Perturbation of the Earth System at the Proterozoic-Phanerozoic transition and the resilience of the biosphere

Lead Research Organisation: University of Bristol
Department Name: Earth Sciences

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Planned Impact

The nature of the research topic means that much of the direct benefit will be for the academic community (see Academic Beneficiaries), however as it tackles the emergence of complex life on Earth there will be significant public interest in the research topic, approach, progress and outputs. Going beyond the topic itself, our approach is non-traditional in that it is highly integrative and seeks to develop and exploit a step change to develop inter-operable multi-parameter datasets and models, impacting how others research similar 'Earth System' topics.

Beyond the academic community (see Academic Beneficiaries) we expect the general public, in UK and China, will be beneficiaries of the research. The 'Cambrian explosion' and the origin of complex life on our planet was listed in an Economist article 'Life, the multiverse and everything, Science has remade the world, but scientists are not finished yet' (6th August 2015) as one of Science's six unsolved mysteries. This highlights that the research topic covered by this proposal is one of the big ones that captures the public's interest. We will develop novel web, using Quick Response (QR) codes and MediaWIKI infrastructure to communicate project science at sites where the rocks outcrop, and museums. We expect this to generate interest in the Earth and Biological Sciences, highlighting how the Earth system has evolved and operated prior to becoming our familiar world, will allow us to engage with the public and get them to think about complexity, feedbacks, and how systems evolve. Whilst the current changes facing the planet are operating at different timescales there are parallels to be made and lessons to be learnt from studying the 'Cambrian explosion'.

The focus on 'data mining and management' within this project allows us to identify those organisations and professional scientific bodies who are invested in developing geoscience 'data management' tools. In the case of this project, such organisations would include the International Commission on Stratigraphy (ICS), the Interdisciplinary Earth Data Alliance (IEDA), and the EARTHTIME Initiative. These organisations will benefit from our engagement with such systems and using this project to accelerate development in identified key areas. These will include aiding the federation of data from the GEOCHRON databased with the stratigraphic data in the GeoBiodiversity Database, and the development of 'age-model' tools within the later.

A third group of beneficiaries represent the industries that are engaged with exploring the resource potential of late Precambrian and earliest Phanerozoic sedimentary successions. The resources in question are primarily hydrocarbons although economic sulphide and phosphorite deposits occur within these successions. With respect to hydrocarbons the late Precambrian is considered a frontier for exploration, and significant accumulations of Precambrian occur in basins such as the South Oman Salt Basin. The primary research we will generate will include information about the geochemistry of specific successions of the South China Platform, information about their palaeogeographic history and information about basin development. Companies and industry funded research consortia will benefit from the approach developed in this research programme. Furthermore, the data generated, placed within the developing global 4D framework will allow us to export information to other basins which may have an economic potential (e.g., Oman, Brazil).

Publications

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Bowles A (2024) Cryogenian origins of multicellularity in Archaeplastida in Genome Biology and Evolution

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Bowles AMC (2023) The origin and early evolution of plants. in Trends in plant science

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Bråte J (2018) Unicellular Origin of the Animal MicroRNA Machinery. in Current biology : CB

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Clark JW (2023) Constraining Whole-Genome Duplication Events in Geological Time. in Methods in molecular biology (Clifton, N.J.)

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Cunningham JA (2017) The origin of animals: Can molecular clocks and the fossil record be reconciled? in BioEssays : news and reviews in molecular, cellular and developmental biology

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Davies TG (2017) Open data and digital morphology. in Proceedings. Biological sciences

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Deline B (2018) Evolution of metazoan morphological disparity. in Proceedings of the National Academy of Sciences of the United States of America

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Donoghue P (2017) Evolution: Divining the Nature of the Ancestral Vertebrate. in Current biology : CB

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Donoghue PCJ (2020) Fossil cells. in Current biology : CB

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Donoghue PCJ (2021) The evolutionary emergence of land plants. in Current biology : CB

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Donoghue Philip C. J. (2020) Fossil cells in CURRENT BIOLOGY

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Dunn FS (2019) Anatomy of the Ediacaran rangeomorph Charnia masoni. in Papers in palaeontology

