Enhanced contrast synchrotron X-ray microtomography for describing skeleton-associated soft tissue defects in zebrafish mutants.

Detailed histological analyses are desirable for zebrafish mutants that are models for human skeletal diseases, but traditional histological techniques are limited to two-dimensional thin sections with orientations highly dependent on careful sample preparation. On the other hand, techniques that provide three-dimensional (3D) datasets including µCT scanning are typically limited to visualizing the bony skeleton and lack histological resolution. We combined diffusible iodine-based contrast enhancement (DICE) and propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SRµCT) to image late larval and juvenile zebrafish, obtaining high-quality 3D virtual histology datasets of the mineralized skeleton and surrounding soft tissues. To demonstrate this technique, we used virtual histological thin sections and 3D segmentation to qualitatively and quantitatively compare wild-type zebrafish and nkx3.2 -/- mutants to characterize novel soft-tissue phenotypes in the muscles and tendons of the jaw and ligaments of the Weberian apparatus, as well as the sinus perilymphaticus associated with the inner ear. We could observe disrupted fiber organization and tendons of the adductor mandibulae and protractor hyoideus muscles associated with the jaws, and show that despite this, the overall muscle volumes appeared unaffected. Ligaments associated with the malformed Weberian ossicles were mostly absent in nkx3.2 -/- mutants, and the sinus perilymphaticus was severely constricted or absent as a result of the fused exoccipital and basioccipital elements. These soft-tissue phenotypes have implications for the physiology of nkx3.2 -/- zebrafish, and demonstrate the promise of DICE-PPC-SRµCT for histopathological investigations of bone-associated soft tissues in small-fish skeletal disease models and developmental studies more broadly.

At the root of the mammalian mind: The sensory organs, brain and behavior of pre-mammalian synapsids.

All modern mammals are descendants of the paraphyletic non-mammaliaform Synapsida, colloquially referred to as the "mammal-like reptiles." It has long been assumed that these mammalian ancestors were essentially reptile-like in their morphology, biology, and behavior, i.e., they had a small brain, displayed simple behavior, and their sensory organs were unrefined compared to those of modern mammals. Recent works have, however, revealed that neurological, sensory, and behavioral traits previously considered typically mammalian, such as whiskers, enhanced olfaction, nocturnality, parental care, and complex social interactions evolved before the origin of Mammaliaformes, among the early-diverging "mammal-like reptiles." In contrast, an enlarged brain did not evolve immediately after the origin of mammaliaforms. As such, in terms of paleoneurology, the last "mammal-like reptiles" were not significantly different from the earliest mammaliaforms. The abundant data and literature published in the last 10 years no longer supports the "three pulses" scenario of synapsid brain evolution proposed by Rowe and colleagues in 2011, but supports the new "outside-in" model of Rodrigues and colleagues proposed in 2018, instead. As Mesozoic reptiles were becoming the dominant taxa within terrestrial ecosystems, synapsids gradually adapted to smaller body sizes and nocturnality. This resulted in a sensory revolution in synapsids as olfaction, audition, and somatosensation compensated for the loss of visual cues. This altered sensory input is aligned with changes in the brain, the most significant of which was an increase in relative brain size.

Ecomorphological patterns in trigeminal canal branching among sauropsids reveal sensory shift in suchians.

The vertebrate trigeminal nerve is the primary mediator of somatosensory information from nerve endings across the face, extending nerve branches through bony canals in the face and mandibles, terminating in sensory receptors. Reptiles evolved several extreme forms of cranial somatosensation in which enhanced trigeminal tissues are present in species engaging in unique mechanosensory behaviors. However, morphology varies by clade and ecology among reptiles. Few lineages approach the extreme degree of tactile somatosensation possessed by crocodylians, the only remaining members of a clade that underwent an ecological transition from the terrestrial to semiaquatic habitat, also evolving a specialized trigeminal system. It remains to be understood how trigeminal osteological correlates inform how adaptations for enhanced cranial sensation evolved in crocodylians. Here we identify an increase in sensory abilities in Early Jurassic crocodylomorphs, preceding the transitions to a semiaquatic habitat. Through quantification of trigeminal neurovascular canal branching patterns in an extant phylogenetic bracket we quantify and identify morphologies associated with sensory behaviors in representative fossil taxa, we find stepwise progression of increasing neurovascular canal density, complexity, and distribution from the primitive archosaurian to the derived crocodilian condition. Model-based inferences of sensory ecologies tested on quantified morphologies of extant taxa with known sensory behaviors indicate a parallel increase in sensory abilities among pseudosuchians. These findings establish patterns of reptile trigeminal ecomorphology, revealing evolutionary patterns of somatosensory ecology.

Palate evolution in early-branching crocodylomorphs: Implications for homology, systematics, and ecomorphology.

Living crocodylomorphs have an ossified secondary palate with a posteriorly positioned choana that enables their semi-aquatic, predatory ecology. In contrast, the earliest branching members of Crocodylomorpha have an open palate with anteriorly positioned choanae. The evolution of an ossified secondary palate and a posteriorly positioned choana features strongly in hypotheses of broad-scale phylogenetic relationships within Crocodylomorpha. Renewed investigations into palatal morphology among extinct members of the clade show surprising variability in the anatomy of the palate, with at least one and potentially a second independent occurrence of "eusuchian-type" palate outside of Eusuchia. Understanding the trajectory of crocodylomorph palatal evolution is, therefore, a key to inferring crocodylomorph interrelationships and ecomorphology. To document early-branching crocodylomorph palatal anatomy, we developed an anatomical comparative dataset using computed tomography scan data and literature, comprising 12 early-branching crocodylomorph taxa. To understand discrete phenotypic changes in palatal structure, we compiled a phylogenetically broadly sampled character-taxon matrix from the existing literature, and revised its palatal characters, adding 10 new palatal characters. Our comparative anatomical investigations allow us to propose an adapted hypothesis for the closure of the palate and the posterior migration of the choana. Our phylogenetic findings corroborate previous research showing that non-crocodyliform crocodylomorphs ("sphenosuchians") are paraphyletic, with the exclusion of the clade Hallopodidae. Non-mesoeucrocodylian crocodyliforms ("protosuchians") are paraphyletic, but form three monophyletic clades: Notochampsoidea, Shartegosuchoidea, and Gobiosuchidae. We find a potential association between secondary palate development and dietary shifts, particularly with regard to hypothesized origins of herbivory.

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.

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.

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.