The osteology of the Late Triassic reptile Scleromochlus taylori from µCT data.

Scleromochlus taylori is one of the most enigmatic members of the herpetofauna from the Lossiemouth Sandstone Formation (Upper Triassic) of Elgin (Moray, Scotland). For many years it was thought to be closely related to pterosaurs and dinosaurs, but the anatomy of this animal is difficult to interpret because of the notoriously poor preservation of the six available specimens, which comprise void space in the sandstone after the bones were destroyed by diagenesis. Historically, these fossils have been studied using physical molds, which provide only incomplete, and potentially distorted, information. Due to these uncertainties, interpretations of the anatomy, phylogenetic relationships, and paleobiology of Scleromochlus taylori have remained contentious. Here, we use microcomputed tomographic (µCT) techniques to redescribe and illustrate the osteology of Scleromochlus in detail, building upon a short redescription of keystone features of the anatomy that we recently published. We digitally visualize, describe, and figure previously inaccessible-and thus unaltered-portions of its skeleton, as well as providing new observations on the exposed parts of each specimen. This work reveals many novel features of the skull, mandible, trunk, tail, girdles, forelimb, and hindlimb (particularly of the manus, femur, and pes), demonstrating that historic molding techniques failed, in some cases, to accurately capture the anatomy of Scleromochlus. Our review sheds light on some of the most controversial aspects of Scleromochlus morphology showing that this taxon retains plesiomorphic features of Avemetatarsalia in the postcranial skeleton, alongside a suite of synapomorphies diagnostic of pterosauromorphs (the broad clade of pterosaurs and taxa more closely related to them than dinosaurs), particularly one subgroup, the lagerpetids. Consistent with recent work, our updated phylogenetic analyses (Maximum Parsimony and Bayesian Inference) demonstrate that Scleromochlus taylori is an avemetatarsalian archosaur that is recovered firmly in an early diverging position within Pterosauromorpha, as a member of Lagerpetidae, thus shedding important information on the origin of pterosaurs, the first group of vertebrates to evolve powered flight.

Scleromochlus and the early evolution of Pterosauromorpha.

Pterosaurs, the first vertebrates to evolve powered flight, were key components of Mesozoic terrestrial ecosystems from their sudden appearance in the Late Triassic until their demise at the end of the Cretaceous1-6. However, the origin and early evolution of pterosaurs are poorly understood owing to a substantial stratigraphic and morphological gap between these reptiles and their closest relatives6, Lagerpetidae7. Scleromochlus taylori, a tiny reptile from the early Late Triassic of Scotland discovered over a century ago, was hypothesized to be a key taxon closely related to pterosaurs8, but its poor preservation has limited previous studies and resulted in controversy over its phylogenetic position, with some even doubting its identification as an archosaur9. Here we use microcomputed tomographic scans to provide the first accurate whole-skeletal reconstruction and a revised diagnosis of Scleromochlus, revealing new anatomical details that conclusively identify it as a close pterosaur relative1 within Pterosauromorpha (the lagerpetid + pterosaur clade). Scleromochlus is anatomically more similar to lagerpetids than to pterosaurs and retains numerous features that were probably present in very early diverging members of Avemetatarsalia (bird-line archosaurs). These results support the hypothesis that the first flying reptiles evolved from tiny, probably facultatively bipedal, cursorial ancestors1.

Middle Jurassic fossils document an early stage in salamander evolution.