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Dunn FS (2018) Ediacaran developmental biology. in Biological reviews of the Cambridge Philosophical Society

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Ferrón HG (2021) Functional assessment of morphological homoplasy in stem-gnathostomes. in Proceedings. Biological sciences

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Gai Z (2022) The Evolution of the Spiracular Region From Jawless Fishes to Tetrapods in Frontiers in Ecology and Evolution

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Guillerme T (2020) Disparities in the analysis of morphological disparity. in Biology letters

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Howard R (2022) The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data in Journal of the Geological Society

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Mills DB (2022) Eukaryogenesis and oxygen in Earth history. in Nature ecology & evolution

 
Description We established a timescale for early animal evolution in which we rationalised the fossil record and the pattern of character evolution in the assembly of animal bodyplans.
Exploitation Route The molecular evolutionary timescale can be used as a framework for calibrating biological evolution to the evolution of the Earth system
Sectors Education

 
Title Data & Scripts from Beavan et al. (2020): Performance of a priori and a posteriori calibration strategies in divergence time estimation. 
Description The data and scripts includes all information necessary to recreate the simulated data of Beavan et al. (2020). In addition, it includes all the parameters and scripts to analyse the data and the original alignments used in the study. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/uopumskkuech206ueqdxpcrif/
 
Title Data from Dong et al. 2022. Internal anatomy of a fossilized embryonic stage of the Cambrian-Ordovician scalidophoran Markuelia. Royal Society Open Science 
Description This dataset contains 7 Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) datasets based on specimens of Markuelia hunanensis from the upper Cambrian (Furongian) Bitiao Formation at Wangcun Section, Yongshun County, Hunan Province, South China. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/za3bxfhxpyct2qsy8ceeriksh/
 
Title Data from Dunn et al. 2021. The developmental biology of Charnia and the eumetazoan affinity of the Ediacaran rangeomorphs. Science Advances 
Description This dataset contains three dimensional X-Ray tomographic datasets and reflectance transformation images of fossilized specimens of Charnia masoni (stem-eumetazoan). The data accompanies the following paper: Frances S. Dunn, Alexander G. Liu, Dmitriy V. Grazhdankin, Philip Vixseboxse, Joseph Flannery-Sutherland, Emily Green, Simon Harris, Philip R. Wilby and Philip C. J. Donoghue. 2021. The developmental biology of Charnia and the eumetazoan affinity of the Ediacaran rangeomorphs. Science Advances 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/mukcdnafukgq2n8oljgar1s23/
 
Title Data from Landon et al. Cellular preservation of excysting developmental stages of new eukaryotes from the early Ediacaran Weng'an Biota 
Description X-ray tomographic slice data from 21 ediacaran microfossils 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Title Data from Liu et al. 2022. Saccorhytus is an early ecdysozoan and not the earliest deuterostome. Nature 
Description This dataset contains 25 Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) datasets based on specimens of Saccorhytus coronarius from the early Cambrian Kuanchuanpu Formation (late Llandovery to early Wenlock, Silurian) of Zhejiang, South China. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/2iha22zobeher2leh936xrktqx/
 
Title Data from Psarras et al. 2023. Three-dimensional reconstruction, taphonomic and petrological data suggest the oldest record of bioturbation is a body fossil coquina. Papers in Palaeontology 
Description This dataset contains an X-Ray microtomographic dataset based on a rock sample containing specimens of Nenoxites from the late Ediacaran Khatyspyt Formation of Arctic Siberia 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/13jspoe3ih1wl2bx94tc6x6uf7/
 
Title Data from Steiner et al. 2021. Exceptionally preserved early Cambrian bilaterian developmental stages from Mongolia. Nature Communications 
Description The data accompanies the paper: Michael Steiner, Ben Yang, Simon Hohl, Da Li, Philip Donoghue. 2021. Exceptionally preserved early Cambrian bilaterian developmental stages from Mongolia. Nature Communications. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/27qu5twt57gu62m9dpk4ntcrfs/
 
