Philip C J Donoghue

University of Bristol | UB · School of Earth Sciences

Theories on the origin of vertebrate teeth have long focused on chondrichthyans as reflecting a primitive condition-but this is better informed by the extinct placoderms, which constitute a sister clade or grade to the living gnathostomes. Here, we show that 'supragnathal' toothplates from the acanthothoracid placoderm Romundina stellina comprise m...

Tardigrada, the water bears, are microscopic animals with walking appendages, that are members of Ecdysozoa, the clade of moulting animals that also includes Nematoda (round worms), Nematomorpha (horsehair worms), Priapulida (penis worms), Kinorhyncha (mud dragons), Loricifera (loricated animals), Arthropoda (insects, spiders centipedes, crustacean...

Teeth are a key vertebrate innovation; their evolution is generally associated with the origin of jawed vertebrates. However, tooth-like structures already occur in jawless stem-gnathostomes; heterostracans bear denticles and morphologically distinct tubercles on their oral plates. We analysed the histology of the heterostracan denticles and plates...

Evolutionary novelties are commonly identified as drivers of lineage diversification, with key innovations potentially triggering adaptive radiation. Nevertheless, testing hypotheses on the role of evolutionary novelties in promoting diversification through deep time has proven challenging. Here we unravel the role of the raptorial appendages, with...

Evolutionary novelties are commonly identified as drivers of lineage diversification, with key innovations potentially triggering adaptive radiation. Nevertheless, testing hypotheses on the role of evolutionary novelties in promoting diversification through deep time has proven challenging. Here we unravel the role of the raptorial appendages, with...

Early vertebrate evolution has been characterized as a gradual shift from passive to more active feeding modes. However, this evolutionary scenario is contingent on poorly constrained inferences of the feeding ecology of extinct stem‐gnathostomes. Heterostracans are among the earliest members of the gnathostome stem‐lineage. Pteraspidiform heterost...

The timescale of animal diversification has been a focus of debate over how evolutionary history should be calibrated to geologic time. Molecular clock analyses have invariably estimated a Cryogenian or Tonian origin of animals while unequivocal animal fossils first occur in the Ediacaran. However, redating of key Ediacaran biotas and the discovery...

Background The sea spiders (Pycnogonida Latreille, 1810) of the Hunsrück Slate (Lower Devonian, ~400 million years ago) are iconic in their abundance, exquisite pyritic preservation, and in their distinctive body plan compared to extant sea spiders (Pantopoda Gerstäcker, 1863). Consequently, the Hunsrück sea spiders are important in understanding t...

The wing is the key evolutionary innovation of pterygote insects and wing morphology is commonly envisaged as finely attuned to functional performance. Here, we use a theoretical morphospace approach to analyse the evolution of disparity and functional optimality in neuropteran wings, thus, investigating how wings are adapted for flight and how var...

Mesoraphidiidae is an extinct family of the order Raphidioptera with an evolutionary history that is largely unexplored. Here, we uncovered the evolutionary history of Mesoraphidiidae using phylogenetic comparative approaches, based on an updated morphological dataset, with an additional description of two new genera and species with distinct cepha...

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has pr...

Knowledge of Cambrian animal anatomy is limited by preservational processes that result in compaction, size bias, and incompleteness. We documented pristine three-dimensional (3D) anatomy of trilobites fossilized through rapid ash burial from a pyroclastic flow entering a shallow marine environment. Cambrian ellipsocephaloid trilobites from Morocco...

Sponges (Porifera) are highly effective ecosystem engineers, playing a critical role in global biogeochemical processes, including the nitrogen, carbon, and silica cycles. Because of that, they have been closely linked to the evolution of Earth's environments. However, determining the evolutionary history of sponges has posed challenges. Molecular...

Vertebrate evolution has been punctuated by three whole genome duplication (WGD) events that have been implicated causally in phenotypic evolution, from the origin of phenotypic novelties to explosive diversification. Arguably the most dramatic of these is the 3R WGD event associated with the origin of teleost fishes which comprise more than half o...

Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720–635 million yea...

The early Ediacaran Weng'an biota (Doushantuo Formation, South China) provides a rare window onto the period of Earth history in which molecular timescales have inferred the initial phase of crown-metazoan diversification. Interpretation of the embryo-like fossils that dominate the biota remains contentious because they are morphologically simple a...

Over the last two decades, advances in molecular phylogenetics have established a new understanding of beetle phylogeny. However, some historically contentious relationships, particularly among early-diverging beetle clades, remain to be resolved. In a recent paper (Cai et al., 2022), we identified model-dependent signals in beetle phylogeny and sh...

Earth was impacted by global glaciations during the Cryogenian (720-635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molec...

