Ecomorphological diversification in squamates from conserved pattern of cranial integration

Ecological limits on the decoupling of prey capture and processing in fishes

Ray-finned fishes have two jaw systems, the oral and pharyngeal jaws, which perform functions associated with prey capture and processing, respectively. The structural independence of the jaw systems is recognized as having broad implications for the functional and ecological diversity of the radiation. Cichlids (and a few other lineages) possess a modified pharyngeal jaw system that enhances prey processing versatility and capacity. This innovation, pharyngognathy, is hypothesized to have freed the oral jaws to diversify in terms of prey capture. We test the relative role of prey capture properties (e.g., evasiveness) and prey processing (e.g., crushing) in driving divergent selection in the oral and pharyngeal jaws using a macroevolutionary model fitting framework. Evolutionary outcomes were asymmetric. All transitions between different properties of prey capture had a corresponding transition in properties of prey processing. In contrast, fewer than half the transitions in the properties of prey processing had a corresponding prey capture transition. This discrepancy was further highlighted by multi-peak models that reflect the opposing function of each jaw system, which fit better than null models for oral jaw traits, but not pharyngeal jaw traits. These results suggest that pharyngeal jaw function can change independently from the function of the oral jaws, but not vice versa. This finding highlights the possibility of ecological limits to the evolutionary decoupling of jaw systems. The independent actions of prey capture and processing may be decoupled, but their respective functional demands (and evolution) are not. Therefore, prey likely impose some degree of coordinated evolution between acquisition and processing functional morphology, even in decoupled jaw systems.

A highly conserved ontogenetic limb allometry and its evolutionary significance in the adaptive radiation of Anolis lizards

Diversifications often proceed along highly conserved, evolutionary trajectories. These patterns of covariation arise in ontogeny, which raises the possibility that adaptive morphologies are biased towards trait covariations that resemble growth trajectories. Here, we test this prediction in the diverse clade of Anolis lizards by investigating the covariation of embryonic growth of 13 fore- and hindlimb bones in 15 species, and compare these to the evolutionary covariation of these limb bones across 267 Anolis species. Our results demonstrate that species differences in relative limb length are established already at hatching, and are resulting from both differential growth and differential sizes of cartilaginous anlagen. Multivariate analysis revealed that Antillean Anolis share a common ontogenetic allometry that is characterized by positive allometric growth of the long bones relative to metapodial and phalangeal bones. This major axis of ontogenetic allometry in limb bones deviated from the major axis of evolutionary allometry of the Antillean Anolis and the two clades of mainland Anolis lizards. These results demonstrate that the remarkable diversification of locomotor specialists in Anolis lizards are accessible through changes that are largely independent from ontogenetic growth trajectories, and therefore likely to be the result of modifications that manifest at the earliest stages of limb development.

How head shape and substrate particle size affect fossorial locomotion in lizards

Granular substrates ranging from silt to gravel cover much of the Earth's land area, providing an important habitat for fossorial animals. Many of these animals use their heads to penetrate the substrate. Although there is considerable variation in head shape, how head shape affects fossorial locomotor performance in different granular substrates is poorly understood. Here, head shape variation for 152 species of fossorial lizards was quantified for head diameter, slope and pointiness of the snout. The force needed to penetrate different substrates was measured using 28 physical models spanning this evolved variation. Ten substrates were considered, ranging in particle size from 0.025 to 4 mm in diameter and consisting of spherical or angular particles. Head shape evolved in a weakly correlated manner, with snouts that were gently sloped being blunter. There were also significant clade differences in head shape among fossorial lizards. Experiments with physical models showed that as head diameter increased, absolute penetration force increased but force normalized by cross-sectional area decreased. Penetration force decreased for snouts that tapered more gradually and were pointier. Larger and angular particles required higher penetration forces, although intermediate size spherical particles, consistent with coarse sand, required the lowest force. Particle size and head diameter effect were largest, indicating that fossorial burrowers should evolve narrow heads and bodies, and select relatively fine particles. However, variation in evolved head shapes and recorded penetration forces suggests that kinematics of fossorial movement are likely an important factor in explaining evolved diversity.

Phylogenetic history influences convergence for a specialized ecology: comparative skull morphology of African burrowing skinks (Squamata; Scincidae)

Background

Skulls serve many functions and as a result, are subject to many different evolutionary pressures. In squamates, many fossorial species occupy a unique region of skull morphospace, showing convergence across families, due to modifications related to head-first burrowing. As different substrates have variable physical properties, particular skull shapes may offer selective advantages in certain substrates. Despite this, studies of variation within burrowers have been limited and are typically focused on a single origin of fossoriality. We focused on seven skink genera (Acontias, Typhlosaurus, Scelotes, Sepsina, Feylinia, Typhlacontias, and Mochlus; 39 sp.) from southern Africa, encompassing at least three independent evolutions of semi-fossoriality/fossoriality. We used microCT scans and geometric morphometrics to test how cranial and mandibular shape were influenced by phylogenetic history, size, and ecology. We also qualitatively described the skulls of four species to look at variation across phylogenetic and functional levels, and assess the degree of convergence.

Results

We found a strong effect of phylogenetic history on cranial and mandibular shape, with size and substrate playing secondary roles. There was a clear gradient in morphospace from less specialized to more specialized burrowers and burrowers in sand were significantly different from those in other substrates. We also created an anatomical atlas for four species with each element described in isolation. Every bone showed some variation in shape and relative scaling of features, with the skull roofing bones, septomaxilla, vomer, and palatine showing the most variation. We showed how broad-scale convergence in traits related to fossoriality can be the result of different anatomical changes.

