The topological organization of the turtle cranium is constrained and conserved over long evolutionary timescales

The cranium of turtles (Testudines) is characterized by the secondary reduction of temporal fenestrae and loss of cranial joints (i.e., characteristics of anapsid, akinetic skulls). Evolution and ontogeny of the turtle cranium are associated with shape changes. Cranial shape variation among Testudines can partially be explained by dietary and functional adaptations (neck retraction), but it is unclear if cranial topology shows similar ecomorphological signal, or if it is decoupled from shape evolution. We assess the topological arrangement of cranial bones (i.e., number, relative positioning, connections), using anatomical network analysis. Non-shelled stem turtles have similar cranial arrangements to archosauromorph outgroups. Shelled turtles (Testudinata) evolve a unique cranial organization that is associated with bone losses (e.g., supratemporal, lacrimal, ectopterygoid) and an increase in complexity (i.e., densely and highly interconnected skulls with low path lengths between bones), resulting from the closure of skull openings and establishment of unusual connections such as a parietal-pterygoid contact in the secondary braincase. Topological changes evolutionarily predate many shape changes. Topological variation and taxonomic morphospace discrimination among crown turtles are low, indicating that cranial topology may be constrained. Observed variation results from repeated losses of nonintegral bones (i.e., premaxilla, nasal, epipterygoid, quadratojugal), and changes in temporal emarginations and palate construction. We observe only minor ontogenetic changes. Topology is not influenced by diet and habitat, contrasting cranial shape. Our results indicate that turtles have a unique cranial topology among reptiles that is conserved after its initial establishment, and shows that cranial topology and shape have different evolutionary histories.

Deep-time invention and hydrodynamic convergences through amniote flipper evolution

The diapsid plesiosaurs were pelagic and inhabited the oceans from the Triassic to the Cretaceous. A key evolutionary character of plesiosaurs is the four wing-like flippers. While it is mostly accepted that plesiosaurs were underwater fliers like marine turtles, penguins, and maybe whales, other swimming styles have been suggested in the past. These are rowing and a combination of rowing and underwater flight (e.g., pig-nosed turtle, sea lion). Underwater fliers use lift in contrast to rowers that employ drag. For efficiently profiting of lift during underwater flying, it is necessary that plesiosaurs twisted their flippers by muscular activity. To research the evolution of flipper twisting in plesiosaurs and functionally analogous taxa, including turtles, we used anatomical network analysis (AnNA) and reassessed distal flipper muscle functions. We coded bone-to-bone and additionally muscle-to-bone contacts in N × N matrices for foreflippers of the plesiosaur, the loggerhead sea turtle, the pig-nosed turtle, the African penguin, the California sea lion, and the humpback whale based on literature data. In "R," "igraph" was run by using a walktrap algorithm to obtain morphofunctional modules. AnNA revealed that muscle-to-bone contacts are needed to detect contributions of modules to flipper motions, whereas only-bone matrices are not informative for that. Furthermore, the plesiosaur, the marine turtles, the seal, and the penguin flipper twisting mechanisms, but the penguin cannot actively twist the flipper trailing edge. Finally, the foreflipper of the pig-nosed turtle and of the whale is not actively twisted during swimming.

Cranial ecomorphology of turtles and neck retraction as a possible trigger of ecological diversification

Turtles have a highly modified body plan, including a rigid shell that constrains postcranial anatomy. Skull morphology and neck mobility may therefore be key to ecological specialization in turtles. However, the ecological signal of turtle skull morphologies has not been rigorously evaluated, leaving uncertainties about the roles of ecological adaptation and convergence. We evaluate turtle cranial ecomorphology using three-dimensional geometric morphometrics and phylogenetic comparative methods. Skull shape correlates with allometry, neck retraction capability, and different aquatic feeding ecologies. We find that ecological variables influence skull shape only, whereas a key functional variable (the capacity for neck retraction) influences both shape and size. Ecology and functional predictions from three-dimensional shape are validated by high success rates for extant species, outperforming previous two-dimensional approaches. We use this to infer ecological and functional traits of extinct species. Neck retraction evolved among crownward stem-turtles by the Late Jurassic, signaling functional decoupling of the skull and neck from the shell, possibly linked to a major episode of ecomorphological diversification. We also find strong evidence for convergent ecological adaptations among marine groups. This includes parallel loss of neck retraction, evidence for active hunting, possible grazing, and suction feeding in extinct marine groups. Our large-scale assessment of dietary and functional adaptation throughout turtle evolution reveals the timing and origin of their distinct ecomorphologies, and highlights the potential for ecology and function to have distinct effects on skull form.