Salamanders are an important group of living amphibians and model organisms for understanding locomotion, development, regeneration, feeding, and toxicity in tetrapods. However, their origin and early radiation remain poorly understood, with early fossil stem-salamanders so far represented by larval or incompletely known taxa. This poor record also limits understanding of the origin of Lissamphibia (i.e., frogs, salamanders, and caecilians). We report fossils from the Middle Jurassic of Scotland representing almost the entire skeleton of the enigmatic stem-salamander Marmorerpeton. We use computed tomography to visualize high-resolution three-dimensional anatomy, describing morphologies that were poorly characterized in early salamanders, including the braincase, scapulocoracoid, and lower jaw. We use these data in the context of a phylogenetic analysis intended to resolve the relationships of early and stem-salamanders, including representation of important outgroups alongside data from high-resolution imaging of extant species. Marmorerpeton is united with Karaurus, Kokartus, and others from the Middle Jurassic-Lower Cretaceous of Asia, providing evidence for an early radiation of robustly built neotenous stem-salamanders. These taxa display morphological specializations similar to the extant cryptobranchid "giant" salamanders. Our analysis also demonstrates stem-group affinities for a larger sample of Jurassic species than previously recognized, highlighting an unappreciated diversity of stem-salamanders and cautioning against the use of single species (e.g., Karaurus) as exemplars for stem-salamander anatomy. These phylogenetic findings, combined with knowledge of the near-complete skeletal anatomy of Mamorerpeton, advance our understanding of evolutionary changes on the salamander stem-lineage and provide important data on early salamanders and the origins of Batrachia and Lissamphibia.

'Ear stones' in crocodylians: a cross-species comparative and ontogenetic survey of otolith structures.

The vestibular system of the inner ear is a crucial sensory organ, involved in the sensation of balance and equilibrium. It consists of three semicircular canals that sense angular rotations of the head and the vestibule that detects linear acceleration and gravity. The vestibule often contains structures, known as the otoliths or 'ear stones'. Otoliths are present in many vertebrates and are particularly well known from the fossil record of fish, but surprisingly have not been described in detail in most tetrapods, living or extinct. Here, we present for the first time a survey of the otoliths of a broad sample of extant crocodylian species, based on computed tomography scans. We find that otoliths are present in numerous crocodylian species of different growth stages, and they continue to increase in size during ontogeny, with positive allometry compared to skull length. Our results confirm that otoliths are a common component of the crocodylian vestibular system, and suggest they play an important role in sensory detection. Otoliths are likely common, but overlooked, constituents of the inner ear in tetrapods, and a broader study of their size, shape and distribution promises insight into sensory abilities.

Rostral neurovasculature indicates sensory trade-offs in Mesozoic pelagic crocodylomorphs.

Metriorhynchoid thalattosuchians were a marine clade of Mesozoic crocodylomorphs that evolved from semi-aquatic, "gharial"-like species into the obligately pelagic subclade Metriorhynchidae. To explore whether the sensory and physiological demands of underwater life necessitates a shift in rostral anatomy, both in neurology and vasculature, we investigate the trigeminal innervation and potential somatosensory abilities of metriorhynchoids by digitally segmenting the rostral neurovascular canals in CT scans of 10 extant and extinct crocodyliforms. The dataset includes the terrestrial, basal crocodyliform Protosuchus haughtoni, two semi-aquatic basal metriorhynchoids, four pelagic metriorhynchids and three extant, semi-aquatic crocodylians. In the crocodylian and basal metriorhynchoid taxa, we find three main neurovascular channels running parallel to one another posteroanteriorly down the length of the snout, whereas in metriorhynchids there are two, and in P. haughtoni only one. Crocodylians appear to be unique in their extensive trigeminal innervation, which is used to supply the integumentary sensory organs (ISOs) involved with their facial somatosensory abilities. Crocodylians have a far higher number of foramina on the maxillary bones than either metriorhynchoids or P. haughtoni, suggesting that the fossil taxa lacked the somatosensory abilities seen in extant species. We posit that the lack of ISO osteological correlates in metriorhynchoids is due to their basal position in Crocodyliformes, rather than a pelagic adaptation. This is reinforced by the hypothesis that extant crocodyliforms, and possibly some neosuchian clades, underwent a long "nocturnal bottleneck"-hinting that their complex network of ISOs evolved in Neosuchia, as a sensory trade-off to compensate for poorer eyesight.

Paranasal sinus system and upper respiratory tract evolution in Mesozoic pelagic crocodylomorphs.