Conclusions

Our study used geometric morphometrics and comparative anatomy to examine how skull morphology changes for a highly specialized and demanding lifestyle. Although there was broad convergence in both shape and qualitative traits, phylogenetic history played a large role and much of this convergence was produced by different anatomical changes, implying different developmental pathways or lineage-specific constraints. Even within a single family, adaptation for a specialized ecology does not follow a singular deterministic path.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01821-w.

Size, microhabitat, and loss of larval feeding drive cranial diversification in frogs

Habitat is one of the most important factors shaping organismal morphology, but it may vary across life history stages. Ontogenetic shifts in ecology may introduce antagonistic selection that constrains adult phenotype, particularly with ecologically distinct developmental phases such as the free-living, feeding larval stage of many frogs (Lissamphibia: Anura). We test the relative influences of developmental and ecological factors on the diversification of adult skull morphology with a detailed analysis of 15 individual cranial regions across 173 anuran species, representing every extant family. Skull size, adult microhabitat, larval feeding, and ossification timing are all significant factors shaping aspects of cranial evolution in frogs, with late-ossifying elements showing the greatest disparity and fastest evolutionary rates. Size and microhabitat show the strongest effects on cranial shape, and we identify a "large size-wide skull" pattern of anuran, and possibly amphibian, evolutionary allometry. Fossorial and aquatic microhabitats occupy distinct regions of morphospace and display fast evolution and high disparity. Taxa with and without feeding larvae do not notably differ in cranial morphology. However, loss of an actively feeding larval stage is associated with higher evolutionary rates and disparity, suggesting that functional pressures experienced earlier in ontogeny significantly impact adult morphological evolution.

Skeletal variation in extant species enables systematic identification of New Zealand's large, subfossil diplodactylids

New Zealand’s diplodactylid geckos exhibit high species-level diversity, largely independent of discernible osteological changes. Consequently, systematic affinities of isolated skeletal elements (fossils) are primarily determined by comparisons of size, particularly in the identification of Hoplodactylus duvaucelii, New Zealand’s largest extant gecko species. Here, three-dimensional geometric morphometrics of maxillae (a common fossilized element) was used to determine whether consistent shape and size differences exist between genera, and if cryptic extinctions have occurred in subfossil ‘Hoplodactylus cf. duvaucelii’. Sampling included 13 diplodactylid species from five genera, and 11 Holocene subfossil ‘H. cf. duvaucelii’ individuals. We found phylogenetic history was the most important predictor of maxilla morphology among extant diplodactylid genera. Size comparisons could only differentiate Hoplodactylus from other genera, with the remaining genera exhibiting variable degrees of overlap. Six subfossils were positively identified as H. duvaucelii, confirming their proposed Holocene distribution throughout New Zealand. Conversely, five subfossils showed no clear affinities with any modern diplodactylid genera, implying either increased morphological diversity in mainland ‘H. cf. duvaucelii’ or the presence of at least one extinct, large, broad-toed diplodactylid species.

Venomous Snakes Reveal Ecological and Phylogenetic Factors Influencing Variation in Gut and Oral Microbiomes

The gastrointestinal tract (GIT) of vertebrates contains a series of organs beginning with the mouth and ending with the anus or cloacal opening. Each organ represents a unique environment for resident microorganisms. Due to their simple digestive anatomy, snakes are good models for studying microbiome variation along the GIT. Cloacal sampling captures the majority of the microbial diversity found in the GIT of snakes—yet little is known about the oral microbiota of snakes. Most research on the snake mouth and gut microbiota are limited to studies of a single species or captive-bred individuals. It therefore remains unclear how a host’s life history, diet, or evolutionary history correlate with differences in the microbial composition within the mouths and guts of wild snakes. We sampled the mouth and gut microbial communities from three species of Asian venomous snakes and utilized 16S rRNA microbial inventories to test if host phylogenetic and ecological differences correlate with distinct microbial compositions within the two body sites. These species occupy three disparate habitat types: marine, semi-arboreal, and arboreal, our results suggest that the diversity of snake mouth and gut microbial communities correlate with differences in both host ecology and phylogeny.

Cranial integration in the ring-necked parakeet, Psittacula krameri (Psittaciformes: Psittaculidae)

The study of integration and modularity aims to describe the organization of components that make up organisms, and the evolutionary, developmental and functional relationships among them. Both have been studied at the interspecific (evolutionary) and intraspecific (phenotypic and ontogenetic) levels to different degrees across various clades. Although evolutionary modularity and integration are well-characterized across birds, knowledge of intraspecific patterns is lacking. Here, we use a high-density, three-dimensional geometric morphometric approach to investigate patterns of integration and modularity in Psittacula krameri, a highly successful invasive parrot species that exhibits the derived vertical palate and cranio-facial hinge of the Psittaciformes. Showing a pattern of nine distinct cranial modules, our results support findings from recent research that uses similar methods to investigate interspecific integration in birds. Allometry is not a significant influence on cranial shape variation within this species; however, within-module integration is significantly negatively correlated with disparity, with high variation concentrated in the weakly integrated rostrum, palate and vault modules. As previous studies have demonstrated differences in beak shape between invasive and native populations, variation in the weakly integrated palate and rostrum may have facilitated evolutionary change in these parts of the skull, contributing to the ring-necked parakeet’s success as an invasive species.