Determination of muscle strength and function in plesiosaur limbs: finite element structural analyses of Cryptoclidus eurymerus humerus and femur

Background

The Plesiosauria (Sauropterygia) are secondary marine diapsids. They are the only tetrapods to have evolved hydrofoil fore- and hindflippers. Once this specialization of locomotion had evolved, it remained essentially unchanged for 135 Ma. It is still controversial whether plesiosaurs flew underwater, rowed, or used a mixture of the two modes of locomotion. The long bones of Tetrapoda are functionally loaded by torsion, bending, compression, and tension during locomotion. Superposition of load cases shows that the bones are loaded mainly by compressive stresses. Therefore, it is possible to use finite element structure analysis (FESA) as a test environment for loading hypotheses. These include muscle reconstructions and muscle lines of action (LOA) when the goal is to obtain a homogeneous compressive stress distribution and to minimize bending in the model. Myological reconstruction revealed a muscle-powered flipper twisting mechanism. The flippers of plesiosaurs were twisted along the flipper length axis by extensors and flexors that originated from the humerus and femur as well as further distal locations.

Methods

To investigate locomotion in plesiosaurs, the humerus and femur of a mounted skeleton of Cryptoclidus eurymerus (Middle Jurassic Oxford Clay Formation from Britain) were analyzed using FE methods based on the concept of optimization of loading by compression. After limb muscle reconstructions including the flipper twisting muscles, LOA were derived for all humerus and femur muscles of Cryptoclidus by stretching cords along casts of the fore- and hindflippers of the mounted skeleton. LOA and muscle attachments were added to meshed volumetric models of the humerus and femur derived from micro-CT scans. Muscle forces were approximated by stochastic iteration and the compressive stress distribution for the two load cases, "downstroke" and "upstroke", for each bone were calculated by aiming at a homogeneous compressive stress distribution.

Results

Humeral and femoral depressors and retractors, which drive underwater flight rather than rowing, were found to exert higher muscle forces than the elevators and protractors. Furthermore, extensors and flexors exert high muscle forces compared to Cheloniidae. This confirms a convergently evolved myological mechanism of flipper twisting in plesiosaurs and complements hydrodynamic studies that showed flipper twisting is critical for efficient plesiosaur underwater flight.

Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting

BACKGROUND

Plesiosaurs, diapsid crown-group Sauropterygia, inhabited the oceans from the Late Triassic to the Late Cretaceous. Their most exceptional characteristic are four hydrofoil-like flippers. The question whether plesiosaurs employed their four flippers in underwater flight, rowing flight, or rowing has not been settled yet. Plesiosaur locomotory muscles have been reconstructed in the past, but neither the pelvic muscles nor the distal fore- and hindflipper musculature have been reconstructed entirely.

METHODS

All plesiosaur locomotory muscles were reconstructed in order to find out whether it is possible to identify muscles that are necessary for underwater flight including those that enable flipper rotation and twisting. Flipper twisting has been proven by hydrodynamic studies to be necessary for efficient underwater flight. So, Cryptoclidus eurymerus fore- and hindflipper muscles and ligaments were reconstructed using the extant phylogenetic bracket (Testudines, Crocodylia, and Lepidosauria) and correlated with osteological features and checked for their functionality. Muscle functions were geometrically derived in relation to the glenoid and acetabulum position. Additionally, myology of functionally analogous Chelonioidea, Spheniscidae, Otariinae, and Cetacea is used to extract general myological adaptations of secondary aquatic tetrapods to inform the phylogenetically inferred muscle reconstructions.