Thalattosuchians were a predominately marine clade of Mesozoic crocodylomorphs, including semi-aquatic teleosauroid and obligately pelagic metriorhynchid subclades. Recent advances in our understanding of thalattosuchian endocranial anatomy have revealed new details of the evolutionary transition from terrestrial to marine to pelagic taxa. Paranasal sinuses, however, have received little attention. Herein, we investigate the evolution of the paranasal sinus system and part of the upper respiratory system (nasopharyngeal ducts) in Thalattosuchia, by reconstructing the nasal and paranasal anatomy in CT scans of seven thalattosuchian skulls: one teleosauroid, two basal metriorhynchoids and four metriorhynchids. Our outgroups were: three extant crocodylian species (including adult and subadult skulls) and the basal crocodyliform Protosuchus. We found thalattosuchians exhibit exceptionally reduced paranasal sinus systems, solely comprising the antorbital sinus, as has been previously proposed. The semi-aquatic basal thalattosuchians Palgiopthalmosuchus gracilirostris and Pelagosaurus typus both have an antorbital sinus partially located medial to a reduced external antorbital fenestra and broadly communicating with the dorsal alveolar canal. In pelagic metriorhynchids, the antorbital cavity is more extensive than in basal taxa and possibly had an active function associated with a hypothesized accessory suborbital diverticulum, but our reconstructions are insufficient to confirm or reject the presence of such a diverticulum. The nasopharyngeal ducts of metriorhynchids are dorsoventrally enlarged, possibly enabling stronger ventilation. The sequence of acquisition of craniofacial adaptations show a mosaic pattern and appears to predate many skeletal adaptations, suggesting these changes occurred early in the thalattosuchian marine transition.

Ontogenetic variation in the crocodylian vestibular system.

Crocodylians today live in tropical to subtropical environments, occupying mostly shallow waters. Their body size changes drastically during ontogeny, as do their skull dimensions and bite forces, which are associated with changes in prey preferences. Endocranial neurosensory structures have also shown to change ontogenetically, but less is known about the vestibular system of the inner ear. Here we use 30 high-resolution computed tomography (CT) scans and three-dimensional geometric morphometrics to investigate the size and shape changes of crocodylian endosseous labyrinths throughout ontogeny, across four stages (hatchling, juvenile, subadult and adult). We find two major patterns of ontogenetic change. First, the labyrinth increases in size during ontogeny, with negative allometry in relation to skull size. Second, labyrinth shape changes significantly, with hatchlings having shorter semicircular canal radii, with thicker diameters and an overall dorsoventrally shorter labyrinth than those of more mature individuals. We argue that the modification of the labyrinth during crocodylian ontogeny is related to constraints imposed by skull growth, due to fundamental changes in the crocodylian braincase during ontogeny (e.g. verticalisation of the basicranium), rather than changes in locomotion, diet, or other biological functions or behaviours.

Evolution of vision and hearing modalities in theropod dinosaurs.

Owls and nightbirds are nocturnal hunters of active prey that combine visual and hearing adaptations to overcome limits on sensory performance in low light. Such sensory innovations are unknown in nonavialan theropod dinosaurs and are poorly characterized on the line that leads to birds. We investigate morphofunctional proxies of vision and hearing in living and extinct theropods and demonstrate deep evolutionary divergences of sensory modalities. Nocturnal predation evolved early in the nonavialan lineage Alvarezsauroidea, signaled by extreme low-light vision and increases in hearing sensitivity. The Late Cretaceous alvarezsauroid Shuvuuia deserti had even further specialized hearing acuity, rivaling that of today's barn owl. This combination of sensory adaptations evolved independently in dinosaurs long before the modern bird radiation and provides a notable example of convergence between dinosaurs and mammals.

Tempo and Pattern of Avian Brain Size Evolution.

