Alan R. T. Spencer | Imperial College London (original) (raw)

Papers by Alan R. T. Spencer

PeerJ, 2017

Most knowledge concerning Mesozoic Era floras has come from compression fossils. This has been au... more 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.

PREMISE OF THE STUDY: Noeggerathiales are an extinct group of heterosporous shrubs and trees that... more 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 taxo-nomic comparisons to their external morphology and spore structure. We here document from the upper Permian of China the fi rst anatomically preserved noeggerathialeans, 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 organization that is echoed in the newly discovered strobili. Dorsalistachya strobili bear highly dissected sporophylls alternately in two vertical rows, suggesting that they are homologs of leaf pinnae. If so, the " strobilus " is strictly a pseudostrobilus and consists of sporangium-bearing units that are one hierarchical level below true sporophylls. The " sporophylls " bear four microsporangia on the lower (abaxial) surface, occasionally interspersed with short longitudinal rows of megasporangia. A single functional megaspore develops within each winged megasporangium, suggesting adaptation for dispersal as a single unit. CONCLUSIONS: Dorsalistachya presents a unique combination of reproductive features that amply justifi es establishment of a new family, Dorsalistachyaceae. Noeg-gerathiales represent a distinct taxonomic Order of free-sporing plants that most resembles early-divergent eusporangiate ferns and the more derived among the extinct progymnosperms. By the early Permian, noeggerathialeans had attained levels of reproductive sophistication similar to the most derived among the Pa-leozoic sphenophytes and lycophytes, but their heterosporous life history may have contributed to their extinction during the Triassic climatic aridifi cation.

Seed plants appear in the fossil record during the Upper Devonian, but in many subsequent floral ... more Seed plants appear in the fossil record during the Upper Devonian, but in many subsequent floral assemblages they are only unequivocally represented by isolated seeds. The study of these seeds is hence of critical importance to studies of the radiation of the clade itself, but previous investigations have been limited by the two-dimensional nature of the majority of materials, and difficulties in visualising the complex three-dimensional nature of others. Our study has utilised new computerised three-dimensional reconstruction methods to re-evaluate anatomically-preserved seeds from the serial-peel collection of Albert Long, which represent the most complete dataset on early seed-plant radiation. A number of early seed taxa including Genomosperma and Stamnostoma have been restudied using both existing serial-peel and new high-resolution serial-section datasets, reconstructed to 3D models using a custom computer software suite (SPIERS). This work highlights the importance of sample i...

Plants fossilised within siderite nodules (FeCO3) are often three-dimensionally preserved – such ... more Plants fossilised within siderite nodules (FeCO3) are often three-dimensionally preserved – such as those from the Mazon Creek Carboniferous terrestrial lagerstätte. Fossils preserved in this way have historically been studied using single-surface observation or destructive investigative methods such as serial peeling/grinding, and thin-sections. These approaches have gradually improved for over a century, but recent advances in scanning technology, matched by rises in computational power and advances in software, have opened a new and exciting set of tools for palaeobotanists. Here we report a case study of a Medullosan ovule in which a novel combination of X-Ray Micro-Tomography (XMT) and orientated precision-sectioning is used, the latter targeted using the former. This technique has allowed correlation of geometries of different layers (seen in the three-dimensional model) with histological characteristics (gathered from wafered sections). The study reveals the ovule to be unusu...

ABSTRACT The Cheirolepidiaceae are an extinct group of conifers with an extensive Mesozoic fossil... more ABSTRACT The Cheirolepidiaceae are an extinct group of conifers with an extensive Mesozoic fossil record well-documented by foliage, wood, pollen and reproductive organs. Three-dimensionally preserved Cheirolepidiaceous ovuliferous cones are rare, with few known species. Here we use X-Ray computed micro-tomography at the Diamond Light Source Synchrotron (Oxfordshire, UK) to non-destructively image the internal anatomy of a recently discovered petrified ovuliferous cone from a Jurassic (Tithonian ~145 Ma) forest in southern England. The cone is derived from a suite of silicified plant materials, most of which were permineralised in situ in a hyper saline lagoonal setting during a shallow transgressive phase. Tomographic datasets were used to fully describe the histology of the cone and produce three-dimensional models of the gross morphology. These images revealed a remarkable degree of information on the internal tissues of the cone by resolving cellular level details. The results demonstrate that the cone belongs to the extinct genus Pararaucaria (Cheirolepidiaceae) that has only previously been reported from South and North America, and forms only the fourth species to be systematically described. This new species extends the known geographic range of Pararaucaria to the Europe and emphasises the wide distribution of Pararaucarian conifers during the Jurassic.

