Dr Imran Rahman: List of publications

The stem-group euarthropod <i>Anomalocaris canadensis</i> is one of the largest Cambrian animals and is often considered the quintessential apex predator of its time. This radiodont is commonly interpreted as a demersal hunter, responsible for inflicting injuries seen in benthic trilobites. However, controversy surrounds the ability of <i>A. canadensis</i> to use its spinose frontal appendages to masticate or even manipulate biomineralized prey. Here, we apply a new integrative computational approach, combining three-dimensional digital modelling, kinematics, finite-element analysis (FEA) and computational fluid dynamics (CFD) to rigorously analyse an <i>A. canadensis</i> feeding appendage and test its morphofunctional limits. These models corroborate a raptorial function, but expose inconsistencies with a capacity for durophagy. In particular, FEA results show that certain parts of the appendage would have experienced high degrees of plastic deformation, especially at the endites, the points of impact with prey. The CFD results demonstrate that outstretched appendages produced low drag and hence represented the optimal orientation for speed, permitting acceleration bursts to capture prey. These data, when combined with evidence regarding the functional morphology of its oral cone, eyes, body flaps and tail fan, suggest that <i>A. canadensis</i> was an agile nektonic predator that fed on soft-bodied animals swimming in a well-lit water column above the benthos. The lifestyle of <i>A. canadensis</i> and that of other radiodonts, including plausible durophages, suggests that niche partitioning across this clade influenced the dynamics of Cambrian food webs, impacting on a diverse array of organisms at different sizes, tiers and trophic levels.

Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms <i>Lagynocystis pyramidalis</i> and <i>Jaekelocarpus oklahomensis</i> using virtual models based on high-resolution X-ray tomography scans of three-dimensionally preserved fossil specimens. Multivariate analyses of the size, spacing and arrangement of the internal bars in these fossils indicate they are substantially more similar to gill bars in modern enteropneust hemichordates and cephalochordates than to other internal bar-like structures in fossil blastozoan echinoderms. The close similarity between the internal bars of the stylophorans <i>L. pyramidalis</i> and <i>J. oklahomensis</i> and the gill bars of extant chordates and hemichordates is strong evidence for their homology. Differences between these internal bars and bar-like elements of the respiratory systems in blastozoans suggest these structures might have arisen through parallel evolution across deuterostomes, perhaps underpinned by a common developmental genetic mechanism.

The colonisation of freshwater and marine ecosystems by land vertebrates has repeatedly occurred in amphibians, reptiles, birds and mammals over the course of 300 million years. Functional interpretations of the fossil record are crucial to understanding the forces shaping these evolutionary transitions. Secondarily aquatic tetrapods have acquired a suite of anatomical, physiological and behavioural adaptations to locomotion in water. However, much of this information is lost for extinct clades, with fossil evidence often restricted to osteological data and a few extraordinary specimens with soft tissue preservation. Traditionally, functional morphology in fossil secondarily aquatic tetrapods was investigated through comparative anatomy and correlation with living functional analogues. However, in the last two decades, biomechanics in palaeobiology has experienced a remarkable methodological shift. Anatomy-based approaches are increasingly rigorous, informed by quantitative techniques for analysing shape. Moreover, the incorporation of physics-based methods has enabled objective tests of functional hypotheses, revealing the importance of hydrodynamic forces as drivers of evolutionary innovation and adaptation. Here, we present an overview of the latest research on the locomotion of extinct secondarily aquatic tetrapods, with a focus on amniotes, highlighting the state-of-the-art experimental approaches used in this field. We discuss the suitability of these techniques for exploring different aspects of locomotory adaptation, analysing their advantages and limitations and laying out recommendations for their application, with the aim to inform future experimental strategies. Furthermore, we outline some unexplored research avenues that have been successfully deployed in other areas of palaeobiomechanical research, such as the use of dynamic models in feeding mechanics and terrestrial locomotion, thus providing a new methodological synthesis for the field of locomotory biomechanics in extinct secondarily aquatic vertebrates. Advances in imaging technology and three-dimensional modelling software, new developments in robotics, and increased availability and awareness of numerical methods like computational fluid dynamics make this an exciting time for analysing form and function in ancient vertebrates.

Most Palaeozoic brittle stars lack the fused arm ossicles (vertebrae) that facilitate the remarkable mode of walking that characterizes living forms. Here we describe a stem ophiuroid from the Herefordshire Lagerstätte (Silurian, Wenlock Series), which is exceptional in preserving the body cavity uncompacted and the long tube feet. We assign the specimen to the order Oegophiurida. The morphology of the arms and attitude of the specimen suggest that locomotion may have been achieved by arm propulsion combined with podial walking. This ophiuroid increases the diversity of echinoderm higher taxa with preserved soft parts represented in the Herefordshire Lagerstätte.