Relative brain sizes in birds can rival those of primates, but large-scale patterns and drivers of avian brain evolution remain elusive. Here, we explore the evolution of the fundamental brain-body scaling relationship across the origin and evolution of birds. Using a comprehensive dataset sampling> 2,000 modern birds, fossil birds, and theropod dinosaurs, we infer patterns of brain-body co-variation in deep time. Our study confirms that no significant increase in relative brain size accompanied the trend toward miniaturization or evolution of flight during the theropod-bird transition. Critically, however, theropods and basal birds show weaker integration between brain size and body size, allowing for rapid changes in the brain-body relationship that set the stage for dramatic shifts in early crown birds. We infer that major shifts occurred rapidly in the aftermath of the Cretaceous-Paleogene mass extinction within Neoaves, in which multiple clades achieved higher relative brain sizes because of a reduction in body size. Parrots and corvids achieved the largest brains observed in birds via markedly different patterns. Parrots primarily reduced their body size, whereas corvids increased body and brain size simultaneously (with rates of brain size evolution outpacing rates of body size evolution). Collectively, these patterns suggest that an early adaptive radiation in brain size laid the foundation for subsequent selection and stabilization.

Inner ear sensory system changes as extinct crocodylomorphs transitioned from land to water.

Major evolutionary transitions, in which animals develop new body plans and adapt to dramatically new habitats and lifestyles, have punctuated the history of life. The origin of cetaceans from land-living mammals is among the most famous of these events. Much earlier, during the Mesozoic Era, many reptile groups also moved from land to water, but these transitions are more poorly understood. We use computed tomography to study changes in the inner ear vestibular system, involved in sensing balance and equilibrium, as one of these groups, extinct crocodile relatives called thalattosuchians, transitioned from terrestrial ancestors into pelagic (open ocean) swimmers. We find that the morphology of the vestibular system corresponds to habitat, with pelagic thalattosuchians exhibiting a more compact labyrinth with wider semicircular canal diameters and an enlarged vestibule, reminiscent of modified and miniaturized labyrinths of other marine reptiles and cetaceans. Pelagic thalattosuchians with modified inner ears were the culmination of an evolutionary trend with a long semiaquatic phase, and their pelagic vestibular systems appeared after the first changes to the postcranial skeleton that enhanced their ability to swim. This is strikingly different from cetaceans, which miniaturized their labyrinths soon after entering the water, without a prolonged semiaquatic stage. Thus, thalattosuchians and cetaceans became secondarily aquatic in different ways and at different paces, showing that there are different routes for the same type of transition.

Comparative analysis of vestibular ecomorphology in birds.

The bony labyrinth of vertebrates houses the semicircular canals. These sense rotational accelerations of the head and play an essential role in gaze stabilisation during locomotion. The sizes and shapes of the semicircular canals have hypothesised relationships to agility and locomotory modes in many groups, including birds, and a burgeoning palaeontological literature seeks to make ecological interpretations from the morphology of the labyrinth in extinct species. Rigorous tests of form-function relationships for the vestibular system are required to support these interpretations. We test the hypothesis that the lengths, streamlines and angles between the semicircular canals are related to body size, wing kinematics and flying style in birds. To do this, we applied geometric morphometrics and multivariate phylogenetic comparative methods to a dataset of 64 three-dimensional reconstructions of the endosseous labyrinth obtained using micro-computed tomography scanning of bird crania. A strong relationship between centroid size of the semicircular canals and body size indicates that larger birds have longer semicircular canals compared with their evolutionary relatives. Wing kinematics related to manoeuvrability (and quantified using the brachial index) explain a small additional portion of the variance in labyrinth size. We also find strong evidence for allometric shape change in the semicircular canals of birds, indicating that major aspects of the shape of the avian labyrinth are determined by spatial constraints. The avian braincase accommodates a large brain, a large eye and large semicircular canals compared with other tetrapods. Negative allometry of these structures means that the restriction of space within the braincase is intense in small birds. This may explain our observation that the angles between planes of the semicircular canals of birds deviate more strongly from orthogonality than those of mammals, and especially from agile, gliding and flying mammals. Furthermore, we find little support for relationships between labyrinth shape and flying style or wing kinematics. Overall, our results suggest that the topological problem of fitting long semicircular canals into a spatially constrained braincase is more important in determining the shape of the avian labyrinth than the specifics of locomotory style or agility. Our results tentatively indicate a link between visual acuity and proportional size of the labyrinth among birds. This suggests that the large labyrinths of birds compared with other tetrapods may result from their generally high visual acuities, and not directly from their ability to fly. The endosseous labyrinths of extinct birds and their close dinosaurian relatives may allow broad inferences about flight or vision, but so far provide few specific insights into detailed aspects of locomotion.

