Dr Imran Rahman: List of publications

Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160 Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing the first quantitative evaluation of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep 'torpedo-shaped' bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics, and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence.

Photoreception and vision are fundamental aspects of animal sensory biology and ecology, but important gaps remain in our understanding of these processes in many species. The colour-changing brittle star Ophiocoma wendtii is iconic in vision research, speculatively possessing a unique whole-body visual system that incorporates information from nerve bundles underlying thousands of crystalline 'microlenses'. The hypothesis that these might form a sophisticated compound eye-like system regulated by chromatophores has been extensively reiterated, with investigations into biomimetic optics and similar supposedly 'visual' structures in living and fossil taxa. However, no photoreceptors or visual behaviours have ever been identified. We present the first evidence of photoreceptor networks in three Ophiocoma species, both with and without microlenses and colour-changing behaviour. High-resolution microscopy, immunohistochemistry and synchrotron tomography demonstrate that putative photoreceptors cover the animals' oral, lateral and aboral surfaces, but are absent at the hypothesized focal points of the microlenses. The structural optics of these crystal 'lenses' are an exaptation and do not fulfil any apparent visual role. This contradicts previous studies, yet the photoreceptor network in Ophiocoma appears even more widespread than previously anticipated, both taxonomically and anatomically.

© The Palaeontological Association Computational fluid dynamics is a method for simulating fluid flows that has been widely used in engineering for decades, and which also has applications for studying function and ecology in fossil taxa. However, despite the possible benefits of this approach, computational fluid dynamics has been used only rarely in palaeontology to date. The theoretical basis underlying the technique is outlined and the main steps involved in carrying out computer simulations of fluid flows are detailed. I also describe previous studies that have applied the method to fossils and discuss their potential for informing future research directions in palaeontology. Computational fluid dynamics can enable large-scale comparative analyses, as well as exacting tests of hypotheses related to the function and ecology of ancient organisms. In this way, it could transform our understanding of many extinct fossil groups.

Functional analysis through computer modeling can inform on how extinct organisms moved and fed, allowing us to test long-standing paleobiological hypotheses. Many such studies are based on digital models derived from computed tomography or surface scanning, but these methods are not appropriate for all fossils. Here, we show that box modeling — 3-D modeling of complex shapes based on simple objects — can be used to reconstruct the morphology of various fossil specimens. Moreover, the results of computational functional analyses utilizing such models are very similar to those for models derived from tomographic or surface-based techniques. Box modeling is more broadly applicable than alternative methods for digitizing specimens, and hence there is great potential for this approach in paleontological functional analysis. Possible applications include large-scale comparative studies, analyses of hypothetical morphologies, and virtually restoring incomplete/distorted specimens.

Establishing how Ediacaran organisms moved and fed is critical to deciphering their ecological and evolutionary significance, but has long been confounded by their non-analogue body plans. Here, we use computational fluid dynamics to quantitatively analyse water flow around the Ediacaran taxon Parvancorina, thereby testing between competing models for feeding mode and mobility. The results show that flow was not distributed evenly across the organism, but was directed towards localized areas; this allows us to reject osmotrophy, and instead supports either suspension feeding or detritivory. Moreover, the patterns of recirculating flow differ substantially with orientation to the current, suggesting that if Parvancorina was a suspension feeder, it would have been most efficient if it was able to re-orient itself with respect to current direction, and thus ensure flow was directed towards feeding structures. Our simulations also demonstrate that the amount of drag varied with orientation, indicating that Parvancorina would have greatly benefited from adjusting its position to minimize drag. Inference of facultative mobility in Parvancorina suggests that Ediacaran benthic ecosystems might have possessed a higher proportion of mobile taxa than currently appreciated from trace fossil studies. Furthermore, this inference of movement suggests the presence of musculature or appendages that are not preserved in fossils, but which would noneltheless support a bilaterian affinity for Parvancorina.

Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

© 2015 Elsevier B.V. Taphonomic analysis and X-ray micro-tomography (μCT) were applied to Clypeaster specimens from the Miocene of Fuente del Jarro (Valencia, Spain). This enabled the identification of various preservational features, including encrustation, bioerosion, abrasion and post-depositional cracking. Approximately 15% of the studied specimens were affected by encrusters and/or borers. Of particular interest was a single intensely-bored specimen preserving numerous cross-cutting bioerosion structures. These structures exhibit a distinctive morphology consisting of clavate or flask-shaped chambers with a circular to oval cross-section, a narrow neck region near the figure-of-eight-shaped aperture and a chimney extending outside the Clypeaster test. The excellent preservation and characteristic morphology, as revealed by the μCT scan, coupled with the observation that (in some cases) articulated bivalve shells are still present within the chambers, allows for the identification of the tracemaker as the boring bivalve Rocellaria, reaffirming these tube-dwelling animals as borers, burrowers and crypt-builders.The trace fossils described herein are semi-endoskeletal dwellings, representing a combination of bioerosion through the plates of the echinoids, bioturbation in the form of burrowing into the sediment infill of the Clypeaster specimen and carbonate secretion resulting in a crypt. The morphologies of the different dwellings are influenced by the limited available space within the echinoid tests. This study confirms the importance of the relatively stable and thick Clypeaster shells as benthic islands in Cenozoic sandy littoral settings. The high degree of multiple colonizations, as well as the uniform orientation of the burrows, suggests a long-term stable position of this secondary substrate at or near the sediment surface.

