23 results found
Cherns L, Spencer A, Rahman IA, et al., 2021, Correlative tomography of exceptionally preserved Jurassic ammonite implies hyponome-propelled swimming, Geology, ISSN: 0091-7613
The extreme rarity of soft tissue preservation in ammonoids has meant there are open questions regarding fundamental aspects of their biology. We report an exceptionally preserved Middle Jurassic ammonite with unrivalled information on soft body organization interpreted through correlative neutron and X-ray tomography. 3D-imaging of muscles and organs of the body mass for the first time in this iconic fossil group provides key insights into functional morphology. We show that paired dorsal muscles withdrew the body into the shell, rather than acting with the funnel controlling propulsion as in Nautilus. This suggests a mobile, retractable body as a defence strategy and necessitates a distinct swimming mechanism of hyponome propulsion, a trait that we infer evolved early in the ammonoid–coleoid lineage.
Strullu-Derrien C, Le Herisse A, Goral T, et al., 2021, THE OVERLOOKED AQUATIC GREEN ALGAL COMPONENT OF EARLY TERRESTRIAL ENVIRONMENTS: TRISKELIA SCOTLANDICA GEN. ET SP. NOV. FROM THE RHYNIE CHERTS, PAPERS IN PALAEONTOLOGY, Vol: 7, Pages: 709-719, ISSN: 2056-2799
Strullu-Derrien C, Geze M, Spencer ART, et al., 2021, An expanded diversity of oomycetes in Carboniferous forests: Reinterpretation of Oochytrium lepidodendri (Renault 1894) from the Esnost chert, Massif Central, France, PLOS ONE, Vol: 16, ISSN: 1932-6203
Strullu-Derrien C, Cleal CJ, Ducassou C, et al., 2021, A rare late Mississippian flora from Northwestern Europe (Maine-et-Loire Coalfield, Pays de la Loire, France), REVIEW OF PALAEOBOTANY AND PALYNOLOGY, Vol: 285, ISSN: 0034-6667
He X-Y, Spencer ART, Wang S-J, et al., 2021, Hydrasperman pteridosperm ovules from the Permian of China: palaeoecological and palaeobiogeographic implications, HISTORICAL BIOLOGY, ISSN: 0891-2963
Spencer A, Garwood R, Sutton MD, 2020, palaeoware/SPIERS: SPIERS v3.1.1
This is a patch release containing fixes for the macOS release. The following has been changed since the last v3.1.0 release. This is now the recommended version.
Garwood R, Spencer A, 2020, palaeoware/trevosim: TREvoSim v1.0.0
This is the first public release of the TREvoSim software. This release and the underlying model has been described in detail in the following paper:Keating, J.N., Sansom, R.S., Sutton, M.D., Knight, C.G., and Garwood, R.J. 2020. Morphological phylogenetics evaluated using novel evolutionary simulations. Systematic Biology.The code is archived on zenodo.org.