Title Data from Sun et al. (2020) Nucleus preservation in early Ediacaran Weng'an embryo-like fossils, experimental taphonomy of nuclei and implications for reading the eukaryote fossil record. Interface Focus. 
Description This dataset contains three dimensional X-Ray tomographic datasets of fossil specimens of Megasphaera from the Ediacaran Weng'an Biota at 54 Quarry, Weng'an County, Guizhou Province, South China. Tom Davies is Deputy Data Steward. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/pxup7vdmg25r2sl3kr00y5cu6/
 
Title Data from Sun et al. 2021. Ultrastructure and in-situ chemical characterization of intracellular granules of embryo-like fossils from the early Ediacaran Weng'an biota. PalZ 
Description This dataset contains three dimensional X-Ray tomographic datasets of fossil specimens of Megasphaera from the Ediacaran Weng'an Biota, 54 Quarry, Weng'an County, Guizhou Province, South China. The data accompanies the following paper: Weichen Sun, Zongjun Yin, Pengju Liu, Philip C. J. Donoghue, Jinhua Li, Maoyan Zhu. 2021. Ultrastructure and in-situ chemical characterization of intracellular granules of embryo-like fossils from the early Ediacaran Weng'an biota. PalZ 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/1smpsrc4bipqi25rytwr9xgujc/
 
Title Data from Yin et al. (2019) The early Ediacaran Caveasphaera foreshadows the evolutionary origin of animal-like embryology. Current Biology 
Description Tomographic data and associated computed tomographic models 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Title Data from Yin et al. (2020) 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). Science Advances 
Description This dataset contains three dimensional X-Ray tomographic datasets of fossil specimens of Helicoforamina wenganica from the Ediacaran Weng'an Biota, Guizhou Province, South China. Tom Davies is Deputy Data Steward. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://data.bris.ac.uk/data/dataset/tznl7b6dt7kr23cd1d5eokvcz/
 
Title Data from: Anatomy of the Ediacaran rangeomorph Charnia masoni 
Description The Ediacaran macrofossil Charnia masoni Ford is perhaps the most iconic member of the Rangeomorpha: a group of seemingly sessile, frondose organisms that dominates late Ediacaran benthic, deep-marine fossil assemblages. Despite C. masoni exhibiting broad palaeogeographical and stratigraphical ranges, there have been few morphological studies that consider the variation observed among populations of specimens derived from multiple global localities. We present an analysis of C. masoni that evaluates specimens from the UK, Canada and Russia, representing the largest morphological study of this taxon to date. We describe substantial morphological variation within C. masoni and present a new morphological model for this species that has significant implications both for interpretation of rangeomorph architecture, and potentially for existing taxonomic schemes. Previous reconstructions of Charnia include assumptions regarding the presence of structures seen in other rangeomorphs (e.g. an internal stalk) and of homogeneity in higher order branch morphology; observations that are not borne out by our investigations. We describe variation in the morphology of third and fourth order branches, as well as variation in gross structure near the base of the frond. The diagnosis of Charnia masoni is emended to take account of these new features. These findings highlight the need for large-scale analyses of rangeomorph morphology in order to better understand the biology of this long-enigmatic group. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.fg14s2r
 
Title Data from: Evolution of fungal phenotypic disparity 
Description 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 seek to test the general relevance of hypotheses on the evolution of animal body plans by characterising the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated, zygomycetous, sac-bearing, and club-bearing. The discontinuity between morphotypes is a consequence of the extinction of phylogenetic intermediates, indicating that a complete record of fungal disparity would present a much more homogeneous distribution of form. Fungal phenotypic variety gradually expands through time for the most part but sharply increases with the emergence of multicellular body plans. Simulations show these temporal trends to be decidedly non-random, and at least partially shaped by hierarchical contingency. Fungal phenotypic distance is decoupled from changes in gene number, genome size, and taxonomic diversity. Only differences in organismal complexity, the number of traits that constitute an organism, at the cellular and multicellular levels present a meaningful relationship with fungal disparity. Both animals and fungi exhibit a gradual increase in disparity through time, resulting in distributions of form made discontinuous by the extinction of phylogenetic intermediates. These congruences hint at a common mode of multicellular body plan evolution. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL http://datadryad.org/stash/dataset/doi:10.5061/dryad.wwpzgmsm9
 