Open data and digital morphology.

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.

The Braincase and Neurosensory Anatomy of an Early Jurassic Marine Crocodylomorph: Implications for Crocodylian Sinus Evolution and Sensory Transitions.

Modern crocodylians are a morphologically conservative group, but extinct relatives (crocodylomorphs) experimented with a wide range of diets, behaviors, and body sizes. Among the most unusual of these fossil groups is the thalattosuchians, an assemblage of marine-dwellers that transitioned from semiaquatic species (teleosaurids and kin) into purely open-ocean forms (metriorhynchids) during the Jurassic and Cretaceous Periods (ca 191-125 million years ago). Thalattosuchians can give insight into the origin of modern crocodylian morphologies and how anatomy and behavior change during a major evolutionary transition into a new habitat. Little is known, however, about their brains, sensory systems, cranial sinuses, and vasculature. We here describe the endocranial anatomy of a well-preserved specimen of the Jurassic semiaquatic teleosaurid Steneosaurus cf. gracilirostris using X-ray micro-CT. We find that this teleosaurid still had an ear well attuned to hear on land, but had developed large internal carotid and orbital arteries that likely supplied salt glands, previously thought to be present in only the fully pelagic metriorhynchids. There is no great gulf in endocranial anatomy between this teleosaurid and the metriorhynchids, and some of the features that later permitted metriorhynchids to invade the oceanic realm were apparently first developed in semiaquatic taxa. Compared to modern crocodylians, Steneosaurus cf. gracilirostris has a more limited set of pharyngotympanic sinuses, but it is unclear whether this relates to its aquatic habitat or represents the primitive condition of crocodylomorphs that was later elaborated. Anat Rec, 299:1511-1530, 2016. © 2016 Wiley Periodicals, Inc.

Best practices for digitally constructing endocranial casts: examples from birds and their dinosaurian relatives.

The rapidly expanding interest in, and availability of, digital tomography data to visualize casts of the vertebrate endocranial cavity housing the brain (endocasts) presents new opportunities and challenges to the field of comparative neuroanatomy. The opportunities are many, ranging from the relatively rapid acquisition of data to the unprecedented ability to integrate critically important fossil taxa. The challenges consist of navigating the logistical barriers that often separate a researcher from high-quality data and minimizing the amount of non-biological variation expressed in endocasts - variation that may confound meaningful and synthetic results. Our purpose here is to outline preferred approaches for acquiring digital tomographic data, converting those data to an endocast, and making those endocasts as meaningful as possible when considered in a comparative context. This review is intended to benefit those just getting started in the field but also serves to initiate further discussion between active endocast researchers regarding the best practices for advancing the discipline. Congruent with the theme of this volume, we draw our examples from birds and the highly encephalized non-avian dinosaurs that comprise closely related outgroups along their phylogenetic stem lineage.

A reappraisal of Cerebavis cenomanica (Aves, Ornithurae), from Melovatka, Russia.

The evolution of the avian brain is of crucial importance to studies of the transition from non-avian dinosaurs to modern birds, but very few avian fossils provide information on brain morphological development during the Mesozoic. An isolated specimen from the Cenomanian of Melovatka in Russia was described by Kurochkin and others as a fossilized brain, designated the holotype of Cerebavis cenomanica Kurochkin and Saveliev and tentatively referred to Enantiornithes. We have previously highlighted that this specimen is an incomplete skull, rendering the diagnostic characters invalid and Cerebavis cenomanica a nomen dubium. We provide here a revised diagnosis of Cerebavis cenomanica based on osteological characters, and a reconstruction of the endocranial morphology (= brain shape) based on µCT investigation of the braincase. Absence of temporal fenestrae indicates an ornithurine affinity for Cerebavis. The brain of this taxon was clearly closer to that of modern birds than to Archaeopteryx and does not represent a divergent evolutionary pathway as originally concluded by Kurochkin and others. No telencephalic wulst is present, suggesting that this advanced avian neurological feature was not recognizably developed 93 million years ago.