Strullu-Derrien C, Bernard S, Spencer ART, et al., 2019, On the structure and chemistry of fossils of the earliest woody plant, PALAEONTOLOGY, Vol: 62, Pages: 1015-1026, ISSN: 0031-0239
Garwood RJ, Oliver H, Spencer ART, 2019, An introduction to the Rhynie chert, Geological Magazine, Pages: 1-18, ISSN: 0016-7568
<jats:title>Abstract</jats:title><jats:p>The terrestrialization of life has profoundly affected the biosphere, geosphere and atmosphere, and the <jats:italic>Geological Magazine</jats:italic> has published key works charting the development of our understanding of this process. Integral to this understanding – and featuring in one of the <jats:italic>Geological Magazine</jats:italic> publications – is the Devonian Rhynie chert Konservat-Lagerstätte located in Aberdeenshire, Scotland. Here we provide a review of the work on this important early terrestrial deposit to date. We begin by highlighting contributions of note in the <jats:italic>Geological Magazine</jats:italic> improving understanding of terrestrialization and Palaeozoic terrestrial ecosystems. We then introduce the Rhynie chert. The review highlights its geological setting: the Caledonian context of the Rhynie Basin and its nature at the time of deposition of the cherts which host its famous fossils. There follows an introduction to the development of the half-graben in which the cherts and host sediments were deposited, the palaeoenvironment this represented and the taphonomy of the fossils themselves. We subsequently provide an overview of the mineralization and geochemistry of the deposit, and then the fossils found within the Rhynie chert. These include: six plant genera, which continue to provide significant insights into the evolution of life on land; a range of different fungi, with recent work starting to probe plant–fungus interactions; lichens, amoebae and a range of unicellular eukaryotes and prokaryotes (algae and cyanobacteria); and finally a range of both aquatic and terrestrial arthropods. Through continued study coupled with methodological advances, Rhynie fossils will continue to provide unique insights into early life on land.</jats:p>
Garwood RJ, Spencer ART, Sutton MD, 2019, REvoSim: Organism-level simulation of macro and microevolution, Palaeontology, Vol: 62, Pages: 339-355, ISSN: 0031-0239
Macroevolutionary processes dictate the generation and loss of biodiversity. Understanding them is a key challenge when interrogating the earth–life system in deep time. Model-based approaches can reveal important macroevolutionary patterns and generate hypotheses on the underlying processes. Here we present and document a novel model called REvoSim (Rapid Evolutionary Simulator) coupled with a software implementation of this model. The latter is available here as both source code (C++/Qt, GNU General Public License) and as distributables for a variety of operating systems. REvoSim is an individual-based model with a strong focus on computational efficiency. It can simulate populations of 10 5 –10 7 digital organisms over geological timescales on a typical desktop computer, and incorporates spatial and temporal environmental variation, recombinant reproduction, mutation and dispersal. Whilst microevolutionary processes drive the model, macroevolutionary phenomena such as speciation and extinction emerge. We present results and analysis of the model focusing on validation, and note a number potential applications. REvoSim can serve as a multipurpose platform for studying both macro and microevolution, and bridges this divide. It will be continually developed by the authors to expand its capabilities and hence its utility.
Spencer A, Garwood R, 2019, palaeoware/SPIERS: SPIERS v3.0.1
Change logThis is a patch release, with a modified SPIERS update notification system. The following has been changed since the last v3.0.0. This is now the recommended version.
Spencer A, Sutton M, Garwood R, 2019, palaeoware/revosim: REvoSim and EnviroGen v2.0.1
This is a patch release of the REvoSim and EnviroGen software containing minor bug fixes and code improvements. This release and the underlying model has been described in detail in the following paper:Garwood, R.J., Spencer A.R.T. and Sutton, M.D. 2019. REvoSim: Organism-level simulation of macro- and microevolution. Palaeontology.The code is archived on zenodo.org:Documentation:REvoSim Online DocumentationEnviroGen Online DocumentationChange log:The following has been changed since the last release.REvoSimUpdate in copyright notice datesMoved licence text to a resource fileEnviroGenUpdate in copyright notice datesMoved licence text to a resource fileGeneralUpdated README file with compile instructions.Updated conditional defines to ensure that the program compiles with pre QT 5.6Updated icons for all operating systemsRelease information: WindowsA zip containing all required binaries can be downloaded from the assets above. Alternatively an installer is provided. See notes below:Note 1: The .zip archive contains all REvoSim programs (REvoSim and EnviroGen). The .zip can be extracted and the programs run by double clicking the .exe files in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.Note 2: The windows installer will not overwrite any pre-existing REvoSim installations. However, it will set the default program for all REvoSim files (.revosim) to to use the newly installed version.MacA zip containing the REvoSim programs (REvoSim and EnviroGen) can be downloaded from the assets above. To install the software, drag and drop the required .app folder(s) into the Applications folder. You may be required to the approve the software in security and privacy settings before it will launch.LinuxAny Linux users willing to test a Linux build should contact email@example.com. A Linux package is planned for release during Q1 2019.
