Philip C. J. Donoghue
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View article: Evolution of chondrichthyan jaw morphology, from ecological generalists to specialists
Evolution of chondrichthyan jaw morphology, from ecological generalists to specialists Open
Living chondrichthyans comprise only a fraction of their historical diversity represented in the fossil record, but together they provide insights into the evolution of this ancient clade. Using a theoretical morphology approach, we sought…
View article: Convergent genome evolution shaped the emergence of terrestrial animals
Convergent genome evolution shaped the emergence of terrestrial animals Open
The challenges associated with the transition of life from water to land are profound 1 , yet they have been met in many distinct animal lineages 2–5 . These constitute a series of independent evolutionary experiments from which we can dec…
View article: A timetree of Fungi dated with fossils and horizontal gene transfers
A timetree of Fungi dated with fossils and horizontal gene transfers Open
Dating the tree of Fungi has been challenging due to a paucity of fossil calibrations and high taxonomic diversity of the group. Here we reconstructed and dated a comprehensive phylogeny comprising 110 fungal species, utilizing 225 phyloge…
View article: Investigating the Morphogenesis and Replacement of Lamprey Toothlets Using Synchrotron Imaging
Investigating the Morphogenesis and Replacement of Lamprey Toothlets Using Synchrotron Imaging Open
Teeth are a key innovation that underpinned the adaptive radiation of jawed vertebrates; however, their evolutionary origin must lie with the diverse tooth‐like structures of living and fossil jawless vertebrates. Most previous studies hav…
View article: A new ‘acanthothoracid’ placoderm from the Arctic Canada (Early Devonian) and its bearing on the evolution of jaws and teeth
A new ‘acanthothoracid’ placoderm from the Arctic Canada (Early Devonian) and its bearing on the evolution of jaws and teeth Open
The origin of jaws and teeth represents one of the most formative episodes in our own evolutionary history. However, this event is poorly understood because of a lack of detailed knowledge of key lineages, including the ‘acanthothoracid’ p…
View article: The emergence of metabolisms through Earth history and implications for biospheric evolution
The emergence of metabolisms through Earth history and implications for biospheric evolution Open
We investigate the evolution of microbial metabolisms from the last universal common ancestor to the extant biota through comparative phylogenomics, reconciling the evolution of the genes that underpin metabolic pathways with a time-calibr…
View article: Morphological constraints in hymenopteran forewings limit flight efficiency optimization
Morphological constraints in hymenopteran forewings limit flight efficiency optimization Open
The evolution of wings and flapping flight was integral to the radiation of Pterygota, but little is known about the factors underpinning the morphological disparity of insect wings. We use a theoretical morphospace approach to investigate…
View article: Uncertainty in the timing of diversification of flowering plants rests with equivocal interpretation of their fossil record
Uncertainty in the timing of diversification of flowering plants rests with equivocal interpretation of their fossil record Open
The timing of the origin of crown-angiosperms exemplifies the impact of competing approaches to establishing evolutionary timescales. Fossils of unequivocal crown-angiosperms are not known from before the Cretaceous, and yet molecular esti…
View article: Morphogenesis of Fractofusus andersoni and the nature of early animal development
Morphogenesis of Fractofusus andersoni and the nature of early animal development Open
Rangeomorphs are among the oldest anatomically complex macroscopic fossil organisms and, originating prior to 574 Ma, they represent the earliest total-group eumetazoans. Rangeomorph morphogenesis is therefore significant for understanding…
View article: Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system
Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system Open
The average long-term impact of Darwinian evolution on Earth’s habitability remains extremely uncertain. Recent attempts to reconcile this uncertainty by “Darwinizing” nonreplicating biogeochemical processes subject to persistence-based se…
View article: The evolution of herbivory, not terrestrialization, drove morphological change in the mandibles of Palaeozoic tetrapods
The evolution of herbivory, not terrestrialization, drove morphological change in the mandibles of Palaeozoic tetrapods Open
The radiation of tetrapods during the Devonian and Early Carboniferous was associated with a transition from aquatic to terrestrial environments, with attendant changes in feeding ecology. Despite this, evidence suggests that feeding morph…
View article: A timescale for the evolutionary history of sea spiders (Arthropoda: Pycnogonida)