Phylogenetic and environmental context of a Tournaisian tetrapod fauna.

The end-Devonian to mid-Mississippian time interval has long been known for its depauperate palaeontological record, especially for tetrapods. This interval encapsulates the time of increasing terrestriality among tetrapods, but only two Tournaisian localities previously produced tetrapod fossils. Here we describe five new Tournaisian tetrapods (Perittodus apsconditus, Koilops herma, Ossirarus kierani, Diploradus austiumensis and Aytonerpeton microps) from two localities in their environmental context. A phylogenetic analysis retrieved three taxa as stem tetrapods, interspersed among Devonian and Carboniferous forms, and two as stem amphibians, suggesting a deep split among crown tetrapods. We also illustrate new tetrapod specimens from these and additional localities in the Scottish Borders region. The new taxa and specimens suggest that tetrapod diversification was well established by the Tournaisian. Sedimentary evidence indicates that the tetrapod fossils are usually associated with sandy siltstones overlying wetland palaeosols. Tetrapods were probably living on vegetated surfaces that were subsequently flooded. We show that atmospheric oxygen levels were stable across the Devonian/Carboniferous boundary, and did not inhibit the evolution of terrestriality. This wealth of tetrapods from Tournaisian localities highlights the potential for discoveries elsewhere.

Avian cerebellar floccular fossa size is not a proxy for flying ability in birds.

Extinct animal behavior has often been inferred from qualitative assessments of relative brain region size in fossil endocranial casts. For instance, flight capability in pterosaurs and early birds has been inferred from the relative size of the cerebellar flocculus, which in life protrudes from the lateral surface of the cerebellum. A primary role of the flocculus is to integrate sensory information about head rotation and translation to stabilize visual gaze via the vestibulo-occular reflex (VOR). Because gaze stabilization is a critical aspect of flight, some authors have suggested that the flocculus is enlarged in flying species. Whether this can be further extended to a floccular expansion in highly maneuverable flying species or floccular reduction in flightless species is unknown. Here, we used micro computed-tomography to reconstruct "virtual" endocranial casts of 60 extant bird species, to extract the same level of anatomical information offered by fossils. Volumes of the floccular fossa and entire brain cavity were measured and these values correlated with four indices of flying behavior. Although a weak positive relationship was found between floccular fossa size and brachial index, no significant relationship was found between floccular fossa size and any other flight mode classification. These findings could be the result of the bony endocranium inaccurately reflecting the size of the neural flocculus, but might also reflect the importance of the flocculus for all modes of locomotion in birds. We therefore conclude that the relative size of the flocculus of endocranial casts is an unreliable predictor of locomotor behavior in extinct birds, and probably also pterosaurs and non-avian dinosaurs.

Inner ear anatomy is a proxy for deducing auditory capability and behaviour in reptiles and birds.

Inferences of hearing capabilities and audition-related behaviours in extinct reptiles and birds have previously been based on comparing cochlear duct dimensions with those of living species. However, the relationship between inner-ear bony anatomy and hearing ability or vocalization has never been tested rigorously in extant or fossil taxa. Here, micro-computed tomographic analysis is used to investigate whether simple endosseous cochlear duct (ECD) measurements can be fitted to models of hearing sensitivity, vocalization, sociality and environmental preference in 59 extant reptile and bird species, selected based on their vocalization ability. Length, rostrocaudal/mediolateral width and volume measurements were taken from ECD virtual endocasts and scaled to basicranial length. Multiple regression of these data with measures of hearing sensitivity, vocal complexity, sociality and environmental preference recovered positive correlations between ECD length and hearing range/mean frequency, vocal complexity, the behavioural traits of pair bonding and living in large aggregations, and a negative correlation between ECD length/rostrocaudal width and aquatic environments. No other dimensions correlated with these variables. Our results suggest that ECD length can be used to predict mean hearing frequency and range in fossil taxa, and that this measure may also predict vocal complexity and large group sociality given comprehensive datasets.