The Intertwined Evolution and Development of Sutures and Cranial Morphology

Phenotypic variation across mammals is extensive and reflects their ecological diversification into a remarkable range of habitats on every continent and in every ocean. The skull performs many functions to enable each species to thrive within its unique ecological niche, from prey acquisition, feeding, sensory capture (supporting vision and hearing) to brain protection. Diversity of skull function is reflected by its complex and highly variable morphology. Cranial morphology can be quantified using geometric morphometric techniques to offer invaluable insights into evolutionary patterns, ecomorphology, development, taxonomy, and phylogenetics. Therefore, the skull is one of the best suited skeletal elements for developmental and evolutionary analyses. In contrast, less attention is dedicated to the fibrous sutural joints separating the cranial bones. Throughout postnatal craniofacial development, sutures function as sites of bone growth, accommodating expansion of a growing brain. As growth frontiers, cranial sutures are actively responsible for the size and shape of the cranial bones, with overall skull shape being altered by changes to both the level and time period of activity of a given cranial suture. In keeping with this, pathological premature closure of sutures postnatally causes profound misshaping of the skull (craniosynostosis). Beyond this crucial role, sutures also function postnatally to provide locomotive shock absorption, allow joint mobility during feeding, and, in later postnatal stages, suture fusion acts to protect the developed brain. All these sutural functions have a clear impact on overall cranial function, development and morphology, and highlight the importance that patterns of suture development have in shaping the diversity of cranial morphology across taxa. Here we focus on the mammalian cranial system and review the intrinsic relationship between suture development and morphology and cranial shape from an evolutionary developmental biology perspective, with a view to understanding the influence of sutures on evolutionary diversity. Future work integrating suture development into a comparative evolutionary framework will be instrumental to understanding how developmental mechanisms shaping sutures ultimately influence evolutionary diversity.

Comparative cranial biomechanics in two lizard species: impact of variation in cranial design

Cranial morphology in lepidosaurs is highly disparate and characterised by the frequent loss or reduction of bony elements. In varanids and geckos, the loss of the postorbital bar is associated with changes in skull shape, but the mechanical principles underlying this variation remain poorly understood. Here, we sought to determine how the overall cranial architecture and the presence of the postorbital bar relate to the loading and deformation of the cranial bones during biting in lepidosaurs. Using computer-based simulation techniques, we compared cranial biomechanics in the varanid Varanus niloticus and the teiid Salvator merianae, two large, active foragers. The overall strain magnitude and distribution across the cranium were similar in the two species, despite lower strain gradients in V. niloticus. In S. merianae, the postorbital bar is important for resistance of the cranium to feeding loads. The postorbital ligament, which in varanids partially replaces the postorbital bar, does not affect bone strain. Our results suggest that the reduction of the postorbital bar impaired neither biting performance nor the structural resistance of the cranium to feeding loads in V. niloticus. Differences in bone strain between the two species might reflect demands imposed by feeding and non-feeding functions on cranial shape. Beyond variation in cranial bone strain related to species-specific morphological differences, our results reveal that similar mechanical behaviour is shared by lizards with distinct cranial shapes. Contrary to the situation in mammals, the morphology of the circumorbital region, calvaria and palate appears to be important for withstanding high feeding loads in these lizards.

Summary:In vivo measurements and computer-based simulations of the cranial mechanics of two large lizards indicate that similar mechanical behaviour is shared by lizards with distinct cranial architecture, and show the importance of the postorbital bar in resisting the feeding loads.

How to become a crab: Phenotypic constraints on a recurring body plan

A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as "carcinization." The repeated loss of this body plan has been identified as "decarcinization." In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.

Sphenotemporal and Fronto-Orbital Dysmorphology in Unilateral Coronal Synostosis Using Geometric Morphometric Curve-Based Analysis

BACKGROUND

Geometric morphometric analysis with Procrustes superimposition is a commonly used method to characterize and study complex dysmorphology. The present study employs an advanced Procrustes-based approach to studying craniofacial dysmorphology in unilateral coronal synostosis and quantitatively describe bony patterns in this disorder, in order to better understand the associated fronto-orbital and sphenotemporal deformities.

METHODS

Forty-one unilateral coronal synostosis (UCS) patients and 41 age- and sex-matched controls underwent high-resolution computed tomography imaging. Thirty-one anatomical landmarks were labeled on each imaging set. Landmarks were used to calculate angle, lengths, and define fronto-orbital and sphenotemporal anatomical curves. A validated geometric morphometric workflow was used to perform a Procrustes superimposition to register landmarks into a common space and perform a principal components analysis.

RESULTS

Supraorbital bar curvature was significantly increased ipsilateral to the fused suture and decreased contralateral, P < 0.0001 for both sides. The sagittal sphenotemporal curve also showed ipsilateral increase in curvature (P < 0.0001) but there was no effect on the contralateral side (P > 0.05).

CONCLUSIONS

Geometric morphometric analysis revealed significant dysmorphology between UCS patients and controls. These results suggest bilateral changes in fronto-orbital curvature and ipsilateral changes in sagittal sphenotemporal curvature, which may be useful in further characterizing the dynamic craniofacial changes in UCS.

