific article published in October 2014

Functional assessment of morphological homoplasy in stem-gnathostomes

scientific article published on 20 January 2021

Galeaspid anatomy and the origin of vertebrate paired appendages

scientific article published on 28 September 2022

Genome duplication, extinction and vertebrate evolution

scientific article

Gondolelloid multielement conodont apparatus ( Nicoraella ) from the Middle Triassic of Yunnan Province, southwestern China

article

Growth and patterning in the conodont skeleton

scientific article (publication date: 29 April 1998)

Growth, function, and the conodont fossil record

scientific article

Histology and affinity of anaspids, and the early evolution of the vertebrate dermal skeleton

scientific article

Histology and affinity of the earliest armoured vertebrate

scientific article (publication date: 22 December 2005)

Histology of "placoderm" dermal skeletons: Implications for the nature of the ancestral gnathostome

scientific article

Histology of the galeaspid dermoskeleton and endoskeleton, and the origin and early evolution of the vertebrate cranial endoskeleton

Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton

scientific article

Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin

scientific article published on 20 August 2018

Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmatodea) reveal a Permian-Triassic co-origination with insectivores

scientific article published on 11 November 2020

Integrated phylogenomics and fossil data illuminate the evolution of beetles

scientific article published in 2022

MOLECULAR PALAEOBIOLOGY

scientific article published in 2007

MicroRNA annotation of plant genomes - Do it right or not at all.

scientific article published on 5 January 2017

MicroRNAs and the advent of vertebrate morphological complexity

scientific article

Microstructural variation in conodont enamel is a functional adaptation

scientific article published in August 2001

Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography

Mitochondrial genomes illuminate the evolutionary history of the Western honey bee (Apis mellifera)

scientific article published on 03 September 2020

Modelling the Conodont Skeleton: A New Reconstruction for the Conodont Mouth

scholarly article

Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals

scientific article (publication date: 2014)

New palaeoscolecid worms from the Furongian (upper Cambrian) of Hunan, South China: is Markuelia an embryonic palaeoscolecid?

article

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)

scholarly article by Filipe de Sousa et al published 9 November 2018 in New Phytologist

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)

scholarly article by Filipe Sousa et al published 7 December 2018 in New Phytologist

Nuclei and nucleoli in embryo-like fossils from the Ediacaran Weng’an Biota

article

Nucleus preservation in early Ediacaran Weng'an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record

scientific article published on 12 June 2020

ONTOGENY AND TAPHONOMY: AN EXPERIMENTAL TAPHONOMY STUDY OF THE DEVELOPMENT OF THE BRINE SHRIMPARTEMIA SALINA

article

Ontogeny and microstructure of the enigmatic Cambrian tommotiid Sunnaginia Missarzhevsky, 1969

scientific article published in 2012

Open data and digital morphology

scientific article (publication date: 12 April 2017)

Origin and early evolution of vertebrate skeletonization

scientific article

Origin and evolution of the integumentary skeleton in non-tetrapod vertebrates

scientific article (publication date: April 2009)

Origin of horsetails and the role of whole-genome duplication in plant macroevolution

scientific article published on 30 October 2019

Palaeontology: embryonic identity crisis

scientific article

Paleontological evidence to date the tree of life

scientific article

Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.

scientific article published in October 2017

Performance of a priori and a posteriori calibration strategies in divergence time estimation

scientific article published on 22 May 2020

Phase-contrast X-ray microtomography links Cretaceous seeds with Gnetales and Bennettitales

scientific article

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

scientific article (publication date: 7 September 2012)

Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye ⬇️

scientific article

Plant Evolution: Assembling Land Plants

scientific article published on 01 January 2020

Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model

scholarly article by Mark N Puttick et al published 19 August 2018 in Palaeontology

Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data

scientific article

Ptychographic nanotomography at the Swiss Light Source

article

RelTime Rates Collapse to a Strict Clock When Estimating the Timeline of Animal Diversification

scientific article published on 25 April 2017

Reply to 'placoderms and the evolutionary origin of teeth': Burrow et al. (2016)

scientific article

Reply to Hedges et al.: Accurate timetrees do indeed require accurate calibrations

article published in the Proceedings of the National Academy of Sciences of the United States of America

Rocks and clocks: calibrating the Tree of Life using fossils and molecules

scientific article (publication date: August 2007)

Romundina and the evolutionary origin of teeth

scientific article

Saccorhytus is an early ecdysozoan and not the earliest deuterostome

scientific article published on 17 August 2022

Saving the stem group—a contradiction in terms?

scientific article published in 2005

Scanning electron microscopy and synchrotron radiation x-ray tomographic microscopy of 330 million year old charcoalified seed fern fertile organs

scientific article

Size is not everything: rates of genome size evolution, not C-value, correlate with speciation in angiosperms

scientific article

Skeletal histology ofBothriolepis canadensis(Placodermi, Antiarchi) and evolution of the skeleton at the origin of jawed vertebrates

scientific article (publication date: November 2009)

