Molecular structure of sauropsid ß-keratins from tuatara (Sphenodon punctatus).

The birds and reptiles, collectively known as the sauropsids, can be subdivided phylogenetically into the archosaurs (birds, crocodiles), the testudines (turtles), the squamates (lizards, snakes) and the rhynchocephalia (tuatara). The structural framework of the epidermal appendages from the sauropsids, which include feathers, claws and scales, has previously been characterised by electron microscopy, infrared spectroscopy and X-ray diffraction analyses, as well as by studies of the amino acid sequences of the constituent ß-keratin proteins (also referred to as the corneous ß-proteins). An important omission in this work, however, was the lack of sequence and structural data relating to the epidermal appendages of the rhynchocephalia (tuatara), one of the two branches of the lepidosaurs. Considerable effort has gone into sequencing the tuatara genome and while this is not yet complete, there are now sufficient sequence data for conclusions to be drawn on the similarity of the ß-keratins from the tuatara to those of other members of the sauropsids. These results, together with a comparison of the X-ray diffraction pattern of tuatara claw with those from seagull feather and goanna claw, confirm that there is a common structural plan in the ß-keratins of all of the sauropsids, and not just those that comprise the archosaurs (birds and crocodiles), the testudines (turtles) and the squamates (lizards and snakes).

Tip-dating and homoplasy: reconciling the shallow molecular divergences of modern gharials with their long fossil record.

Simultaneously analysing morphological, molecular and stratigraphic data suggests a potential resolution to a major remaining inconsistency in crocodylian evolution. The ancient, long-snouted thoracosaurs have always been placed near the Indian gharial Gavialis, but their antiquity (ca 72 Ma) is highly incongruous with genomic evidence for the young age of the Gavialis lineage (ca 40 Ma). We reconcile this contradiction with an updated morphological dataset and novel analysis, and demonstrate that thoracosaurs are an ancient iteration of long-snouted stem crocodylians unrelated to modern gharials. The extensive similarities between thoracosaurs and Gavialis are shown to be an almost 'perfect storm' of homoplasy, combining convergent adaptions to fish-eating, as well resemblances between genuinely primitive traits (thoracosaurs) and atavisms (Gavialis). Phylogenetic methods that ignore stratigraphy (parsimony and undated Bayesian methods) are unable to tease apart these similarities and invariably unite thoracosaurs and Gavialis. However, tip-dated Bayesian approaches additionally consider the large temporal gap separating ancient (thoracosaurs) and modern (Gavialis) iterations of similar long-snouted crocodyliforms. These analyses robustly favour a phylogeny which places thoracosaurs basal to crocodylians, far removed from modern gharials, which accordingly are a very young radiation. This phylogenetic uncoupling of ancient and modern gharial-like crocs is more consistent with molecular clock divergence estimates, and also the bulk of the crocodylian fossil record (e.g. all unequivocal gharial fossils are very young). Provided that the priors and models attribute appropriate relative weights to the morphological and stratigraphic signals-an issue that requires investigation-tip-dating approaches are potentially better able to detect homoplasy and improve inferences about phylogenetic relationships, character evolution and divergence dates.

Filamentous Structure of Hard ß-Keratins in the Epidermal Appendages of Birds and Reptiles.

The structures of avian and reptilian epidermal appendages, such as feathers, claws and scales, have been modelled using X-ray diffraction and electron microscopy data, combined with sequence analyses. In most cases, a family of closely related molecules makes up the bulk of the appendage, and each of these molecules contains a central ß-rich 34-residue segment, which has been identified as the principal component of the framework of the 3.4 nm diameter filaments. The N- and C-terminal segments form the matrix component of the filament/matrix complex. The 34-residue ß-rich central domains occur in pairs, related by either a parallel dyad or a perpendicular dyad axis, and form a ß-sandwich stabilized by apolar interactions. They are also twisted in a right-handed manner. In feather, the filaments are packed into small sheets and it is possible to determine their likely orientation within the sheets from the low-angle X-ray diffraction data. The physical properties of the various epidermal appendages can be related to the amino acid sequence and composition of defined molecular segments characteristic of the chains concerned.

Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs.

Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modeling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, to estimate metabolic rates of fossil archosauromorphs. This modeling procedure serves as a case study for eigenvector-based predictive modeling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share a higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e., endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous.