Spencer A, Garwood R, Sutton M, 2019, palaeoware/revosim: REvoSim and EnviroGen v2.0.0
This is the first public release of the REvoSim and EnviroGen software. This release and the underlying model has been described in detail in the following paper:Garwood, R.J., Spencer A.R.T. and Sutton, M.D. 2019. REvoSim: Organism-level simulation of macro- and microevolution. Palaeontology.Change log:The following has been changed since the last release.REvoSimInitial public release.EnviroGen:Initial public release.Release information: LinuxAny Linux users willing to test a Linux build should contact firstname.lastname@example.org.WindowsA zip containing all required binaries can be downloaded from the assets above. Alternatively an installer is provided. See notes below:Note 1: the .zip archive contains all REvoSim programs (REvoSim and EnviroGen). The .zip can be extracted and the programs run by double clicking the .exe files in the ./bin folder. All the required libraries have been included and are found in the ./bin folder.Note 2: The windows installer will not overwrite any pre-existing REvoSim installations. However, it will set the default program for all REvoSim files (.revosim) to to use the newly installed version.MacWe are working on a Mac release and hope to have it released soon.
Burca G, Nagella S, Clark T, et al., 2018, Exploring the potential of neutron imaging for life sciences on IMAT, Journal of Microscopy, Vol: 272, Pages: 242-247, ISSN: 0022-2720
Neutron imaging has been employed in life sciences in recent years and has proven to be a viable technique for studying internal features without compromising integrity and internal structure of samples in addition to being complementary to other methods such as X-ray or magnetic resonance imaging. Within the last decade, a neutron imaging beamline, IMAT, was designed and built at the ISIS Neutron and Muon Source, UK, to meet the increasing demand for neutron imaging applications in various fields spanning from materials engineering to biology. In this paper, we present the first neutron imaging experiments on different biological samples during the scientific commissioning of the IMAT beamline mainly intended to explore the beamline's capabilities and its potential as a noninvasive investigation tool in fields such as agriculture (soil-plants systems), palaeontology and dentistry. Lay Description: Neutrons form a highly penetrating radiation passing through matter without damaging or structurally modifying it, a property that makes them the ideal tool for many kinds of complementary material investigations. Moreover, the strong interaction of neutrons with hydrogen and their ability to distinguish between hydrogen and deuterium with no radiation damage make neutrons a good probe for imaging biological specimens. The recent technological developments of sources and detectors improved the capabilities of neutron imaging instruments and also have facilitated the use of neutron imaging on a much wider scale than before. Neutron imaging is proving its advantages as being complementary to other known methods of investigation such as X-ray imaging or magnetic resonance imaging and it is no surprise that it is not only employed in engineering or archaeology, but also in life sciences. This definitely opens new perspectives for a more interdisciplinary approach in contemporary science. Within the last decade a neutron imaging beamline, IMAT, was designed and built at the IS
Strullu-Derrien C, Spencer ART, Goral T, et al., 2018, New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 373, ISSN: 0962-8436
Spencer ART, Garwood RJ, Rees AR, et al., 2017, New insights into Mesozoic cycad evolution: an exploration of anatomically preserved Cycadaceae seeds from the Jurassic Oxford Clay biota, PeerJ, Vol: 5, ISSN: 2167-8359
Most knowledge concerning Mesozoic Era floras has come from compression fossils. This has been augmented in the last 20 years by rarer permineralized material showing cellular preservation. Here, we describe a new genus of anatomically preserved gymnosperm seed from the Callovian–Oxfordian (Jurassic) Oxford Clay Formation (UK), using a combination of traditional sectioning and synchrotron radiation X-ray micro-tomography (SRXMT). Oxfordiana motturii gen. et sp. nov. is large and bilaterally symmetrical. It has prominent external ribs, and has a three-layered integument comprising: a narrow outer layer of thick walled cells; a thick middle parenchymatous layer; and innermost a thin fleshy layer. The integument has a longitudinal interior groove and micropyle, enveloping a nucellus with a small pollen chamber. The large size, bilateral symmetry and integumentary groove demonstrate an affinity for the new species within the cycads. Moreover, the internal groove in extant taxa is an autapomorphy of the genus Cycas, where it facilitates seed germination. Based upon the unique seed germination mechanism shared with living species of the Cycadaceae, we conclude that O. motturii is a member of the stem-group lineage leading to Cycas after the Jurassic divergence of the Cycadaceae from other extant cycads. SRXMT—for the first time successfully applied to fossils already prepared as slides—reveals the distribution of different mineral phases within the fossil, and allows us to evaluate the taphonomy of Oxfordiana. An early pyrite phase replicates the external surfaces of individual cells, a later carbonate component infilling void spaces. The resulting taphonomic model suggests that the relatively small size of the fossils was key to their exceptional preservation, concentrating sulfate-reducing bacteria in a locally closed microenvironment and thus facilitating soft-tissue permineralization.