Three-dimensional geometric morphometric analysis of the skull of Protoceratops andrewsi supports a socio-sexual signalling role for the ceratopsian frill

Socio-sexual selection is predicted to be an important driver of evolution, influencing speciation, extinction and adaptation. The fossil record provides a means of testing these predictions, but detecting its signature from morphological data alone is difficult. There are, nonetheless, some specific patterns of growth and variation which are expected of traits under socio-sexual selection. The distinctive parietal-squamosal frill of ceratopsian dinosaurs has previously been suggested as a socio-sexual display trait, but evidence for this has been limited. Here, we perform a whole-skull shape analysis of an unprecedentedly large sample of specimens of Protoceratops andrewsi using a high-density landmark-based geometric morphometric approach to test four predictions regarding a potential socio-sexual signalling role for the frill. Three predictions-low integration with the rest of the skull, significantly higher rate of change in size and shape during ontogeny, and higher morphological variance than other skull regions-are supported. One prediction, sexual dimorphism in shape, is not supported, suggesting that sexual differences in P. andrewsi are likely to be small. Together, these findings are consistent with mutual mate choice or selection for signalling quality in more general social interactions, and support the hypothesis that the frill functioned as a socio-sexual signal in ceratopsian dinosaurs.

A farewell to arms and legs: a review of limb reduction in squamates

Elongated snake-like bodies associated with limb reduction have evolved multiple times throughout vertebrate history. Limb-reduced squamates (lizards and snakes) account for the vast majority of these morphological transformations, and thus have great potential for revealing macroevolutionary transitions and modes of body-shape transformation. Here we present a comprehensive review on limb reduction, in which we examine and discuss research on these dramatic morphological transitions. Historically, there have been several approaches to the study of squamate limb reduction: (i) definitions of general anatomical principles of snake-like body shapes, expressed as varying relationships between body parts and morphometric measurements; (ii) framing of limb reduction from an evolutionary perspective using morphological comparisons; (iii) defining developmental mechanisms involved in the ontogeny of limb-reduced forms, and their genetic basis; (iv) reconstructions of the evolutionary history of limb-reduced lineages using phylogenetic comparative methods; (v) studies of functional and biomechanical aspects of limb-reduced body shapes; and (vi) studies of ecological and biogeographical correlates of limb reduction. For each of these approaches, we highlight their importance in advancing our understanding, as well as their weaknesses and limitations. Lastly, we provide suggestions to stimulate further studies, in which we underscore the necessity of widening the scope of analyses, and of bringing together different perspectives in order to understand better these morphological transitions and their evolution. In particular, we emphasise the importance of investigating and comparing the internal morphology of limb-reduced lizards in contrast to external morphology, which will be the first step in gaining a deeper insight into body-shape variation.

Heading for higher ground: Developmental origins and evolutionary diversification of the amniote face

Amniotes, a clade of terrestrial vertebrates, which includes all of the descendants of the last common ancestor of the reptiles (including dinosaurs and birds) and mammals, is one of the most successful group of animals on our planet. In addition to having an egg equipped with an amnion, an adaptation to lay eggs on land, amniotes possess a number of other major morphological characteristics. Chief among them is the amniote skull, which can be classified into several major types distinguished by the presence and number of temporal fenestrae (windows) in the posterior part. Amniotes evolved from ancestors who possessed a skull composed of a complex mosaic of small bones separated by sutures. Changes in skull composition underlie much of the large-scale evolution of amniotes with many lineages showing a trend in reduction of cranial elements known as the "Williston's Law." The skull of amniotes is also arranged into a set of modules of closely co-evolving bones as revealed by modularity and integration tests. One of the most consistently recovered and at the same time most versatile modules is the "face," anatomically defined as the anterior portion of the head. The faces of amniotes display extraordinary amount of variation, with many adaptive radiations showing parallel tendencies in facial scaling, e.g., changes in length or width. This review explores the natural history of the amniote face and discusses how a better understanding of its anatomy and developmental biology helps to explain the outstanding scale of adaptive facial diversity. We propose a model for facial evolution in the amniotes, based on the differential rate of cranial neural crest cell proliferation and the timing of their skeletal differentiation.

Differing limb functions and their potential influence upon the diversification of the mustelid hindlimb skeleton

Though form-function relationships of the mammalian locomotor system have been investigated for over a century, recent models of trait evolution have hitherto been seldom used to identify likely evolutionary processes underlying the locomotor system’s morphological diversity. Using mustelids, an ecologically diverse carnivoran lineage, I investigated whether variation in hindlimb skeletal morphology functionally coincides with climbing, digging, swimming and generalized locomotor habits by using 15 linear traits of the femur, tibia, fibula, calcaneum and metatarsal III across 44 species in a principal component analysis. I subsequently fit different models of Brownian motion and adaptive trait diversification individually to each trait. Climbing, digging and swimming mustelids occupy distinct regions of phenotypic space characterized by differences in bone robustness. Models of adaptive and neutral evolution are, respectively, the best fits for long bone lengths and muscle in-levers, suggesting that different kinds of traits may be associated with different evolutionary processes. However, simulations based upon models of best fit reveal low statistical power to rank the models. Though differences in mustelid hindlimb skeletal morphology appear to coincide with locomotor habits, further study, with sampling expanded beyond the Mustelidae, is necessary to better understand to what degree adaptive evolution shapes morphological diversity of the locomotor system.