Evolution of Sound Source Localization Circuits in the Nonmammalian Vertebrate Brainstem.

The earliest vertebrate ears likely subserved a gravistatic function for orientation in the aquatic environment. However, in addition to detecting acceleration created by the animal's own movements, the otolithic end organs that detect linear acceleration would have responded to particle movement created by external sources. The potential to identify and localize these external sources may have been a major selection force in the evolution of the early vertebrate ear and in the processing of sound in the central nervous system. The intrinsic physiological polarization of sensory hair cells on the otolith organs confers sensitivity to the direction of stimulation, including the direction of particle motion at auditory frequencies. In extant fishes, afferents from otolithic end organs encode the axis of particle motion, which is conveyed to the dorsal regions of first-order octaval nuclei. This directional information is further enhanced by bilateral computations in the medulla and the auditory midbrain. We propose that similar direction-sensitive neurons were present in the early aquatic tetrapods and that selection for sound localization in air acted upon preexisting brain stem circuits like those in fishes. With movement onto land, the early tetrapods may have retained some sensitivity to particle motion, transduced by bone conduction, and later acquired new auditory papillae and tympanic hearing. Tympanic hearing arose in parallel within each of the major tetrapod lineages and would have led to increased sensitivity to a broader frequency range and to modification of the preexisting circuitry for sound source localization.

Amino acid sequence homologies in the hard keratins of birds and reptiles, and their implications for molecular structure and physical properties.

Avian and reptilian epidermal appendages such as feathers, claws and scales exhibit a filament-matrix texture. Previous studies have established that both components reside within the same single-chain molecule. In the present study the homology in a wide range of aligned sequences is used to gain insights into the structure and function of the molecular segments associated with the filament and with the matrix. The notion that all molecules contain a ß-rich 34-residue segment associated with the framework of the filament is reinforced by the present study. In addition, the residues involved in the polymerization of the molecules to form filaments are identified. In the Archosaurs (birds, crocodiles and turtles), and the Squamates (snakes and lizards) segments rich in glycine and tyrosine can be identified in the C-terminal domain. In Rhynocephalians (tuataras) and Squamates a similar segment is inserted at a specific point in the N-terminal domain. In some Archosaurian appendages (both avian and reptilian) segments rich in charged residues and cysteine are found in the N-terminal domain. The likely effect of these segments will be to soften the tissue without compromising its insolubility. The structure and role of the various molecular segments identified in this study and the way in which they might manifest themselves in terms of the physical properties of the particular epidermal appendage in which they appear are also discussed.

Locomotion and the early Mesozoic success of Archosauromorpha.

The Triassic was a time of ecological upheaval as life recovered from the Permian-Triassic mass extinction. Archosauromorphs were a key component of the recovery, diversifying substantially during the Triassic and encompassing the origins of dinosaurs, pterosaurs and crocodylomorphs. Here, we explore the evolution of locomotion in Archosauromorpha to test whether dinosaurs show any distinctive locomotory features that might explain their success. We implement geometric morphometrics on limb bone shapes and use limb ratios to calculate bipedality and cursoriality metrics. We find that the Avemetatarsalia (dinosaurs, pterosaurs and relatives) exhibit more variable limb form and limb ratios than any other group, indicating a wider range of locomotory modes. The earliest avemetatarsalians were bipedal and cursorial, and their range of form increased through the Triassic with notable diversification shifts following extinction events. This is especially true of dinosaurs, even though these changes cannot be discriminated from a stochastic process. By contrast, the Pseudosuchia (crocodilians and relatives) were more restricted in limb form and locomotor mode with disparity decreasing through time, suggesting more limited locomotor adaptation and vulnerability to extinction. Perhaps the greater locomotor plasticity of dinosaurs gave them a competitive advantage in the changing climates of the Late Triassic.

Liver mitochondrial coupling efficiency and its relationship to oxidative capacity and adenine nucleotide translocase content: A comparative study among crocodiles, birds and mammals.