Wang S-J, Bateman RM, Spencer ART, et al., 2017, Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities, American Journal of Botany, Vol: 104, Pages: 127-149, ISSN: 0002-9122
PREMISE OF THE STUDY: Noeggerathiales are an extinct group of heterosporous shrubs and trees that were widespread and diverse during the Pennsylvanian–Permian Epochs (323–252 Ma) but are of controversial taxonomic affi nity. Groups proposed as close relatives include leptosporangiate ferns, sphenopsids,progymnosperms, or the extant eusporangiate fern Tmesipteris . Previously identifi ed noeggerathialeans lacked anatomical preservation, limiting taxonomiccomparisons to their external morphology and spore structure. We here document from the upper Permian of China the fi rst anatomically preservednoeggerathialeans, which enhance the perceived distinctiveness of the group and better indicate its systematic affi nity.METHODS: We describe in detail the newly discovered, anatomically preserved heterosporous strobilus Dorsalistachya quadrisegmentorum , gen. et sp. nov.,and redescribe its suspected foliar correlate, the pinnate leaf Plagiozamites oblongifolius .KEY RESULTS: Plagiozamites possesses an omega ( Ω )-shaped vascular trace and prominent cortical secretory cavities—a distinctive anatomical organizationthat is echoed in the newly discovered strobili. Dorsalistachya strobili bear highly dissected sporophylls alternately in two vertical rows, suggestingthat they are homologs of leaf pinnae. If so, the “strobilus” is strictly a pseudostrobilus and consists of sporangium-bearing units that are one hierarchicallevel below true sporophylls. The “sporophylls” bear four microsporangia on the lower (abaxial) surface, occasionally interspersed with short longitudinalrows of megasporangia. A single functional megaspore develops within each winged megasporangium, suggesting adaptation for dispersal as asingle unit.CONCLUSIONS: Dorsalistachya presents a unique combination of reproductive features that amply justifi es establishment of a new family, Dorsalistachyaceae. Noeggerathialesrepresent a distinct taxonomic Order of free-spo
Garwood RJ, Dunlop JA, Spencer ART, et al., 2016, Almost a spider: a 305-million-year-old fossil arachnid and spider origins, Proceedings of the Royal Society of London. Series B, Biological Sciences, Vol: 283, ISSN: 0080-4649
Spiders are an important animal group, with a long history. Details of their origins remain limited, with little knowledge of their stem group, and no insights into the sequence of character acquisition during spider evolution. We describe a new fossil arachnid, Idmonarachne brasieri gen. et sp. nov. from the Late Carboniferous (Stephanian, ca 305–299 Ma) of Montceau-les-Mines, France. It is three-dimensionally preserved within a siderite concretion, allowing both laboratory- and synchrotron-based phase-contrast computed tomography reconstruction. The latter is a first for siderite-hosted fossils and has allowed us to investigate fine anatomical details. Although distinctly spider-like in habitus, this remarkable fossil lacks a key diagnostic character of Araneae: spinnerets on the underside of the opisthosoma. It also lacks a flagelliform telson found in the recently recognized, spider-related, Devonian–Permian Uraraneida. Cladistic analysis resolves our new fossil as sister group to the spiders: the spider stem-group comprises the uraraneids and I. brasieri. While we are unable to demonstrate the presence of spigots in this fossil, the recovered phylogeny suggests the earliest character to evolve on the spider stem-group is the secretion of silk. This would have been followed by the loss of a flagelliform telson, and then the ability to spin silk using spinnerets. This last innovation defines the true spiders, significantly post-dates the origins of silk, and may be a key to the group's success. The Montceau-les-Mines locality has previously yielded a mesothele spider (with spinnerets). Evidently, Late Palaeozoic spiders lived alongside Palaeozoic arachnid grades which approached the spider condition, but did not express the full suite of crown-group autapomorphies.