The radiation of tetrapods during the Devonian and Carboniferous was associated with a transition from aquatic to terrestrial environments, with attendant changes in feeding ecology that are poorly characterized. Using a theoretical morphospace and functional optimality approach, we characterize the functional evolution of tetrapod mandibles, findi...

Tortilicaulis D.Edwards is a genus of long-standing unknown affinity in which there are two species: the holotype T. transwalliensis D.Edwards, known only from coalified compressions and T. offaeus D.Edwards, Fanning et J.B.Richardson, known from an assemblage of minute, exceptionally well preserved charcoalified fossils from a Lochkovian deposit i...

Articulated natural assemblages contain direct evidence of the element numbers, morphologies, positions and structures for reconstructing the feeding apparatuses of conodont animals, but these kind of materials are very rare in fossil records. Here we report ten new conodont natural assemblages from Member II of the Guanling Formation in Luoping Co...

The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting...

Fossil material assigned to Nenoxites from the late Ediacaran Khatyspyt Formation of Arctic Siberia (550–544 Ma) has been presented as evidence for bioturbation prior to the basal Cambrian boundary. However, that ichnological interpretation has been challenged, and descriptions of similar material from other global localities support a body fossil...

Contemporary glaciers and ice sheets are home to communities of streptophyte glacier algae that must balance their requirements for photosynthesis and growth with tolerance of extremes in temperature, desiccation and UV radiation. These same environmental challenges have been hypothesized as the driving force behind the evolution of land plants fro...

The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates a...

Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordate and larval lampreys with active predation in living jawed vertebrates. Of the extinct jawless vertebrates that phylogenetically intercalate these living groups,...

Most of life’s diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time. However, the co-evolution of life and the Earth system has left signatures of bacterial metabolism in the geochemical record, most conspicuously the Great Oxidation Event (GOE) ∼2.33 billion years ago...

Analyses of morphological disparity can incorporate living and fossil taxa to facilitate the exploration of how phenotypic variation changes through time. However, taphonomic processes introduce non-random patterns of data loss in fossil data and their impact on perceptions of disparity is unclear. To address this, we characterize how measures of d...

The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence...

The timing of early cellular evolution from the divergence of Archaea and Bacteria to the origin of eukaryotes remains poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and root...

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the veracity and timing of the 2R event relative to the divergence of g...

Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations ¹ . The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution 2,3 . However, the veracity and timing of the 2R event relative to the diverge...

Galeaspids are extinct jawless relatives of living jawed vertebrates whose contribution to understanding the evolutionary assembly of the gnathostome bodyplan has been limited by absence of postcranial remains. Here, we describe Foxaspis novemura gen. et sp. nov., based on complete articulated remains from a newly discovered Konservat-Lagerstätte i...

The timing of whole-genome duplication (WGD) events is crucial to understanding their role in evolution and underpins many hypotheses linking WGD to increased diversity and complexity. As such, means of estimating the timing of the WGD events relative to their macroevolutionary outcomes are of considerable importance. Molecular clock methods facili...

Panarthropoda, the clade comprising the phyla Onychophora, Tardigrada and Euarthropoda, encompasses the largest majority of animal biodiversity. The relationships among the phyla are contested and resolution is key to understanding the evolutionary assembly of panarthropod bodyplans. Molecular phylogenetic analyses generally support monophyly of On...

Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes – re...

The Wangcun fossil Lagerstätte in Hunan, South China, has yielded hundreds of fossilized embryos of Markuelia hunanensis representing different developmental stages. Internal tissues have only rarely been observed, impeding further understanding of the soft tissue anatomy, phylogenetic affinity and evolutionary significance of Markuelia. In this st...

The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phyl...

Paired fins are a major innovation1,2 that evolved in the jawed vertebrate lineage after divergence from living jawless vertebrates³. Extinct jawless armoured stem gnathostomes show a diversity of paired body-wall extensions, ranging from skeletal processes to simple flaps⁴. By contrast, osteostracans (a sister group to jawed vertebrates) are inter...

The ecological context of early vertebrate evolution is envisaged as a long-term trend towards increasingly active food acquisition and enhanced locomotory capabilities culminating in the emergence of jawed vertebrates. However, support for this hypothesis has been anecdotal and drawn almost exclusively from the ecology of living taxa, despite know...

The early history of deuterostomes, the group composed of the chordates, echinoderms and hemichordates1, is still controversial, not least because of a paucity of stem representatives of these clades2–5. The early Cambrian microscopic animal Saccorhytus coronarius was interpreted as an early deuterostome on the basis of purported pharyngeal opening...

Organismal-grade multicellularity has been achieved only in animals, plants and fungi. All three kingdoms manifest phenotypically disparate body plans but their evolution has only been considered in detail for animals. Here we tested the general relevance of hypotheses on the evolutionary assembly of animal body plans by characterizing the evolutio...