Spiders are an important animal group, with a long history. Details of their origins remain limit... more 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 postdates 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.

• Premise of the study: Triassic and Jurassic fossils record structural changes in conifer seed c... more • 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.

PeerJ, Oct 23, 2014

We document a new species of ovulate cone (Pararaucaria collinsonae) on the basis of silicified f... more 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 bares 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 in Europe. 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.

The medullosan pteridosperm ovule Stephanospermum Brongniart is a well-known component of Carboni... more 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.

A new species of Medullosan ovule from the Mazon Creek Carboniferous lagerstätte is documented us... more 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.

The Carboniferous Period is a fascinating time in earth history. It spanned 60myrs (359.2 to 299.... more The Carboniferous Period is a fascinating time in earth history. It spanned 60myrs (359.2 to 299.0mya), towards the end of the Palaeozoic era, falling between the Devonian and Permian. During the Carboniferous, the supercontinent Pangaea was assembling and the oceans were home to invertebrates such as corals, bryozoa, ammonoids, echinoderms, trilobites and crustaceans. Fish were also well represented (especially sharks), which were rapidly diversifying at the time. The continents were no barren wasteland either – they were host to some of the first widespread terrestrial forest and swamp ecosystems. In these lived both invertebrates, which had crawled onto land by the Silurian period (at least 423mya) and vertebrates, which were relative newcomers to this realm. This article provides us with an excuse to write about the Carboniferous. We will first introduce the geology and palaeogeography of the Carboniferous, including an overview of the most common mode of preservation we see in terrestrial fossils. Then, we will provide an overview of terrestrial life during the period, as land-based ecosystems of this age are among the best known from the Palaeozoic and an exciting time in the history of life.

Thesis Chapters by Alan R. T. Spencer

Fossil plants are commonly found preserved as impression/compression fossils; rarer but more info... more Fossil plants are commonly found preserved as impression/compression fossils; rarer but more informative are three-dimensional fossils, which can preserve the full or partial anatomy. Traditional palaeobotanical techniques for studying these 3D fossils – through physical sectioning to reveal surfaces for inspection – destroy some part of the fossil during preparation, resulting in data-loss. Tomography combined with ‘virtual palaeontology’ can overcome such limitations. This thesis documents the application of tomography to a number of different plant specimens, in various forms of preservation, with the aid of six case-studies. The first five case-studies demonstrate the use of tomographical methods to elucidate anatomical details of fossil plant organs; with each method improving data acquisition compared to the previous. The first details Physical Optical Tomography (POT) as a technique for extracting morphology from specimens where non-invasive x-rays are not amenable or historical physical dataset used. The second shows the advantages of non-destructive X-ray Micro-Tomography (XMT) in revealing the large scale structures of palaeobotanical material. The third investigates XMT combined with traditional destructive techniques to recover both the maximum morphology and cellular detail. The fourth uses XMT combined with Synchrotron Radiation X-ray Micro-Tomography (SRXMT), resulting in improvements to the visualisation of cellular anatomy. The fifth demonstrates that undescribed macro-sized palaeobotanical material may be fully taxonomically described through non-destructive SRXMT alone. The final case-study investigates the advantages and disadvantages of re-studying a pre-existing tomographic dataset and demonstrates that modern software and hardware enable enhanced data extraction. Discussion of the strengths and weaknesses of each method is undertaken, with details presented for the numerous experimental non-destructive XMT and SRXMT scans performed, informing which technique to use for a given fossil. Furthermore, differences in visualisation technique and problems associated with 3D modelling are discussed.

PeerJ, 2017

PeerJ, Oct 23, 2014