Ontogenetic origins of cranial convergence between the extinct marsupial thylacine and placental gray wolf

Phenotypic convergence, describing the independent evolution of similar characteristics, offers unique insights into how natural selection influences developmental and molecular processes to generate shared adaptations. The extinct marsupial thylacine and placental gray wolf represent one of the most extraordinary cases of convergent evolution in mammals, sharing striking cranial similarities despite 160 million years of independent evolution. We digitally reconstructed their cranial ontogeny from birth to adulthood to examine how and when convergence arises through patterns of allometry, mosaicism, modularity, and integration. We find the thylacine and wolf crania develop along nearly parallel growth trajectories, despite lineage-specific constraints and heterochrony in timing of ossification. These constraints were found to enforce distinct cranial modularity and integration patterns during development, which were unable to explain their adult convergence. Instead, we identify a developmental origin for their convergent cranial morphologies through patterns of mosaic evolution, occurring within bone groups sharing conserved embryonic tissue origins. Interestingly, these patterns are accompanied by homoplasy in gene regulatory networks associated with neural crest cells, critical for skull patterning. Together, our findings establish empirical links between adaptive phenotypic and genotypic convergence and provides a digital resource for further investigations into the developmental basis of mammalian evolution.

Weak genetic signal for phenotypic integration implicates developmental processes as major regulators of trait covariation

Phenotypic integration is an important metric that describes the degree of covariation among traits in a population, and is hypothesized to arise due to selection for shared functional processes. Our ability to identify the genetic and/or developmental underpinnings of integration is marred by temporally overlapping cell-, tissue- and structure-level processes that serve to continually 'overwrite' the structure of covariation among traits through ontogeny. Here, we examine whether traits that are integrated at the phenotypic level also exhibit a shared genetic basis (e.g. pleiotropy). We micro-CT scanned two hard tissue traits, and two soft tissue traits (mandible, pectoral girdle, atrium and ventricle, respectively) from an F5 hybrid population of Lake Malawi cichlids, and used geometric morphometrics to extract 3D shape information from each trait. Given the large degree of asymmetric variation that may reflect developmental instability, we separated symmetric from asymmetric components of shape variation. We then performed quantitative trait loci (QTL) analysis to determine the degree of genetic overlap between shapes. While we found ubiquitous associations among traits at the phenotypic level, except for a handful of notable exceptions, our QTL analysis revealed few overlapping genetic regions. Taken together, this indicates developmental interactions can play a large role in determining the degree of phenotypic integration among traits, and likely obfuscate the genotype to phenotype map, limiting our ability to gain a comprehensive picture of the genetic contributors responsible for phenotypic divergence.

First evidence of convergent lifestyle signal in reptile skull roof microanatomy

BACKGROUND

The study of convergently acquired adaptations allows fundamental insight into life's evolutionary history. Within lepidosaur reptiles-i.e. lizards, tuatara, and snakes-a fully fossorial ('burrowing') lifestyle has independently evolved in most major clades. However, despite their consistent use of the skull as a digging tool, cranial modifications common to all these lineages are yet to be found. In particular, bone microanatomy, although highly diagnostic for lifestyle, remains unexplored in the lepidosaur cranium. This constitutes a key gap in our understanding of their complexly interwoven ecology, morphology, and evolution. In order to bridge this gap, we reconstructed the acquisition of a fossorial lifestyle in 2813 lepidosaurs and assessed the skull roof compactness from microCT cross-sections in a representative subset (n = 99). We tested this and five macroscopic morphological traits for their convergent evolution.

RESULTS

We found that fossoriality evolved independently in 54 lepidosaur lineages. Furthermore, a highly compact skull roof, small skull diameter, elongate cranium, and low length ratio of frontal and parietal were repeatedly acquired in concert with a fossorial lifestyle.

CONCLUSIONS

We report a novel case of convergence that concerns lepidosaur diversity as a whole. Our findings further indicate an early evolution of fossorial modifications in the amphisbaenian 'worm-lizards' and support a fossorial origin for snakes. Nonetheless, our results suggest distinct evolutionary pathways between fossorial lizards and snakes through different contingencies. We thus provide novel insights into the evolutionary mechanisms and constraints underlying amniote diversity and a powerful tool for the reconstruction of extinct reptile ecology.

Morphological integration and modularity in the hyperkinetic feeding system of aquatic-foraging snakes

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of eight bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 μCT-scanned skulls and high-density geometric morphometric methods to address the origin and patterns of variation and integration in the feeding bones of aquatic-foraging snakes. By comparing alternate superimposition protocols allowing us to analyze the entire kinetic feeding system simultaneously, we find that the feeding bones are highly integrated, driven predominantly by functional selective pressures. The most supported pattern of modularity contains four modules, each associated with distinct functional roles: the mandible, the palatopterygoid arch, the maxilla, and the suspensorium. Further, the morphological disparity of each bone is not linked to its magnitude of integration, indicating that integration within the feeding system does not strongly constrain morphological evolution, and that adequate biomechanical solutions to a wide range of feeding ecologies and behaviors are readily evolvable within the constraint due to integration in the snake feeding system.

Phenotypic integration in feliform carnivores: Covariation patterns and disparity in hypercarnivores versus generalists

The skeleton is a complex arrangement of anatomical structures that covary to various degrees depending on both intrinsic and extrinsic factors. Among the Feliformia, many species are characterized by predator lifestyles providing a unique opportunity to investigate the impact of highly specialized hypercarnivorous diet on phenotypic integration and shape diversity. To do so, we compared the shape of the skull, mandible, humerus, and femur of species in relation to their feeding strategies (hypercarnivorous vs. generalist species) and prey preference (predators of small vs. large prey) using three-dimensional geometric morphometric techniques. Our results highlight different degrees of morphological integration in the Feliformia depending on the functional implication of the anatomical structure, with an overall higher covariation of structures in hypercarnivorous species. The skull and the forelimb are not integrated in generalist species, whereas they are integrated in hypercarnivores. These results can potentially be explained by the different feeding strategies of these species. Contrary to our expectations, hypercarnivores display a higher disparity for the skull than generalist species. This is probably due to the fact that a specialization toward high-meat diet could be achieved through various phenotypes. Finally, humeri and femora display shape variations depending on relative prey size preference. Large species feeding on large prey tend to have robust long bones due to higher biomechanical constraints.