© 2018 The Authors. The first diverse and morphologically complex macroscopic communities appear in the late Ediacaran period, 575 to 541 million years ago (Ma). The enigmatic organisms that make up these communities are thought to have formed simple ecosystems characterized by a narrow range of feeding modes, with most restricted to the passive absorption of organic particles (osmotrophy). We test between competing feeding models for the iconic Ediacaran organism Tribrachidium heraldicum using computational fluid dynamics. We show that the external morphology of Tribrachidium passively directs water flow toward the apex of the organism and generates low-velocity eddies above apical "pits." These patterns of fluid flow are inconsistent with osmotrophy and instead support the interpretation of Tribrachidium as a passive suspension feeder. This finding provides the oldest empirical evidence for suspension feeding at 555 to 550 Ma, ∼10 million years before the Cambrian explosion, and demonstrates that Ediacaran organisms formed more complex ecosystems in the latest Precambrian, involving a larger number of ecological guilds, than currently appreciated.

It is now clear in many species that male and female genital evolution has been shaped by sexual selection. However, it has historically been difficult to confirm correlations between morphology and fitness, as genital traits are complex and manipulation tends to impair function significantly. In this study, we investigate the functional morphology of the elongate male intromittent organ (or processus) of the seed bug Lygaeus simulans, in two ways. We first use micro-computed tomography (micro-CT) and flash-freezing to reconstruct in high resolution the interaction between the male intromittent organ and the female internal reproductive anatomy during mating. We successfully trace the path of the male processus inside the female reproductive tract. We then confirm that male processus length influences sperm transfer by experimental ablation and show that males with shortened processi have significantly reduced post-copulatory reproductive success. Importantly, male insemination function is not affected by this manipulation per se. We thus present rare, direct experimental evidence that an internal genital trait functions to increase reproductive success and show that, with appropriate staining, micro-CT is an excellent tool for investigating the functional morphology of insect genitalia during copulation.

Complete, articulated crinoids from the Ordovician peri-Gondwanan margin are rare. Here, we describe a new species, Iocrinus africanus sp. nov., from the Darriwilian-age Taddrist Formation of Morocco. The anatomy of this species was studied using a combination of traditional palaeontological methods and non-destructive X-ray micro-tomography (micro-CT). This revealed critical features of the column, distal arms, and aboral cup, which were hidden in the surrounding rock and would have been inaccessible without the application of micro-CT. Iocrinus africanus sp. nov. is characterized by the presence of seven to thirteen tertibrachials, three in-line bifurcations per ray, and an anal sac that is predominantly unplated or very lightly plated. Iocrinus is a common genus in North America (Laurentia) and has also been reported from the United Kingdom (Avalonia) and Oman (middle east Gondwana). Together with Merocrinus, it represents one of the few geographically widespread crinoids during the Ordovician and serves to demonstrate that faunal exchanges between Laurentia and Gondwana occurred at this time. This study highlights the advantages of using both conventional and cutting-edge techniques (such as micro-CT) to describe the morphology of new fossil specimens.

A new cinctan echinoderm, Graciacystis ambigua gen. et sp. nov. from Cambrian Series 3 rocks of Spain, is described based on more than 100 articulated specimens that range from 6 to 14.5mm in thecal length. This material shows that Graciacystis ambigua, while plastic in thecal shape, is highly conservative in its thecal construction, with a fixed number of marginal plates and very limited addition of plates in the stele and ventral membrane through ontogeny. Ventral swellings on marginal elements are absent from the smallest specimens and become gradually more marked during growth. A cladistic analysis shows Graciacystis to be a basal cinctan, more derived than Sotocinctus and the Trochocystitidae and as sister group to a large clade formed by Sucocystidae+Gyrocystidae. The determinate growth pattern seen in Graciacystis seems to be the general pattern for all cinctans. © The Palaeontological Association.

Dehmicystis globulus is a very poorly known Lower Devonian solute echinoderm from the Hunsrück Slate of Germany. To date, only the holotype has been formally described; however, it is incomplete and does not preserve important characters of the group. We report three new individuals on the same slab of slate, one of which is almost complete. This material informs a full systematic redescription of the genus. The orientation and mode of life of solutes are contentious; our new morphofunctional data strongly suggest that Dehmicystis was oriented with the ambulacrum on the upper surface. Such a position implies a suspension feeding mode of life, with food particles captured from the current using the ambulacrum. The stele may have enabled limited movement on the sea floor but was principally responsible for support, anchorage, and (facultative) attachment. © 2011 Springer-Verlag.