Spencer ART, Mapes G, Bateman RM, et al., 2015, Middle Jurassic evidence for the origin of Cupressaceae: A paleobotanical context for the roles of regulatory genetics and development in the evolution of conifer seed cones, American Journal of Botany, Vol: 102, Pages: 942-961, ISSN: 1537-2197
• Premise of the study: Triassic and Jurassic fossils record structural changes in conifer seed cones through time, provide the earliest evidence for crown-group conifer clades, and further clarify sister-group relationships of modern conifer families. A new and distinct seed-cone from the Isle of Skye in western Scotland provides the oldest detailed evidence for the ancestral morphology of the phylogenetically contentious family Cupressaceae.• Methods: A single isolated cone was prepared as serial sections by the cellulose acetate peel technique, mounted on microscope slides, and viewed and photographed using transmitted light. The three-dimensional structure of the cone was first reconstructed from the serial sections and then refined through imaging with x-ray microtomography.• Key results: Scitistrobus duncaanensis, gen. et sp. nov., is a 7.5 mm-diameter cylindrical seed cone with helically arranged bract–scale complexes in which three scale tips separate from a large bract, each tip bearing one adaxial seed. Seeds are near-inverted, show 180° rotational symmetry, and have a diminutive wing in the major plane.• Conclusions: Scitistrobus duncaanensis extends the fossil record for anatomically preserved seed cones of the Cupressaceae backward from the Upper Jurassic to the Aalenian Stage of the Middle Jurassic. The cone displays a previously unknown combination of characters that we regard as diagnostic for seed cones of early-divergent Cupressaceae and helps to clarify the sequence of structural changes that occurred during the transition from ancestral voltzialean conifers to morphologically recognizable Cupressaceae. Hypotheses of homology underpinning such transformational series can be tested by ongoing reciprocal illumination between the morphology of fossil taxa and the morphogenesis and developmental genetics of their extant crown-group relatives.
Steart DC, Spencer ART, Garwood RJ, et al., 2014, X-ray Synchrotron Microtomography of a silicified Jurassic Cheirolepidiaceae (Conifer) cone: histology and morphology of Pararaucaria collinsonae sp. nov., PeerJ, Vol: 2, ISSN: 2167-8359
We document a new species of ovulate cone (Pararaucaria collinsonae) on the basis of silicified fossils from the Late Jurassic Purbeck Limestone Group of southern England (Tithonian Stage: ca. 145 million years). Our description principally relies on the anatomy of the ovuliferous scales, revealed through X-ray synchrotron microtomography (SRXMT) performed at the Diamond Light Source (UK). This study represents the first application of SRXMT to macro-scale silicified plant fossils, and demonstrates the significant advantages of this approach, which can resolve cellular structure over lab-based X-Ray computed microtomography (XMT). The method enabled us to characterize tissues and precisely demarcate their boundaries, elucidating organ shape, and thus allowing an accurate assessment of affinities. The cones are broadly spherical (ca. 1.3 cm diameter), and are structured around a central axis with helically arranged bract/scale complexes, each of which bare a single ovule. A three-lobed ovuliferous scale and ovules enclosed within pocket-forming tissue, demonstrate an affinity with Cheirolepidiaceae. Details of vascular sclerenchyma bundles, integument structure, and the number and attachment of the ovules indicate greatest similarity to P. patagonica and P. carrii. This fossil develops our understanding of the dominant tree element of the Purbeck Fossil Forest, providing the first evidence for ovulate cheirolepidiaceous cones from this locality. Alongside recent discoveries in North America, this significantly extends the known palaeogeographic range of Pararaucaria, supporting a mid-palaeolatitudinal distribution in both Gondwana and Laurasia during the Late Jurassic. Palaeoclimatic interpretations derived from contemporaneous floras, climate sensitive sediments, and general circulation climate models indicate that Pararaucaria was a constituent of low diversity floras in semi-arid Mediterranean-type environments.