RESULTS

A total of 52 plesiosaur fore- and hindflipper muscles were reconstructed. Amongst these are flipper depressors, elevators, retractors, protractors, and rotators. These muscles enable a fore- and hindflipper downstroke and upstroke, the two sequences that represent an underwater flight flipper beat cycle. Additionally, other muscles were capable of twisting fore- and hindflippers along their length axis during down- and upstroke accordingly. A combination of these muscles that actively aid in flipper twisting and intermetacarpal/intermetatarsal and metacarpodigital/metatarsodigital ligament systems, that passively engage the successive digits, could have accomplished fore-and hindflipper length axis twisting in plesiosaurs that is essential for underwater flight. Furthermore, five muscles that could possibly actively adjust the flipper profiles for efficient underwater flight were found, too.

An early bothremydid from the Arlington Archosaur Site of Texas

Four turtle taxa are previously documented from the Cenomanian Arlington Archosaur Site (AAS) of the Lewisville Formation (Woodbine Group) in Texas. Herein, we describe a new side-necked turtle (Pleurodira), Pleurochayah appalachius gen. et sp. nov., which is a basal member of the Bothremydidae. Pleurochayah appalachius gen. et sp. nov. shares synapomorphic characters with other bothremydids, including shared traits with Kurmademydini and Cearachelyini, but has a unique combination of skull and shell traits. The new taxon is significant because it is the oldest crown pleurodiran turtle from North America and Laurasia, predating bothremynines Algorachelus peregrinus and Paiutemys tibert from Europe and North America respectively. This discovery also documents the oldest evidence of dispersal of crown Pleurodira from Gondwana to Laurasia. Pleurochayah appalachius gen. et sp. nov. is compared to previously described fossil pleurodires, placed in a modified phylogenetic analysis of pelomedusoid turtles, and discussed in the context of pleurodiran distribution in the mid-Cretaceous. Its unique combination of characters demonstrates marine adaptation and dispersal capability among basal bothremydids.

Origin and Evolution of the Turtle Body Plan

The origin of turtles and their uniquely shelled body plan is one of the longest standing problems in vertebrate biology. The unfulfilled need for a hypothesis that both explains the derived nature of turtle anatomy and resolves their unclear phylogenetic position among reptiles largely reflects the absence of a transitional fossil record. Recent discoveries have dramatically improved this situation, providing an integrated, time-calibrated model of the morphological, developmental, and ecological transformations responsible for the modern turtle body plan. This evolutionary trajectory was initiated in the Permian (>260 million years ago) when a turtle ancestor with a diapsid skull evolved a novel mechanism for lung ventilation. This key innovation permitted the torso to become apomorphically stiff, most likely as an adaption for digging and a fossorial ecology. The construction of the modern turtle body plan then proceeded over the next 100 million years following a largely stepwise model of osteological innovation.

Comparative analysis of the shape and size of the middle ear cavity of turtles reveals no correlation with habitat ecology

The middle ear of turtles differs from other reptiles in being separated into two distinct compartments. Several ideas have been proposed as to why the middle ear is compartmentalized in turtles, most suggesting a relationship with underwater hearing. Extant turtle species span fully marine to strictly terrestrial habitats, and ecomorphological hypotheses of turtle hearing predict that this should correlate with variation in the structure of the middle ear due to differences in the fluid properties of water and air. We investigate the shape and size of the air-filled middle ear cavity of 56 extant turtles using 3D data and phylogenetic comparative analysis to test for correlations between habitat preferences and the shape and size of the middle ear cavity. Only weak correlations are found between middle ear cavity size and ecology, with aquatic taxa having proportionally smaller cavity volumes. The middle ear cavity of turtles exhibits high shape diversity among species, but we found no relationship between this shape variation and ecology. Surprisingly, the estimated acoustic transformer ratio, a key functional parameter of impedance-matching ears in vertebrates, also shows no relation to habitat preferences (aquatic/terrestrial) in turtles. We suggest that middle ear cavity shape may be controlled by factors unrelated to hearing, such as the spatial demands of surrounding cranial structures. A review of the fossil record suggests that the modern turtle ear evolved during the Early to Middle Jurassic in stem turtles broadly adapted to freshwater and terrestrial settings. This, combined with our finding that evolutionary transitions between habitats caused only weak evolutionary changes in middle ear structure, suggests that tympanic hearing in turtles evolved as a compromise between subaerial and underwater hearing.