A 3D ontogenetic atlas of Alligator mississippiensis cranial nerves and their significance for comparative neurology of reptiles

Cranial nerves are key features of the nervous system and vertebrate body plan. However, little is known about the anatomical relationships and ontogeny of cranial nerves in crocodylians and other reptiles, hampering understanding of adaptations, evolution, and development of special senses, somatosensation, and motor control of cranial organs. Here we share three dimensional (3D) models an of the cranial nerves and cranial nerve targets of embryonic, juvenile, and adult American Alligators (Alligator mississippiensis) derived from iodine-contrast CT imaging, for the first time, exploring anatomical patterns of cranial nerves across ontogeny. These data reveal the tradeoffs of using contrast-enhanced CT data as well as patterns in growth and development of the alligator cranial nervous system. Though contrast-enhanced CT scanning allows for reconstruction of numerous tissue types in a nondestructive manner, it is still limited by size and resolution. The position of alligator cranial nerves varies little with respect to other cranial structures yet grow at different rates as the skull elongates. These data constrain timing of trigeminal and sympathetic ganglion fusion and reveal morphometric differences in nerve size and path during growth. As demonstrated by these data, alligator cranial nerve morphology is useful in understanding patterns of neurological diversity and distribution, evolution of sensory and muscular innervation, and developmental homology of cranial regions, which in turn, lead to inferences of physiology and behavior.

Skull shape of a widely distributed, endangered marsupial reveals little evidence of local adaptation between fragmented populations

The biogeographic distribution of diversity among populations of threatened mammalian species is generally investigated using population genetics. However, intraspecific phenotypic diversity is rarely assessed beyond taxonomy-focused linear measurements or qualitative descriptions. Here, we use a technique widely used in the evolutionary sciences-geometric morphometrics-to characterize shape diversity in the skull of an endangered marsupial, the northern quoll, across its 5,000 km distribution range along Northern Australia. Skull shape is a proxy for feeding, behavior, and phenotypic differentiation, allowing us to ask whether populations can be distinguished and whether patterns of variation indicate adaptability to changing environmental conditions. We analyzed skull shape in 101 individuals across four mainland populations and several islands. We assessed the contribution of population, size, sex, rainfall, temperature, and geography to skull shape variation using principal component analysis, Procrustes ANOVA, and variation partitioning analyses. The populations harbor similar amounts of broadly overlapping skull shape variation, with relatively low geographic effects. Size predicted skull shape best, coinciding with braincase size variation and differences in zygomatic arches. Size-adjusted differences in populations explained less variation with far smaller effect sizes, relating to changes in the insertion areas of masticatory muscles, as well as the upper muzzle and incisor region. Climatic and geographic variables contributed little. Strikingly, the vast majority of shape variation-76%-remained unexplained. Our results suggest a uniform intraspecific scope for shape variation, possibly due to allometric constraints or phenotypic plasticity beyond the relatively strong allometric effect. The lack of local adaptation indicates that cross-breeding between populations will not reduce local morphological skull (and probably general musculoskeletal) adaptation because none exists. However, the potential for heritable morphological variation (e.g., specialization to local diets) seems exceedingly limited. We conclude that 3D geometric morphometrics can provide a comprehensive, statistically rigorous phenomic contribution to genetic-based conservation studies.

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

High-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

Decelerated dinosaur skull evolution with the origin of birds

The evolutionary radiation of birds has produced incredible morphological variation, including a huge range of skull form and function. Investigating how this variation arose with respect to non-avian dinosaurs is key to understanding how birds achieved their remarkable success after the Cretaceous-Paleogene extinction event. Using a high-dimensional geometric morphometric approach, we quantified the shape of the skull in unprecedented detail across 354 extant and 37 extinct avian and non-avian dinosaurs. Comparative analyses reveal fundamental differences in how skull shape evolved in birds and non-avian dinosaurs. We find that the overall skull shape evolved faster in non-avian dinosaurs than in birds across all regions of the cranium. In birds, the anterior rostrum is the most rapidly evolving skull region, whereas more posterior regions-such as the parietal, squamosal, and quadrate-exhibited high rates in non-avian dinosaurs. These fast-evolving elements in dinosaurs are strongly associated with feeding biomechanics, forming the jaw joint and supporting the jaw adductor muscles. Rapid pulses of skull evolution coincide with changes to food acquisition strategies and diets, as well as the proliferation of bony skull ornaments. In contrast to the appendicular skeleton, which has been shown to evolve more rapidly in birds, avian cranial morphology is characterised by a striking deceleration in morphological evolution relative to non-avian dinosaurs. These results may be due to the reorganisation of skull structure in birds-including loss of a separate postorbital bone in adults and the emergence of new trade-offs with development and neurosensory demands. Taken together, the remarkable cranial shape diversity in birds was not a product of accelerated evolution from their non-avian relatives, despite their frequent portrayal as an icon of adaptive radiations.