Title Data from: Probabilistic methods outperform parsimony in the phylogenetic analysis of data simulated without a probabilistic model 
Description In order to understand patterns and processes of the diversification of life we require an accurate understanding of taxa interrelationships. Recent studies have suggested that analyses of morphological character data using the Bayesian and Maximum likelihood Mk model provide phylogenies of higher accuracy compared to parsimony methods. These studies have proved controversial, particularly simulating morphology-data under Markov models that assume shared branch lengths for characters, as it is claimed this leads to bias favouring the Bayesian or Maximum likelihood Mk model over parsimony models which do not explicitly make this assumption. We avoid these potential issues by employing a simulation protocol in which character states are randomly assigned to tips, but datasets are constrained to an empirically-realistic distribution of homoplasy as measured by the Consistency Index. Datasets were analysed with equal-weights and implied weights parsimony, and the Maximum Likelihood and Bayesian Mk model. We find that consistent (low homoplasy) datasets render method choice largely irrelevant, as all methods perform well with high consistency (low homoplasy) datasets, but the largest discrepancies in accuracy occur with low consistency datasets (high homoplasy). In such cases, the Bayesian Mk model is significantly more accurate than alternative models, and Implied weights parsimony never significantly out-performs the Bayesian Mk model. When poorly-supported branches are collapsed, the Bayesian Mk model recovers trees with higher resolution compared to other methods. Since it is not possible to assess homoplasy independently of a tree estimate, the Bayesian Mk model emerges as the most reliable method for categorical morphological analyses. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.h8r2629
 
Title Data from: Probabilistic methods surpass parsimony when assessing clade support in phylogenetic analyses of discrete morphological data 
Description Fossil taxa are critical to inferences of historical diversity and the origins of modern biodiversity, but realizing their evolutionary significance is contingent on restoring fossil species to their correct position within the tree of life. For most fossil species, morphology is the only source of data for phylogenetic inference; this has traditionally been analysed using parsimony, the predominance of which is currently challenged by the development of probabilistic models that achieve greater phylogenetic accuracy. Here, based on simulated and empirical datasets, we explore the relative efficacy of competing phylogenetic methods in terms of clade support. We characterize clade support using bootstrapping for parsimony and Maximum Likelihood, and intrinsic Bayesian posterior probabilities, collapsing branches that exhibit less than 50% support. Ignoring node support, Bayesian inference is the most accurate method in estimating the tree used to simulate the data. After assessing clade support, Bayesian and Maximum Likelihood exhibit comparable levels of accuracy, and parsimony remains the least accurate method. However, Maximum Likelihood is less precise than Bayesian phylogeny estimation, and Bayesian inference recaptures more correct nodes with higher support compared to all other methods, including Maximum Likelihood. We assess the effects of these findings on empirical phylogenies. Our results indicate probabilistic methods should be favoured over parsimony. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.8dd39
 
Title Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution 
Description Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.5706p
 
Title Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution 
Description This repository contains simulated data and Bayesian MCMC output from *Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution* by Rachel CM Warnock, Ziheng Yang and Philip CJ Donoghue. (2017) **Proc. R. Soc. B** 284 (1857). This data is associated with the following paper: http://rspb.royalsocietypublishing.org/content/284/1857/20170227. This data is also associated with code available on dryad: http://datadryad.org/resource/doi:10.5061/dryad.5706p. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
 
Title Data from: The effect of fossil sampling on the estimation of divergence times with the fossilised birth death process 
Description Timescales are of fundamental importance to evolutionary biology as they facilitate hypothesis tests of historical evolutionary processes. Through the incorporation of fossil occurrence data, the fossilised birth-death (FBD) process provides a framework for estimating divergence times using more palaeontological data than traditional node calibration approaches have allowed. The inclusion of more data can refine evolutionary timescale estimates, but for many taxonomic groups it is computationally infeasible to include all fossil occurrence data. Here, we utilise both empirical data and a simulation framework to identify approaches to subsampling fossil occurrence data that result in the most accurate estimates of divergence times. To achieve this we assess the performance of the FBD-Skyline model when implementing multiple approaches to incorporating subsampled fossil occurrences. Our results demonstrate that it is necessary to account for all available fossil occurrence data to achieve the most accurate estimates of clade age. We show that this can be achieved if an empirical Bayes approach to account for fossil sampling through time is applied to the FBD process. Random subsampling of occurrence data can lead to estimates of clade age that are incompatible with fossil evidence if no control over the affinities of fossil occurrences is enforced. Our results call into question the accuracy of previous divergence time studies incorporating the FBD process that have used only a subsample of all available fossil occurrence data. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.g7s0hk3
 