Microanatomy of the stem-turtle Pappochelys rosinae indicates a predominantly fossorial mode of life and clarifies early steps in the evolution of the shell

Unlike any other tetrapod, turtles form their dorsal bony shell (carapace) not from osteoderms, but by contribution of the ribs and vertebrae that expand into the dermis to form plate-like shell components. Although this was known from embryological studies in extant turtles, important steps in this evolutionary sequence have recently been highlighted by the Triassic taxa Pappochelys, Eorhynchochelys and Odontochelys, and the Permian Eunotosaurus. The discovery of Pappochelys shed light on the origin of the ventral bony shell (plastron), which formed from enlarged gastralia. A major question is whether the turtle shell evolved in the context of a terrestrial or aquatic environment. Whereas Odontochelys was controversially interpreted as aquatic, a terrestrial origin of turtles was proposed based on evidence of fossorial adaptations in Eunotosaurus. We report palaeohistological data for Pappochelys, a taxon that exemplifies earlier evolutionary stages in the formation of the bony shell than Odontochelys. Bone histological evidence reveals (1) evolutionary changes in bone microstructure in ribs and gastralia approaching the turtle condition and (2) evidence for a predominantly amphibious or fossorial mode of life in Pappochelys, which support the hypothesis that crucial steps in the evolution of the shell occurred in a terrestrial rather than fully aquatic environment.

The palatal dentition of tetrapods and its functional significance

The presence of a palatal dentition is generally considered to be the primitive condition in amniotes, with each major lineage showing a tendency toward reduction. This study highlights the variation in palatal tooth arrangements and reveals clear trends within the evolutionary history of tetrapods. Major changes occurred in the transition between early tetrapods and amphibians on the one hand, and stem amniotes on the other. These changes reflect the function of the palatal dentition, which can play an important role in holding and manipulating food during feeding. Differences in the arrangement of palatal teeth, and in their pattern of loss, likely reflect differences in feeding strategy but also changes in the arrangement of cranial soft tissues, as the palatal dentition works best with a well-developed mobile tongue. It is difficult to explain the loss of palatal teeth in terms of any single factor, but palatal tooth patterns have the potential to provide new information on diet and feeding strategy in extinct taxa.

MUSCULAR ANATOMY OF THE PECTORAL AND FORELIMB OF Caiman crocodilus crocodilus (LINNAEUS, 1758) (CROCODYLIA: ALLIGATORIDAE)

Abstract Among the Brazilian crocodilian, Caiman crocodilus crocodilus is widely distributed, given its adaptation to diverse habitats and their generalist diet. Information about the reproductive and ethological character of this species is abundant, whereas morphological data are still scarce. This study aimed to identify and report the muscles and their origin and the insertion into the pectoral and forelimb of C. crocodilus crocodilus. We used two male specimens, adults, belonging to the collection of the UFG - Jataí. We performed usual procedures for dissection and further individualization, withdrawal of members, and observation of muscle origins and insertions. The musculature of C. crocodilus crocodilus generally conservative is similar to C. latirostris and A. mississippiensis. The muscles of the pectoral girdle showed little variation among crocodilians. In the forelimb, the triceps muscle has five distinct heads and biceps has only one. The extensor and flexor surface of the hand showed similar topography to A. mississippiensis. We described some differences in the origin and insertion of certain muscles, as well as the classification and topography of some flexor and extensor muscles in the forearm segment. The distal segments showed more variations, which probably reflects the variety of locomotor habits among crocodilians.

The integumental appendages of the turtle shell: an evo-devo perspective

The turtle shell is composed of dorsal armor (carapace) and ventral armor (plastron) covered by a keratinized epithelium. There are two epithelial appendages of the turtle shell: scutes (large epidermal shields separated by furrows and forming a unique mosaic) and tubercles (numerous small epidermal bumps located on the carapaces of some species). In our perspective, we take a synthetic, comparative approach to consider the homology and evolution of these integumental appendages. Scutes have been more intensively studied, as they are autapomorphic for turtles and can be diagnostic taxonomically. Their pattern of tessellation is stable phylogenetically, but labile in the individual. We discuss the history of developmental investigations of these structures and hypotheses of evolutionary and anomalous variation. In our estimation, the scutes of the turtle shell are an evolutionary novelty, whereas the tubercles found on the shells of some turtles are homologous to reptilian scales.