The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontolo...

The spiracular region, comprising the hyomandibular pouch together with the mandibular and hyoid arches, has a complex evolutionary history. In living vertebrates, the embryonic hyomandibular pouch may disappear in the adult, develop into a small opening between the palatoquadrate and hyomandibula containing a single gill-like pseudobranch, or crea...

The endosymbiotic origin of mitochondria during eukaryogenesis has long been viewed as an adaptive response to the oxygenation of Earth’s surface environment, presuming a fundamentally aerobic lifestyle for the free-living bacterial ancestors of mitochondria. This oxygen-centric view has been robustly challenged by recent advances in the Earth and...

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-codi...

The Siluro-Devonian adaptive radiation of jawed vertebrates, which underpins almost all living vertebrate biodiversity, is characterized by the evolutionary innovation of the lower jaw. Multiple lines of evidence have suggested that the jaw evolved from a rostral gill arch, but when the jaw took on a feeding function remains unclear. We quantified...

Understanding the relationship between form, function and diet in feeding structures is critical to constraining the roles of organisms in their ecosystem and adaptive responses to food resources. Yet, analysis of this relationship in invertebrates has been hampered by a reliance on descriptive and qualitative characterisation of the shapes of feed...

High-throughput sequencing projects generate genome-scale sequence data for species-level phylogenies1–3. However, state-of-the-art Bayesian methods for inferring timetrees are computationally limited to small datasets and cannot exploit the deluge of new genomes⁴. In the case of mammals, molecular-clock analyses of limited datasets have produced c...

Ecdysozoans (Phyla Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Priapulida, Tardigrada) are invertebrates bearing a tough, periodically moulted cuticle that predisposes them to exceptional preservation. Ecdysozoans dominate the oldest exceptionally-preserved bilaterian animal biotas in the early-mid Cambrian (∼520–508 M...

Embryo-like fossils from the early Ediacaran Weng’an biota provide a window of exceptional fossil preservation onto the period of life history in which molecular clocks estimate the fundamental animal lineages to have diverged. However, their diversity and biological affinities have proven controversial, because they are morphologically simple and,...

The origin of plants and their colonization of land resulted in the transformation of the terrestrial environment. Here we investigate the evolution of the land plants (embryophytes) and their two main lineages, the tracheophytes (vascular plants) and bryophytes (non vascular plants). We used new fossil calibrations, relative lineage dating implied...

Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our un...

There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant...

With over 380,000 described species and possibly several million more yet unnamed, beetles represent the most biodiverse animal order. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here we use a dataset of 68 single-copy nuclear protein codin...

The evolution of wings propelled insects to their present mega-diversity. However, interordinal relationships of early-diverging winged insects and the timescale of their evolution are difficult to resolve, in part due to uncertainties in the placement of the enigmatic and species-poor order Zoraptera. The 'Zoraptera problem' has remained a content...

Conodont elements, microfossil remains of extinct primitive vertebrates, are commonly exploited as mineral archives of ocean chemistry, yielding fundamental insights into the palaeotemperature and chemical composition of past oceans. Geochemical assays have been traditionally focused on the so-called lamellar and white matter crown tissues; however...

Cladistic character matrices are routinely repurposed in analyses of morphological disparity. Unfortunately, the sampling of taxa and characters within such datasets reflects their intended application (to resolve phylogeny, rather than distinguish between phenotypes) resulting in tree shapes that often misrepresent broader taxonomic and morphologi...

The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian total-evidence dating methods, which use fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic proce...

Chondrichthyan dentitions are conventionally interpreted to reflect the ancestral gnathostome condition but interpretations of osteichthyan dental evolution in this light have proved unsuccessful, perhaps because chondrichthyan dentitions are equally specialized, or else evolved independently. Ischnacanthid acanthodians are stem-Chondrichthyes; as...

Molecular timescales estimate that early animal lineages diverged tens of millions of years before their earliest unequivocal fossil evidence. The Ediacaran macrobiota (~574 to 538 million years ago) are largely eschewed from this debate, primarily due to their extreme phylogenetic uncertainty, but remain germane. We characterize the development of...

The role of time (i.e. taxa ages) in phylogeny has been a source of intense debate within palaeontology for decades and has not yet been resolved fully. The fossilised birth-death range process is a model that explicitly accounts for information about species through time. It presents a fresh opportunity to examine the role of stratigraphic data in...

Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the...

Cladistic datasets of morphological characters are comprised of observations that exhibit varying degrees of consistency with underlying phylogenetic hypotheses, reflecting the acquisition and retention of character states (highly consistent characters), or the convergent evolution and loss of character states (less consistent characters). The cons...

In a recent paper we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. App...