&lt;jats:p&gt; The biological pump is crucial for transporting nutrients fixed by surface-dwelling primary producers to demersal animal communities. Indeed, the establishment of an efficient biological pump was likely a key factor enabling the diversification of animals over 500 Myr ago during the Cambrian explosion. The modern biological pump operates through two main vectors: the passive sinking of aggregates of organic matter, and the active vertical migration of animals. The coevolution of eukaryotes and sinking aggregates is well understood for the Proterozoic and Cambrian; however, little attention has been paid to the establishment of the vertical migration of animals. Here we investigate the morphological variation and hydrodynamic performance of the Cambrian euarthropod &lt;jats:italic&gt;Isoxys&lt;/jats:italic&gt; . We combine elliptical Fourier analysis of carapace shape with computational fluid dynamics simulations to demonstrate that &lt;jats:italic&gt;Isoxys&lt;/jats:italic&gt; species likely occupied a variety of niches in Cambrian oceans, including vertical migrants, providing the first quantitative evidence that some Cambrian animals were adapted for vertical movement in the water column. Vertical migration was one of several early Cambrian metazoan innovations that led to the biological pump taking on a modern-style architecture over 500 Myr ago. &lt;/jats:p&gt;

&lt;jats:title&gt;Abstract&lt;/jats:title&gt;&lt;jats:p&gt;Suspension feeding is a key ecological strategy in modern oceans that provides a link between pelagic and benthic systems. Establishing when suspension feeding first became widespread is thus a crucial research area in ecology and evolution, with implications for understanding the origins of the modern marine biosphere. Here, we use three-dimensional modelling and computational fluid dynamics to establish the feeding mode of the enigmatic Ediacaran pentaradial eukaryote &lt;jats:italic&gt;Arkarua&lt;/jats:italic&gt;. Through comparisons with two Cambrian echinoderms, &lt;jats:italic&gt;Cambraster&lt;/jats:italic&gt; and &lt;jats:italic&gt;Stromatocystites&lt;/jats:italic&gt;, we show that flow patterns around &lt;jats:italic&gt;Arkarua&lt;/jats:italic&gt; strongly support its interpretation as a passive suspension feeder. &lt;jats:italic&gt;Arkarua&lt;/jats:italic&gt; is added to the growing number of Ediacaran benthic suspension feeders, suggesting that the energy link between pelagic and benthic ecosystems was likely expanding in the White Sea assemblage (~&#x2009;558&#x2013;550&#xA0;Ma). The advent of widespread suspension feeding could therefore have played an important role in the subsequent waves of ecological innovation and escalation that culminated with the Cambrian explosion.&lt;/jats:p&gt;

Computational fluid dynamics (CFD), which involves using computers to simulate fluid flow, is emerging as a powerful approach for elucidating the palaeobiology of ancient organisms. Here, Imran A. Rahman describes its applications for studying fossil echinoderms. When properly configured, CFD simulations can be used to test functional hypotheses in extinct species, informing on aspects such as feeding and stability. They also show great promise for addressing ecological questions related to the interaction between organisms and their environment. CFD has the potential to become an important tool in echinoderm palaeobiology over the coming years.

Over 3.7 billion years of Earth history, life has evolved complex adaptations to help navigate and interact with the fluid environment. Consequently, fluid dynamics has become a powerful tool for studying ancient fossils, providing insights into the palaeobiology and palaeoecology of extinct organisms from across the tree of life. In recent years, this approach has been extended to the Ediacara biota, an enigmatic assemblage of Neoproterozoic soft‐bodied organisms that represent the first major radiation of macroscopic eukaryotes. Reconstructing the ways in which Ediacaran organisms interacted with the fluids provides new insights into how these organisms fed, moved, and interacted within communities. Here, we provide an in‐depth review of fluid physics aimed at palaeobiologists, in which we dispel misconceptions related to the Reynolds number and associated flow conditions, and specify the governing equations of fluid dynamics. We then review recent advances in Ediacaran palaeobiology resulting from the application of computational fluid dynamics (CFD). We provide a worked example and account of best practice in CFD analyses of fossils, including the first large eddy simulation (LES) experiment performed on extinct organisms. Lastly, we identify key questions, barriers, and emerging techniques in fluid dynamics, which will not only allow us to understand the earliest animal ecosystems better, but will also help to develop new palaeobiological tools for studying ancient life.

Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible, enabling continued evolutionary innovation throughout the clades’ history.