Morphology and function of the palatal dentition in Choristodera

Choristoderes are a group of extinct freshwater reptiles that were distributed throughout Laurasia from the Middle Jurassic to the Miocene. They are inferred to have had a lifestyle similar to that of extant gavialid crocodiles, but they differed from crocodiles in retaining an extensive palatal dentition. All choristoderes had teeth on the vomers, palatines and pterygoids, and teeth are rarely present on the parasphenoid. Palatal teeth are conical, as in the marginal dentition, and form longitudinal and transverse rows. Detailed examination of different genera shows that the orientation of the palatal tooth crowns changes with their position on the palate, supporting the view that they are involved in intra-oral food transportation, presumably in combination with a fleshy tongue. Moreover, observed variation in palatal tooth shape and the width of palatal tooth batteries may provide additional clues about diet. The European Simoedosaurus lemoinei has sharper palatal teeth than its North American counterpart, S. dakotensis, suggesting a preference for softer prey - a conclusion consistent with the more gracile teeth and narrower snout.

The origin of turtles: a paleontological perspective

The origin of turtles and their unusual body plan has fascinated scientists for the last two centuries. Over the course of the last decades, a broad sample of molecular analyses have favored a sister group relationship of turtles with archosaurs, but recent studies reveal that this signal may be the result of systematic biases affecting molecular approaches, in particular sampling, non-randomly distributed rate heterogeneity among taxa, and the use of concatenated data sets. Morphological studies, by contrast, disfavor archosaurian relationships for turtles, but the proposed alternative topologies are poorly supported as well. The recently revived paleontological hypothesis that the Middle Permian Eunotosaurus africanus is an intermediate stem turtle is now robustly supported by numerous characters that were previously thought to be unique to turtles and that are now shown to have originated over the course of tens of millions of years unrelated to the origin of the turtle shell. Although E. africanus does not solve the placement of turtles within Amniota, it successfully extends the stem lineage of turtles to the Permian and helps resolve some questions associated with the origin of turtles, in particular the non-composite origin of the shell, the slow origin of the shell, and the terrestrial setting for the origin of turtles.

Emerging from the rib: resolving the turtle controversies

Two of the major controversies in the present study of turtle shell development involve the mechanism by which the carapacial ridge initiates shell formation and the mechanism by which each rib forms the costal bones adjacent to it. This paper claims that both sides of each debate might be correct-but within the species examined. Mechanism is more properly "mechanisms," and there is more than one single way to initiate carapace formation and to form the costal bones. In the initiation of the shell, the rib precursors may be kept dorsal by either "axial displacement" (in the hard-shell turtles) or "axial arrest" (in the soft-shell turtle Pelodiscus), or by a combination of these. The former process would deflect the rib into the dorsal dermis and allow it to continue its growth there, while the latter process would truncate rib growth. In both instances, though, the result is to keep the ribs from extending into the ventral body wall. Our recent work has shown that the properties of the carapacial ridge, a key evolutionary innovation of turtles, differ greatly between these two groups. Similarly, the mechanism of costal bone formation may differ between soft-shell and hard-shell turtles, in that the hard-shell species may have both periosteal flattening as well as dermal bone induction, while the soft-shelled turtles may have only the first of these processes.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

On the homology of the shoulder girdle in turtles

The shoulder girdle in turtles is encapsulated in the shell and has a triradiate morphology. Due to its unique configuration among amniotes, many theories have been proposed about the skeletal identities of the projections for the past two centuries. Although the dorsal ramus represents the scapular blade, the ventral two rami remain uncertain. In particular, the ventrorostral process has been compared to a clavicle, an acromion, and a procoracoid based on its morphology, its connectivity to the rest of the skeleton and to muscles, as well as with its ossification center, cell lineage, and gene expression. In making these comparisons, the shoulder girdle skeleton of anurans has often been used as a reference. This review traces the history of the debate on the homology of the shoulder girdle in turtles. And based on the integrative aspects of developmental biology, comparative morphology, and paleontology, we suggest acromion and procoracoid identities for the two ventral processes.

Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister-relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super-alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.

The evolutionary origin of the turtle shell and its dependence on the axial arrest of the embryonic rib cage

Turtles are characterized by their possession of a shell with dorsal and ventral moieties: the carapace and the plastron, respectively. In this review, we try to provide answers to the question of the evolutionary origin of the carapace, by revising morphological, developmental, and paleontological comparative analyses. The turtle carapace is formed through modification of the thoracic ribs and vertebrae, which undergo extensive ossification to form a solid bony structure. Except for peripheral dermal elements, there are no signs of exoskeletal components ontogenetically added to the costal and neural bones, and thus the carapace is predominantly of endoskeletal nature. Due to the axial arrest of turtle rib growth, the axial part of the embryo expands laterally and the shoulder girdle becomes encapsulated in the rib cage, together with the inward folding of the lateral body wall in the late phase of embryogenesis. Along the line of this folding develops a ridge called the carapacial ridge (CR), a turtle-specific embryonic structure. The CR functions in the marginal growth of the carapacial primordium, in which Wnt signaling pathway might play a crucial role. Both paleontological and genomic evidence suggest that the axial arrest is the first step toward acquisition of the turtle body plan, which is estimated to have taken place after the divergence of a clade including turtles from archosaurs. The developmental relationship between the CR and the axial arrest remains a central issue to be solved in future.

The origin and early evolution of Sauria: reassessing the permian Saurian fossil record and the timing of the crocodile-lizard divergence

Sauria is the crown-group of Diapsida and is subdivided into Lepidosauromorpha and Archosauromorpha, comprising a high percentage of the diversity of living and fossil tetrapods. The split between lepidosauromorphs and archosauromorphs (the crocodile-lizard, or bird-lizard, divergence) is considered one of the key calibration points for molecular analyses of tetrapod phylogeny. Saurians have a very rich Mesozoic and Cenozoic fossil record, but their late Paleozoic (Permian) record is problematic. Several Permian specimens have been referred to Sauria, but the phylogenetic affinity of some of these records remains questionable. We reexamine and review all of these specimens here, providing new data on early saurian evolution including osteohistology, and present a new morphological phylogenetic dataset. We support previous studies that find that no valid Permian record for Lepidosauromorpha, and we also reject some of the previous referrals of Permian specimens to Archosauromorpha. The most informative Permian archosauromorph is Protorosaurus speneri from the middle Late Permian of Western Europe. A historically problematic specimen from the Late Permian of Tanzania is redescribed and reidentified as a new genus and species of basal archosauromorph: Aenigmastropheus parringtoni. The supposed protorosaur Eorasaurus olsoni from the Late Permian of Russia is recovered among Archosauriformes and may be the oldest known member of the group but the phylogenetic support for this position is low. The assignment of Archosaurus rossicus from the latest Permian of Russia to the archosauromorph clade Proterosuchidae is supported. Our revision suggests a minimum fossil calibration date for the crocodile-lizard split of 254.7 Ma. The occurrences of basal archosauromorphs in the northern (30°N) and southern (55°S) parts of Pangea imply a wider paleobiogeographic distribution for the group during the Late Permian than previously appreciated. Early archosauromorph growth strategies appear to be more diverse than previously suggested based on new data on the osteohistology of Aenigmastropheus.

The endoskeletal origin of the turtle carapace

The turtle body plan, with its solid shell, deviates radically from those of other tetrapods. The dorsal part of the turtle shell, or the carapace, consists mainly of costal and neural bony plates, which are continuous with the underlying thoracic ribs and vertebrae, respectively. Because of their superficial position, the evolutionary origins of these costo-neural elements have long remained elusive. Here we show, through comparative morphological and embryological analyses, that the major part of the carapace is derived purely from endoskeletal ribs. We examine turtle embryos and find that the costal and neural plates develop not within the dermis, but within deeper connective tissue where the rib and intercostal muscle anlagen develop. We also examine the fossils of an outgroup of turtles to confirm that the structure equivalent to the turtle carapace developed independently of the true osteoderm. Our results highlight the hitherto unravelled evolutionary course of the turtle shell.