Title Data from: The efficacy of consensus tree methods for summarising phylogenetic relationships from a posterior sample of trees estimated from morphological data 
Description Consensus trees are required to summarise trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are co-estimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility contains an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarising diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological datasets contributes to the inability of MCC and MAP trees to present an accurate summary of the posterior distribution. Conversely, majority-rule consensus (MRC) trees report a lower proportion of incorrect nodes when summarising the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarise the results of Bayesian phylogenetic analyses of morphological data. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.66s9h
 
Title Data from: The impact of fossil stratigraphic ranges on tip-calibration, and the accuracy and precision of divergence time estimates 
Description The molecular clock provides the only viable means of establishing realistic evolutionary timescales but it remains unclear how best to calibrate divergence time analyses. Calibrations can be applied to the tips and/or to the nodes of a phylogeny. Tip-calibration is an attractive approach since it allows fossil species to be included alongside extant relatives in molecular clock analyses. However, most fossil species are known from multiple stratigraphical horizons and it remains unclear how such age ranges should be interpreted to codify tip-calibrations. We use simulations and empirical data to explore the impact on precision and accuracy of different approaches to informing tip-calibrations. In particular, we focus on the effect of using tip-calibrations defined using the oldest vs youngest stratigraphic occurrences, the full stratigraphical range, as well as confidence intervals on these data points. The results of our simulations show that using different calibration approaches leads to different divergence-time estimates and demonstrate that concentrating tip-calibrations near the root of the dated phylogeny improves both precision and accuracy of estimated divergence times. Finally, our results indicate that the highest levels of accuracy and precision are achieved when fossil tips are calibrated based on the fossil occurrence from which the morphological data were derived. These trends were corroborated by analysis of an empirical dataset for Ursidae. Overall, we conclude that tip-dating analyses should, in particular, employ tip calibrations close to the root of the tree and they should be calibrated based on the age of the fossil used to inform the morphological data used in Total Evidence Dating. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.7kh57t5
 
Title Electronic supplementary material from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history. A response to Brown et al. 
Description Literature reviewed 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/dataset/Electronic_supplementary_material_from_Parsimony_and_maximu...
 
Title Literature reviewed from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.
Description ESM 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/dataset/Electronic_supplementary_material_from_Parsimony_and_maximu...
 
Title Literature reviewed from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown et al.
Description ESM 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/dataset/Electronic_supplementary_material_from_Parsimony_and_maximu...
 
Title Molecular clock fossil calibration database 
Description A database of fully researched and evidenced fossil calibrations for molecular clock analyses. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact There are a number of launch publications associated, it is changing best practice in divergence time estimation, and it fostering links between palaeontologists and molecular biologists. 
URL http://www.nescent.org/science/awards_summary.php?id=259
 