Synchrotron X-ray tomographic microscopy of fossil embryos

scientific article

Tectonic blocks and molecular clocks

scientific article

Teeth before jaws? Comparative analysis of the structure and development of the external and internal scales in the extinct jawless vertebrate Loganellia scotica.

scientific article published in November 2011

Testing microstructural adaptation in the earliest dental tools

scientific article

Testing models of dental development in the earliest bony vertebrates, Andreolepis and Lophosteus

scientific article (publication date: 23 October 2012)

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

scientific article published in June 2017

The Early Ediacaran Caveasphaera Foreshadows the Evolutionary Origin of Animal-like Embryology

scientific article published on 19 November 2019

The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data

scientific article published on 10 March 2022

The Effect of Fossil Sampling on the Estimation of Divergence Times with the Fossilized Birth-Death Process

scientific article published on 01 January 2020

The Efficacy of Consensus Tree Methods for Summarising Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data

scientific article published on 2 November 2017

The Evolutionary Emergence of Vertebrates From Among Their Spineless Relatives

The Fossil Calibration Database-A New Resource for Divergence Dating

scientific article

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

scientific article

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference ⬇️

scientific article

The Weng'an Biota (Doushantuo Formation): an Ediacaran window on soft-bodied and multicellular microorganisms

scientific article published in 2017

The anatomy, affinity and phylogenetic significance ofIlemoraspis kirkinskayae(Osteostraci) from the Devonian of Siberia

article

The anatomy, affinity, and phylogenetic significance of Markuelia

scientific article published in September 2005

The anatomy, taphonomy, taxonomy and systematic affinity of Markuelia: Early Cambrian to Early Ordovician scalidophorans

article

The apparatus composition and architecture of Erismodus quadridactylus and the implications for element homology in prioniodinin conodonts

article

The circulatory system of Galeaspida (Vertebrata; stem-Gnathostomata) revealed by synchrotron X-ray tomographic microscopy

scholarly article by Zhi-Kun Gai et al published April 2019 in Palaeoworld

The dermal skeleton of the jawless vertebrate Tremataspis mammillata (Osteostraci, stem‐Gnathostomata)

scientific article published on 08 May 2019

The developmental biology of and the eumetazoan affinity of the Ediacaran rangeomorphs

scientific article

The earliest fossil embryos begin to mature

scientific article published in May 2007

The early Cambrian fossil embryo Pseudooides is a direct-developing cnidarian, not an early ecdysozoan.

scientific article published in December 2017

The evolution of methods for establishing evolutionary timescales

scientific article

The homology and phylogeny of chondrichthyan tooth enameloid

scientific article

The impact of fossil stratigraphic ranges on tip‐calibration, and the accuracy and precision of divergence time estimates

scientific article published in 2019

The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times

scientific article

The ins and outs of the evolutionary origin of teeth

scientific article

The interrelationships of ‘complex’ conodonts (Vertebrata)

scholarly article by Philip Donoghue et al published January 2008 in Journal of Systematic Palaeontology

The nature of aspidin and the evolutionary origin of bone

scientific article published in 2018

The nature of the last universal common ancestor and its impact on the early Earth system ⬇️

journal article from 'Nature Ecology & Evolution' published in 2024

The origin and evolution of the neural crest

scientific article (publication date: June 2008)

The origin of animals: Can molecular clocks and the fossil record be reconciled?

scientific article

The origin of conodonts and of vertebrate mineralized skeletons

scientific article published on 16 October 2013

The sharpest tools in the box? Quantitative analysis of conodont element functional morphology

scientific article (publication date: 22 July 2012)

The spatial and temporal diversification of Early Palaeozoic vertebrates

The timescale of early land plant evolution.

scientific article published on 20 February 2018

The trouble with topology: phylogenies without fossils provide a revisionist perspective of evolutionary history in topological analyses of diversity

scientific article

The ‘Orsten’—More than a Cambrian Konservat-Lagerstätte yielding exceptional preservation

article

There is no general model for occlusal kinematics in conodonts

scientific article published in 2014

Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

scientific article

Tooth replacement in early sarcopterygians

scientific article published on 13 November 2019

Translating taxonomy into the evolution of conodont feeding ecology

scholarly article

Tubular microfossils from the Ediacaran Weng’an Biota (Doushantuo Formation, South China) are not early animals

article

Ultrastructure and in-situ chemical characterization of intracellular granules of embryo-like fossils from the early Ediacaran Weng’an biota

scientific article

Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data

scientific article (publication date: 11 January 2017)

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

scientific article

Unicellular Origin of the Animal MicroRNA Machinery

Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. ⬇️

scientific article published in June 2018

Whole-Genome Duplication and Plant Macroevolution

scientific article published on 16 August 2018

X-ray nanotomography and electron backscatter diffraction demonstrate the crystalline, heterogeneous and impermeable nature of conodont white matter

scientific article

miRNAs: small genes with big potential in metazoan phylogenetics

scientific article

microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

scientific article

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