Spencer ART, Wang S-J, Dunn MT, et al., 2013, Species of the medullosan ovule Stephanospermum from the Lopingian (late Permian) floras of China, Journal of Asian Earth Sciences
The medullosan pteridosperm ovule Stephanospermum Brongniart is a well-known component of Carboniferous aged coal-ball and siderite nodule floras from North America and Europe but also occurs in the Permian floras of Cathaysia where it is represented by the Lopingian (late Permian) aged species Stephanospermum trunctatum (Li) Wang et al. (2009) from coal-balls in the Wangjiazhai Formation in Southern China. We provide a detailed emendation of S. trunctatum and illustrate it comprehensively for the first time, and document an additional specimen from the Wangjiazhai Formation coal-ball assemblage that we assign to Stephanospermum shuichengensis sp. nov. S. shuichengensis is distinguished from S. trunctatum by the absence of apical teeth in the sclerotesta and non-obovate base. The two species of Stephanospermum from the Wangjiazhai Formation are important as they extend the stratigraphic and geographical range of the genus from the Pennsylvanian of Euramerica into the Lopingian of Southern China, and demonstrate that the genus persisted in wetland, peat forming environments in the run up to the end-Permian mass extinction event. The 44 MY stratigraphic discontinuity between the Euramerican and the Cathaysian species, here named the Stephanospermum gap, leads us to infer that the genus was likely to have occurred in the Pennsylvanian–Permian successions of southern Russia and northern China that are geographically and stratigraphically intermediate to the known occurrences but from which the genus has yet to be discovered. Medullosan pteridosperms appear to have become extinct at or immediately prior to the Permian-Triassic boundary that coincides with the Permo–Trias mass extinction event; although the exact causes of this loss in plant diversity remains unknown, a response to regional climatic drying is likely to have been a contributing factor.
Spencer ART, Hilton J, Sutton MD, 2012, Combined methodologies for three-dimensional reconstruction of fossil plants preserved in siderite nodules: Stephanospermum braidwoodensis nov. sp. (Medullosales) from the Mazon Creek lagerstätte, Review of Palaeobotany and Palynology
A new species of Medullosan ovule from the Mazon Creek Carboniferous lagerstätte is documented using a novel combination of non-invasive X-Ray Micro-Tomography (XMT) and orientated precision sectioning based on the XMT results. 3-D reconstruction of the ovule has correlated geometries of different layers with tissue characteristics gathered from wafered sections, with the methodological combination presenting a virtual reconstruction of the specimen and also enabling positioning of serial sections of the holotype in pre-determined positions. Stephanospermum braidwoodensis sp. nov. has four longitudinally orientated sarcotestal wings, two to each side of the major plane that demonstrate 180° rotational (bilateral) symmetry, while the sclerotesta has three prominent longitudinal commissural ribs and the pollen chamber has three small ribs and triangular nucellar beak, both demonstrating radial (threefold) symmetry. This demonstration of both radial and bilateral symmetries in different tissues emphasises the complexities of inferring systematic affinities of fossil seeds from symmetry alone. We consider S. braidwoodensis to be closely related to the co-occurring S. konopeonus Drinnan et al., and postulate that it was born on a fertile truss similar to that of the latter species. Finally implications of our findings for the utility of these methods in identifying additional species from the Mazon Creek biota are discussed, and the advantages and disadvantages of different methods of nodule preparation are considered. We conclude that additional species are likely to be recognised from the Mazon Creek flora by application of the same methodologies used in this investigation.
Garwood RJ, Spencer ART, 2011, The geology and terrestrial life of the Carboniferous, Deposits Magazine, Vol: 28, Pages: 38-47
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