A new stylophoran (Ceratocystis prosthiakida sp. nov.) from the early Middle Cambrian of the Franconian Forest (north-east Bavaria, Germany) is described with the aid of computed tomography, a powerful means of visualizing fossil anatomy. Investigation in this manner enabled previously inaccessible, buried parts of the fossil to be imaged and studied. In addition, a procedure for digitally correcting plate articulations was implemented. Ceratocystis prosthiakida sp. nov. possesses a thin anterior right spine which clearly differentiates it from other species of Ceratocystis. Similar to other Ceratocystis species, C. prosthiakida sp. nov. lived in storm-dominated shallow marine conditions. The species is from the Galgenberg Formation, which has an early Agdzian age in the unified West Gondwanan chronostratigraphy. As a result, it represents the oldest stylophoran known to date. © 2009 Springer-Verlag.

Cruziana, Gordia, Planolites, Rusophycus, and Trichophycus are common ichnological elements of the Kaili Biota. New discoveries based on the examination of 323 specimens include eldoniids, echinoderms, trilobites, monoplacophorans, and non-biomineralizing arthropods that are associated with trace fossils. Based on the observed effects of bioturbation on the preservation of five different animal groups, it is clear that infaunal scavengers/deposit feeders were periodically active on the Kaili sea floor and were able to reach historic layers yielding exceptionally preserved fossils. In general, the average level of infaunal activity is absent to moderate (Ichnofabric Index [i.i.]=1 to 3) in the Kaili substrate; by contrast, the "Phycodes beds" are completely disturbed by infaunal activity (i.i.=5). Observed burrow diameter ranges from diminutive (~0.2 mm) to normal (up to 4.2 mm). Computed tomography allows us to visualize the precise geometry of the trace fossil-body fossil association in three dimensions. We concluded that although some Kaili infaunal animals could bore through the biomineralized echinoderms, they did not appear to have scavenged upon these echinoderms based on our three-dimensional reconstruction. Furthermore, Kaili burrowers can reach the historic layers containing exceptionally preserved fossils without altering soft-tissue preservation. On the other hand, we used conventional techniques to reveal that one burrow is filled with fecal pellets (100-200 μm) at its terminal end. Because most burrows are filled with yellow/brown "coarse sediment", and because there is no compositional difference between the fecal pellets and the surrounding coarse sediment within the burrow, the origin of the yellow/brown "coarse sediment" is interpreted here as parautochthonous and/or autochthonous and as a result of sediment reworking by deposit (or suspension) feeders. The relative scarcity of soft-part preservation in the Kaili Biota compared to the older Chengjiang Biota and the younger Burgess Shale Biota may be the result of post-burial bio-disturbance due to the relatively high intensity of local bioturbation. It is plausible that oxygenation in deeper sediments (facilitated by bioturbation) allowed carcasses in the Kaili biota to undergo a more extensive period of 'normal' decay prior to final burial than in other Cambrian Konservat-Lagerstätten. © 2010 Elsevier B.V. All rights reserved.

SYNOPSIS Ctenocystoids are a poorly understood group of fossil deuterostomes, with little known about their morphology, palaeobiology or affinities. A three-dimensional specimen of the ctenocystoid Ctenocystis utahensis from the Middle Cambrian Spence Shale (western USA) was imaged using X-ray microtomography and digitally reconstructed. This allowed the species to be described in greater detail than previously possible, providing a number of morphofunctional insights. Two openings are identified: (i) an anterior opening controlled by moveable plates in the distinctive ctenoid apparatus and (ii) a wide posterior periproct. A putative third body opening (hydropore and/or gonopore) is not present, contrary to previous reconstructions. Ctenocystis utahensis was most probably epibenthic, facing into water currents during life. Suspended food particles entered paired lateral grooves within the ctenoid apparatus through gaps between neighbouring ctenoid plates; when the ctenoid apparatus was open, material could pass from these lateral grooves to an internal chamber, which led into the main body cavity. Our reconstruction demonstrates that the plates of the ctenoid apparatus and the lateral feeding grooves are not homologous with paired brachioles, refuting suggestions that ctenocystoids are derived blastozoans. Instead, it is probable that ctenocystoids are basal stem-group echinoderms, sharing several plesiomorphies (a bilateral body plan, pharyngeal gill slits and a paired water vascular system) with the latest common ancestor of echinoderms plus hemichordates. Reconstructing the anatomy of ctenocystoids in three-dimensions is critical to a full understanding of their palaeobiology and phylogenetic position. © 2009 The Natural History Museum.

Mitrates are a controversial group of extinct deuterostomes; there is little agreement over their affinities, functional morphology or even the orientation of their upper and lower surfaces. Four slabs of slate from the Lower Devonian Hunsrück Slate (Bundenbach, Germany) are here described, showing trace fossils (Vadichnites transversus igen. et isp. nov.) associated with the mitrate Rhenocystis latipedunculata. These new findings clearly demonstrate that the mitrate appendage was used in locomotion and that this movement took place appendage-first. Such a functional interpretation suggests that mitrates were oriented with the flat body surface upwards in life and argues against a phylogenetic position in the echinoderm crown-group. © The Palaeontological Association, 2009.