Phylogeny and evolution of unique skull morphologies in dietary specialist African shovel-snouted snakes (Lamprophiidae: Prosymna)

Prosymna is a specialized African snake genus lacking close relatives. The evolutionary relationships and history within Prosymna are poorly understood. Here we assembled a multi-gene data set including representatives for 11 of 16 species to investigate the phylogenetic relationships of this group. Our analyses support the monophyly of Prosymna and are congruent with species groups previously recognized on the basis of external morphology. Divergences among extant Prosymna began in the mid-Cenozoic, with the earliest divergence splitting northern from southern lineages. High-resolution computed tomography scans confirm that a specialized skull morphology is found across the genus and was probably present in the common ancestor of Prosymna. This specialization is exemplified by dentition featuring reduced anterior but greatly enlarged, blade-like posterior maxillary teeth and an unusually high degree of fusion of cranial bones. One species, P. visseri, has a hammer-like maxilla unlike that of any other known snake. Evidence for oophagy in Prosymna and the possible roles of morphological specializations in egg-slitting or egg-crushing feeding mechanisms are discussed.

Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles

The origin of phenotypic diversity among higher clades is one of the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates of evolution and phenotypic disparity across broad scales of time to understand the evolutionary dynamics behind the origin and early evolution of new clades. Here, we provide a total-evidence dating approach to this problem in diapsid reptiles. We find major chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expansion in phenotypic disparity in reptile evolution. Importantly, many instances of accelerated phenotypic evolution are detected at the origin of major clades and body plans, but not concurrent with previously proposed periods of adaptive radiation. Furthermore, strongly heterogenic rates of evolution mark the acquisition of similarly adapted functional types, and the origin of snakes is marked by the highest rates of phenotypic evolution in diapsid history.

Exploring the functional meaning of head shape disparity in aquatic snakes

Phenotypic diversity, or disparity, can be explained by simple genetic drift or, if functional constraints are strong, by selection for ecologically relevant phenotypes. We here studied phenotypic disparity in head shape in aquatic snakes. We investigated whether conflicting selective pressures related to different functions have driven shape diversity and explore whether similar phenotypes may give rise to the same functional output (i.e., many-to-one mapping of form to function). We focused on the head shape of aquatically foraging snakes as they fulfill several fitness-relevant functions and show a large amount of morphological variability. We used 3D surface scanning and 3D geometric morphometrics to compare the head shape of 62 species in a phylogenetic context. We first tested whether diet specialization and size are drivers of head shape diversification. Next, we tested for many-to-one mapping by comparing the hydrodynamic efficiency of head shape characteristic of the main axes of variation in the dataset. We 3D printed these shapes and measured the forces at play during a frontal strike. Our results show that diet and size explain only a small amount of shape variation. Shapes did not fully functionally converge as more specialized aquatic species evolved a more efficient head shape than others. The shape disparity observed could thus reflect a process of niche specialization.

Metamorphosis shapes cranial diversity and rate of evolution in salamanders

Metamorphosis is widespread across the animal kingdom and induces fundamental changes in the morphology, habitat and resources used by an organism during its lifetime. Metamorphic species are likely to experience more dynamic selective pressures through ontogeny compared with species with single-phase life cycles, which may drive divergent evolutionary dynamics. Here, we reconstruct the cranial evolution of the salamander using geometric morphometric data from 148 species spanning the order's full phylogenetic, developmental and ecological diversity. We demonstrate that life cycle influences cranial shape diversity and rate of evolution. Shifts in the rate of cranial evolution are consistently associated with transitions from biphasic to either direct-developing or paedomorphic life cycle strategies. Direct-developers exhibit the slowest rates of evolution and the lowest disparity, and paedomorphic species the highest. Species undergoing complete metamorphosis (biphasic and direct-developing) exhibit greater cranial modularity (evolutionary independence among regions) than do paedomorphic species, which undergo differential metamorphosis. Biphasic and direct-developing species also display elevated disparity relative to the evolutionary rate for bones associated with feeding, whereas this is not the case for paedomorphic species. Metamorphosis has profoundly influenced salamander cranial evolution, requiring greater autonomy of cranial elements and facilitating the rapid evolution of regions that are remodelled through ontogeny. Rather than compounding functional constraints on variation, metamorphosis seems to have promoted the morphological evolution of salamanders over 180 million years, which may explain the ubiquity of this complex life cycle strategy across disparate organisms.

Cranial integration in the fire salamander, Salamandra salamandra (Caudata: Salamandridae)

Phenotypic integration and modularity are concepts that represent the pattern of connectivity of morphological structures within an organism. Integration describes the coordinated variation of traits, and analyses of these relationships among traits often reveals the presence of modules, sets of traits that are highly integrated but relatively independent of other traits. Phenotypic integration and modularity have been studied at both the evolutionary and static level across a variety of clades, although most studies thus far are focused on amniotes, and especially mammals. Using a high-dimensional geometric morphometric approach, we investigated the pattern of cranial integration and modularity of the Italian fire salamander (Salamandra salamandra giglioli). We recovered a highly modular pattern, but this pattern did not support either entirely developmental or functional hypotheses of cranial organisation, possibly reflecting complex interactions amongst multiple influencing factors. We found that size had no significant effect on cranial shape, and that morphological variance of individual modules had no significant relationship with degree of within-module integration. The pattern of cranial integration in the fire salamander is similar to that previously recovered for caecilians, with highly integrated jaw suspensorium and occipital regions, suggesting possible conservation of patterns across lissamphibians.