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 form a sophisticated compound eye-like system regulated by chromatophore movement has been extensively reiterated, with consequent investigations into biomimetic optics and similar ‘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 hypothesised 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 Cambrian, characterized by the global appearance of diverse biomineralized metazoans in the fossil record for the first time, represents a pivotal point in the history of life. This period also documents a major change in the nature of the sea floor: Neoproterozoic-type substrates stabilized by microbial mats were replaced by unconsolidated soft substrates with a well-developed mixed layer. The effect of this transition on the ecology and evolution of benthic metazoans is termed the Cambrian Substrate Revolution (CSR), and this is thought to have impacted greatly on early suspension-feeding echinoderms in particular. According to this paradigm, most echinoderms rested directly on non-bioturbated soft substrates as sediment attachers and stickers during the Cambrian Epoch 2. As the substrates became increasingly disturbed by burrowing, forming a progressively thickening mixed layer, echinoderms developed new strategies for attaching to firm and hard substrates. To test this model, we evaluated the mode of attachment of 83 Cambrian suspension-feeding echinoderm species; attachment mode was inferred based on direct evidence in fossil specimens and interpretations of functional morphology. These data were analyzed quantitatively to explore trends in attachment throughout the Cambrian. In contrast to previous studies, the majority of Cambrian clades (eocrinoids, helicoplacoids, helicocystoids, isorophid edrioasteroids, and solutes) are now interpreted as hard (shelly) substrate attachers. Only early edrioasteroids attached directly to firm substrates stabilized by microbially induced sedimentary structures. Contrary to the predictions of the CSR paradigm, our study demonstrates that Cambrian echinoderms were morphologically pre-adapted to the substrate changes that occurred during the Cambrian, allowing them to fully exploit the appearance of hardgrounds in the Furongian. We find no support for the claim that the CSR explains the peak in echinoderm diversity during Cambrian Epochs 2–3, or that it caused the extinction of helicoplacoids.

Trilobites were capable of enrolling in different ways based on the flexible articulation of thoracic segments and associated interlocking devices; the type of enrolment (spiral or sphaeroidal) is thought to have largely depended on the coaptative devices that each trilobite used to enclose the body. Based on X-ray microtomography scans of complete enrolled specimens from the Cambrian, we created three-dimensional (3-D) computer models to assess the kinematics needed to achieve both enrolment types. We demonstrate that closely related trilobites with little morphological variation (Bailiaspis?, Conocoryphe and Parabailiella) developed different enrolment types as a result of small variations in the number of thoracic segments and the angle between adjacent segments. Moreover, our models indicate that sphaeroidal enrolment, which is associated with a smaller number of thoracic segments, enabled faster encapsulation. This supports the hypothesis that there was a trend in the evolution of trilobites towards reduction in the number of thoracic segments in phylogenetically derived taxa in order to enhance the efficiency of enrolment.

Echinoderms are characterized by a calcite endoskeleton with a unique microstructure, which is optimized for multiple functions. For instance, some light-sensitive ophiuroids (Ophiuroidea) and asteroids (Asteroidea) possess skeletal plates with multi-lens arrays that are thought to act as photosensory organs. The origins of these lens-like microstructures have long been unclear. It was recently proposed that the complex photosensory systems in certain modern ophiuroids and asteroids could be traced back to at least the Late Cretaceous (ca. 79 Ma). Here, we document similar structures in ophiuroids and asteroids from the Early Cretaceous of Poland (ca. 136 Ma) that are approximately 57 million years older than the oldest asterozoans with lens-like microstructures described thus far. We use scanning electron microscopy, synchrotron tomography, and electron backscatter diffraction combined with focused ion beam microscopy to describe the morphology and crystallography of these structures in exceptional detail. The results indicate that, similar to Recent light-sensitive ophiuroids, putative microlenses in Cretaceous ophiuroids and asteroids exhibit a shape and crystal orientation that would have minimized spherical aberration and birefringence. We suggest that these lens-like microstructures evolved by secondary deposition of calcite on pre-existing porous tubercles that were already present in ancestral Jurassic forms.

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.

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.

Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.

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.

Echinoderms are a major group of invertebrate deuterostomes that have been an important component of marine ecosystems throughout the Phanerozoic. Their fossil record extends back to the Cambrian, when several disparate groups appear in different palaeocontinents at about the same time. Many of these early forms exhibit character combinations that differ radically from extant taxa, and thus their anatomy and phylogeny have long been controversial. Deciphering the earliest evolution of echinoderms therefore requires a detailed understanding of the morphology of Cambrian fossils, as well as the selection of an appropriate root and the identification of homologies for use in phylogenetic analysis. Based on the sister‐group relationships and ontogeny of modern species and new fossil discoveries, we now know that the first echinoderms were bilaterally symmetrical, represented in the fossil record by Ctenoimbricata and some early ctenocystoids. The next branch in echinoderm phylogeny is represented by the asymmetrical cinctans and solutes, with an echinoderm‐type ambulacral system originating in the more crownward of these groups (solutes). The first radial echinoderms are the helicoplacoids, which possess a triradial body plan with three ambulacra radiating from a lateral mouth. Helicocystoids represent the first pentaradial echinoderms and have the mouth facing upwards with five radiating recumbent ambulacra. Pentaradial echinoderms diversified rapidly from the beginning of their history, and the most significant differences between groups are recorded in the construction of the oral area and ambulacra, as well as the nature of their feeding appendages. Taken together, this provides a clear narrative of the early evolution of the echinoderm body plan.

Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them.