A timescale for the evolutionary history of sea spiders (Arthropoda: Pycnogonida) Open
Sea spiders (Arthropoda: Pycnogonida) are an ancient lineage of chelicerates represented by a single living order, Pantopoda, and a patchy fossil record that provides limited information of their evolutionary timescale. The sudden appearan…
View article: CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora
CAT-Posterior Mean Site Frequencies Improves Phylogenetic Modeling Under Maximum Likelihood and Resolves Tardigrada as the Sister of Arthropoda Plus Onychophora Open
Tardigrada, the water bears, are microscopic animals with walking appendages that are members of Ecdysozoa, the clade of molting animals that also includes Nematoda (round worms), Nematomorpha (horsehair worms), Priapulida (penis worms), K…
View article: Morphogenesis of pteraspid heterostracan oral plates and the evolutionary origin of teeth
Morphogenesis of pteraspid heterostracan oral plates and the evolutionary origin of teeth Open
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 morphological…
View article: Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa
Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa Open
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 unequ…
View article: Finite element and microstructural analyses indicate that pteraspid heterostracan oral plate microstructure was adapted to a mechanical function
Finite element and microstructural analyses indicate that pteraspid heterostracan oral plate microstructure was adapted to a mechanical function Open
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‐gnath…
View article: New insights into the Devonian sea spiders of the Hunsrück Slate (Arthropoda: Pycnogonida)
New insights into the Devonian sea spiders of the Hunsrück Slate (Arthropoda: Pycnogonida) Open
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 se…
View article: Widespread convergence towards functional optimization in the lower jaws of crocodile-line archosaurs
Widespread convergence towards functional optimization in the lower jaws of crocodile-line archosaurs Open
Extant crocodilian jaws are subject to functional demands induced by feeding and hydrodynamics. However, the morphological and ecological diversity of extinct crocodile-line archosaurs is far greater than that of living crocodilians, featu…
View article: Independent origins of spicules reconcile palaeontological and molecular evidence of the evolutionary history of sponges
Independent origins of spicules reconcile palaeontological and molecular evidence of the evolutionary history of sponges Open
Sponges (Porifera) play a critical role in global biogeochemical processes. However, their evolutionary timeline remains unclear hampering our understanding of Neoproterozoic paleoecology. Molecular data suggest a Tonian or Cryogenian orig…
View article: Molecular Dating of the Teleost Whole Genome Duplication (3R) Is Compatible With the Expectations of Delayed Rediploidization
Molecular Dating of the Teleost Whole Genome Duplication (3R) Is Compatible With the Expectations of Delayed Rediploidization Open
Vertebrate evolution has been punctuated by three whole genome duplication events that have been implicated causally in phenotypic evolution, from the origin of phenotypic novelties to explosive diversification. Arguably, the most dramatic…
View article: Metagenome‐assembled genome of the glacier alga <i>Ancylonema</i> yields insights into the evolution of streptophyte life on ice and land
Metagenome‐assembled genome of the glacier alga <i>Ancylonema</i> yields insights into the evolution of streptophyte life on ice and land Open
Summary 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 dri…
View article: Developmental biology of <i>Spiralicellula</i> and the Ediacaran origin of crown metazoans
Developmental biology of <i>Spiralicellula</i> and the Ediacaran origin of crown metazoans Open
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 o…
View article: The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes
The three-dimensionally articulated oral apparatus of a Devonian heterostracan sheds light on feeding in Palaeozoic jawless fishes Open
Attempts to explain the origin and diversification of vertebrates have commonly invoked the evolution of feeding ecology, contrasting the passive suspension feeding of invertebrate chordates and larval lampreys with active predation in liv…
View article: Functional constraints on tetrapod feeding ecology were released long after terrestrialisation
Functional constraints on tetrapod feeding ecology were released long after terrestrialisation Open
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 morpho…
View article: Cryogenian Origins of Multicellularity in Archaeplastida
Cryogenian Origins of Multicellularity in Archaeplastida Open
Earth was impacted by global glaciations during the Cryogenian (720 to 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 tempor…