Title Pseudooidesmatrixfinal.txt from The early Cambrian fossil embryo Pseudooides is a direct-developing cnidarian, not an early ecdysozoan 
Description Early Cambrian Pseudooides prima has been described from embryonic and post-embryonic stages of development, exhibiting long germ-band development. There has been some debate about the pattern of segmentation, but this interpretation, as among the earliest records of ecdysozoans, has been generally accepted. Here, we show that the 'germ band' of P. prima embryos separates along its mid axis during development, with the transverse furrows between the 'somites' unfolding into the polar aperture of the hexa-radial theca of Hexaconularia sichuanensis, conventionally interpreted as a scyphozoan cnidarian; co-occurring post-embryonic remains of ecdysozoans are unrelated. We recognize H. sichuanensis as a junior synonym of P. prima as a consequence of identifying these two-form taxa as distinct developmental stages of the same organism. Direct development in P. prima parallels the co-occuring olivooids Olivooides, and Quadrapyrgites and Bayesian phylogenetic analysis of a novel phenotype dataset indicates that, despite differences in their tetra-, penta- and hexa-radial symmetry, these hexangulaconulariids comprise a clade of scyphozoan medusozoans, with Arthrochites and conulariids, that all exhibit direct development from embryo to thecate polyp. The affinity of hexangulaconulariids to extant scyphozoan medusozoans indicates that the prevalence of tetraradial symmetry and indirect development are a vestige of a broader spectrum of body-plan symmetries and developmental modes that was manifest in their early Phanerozoic counterparts. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/Pseudooidesmatrixfinal_txt_from_The_early_Cambrian_fossil_embryo_i_...
 
Title Pseudooidesmatrixfinal.txt from The early Cambrian fossil embryo Pseudooides is a direct-developing cnidarian, not an early ecdysozoan 
Description Early Cambrian Pseudooides prima has been described from embryonic and post-embryonic stages of development, exhibiting long germ-band development. There has been some debate about the pattern of segmentation, but this interpretation, as among the earliest records of ecdysozoans, has been generally accepted. Here, we show that the 'germ band' of P. prima embryos separates along its mid axis during development, with the transverse furrows between the 'somites' unfolding into the polar aperture of the hexa-radial theca of Hexaconularia sichuanensis, conventionally interpreted as a scyphozoan cnidarian; co-occurring post-embryonic remains of ecdysozoans are unrelated. We recognize H. sichuanensis as a junior synonym of P. prima as a consequence of identifying these two-form taxa as distinct developmental stages of the same organism. Direct development in P. prima parallels the co-occuring olivooids Olivooides, and Quadrapyrgites and Bayesian phylogenetic analysis of a novel phenotype dataset indicates that, despite differences in their tetra-, penta- and hexa-radial symmetry, these hexangulaconulariids comprise a clade of scyphozoan medusozoans, with Arthrochites and conulariids, that all exhibit direct development from embryo to thecate polyp. The affinity of hexangulaconulariids to extant scyphozoan medusozoans indicates that the prevalence of tetraradial symmetry and indirect development are a vestige of a broader spectrum of body-plan symmetries and developmental modes that was manifest in their early Phanerozoic counterparts. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
URL https://rs.figshare.com/articles/Pseudooidesmatrixfinal_txt_from_The_early_Cambrian_fossil_embryo_i_...
 
Title Unicellular origin of the animal microRNA machinery. Bråte et al. 
Description  
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
URL https://data.mendeley.com/datasets/h96s28wcx9/1
 
Title Unicellular origin of the animal microRNA machinery. Bråte et al. 
Description  
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
URL https://data.mendeley.com/datasets/h96s28wcx9
 
Description Conference presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference presentation
Year(s) Of Engagement Activity 2017
 
Description Elizabeth Pennisi: Yu et al. (2024) NEE Science Magazine https://www.science.org/content/article/slimy-hagfish-help-solve-mysteries-genome-duplication 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Interview with a journalist resulting in the following output:

Elizabeth Pennisi: Yu et al. (2024) NEE Science Magazine
https://www.science.org/content/article/slimy-hagfish-help-solve-mysteries-genome-duplication
Year(s) Of Engagement Activity 2024
URL https://www.science.org/content/article/slimy-hagfish-help-solve-mysteries-genome-duplication
 
Description Press release and associated interviews 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press releases associated with three consecutive papers and associated interviews
Year(s) Of Engagement Activity 2018
 
Description Public 'Great Debate' at Oxford University Museum of Natural History on 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 250 people present on the evening, booked ahead plus others watching the event streamed and still others watching it offline. e-polls taken before an after the event - on the timing and nature of the Cambrian Explosion - showed that people had changed their views
Year(s) Of Engagement Activity 2020
URL https://oumnh.ox.ac.uk/event/the-first-animals-when-where-and-how
 
Description Westbury on Trym C of E primary Academy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Science Week school presentation
Year(s) Of Engagement Activity 2017