Reproductive phenotype predicts adult bite-force performance in sex-reversed dragons (Pogona vitticeps)

Sex-related differences in morphology and behavior are well documented, but the relative contributions of genes and environment to these traits are less well understood. Species that undergo sex reversal, such as the central bearded dragon (Pogona vitticeps), offer an opportunity to better understand sexually dimorphic traits because sexual phenotypes can exist on different chromosomal backgrounds. Reproductively female dragons with a discordant sex chromosome complement (sex reversed), at least as juveniles, exhibit traits in common with males (e.g., longer tails and greater boldness). However, the impact of sex reversal on sexually dimorphic traits in adult dragons is unknown. Here, we investigate the effect of sex reversal on bite-force performance, which may be important in resource acquisition (e.g., mates and/or food). We measured body size, head size, and bite force of the three sexual phenotypes in a colony of captive animals. Among adults, we found that males (ZZm) bite more forcefully than either chromosomally concordant females (ZWf) or sex-reversed females (ZZf), and this difference is associated with having relatively larger head dimensions. Therefore, adult sex-reversed females, despite apparently exhibiting male traits as juveniles, do not develop the larger head and enhanced bite force of adult male bearded dragons. This pattern is further illustrated in the full sample by a lack of positive allometry of bite force in sex-reversed females that is observed in males. The results reveal a close association between reproductive phenotype and bite force performance, regardless of sex chromosome complement.

Sex biases in bird and mammal natural history collections

Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.

High-Density Morphometric Analysis of Shape and Integration: The Good, the Bad, and the Not-Really-a-Problem

The field of comparative morphology has entered a new phase with the rapid generation of high-resolution three-dimensional (3D) data. With freely available 3D data of thousands of species, methods for quantifying morphology that harness this rich phenotypic information are quickly emerging. Among these techniques, high-density geometric morphometric approaches provide a powerful and versatile framework to robustly characterize shape and phenotypic integration, the covariances among morphological traits. These methods are particularly useful for analyses of complex structures and across disparate taxa, which may share few landmarks of unambiguous homology. However, high-density geometric morphometrics also brings challenges, for example, with statistical, but not biological, covariances imposed by placement and sliding of semilandmarks and registration methods such as Procrustes superimposition. Here, we present simulations and case studies of high-density datasets for squamates, birds, and caecilians that exemplify the promise and challenges of high-dimensional analyses of phenotypic integration and modularity. We assess: (1) the relative merits of "big" high-density geometric morphometrics data over traditional shape data; (2) the impact of Procrustes superimposition on analyses of integration and modularity; and (3) differences in patterns of integration between analyses using high-density geometric morphometrics and those using discrete landmarks. We demonstrate that for many skull regions, 20-30 landmarks and/or semilandmarks are needed to accurately characterize their shape variation, and landmark-only analyses do a particularly poor job of capturing shape variation in vault and rostrum bones. Procrustes superimposition can mask modularity, especially when landmarks covary in parallel directions, but this effect decreases with more biologically complex covariance patterns. The directional effect of landmark variation on the position of the centroid affects recovery of covariance patterns more than landmark number does. Landmark-only and landmark-plus-sliding-semilandmark analyses of integration are generally congruent in overall pattern of integration, but landmark-only analyses tend to show higher integration between adjacent bones, especially when landmarks placed on the sutures between bones introduces a boundary bias. Allometry may be a stronger influence on patterns of integration in landmark-only analyses, which show stronger integration prior to removal of allometric effects compared to analyses including semilandmarks. High-density geometric morphometrics has its challenges and drawbacks, but our analyses of simulated and empirical datasets demonstrate that these potential issues are unlikely to obscure genuine biological signal. Rather, high-density geometric morphometric data exceed traditional landmark-based methods in characterization of morphology and allow more nuanced comparisons across disparate taxa. Combined with the rapid increases in 3D data availability, high-density morphometric approaches have immense potential to propel a new class of studies of comparative morphology and phenotypic integration.

A Practical Guide to Sliding and Surface Semilandmarks in Morphometric Analyses

Advances in imaging technologies, such as computed tomography (CT) and surface scanning, have facilitated the rapid generation of large datasets of high-resolution three-dimensional (3D) specimen reconstructions in recent years. The wealth of phenotypic information available from these datasets has the potential to inform our understanding of morphological variation and evolution. However, the ever-increasing ease of compiling 3D datasets has created an urgent need for sophisticated methods of capturing high-density shape data that reflect the biological complexity in form. Landmarks often do not take full advantage of the rich shape information available from high-resolution 3D specimen reconstructions, as they are typically restricted to sutures or processes that can be reliably identified across specimens and exclude most of the surface morphology. The development of sliding and surface semilandmark techniques has greatly enhanced the quantification of shape, but their application to diverse datasets can be challenging, especially when dealing with the variable absence of some regions within a structure. Using comprehensive 3D datasets of crania that span the entire clades of birds, squamates and caecilians, we demonstrate methods for capturing morphology across incredibly diverse shapes. We detail many of the difficulties associated with applying semilandmarks to comparable regions across highly disparate structures, and provide solutions to some of these challenges, while considering the consequences of decisions one makes in applying these approaches. Finally, we analyze the benefits of high-density sliding semilandmark approaches over landmark-only studies for capturing shape across diverse organisms and discuss the promise of these approaches for the study of organismal form.