The evolutionary origins of the costal and neural bony plates of the turtle shell have long remained elusive. Here the authors show, through comparative morphological and embryological analyses, that the most of the carapace is derived from endoskeletal ribs.

Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles

The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.

The hooked element in the pes of turtles (Testudines): a global approach to exploring primary and secondary homology

The hooked element in the pes of turtles was historically identified by most palaeontologists and embryologists as a modified fifth metatarsal, and often used as evidence to unite turtles with other reptiles with a hooked element. Some recent embryological studies, however, revealed that this element might represent an enlarged fifth distal tarsal. We herein provide extensive new myological and developmental observations on the hooked element of turtles, and re-evaluate its primary and secondary homology using all available lines of evidence. Digital count and timing of development are uninformative. However, extensive myological, embryological and topological data are consistent with the hypothesis that the hooked element of turtles represents a fusion of the fifth distal tarsal with the fifth metatarsal, but that the fifth distal tarsal dominates the hooked element in pleurodiran turtles, whereas the fifth metatarsal dominates the hooked element of cryptodiran turtles. The term 'ansulate bone' is proposed to refer to hooked elements that result from the fusion of these two bones. The available phylogenetic and fossil data are currently insufficient to clarify the secondary homology of hooked elements within Reptilia.

Origin of the unique morphology of the shoulder girdle in turtles

The shoulder girdle of turtles has a triradiate morphology. Although its dorsal process represents the scapular blade, the skeletal identities of the two ventral processes remain uncertain. To elucidate the question, developmental patterns of the girdles were compared between Chinese soft-shelled turtles, chickens, and mice. Despite the morphological diversity of adults, the initial primordia of the shoulder girdles showed similar morphological patterns. The ventral two processes developed from the anlagen comparable to those of the acromion and the coracoid in other amniotes. The developmental pattern of the acromion is very similar among embryos, whereas that of the coracoid in mammals differs from that in non-mammals, implying that coracoids are not homologous between non-mammals and mammals. Therefore, amniotes have retained the ancestral pattern of the girdle anlage, and the shoulder girdle of turtles has been achieved through a transformation of the pattern in the late ontogenic period.

Middle ear cavity morphology is consistent with an aquatic origin for testudines

The position of testudines in vertebrate phylogeny is being re-evaluated. At present, testudine morphological and molecular data conflict when reconstructing phylogenetic relationships. Complicating matters, the ecological niche of stem testudines is ambiguous. To understand how turtles have evolved to hear in different environments, we examined middle ear morphology and scaling in most extant families, as well as some extinct species, using 3-dimensional reconstructions from micro magnetic resonance (MR) and submillimeter computed tomography (CT) scans. All families of testudines exhibited a similar shape of the bony structure of the middle ear cavity, with the tympanic disk located on the rostrolateral edge of the cavity. Sea Turtles have additional soft tissue that fills the middle ear cavity to varying degrees. When the middle ear cavity is modeled as an air-filled sphere of the same volume resonating in an underwater sound field, the calculated resonances for the volumes of the middle ear cavities largely fell within testudine hearing ranges. Although there were some differences in morphology, there were no statistically significant differences in the scaling of the volume of the bony middle ear cavity with head size among groups when categorized by phylogeny and ecology. Because the cavity is predicted to resonate underwater within the testudine hearing range, the data support the hypothesis of an aquatic origin for testudines, and function of the middle ear cavity in underwater sound detection.

A unified anatomy ontology of the vertebrate skeletal system

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

The head and neck anatomy of sea turtles (Cryptodira: Chelonioidea) and skull shape in Testudines

BACKGROUND

Sea turtles (Chelonoidea) are a charismatic group of marine reptiles that occupy a range of important ecological roles. However, the diversity and evolution of their feeding anatomy remain incompletely known.