The primary objective of this study was to assess whether adenine nucleotide translocase (ANT) content could be associated with phylogenetic disparities in mitochondrial coupling efficiency, within liver mitochondria obtained from rats, crocodiles, and ducklings. Our measurements included mitochondrial membrane conductance, ANT content, and oxidative phosphorylation fluxes at various steady-state rates. We observed significant variations in liver mitochondrial coupling efficiency across the three species. These variations correlated with interspecific differences in mitochondrial oxidative capacity and, to a lesser extent, the ANT content of liver mitochondria. These findings expand upon previous research by highlighting the pivotal role of oxidative capacity and ANT in modulating mitochondrial efficiency on an interspecific scale.

Morphometrics of the Spinal Cord and Surrounding Structures in Alligator mississippiensis.

Understanding the fluid dynamics of the cerebrospinal fluid requires a quantitative description of the spaces in which it flows, including the spinal cord and surrounding meninges. The morphometrics of the spinal cord and surrounding tissues were studied in specimens of the American alligator (Alligator mississippiensis) ranging from hatchlings through adults. Within any size class of alligators (i.e., hatchlings), along the axial length there are significant differences in the size of the spinal cord, meninges, and vertebral canal; these differences can be used to define discrete cervical, thoracic, lumbar and caudal regions. When compared across the range of body sizes in Alligator, every structure in each spinal region had a distinctive growth rate; thus, the physical arrangements between the structures changed as the alligator grew. The combination of regional differentiation and differential growth rates was particularly apparent in the lumbar meninges where a unique form of lumbar cistern could be identified and shown to decrease in relative size as the alligator ages. This analysis of the spinal cord and surrounding tissues was undertaken to develop a data set that could be used for computational flow dynamics of the crocodilian cerebrospinal fluid, and also to assist in the analysis of fossil archosaurs.

Ontogenetic endocranial shape change in alligators and ostriches and implications for the development of the non-avian dinosaur endocranium.

Birds and crocodiles show radically different patterns of brain development, and it is of interest to compare these to determine the pattern of brain growth expected in dinosaurs. Here we provide atlases of 3D brain (endocast) reconstructions for Alligator mississippiensis (alligator) and Struthio camelus (ostrich) through ontogeny, prepared as digital restorations from CT scans of stained head and dry skull specimens. Our morphometric analysis confirms that ostrich brains do not change significantly in shape during postnatal growth, whereas alligator brains unfold from a cramped bird-like shape in the hatchling to an elongate, straight structure in the adult. We confirm that birds exhibit paedomorphic dinosaur endocranial traits such as retaining an enlarged and compact brain shape in the adult, whereas crocodiles show peramorphic traits where the brain elongates with growth as the skull elongates. These atlases of ontogenetic stages of modern bird and crocodilian endocrania provide a basis for comparison of non-avian dinosaur endocasts and consideration of the divergence of the "avian" and "crocodilian" modes of brain development and heterochronic change on phylogenies.

Deep evolutionary diversification of semicircular canals in archosaurs.

Living archosaurs (birds and crocodylians) have disparate locomotor strategies that evolved since their divergence ∼250 mya. Little is known about the early evolution of the sensory structures that are coupled with these changes, mostly due to limited sampling of early fossils on key stem lineages. In particular, the morphology of the semicircular canals (SCCs) of the endosseous labyrinth has a long-hypothesized relationship with locomotion. Here, we analyze SCC shapes and sizes of living and extinct archosaurs encompassing diverse locomotor habits, including bipedal, semi-aquatic, and flying taxa. We test form-function hypotheses of the SCCs and chronicle their evolution during deep archosaurian divergences. We find that SCC shape is statistically associated with both flight and bipedalism. However, this shape variation is small and is more likely explained by changes in braincase geometry than by locomotor changes. We demonstrate high disparity of both shape and size among stem-archosaurs and a deep divergence of SCC morphologies at the bird-crocodylian split. Stem-crocodylians exhibit diverse morphologies, including aspects also present in birds and distinct from other reptiles. Therefore, extant crocodylian SCC morphologies do not reflect retention of a "primitive" reptilian condition. Key aspects of bird SCC morphology that hitherto were interpreted as flight related, including large SCC size and enhanced sensitivity, appeared early on the bird stem-lineage in non-flying dinosaur precursors. Taken together, our results indicate a deep divergence of SCC traits at the bird-crocodylian split and that living archosaurs evolved from an early radiation with high sensory diversity. VIDEO ABSTRACT.