METHODOLOGY/PRINCIPAL FINDINGS

Using computed tomography and classical comparative anatomy we describe the cranial anatomy in two sea turtles, the loggerhead (Caretta caretta) and Kemp's ridley (Lepidochelys kempii), for a better understanding of sea turtle functional anatomy and morphological variation. In both taxa the temporal region of the skull is enclosed by bone and the jaw joint structure and muscle arrangement indicate that palinal jaw movement is possible. The tongue is relatively small, and the hyoid apparatus is not as conspicuous as in some freshwater aquatic turtles. We find several similarities between the muscles of C. caretta and L. kempii, but comparison with other turtles suggests only one of these characters may be derived: connection of the m. adductor mandibulae internus into the Pars intramandibularis via the Zwischensehne. The large fleshy origin of the m. adductor mandibulae externus Pars superficialis from the jugal seems to be a characteristic feature of sea turtles.

CONCLUSIONS/SIGNIFICANCE

In C. caretta and L. kempii the ability to suction feed does not seem to be as well developed as that found in some freshwater aquatic turtles. Instead both have skulls suited to forceful biting. This is consistent with the observation that both taxa tend to feed on relatively slow moving but sometimes armoured prey. The broad fleshy origin of the m. adductor mandibulae externus Pars superficialis may be linked to thecheek region being almost fully enclosed in bone but the relationship is complex.

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

BACKGROUND

The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes.

RESULTS

In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation.

CONCLUSIONS

These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.

Specialization for underwater hearing by the tympanic middle ear of the turtle, Trachemys scripta elegans

Turtles, like other amphibious animals, face a trade-off between terrestrial and aquatic hearing. We used laser vibrometry and auditory brainstem responses to measure their sensitivity to vibration stimuli and to airborne versus underwater sound. Turtles are most sensitive to sound underwater, and their sensitivity depends on the large middle ear, which has a compliant tympanic disc attached to the columella. Behind the disc, the middle ear is a large air-filled cavity with a volume of approximately 0.5 ml and a resonance frequency of approximately 500 Hz underwater. Laser vibrometry measurements underwater showed peak vibrations at 500-600 Hz with a maximum of 300 µm s(-1) Pa(-1), approximately 100 times more than the surrounding water. In air, the auditory brainstem response audiogram showed a best sensitivity to sound of 300-500 Hz. Audiograms before and after removing the skin covering reveal that the cartilaginous tympanic disc shows unchanged sensitivity, indicating that the tympanic disc, and not the overlying skin, is the key sound receiver. If air and water thresholds are compared in terms of sound intensity, thresholds in water are approximately 20-30 dB lower than in air. Therefore, this tympanic ear is specialized for underwater hearing, most probably because sound-induced pulsations of the air in the middle ear cavity drive the tympanic disc.

Sequência de ossificação do sincrânio e hioide em embriões de Caiman yacare (Crocodylia, Alligatoridae)

O crânio representa uma estrutura única e complexa dos vertebrados, sendo foco relevante objeto de estudos morfológicos e sistemáticos. Embora os crocodilianos constituam um importante grupo representante dos Archosauria, nossos conhecimentos acerca de seu desenvolvimento e homologias ainda são escassos. Aqui descrevemos uma sequência detalhada de ossificação dos ossos do crânio de Caiman yacare (Daudin, 1802), objetivando contribuir com informações de foco anatômico. Coletaram-se ao acaso embriões em intervalos regulares durante todo o período de incubação, sendo estes posteriormente submetidos a protocolo de diafanização e coloração de ossos. O padrão de ossificação em C. yacare segue parâmetros gerais em répteis e outros tetrápodes. Os primeiros centros de ossificação correspondem aos ossos dérmicos, envolvidos com funções primárias como a alimentação e respiração (e.g. maxila, dentário, esplenial, angular, pterigoide, ectopterigoide e jugal, incluindo ainda os dentes). Os ossos da porção dorsal do neurocrânio se ossificam posteriormente, evidenciando uma fontanela cranial que permanece até o momento da eclosão. Os ossos parietal, frontal e opstótico possuem mais de um centro de ossificação que se fundem durante a ontogenia. O centro de ossificação do parisfenoide está ausente, e apenas um centro de ossificação está presente para o basisfenoide. A porção posterior do crânio é formada por centros de substituição do condrocrânio que se ossificam em estágios posteriores.