Palaeophysiology of pH regulation in tetrapods.

The involvement of mineralized tissues in acid-base homeostasis was likely important in the evolution of terrestrial vertebrates. Extant reptiles encounter hypercapnia when submerged in water, but early tetrapods may have experienced hypercapnia on land due to their inefficient mode of lung ventilation (likely buccal pumping, as in extant amphibians). Extant amphibians rely on cutaneous carbon dioxide elimination on land, but early tetrapods were considerably larger forms, with an unfavourable surface area to volume ratio for such activity, and evidence of a thick integument. Consequently, they would have been at risk of acidosis on land, while many of them retained internal gills and would not have had a problem eliminating carbon dioxide in water. In extant tetrapods, dermal bone can function to buffer the blood during acidosis by releasing calcium and magnesium carbonates. This review explores the possible mechanisms of acid-base regulation in tetrapod evolution, focusing on heavily armoured, basal tetrapods of the Permo-Carboniferous, especially the physiological challenges associated with the transition to air-breathing, body size and the adoption of active lifestyles. We also consider the possible functions of dermal armour in later tetrapods, such as Triassic archosaurs, inferring palaeophysiology from both fossil record evidence and phylogenetic patterns, and propose a new hypothesis relating the archosaurian origins of the four-chambered heart and high systemic blood pressures to the perfusion of the osteoderms. This article is part of the theme issue 'Vertebrate palaeophysiology'.

Disparate Growth Strategies within Aetosauria: Novel Histologic Data from the Aetosaur Coahomasuchus chathamensis.

Aetosaurs comprise a clade of quadrupedal, armored, omnivores to herbivores that lived across much of the supercontinent of Pangea during the Late Triassic. Their relative abundance in many units, and the rarity of other Triassic herbivores, points to them as key components of Late Triassic ecosystems. Debate persists about whether they were growing more or less slowly when compared to extant crocodylians, and bone histology is sparsely sampled within the group. We undertook a histological examination of Coahomasuchus chathamensis to address its ontogenetic trajectory and characterize its histology. We sampled a paramedian osteoderm from the holotype specimen, as well as five osteoderms (two paramedian, one lateral, and two of uncertain position) and two incomplete limb bones (radius and fibula), from referred specimens discovered at the type locality. Using these we estimated specimen ages with lines of arrested growth (LAGs) to determine that the study individuals reached from 2 to 7 years old. All of the sampled elements contained woven-fibered bone with extensive vasculature within the internal cortex. In some specimens, more poorly vascularized, parallel-fibered bone is evident externally. The holotype of C. chathamensis represents a juvenile individual, and raises the possibility that the holotype of C. kahleorum is a juvenile as well, complicating aetosaur systematics and diversity. When compared to aetosaurs of similar size, it is clear that C. chathamensis was growing comparatively rapidly, about 3 times the rate of similarly sized specimens of Aetosauroides scagliai from Argentina. This discovery reveals the presence of disparate growth strategies within Aetosauria. Anat Rec, 302:1504-1515, 2019. © 2018 American Association for Anatomy.

A phenology of the evolution of endothermy in birds and mammals.

Recent palaeontological data and novel physiological hypotheses now allow a timescaled reconstruction of the evolution of endothermy in birds and mammals. A three-phase iterative model describing how endothermy evolved from Permian ectothermic ancestors is presented. In Phase One I propose that the elevation of endothermy - increased metabolism and body temperature (Tb ) - complemented large-body-size homeothermy during the Permian and Triassic in response to the fitness benefits of enhanced embryo development (parental care) and the activity demands of conquering dry land. I propose that Phase Two commenced in the Late Triassic and Jurassic and was marked by extreme body-size miniaturization, the evolution of enhanced body insulation (fur and feathers), increased brain size, thermoregulatory control, and increased ecomorphological diversity. I suggest that Phase Three occurred during the Cretaceous and Cenozoic and involved endothermic pulses associated with the evolution of muscle-powered flapping flight in birds, terrestrial cursoriality in mammals, and climate adaptation in response to Late Cenozoic cooling in both birds and mammals. Although the triphasic model argues for an iterative evolution of endothermy in pulses throughout the Mesozoic and Cenozoic, it is also argued that endothermy was potentially abandoned at any time that a bird or mammal did not rely upon its thermal benefits for parental care or breeding success. The abandonment would have taken the form of either hibernation or daily torpor as observed in extant endotherms. Thus torpor and hibernation are argued to be as ancient as the origins of endothermy itself, a plesiomorphic characteristic observed today in many small birds and mammals.

Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs.

In a number of recent studies we used computer modeling to investigate the evolution of muscle leverage (moment arms) and function in extant and extinct archosaur lineages (crocodilians, dinosaurs including birds and pterosaurs). These studies sought to quantify the level of disparity and convergence in muscle moment arms during the evolution of bipedal and quadrupedal posture in various independent archosaur lineages, and in doing so further our understanding of changes in anatomy, locomotion and ecology during the group's >250 million year evolutionary history. Subsequent work by others has led us to re-evaluate our models, which revealed a methodological error that impacted on the results obtained from the abduction-adduction and long-axis rotation moment arms in our published studies. In this paper we present corrected abduction-adduction and long axis rotation moment arms for all our models, and evaluate the impact of this new data on the conclusions of our previous studies. We find that, in general, our newly corrected data differed only slightly from that previously published, with very few qualitative changes in muscle moments (e.g., muscles originally identified as abductors remained abductors). As a result the majority of our previous conclusions regarding the functional evolution of key muscles in these archosaur groups are upheld.

The natural history of sound localization in mammals--a story of neuronal inhibition.

Our concepts of sound localization in the vertebrate brain are widely based on the general assumption that both the ability to detect air-borne sounds and the neuronal processing are homologous in archosaurs (present day crocodiles and birds) and mammals. Yet studies repeatedly report conflicting results on the neuronal circuits and mechanisms, in particular the role of inhibition, as well as the coding strategies between avian and mammalian model systems. Here we argue that mammalian and avian phylogeny of spatial hearing is characterized by a convergent evolution of hearing air-borne sounds rather than by homology. In particular, the different evolutionary origins of tympanic ears and the different availability of binaural cues in early mammals and archosaurs imposed distinct constraints on the respective binaural processing mechanisms. The role of synaptic inhibition in generating binaural spatial sensitivity in mammals is highlighted, as it reveals a unifying principle of mammalian circuit design for encoding sound position. Together, we combine evolutionary, anatomical and physiological arguments for making a clear distinction between mammalian processing mechanisms and coding strategies and those of archosaurs. We emphasize that a consideration of the convergent nature of neuronal mechanisms will significantly increase the explanatory power of studies of spatial processing in both mammals and birds.

Bone histology of phytosaur, aetosaur, and other archosauriform osteoderms (Eureptilia, Archosauromorpha).

As in other archosauriforms, phytosaurs and aetosaurs are characterized by the presence of well-developed osteoderms. Here we provide a comparative study on the microstructure of phytosaur (five taxa) and aetosaur (thirteen taxa) osteoderms. For outgroup comparison, we sampled osteoderms of the sister taxon to Aetosauria, Revueltosaurus callenderi, and the doswelliid Jaxtasuchus salomoni. Phytosaur, aetosaur, and Jaxtasuchus osteoderms are composed of a diploe structure, whereas the Revueltosaurus osteoderm microanatomy is more compact. The external cortex of phytosaurs, Revueltosaurus and Jaxtasuchus osteoderms is mainly composed of parallel-fibered bone. In aetosaurs, the external cortex mainly consists of lamellar bone, with lines of resorption within the primary bone indicating successive cycles of bone erosion and deposition. The basal cortex in all the specimens is composed of parallel-fibered bone, with the cancellous internal core being more strongly developed in aetosaurs than in phytosaurs. Woven or fibro-lamellar bone was recorded in both phytosaurian and aetosaurian taxa, as well as in Jaxtasuchus. Structural fibers, which at least partly suggest metaplastic origin, were only recorded in the internal core of two phytosaurs and in the basal cortex of one aetosaur. Osteoderm thickness and cancellous to compact bone ratios appear to be subject to ontogenetic change. Minimum growth mark counts in osteoderms sampled indicate that some aetosaurs and phytosaurs lived for at least two decades. Bone microstructures are more uniform in phytosaur osteoderms and show a higher level of disparity among aetosaur osteoderms, and at least in the latter, histological features are potentially apomorphic for species/genus level.