A Cretaceous terrestrial snake with robust hindlimbs and a sacrum

Convergent Evolution Has Led to the Loss of Claw Proteins in Snakes and Worm Lizards

The evolution of cornified skin appendages, such as hair, feathers, and claws, is closely linked to the evolution of proteins that establish the unique mechanical stability of these epithelial structures. We hypothesized that the evolution of the limbless body anatomy of the Florida worm lizard (Rhineura floridana) and the concomitant loss of claws had led to the degeneration of genes with claw-associated functions. To test this hypothesis, we investigated the evolution of three gene families implicated in epithelial cell architecture, namely type I keratins, type II keratins, and genes of the epidermal differentiation complex in R. floridana in comparison with other squamates. We report that the orthologs of mammalian hair and nail keratins have undergone pseudogenization in R. floridana. Likewise, the epidermal differentiation complex genes tentatively named EDYM1 and EDCCs have been lost in R. floridana. The aforementioned genes are conserved in various lizards with claws, but not in snakes. Proteomic analysis of the cornified claws of the bearded dragon (Pogona vitticeps) confirmed that type I and type II hair keratin homologs, EDYM1 and EDCCs, are protein components of claws in squamates. We conclude that the convergent evolution of a limbless body was associated with the convergent loss of claw keratins and differentiation genes in squamates.

Embryonic development of the pelvic girdle and hindlimb skeletal elements in Anilius scytale (Linnaeus, 1758) (Serpentes: Aniliidae)

Anilius scytale is the sister lineage of all other alethinophidian snakes. Morphology of the hind limb complex in adult A. scytale (Aniliidae) has been documented. We herein, for the first time, describe the embryology of the skeletal elements of its hind limb and pelvic girdle and contextualize the evolution of these structures. We identified pregnant females of A. scytale in the Herpetology Collection of the Museu Paraense Emílio Goeldi and separated 40 embryos. The embryos were sequentially staged using external and internal anatomy, collectively comprising a developmental series representing six stages. We cleared-stained one specimen of stages 31, 34, 36, and 37. Using the embryological information gleaned from A. scytale, we reinterpret evidence relating to the ossification of the pelvis and hindlimbs. In A. scytale hindlimb buds develop as transient structures that developed before Stage 30 and regresses in subsequent stages. There is no external or internal evidence of the forelimb or scapular girdle. From Stage 31 onwards the ischium, pubis, ilium, femur and zeugopodial cartilages are visible. Pubis and femur ossify towards the end of embryonic life, and cloacal spurs do not develop in the embryo. Skeletal elements of the hindlimb and pelvic girdle develop initially in the ventral zone of the cloaca-tail region. In subsequent stages the hindlimb and pelvic girdle elements migrate dorsally, with the pubis/ischium positioned medial to the ribs. A similar process may be associated with the achievement of the condition of the pelvic girdle in adults of scolecophidians, pythonids and boids.

Reconstructing the origin and early evolution of the snake brain

Snakes represent one-eighth of terrestrial vertebrate diversity, encompassing various lifestyles, ecologies, and morphologies. However, the ecological origins and early evolution of snakes are controversial topics in biology. To address the paucity of well-preserved fossils and the caveats of osteological traits for reconstructing snake evolution, we applied a different ecomorphological hypothesis based on high-definition brain reconstructions of extant Squamata. Our predictive models revealed a burrowing lifestyle with opportunistic behavior at the origin of crown snakes, reflecting a complex ancestral mosaic brain pattern. These findings emphasize the importance of quantitatively tracking the phenotypic diversification of soft tissues-including the accurate definition of intact brain morphological traits such as the cerebellum-in understanding snake evolution and vertebrate paleobiology. Furthermore, our study highlights the power of combining extant and extinct species, soft tissue reconstructions, and osteological traits in tracing the deep evolution of not only snakes but also other groups where fossil data are scarce.

Large-scale snake genome analyses provide insights into vertebrate development

Snakes are a remarkable squamate lineage with unique morphological adaptations, especially those related to the evolution of vertebrate skeletons, organs, and sensory systems. To clarify the genetic underpinnings of snake phenotypes, we assembled and analyzed 14 de novo genomes from 12 snake families. We also investigated the genetic basis of the morphological characteristics of snakes using functional experiments. We identified genes, regulatory elements, and structural variations that have potentially contributed to the evolution of limb loss, an elongated body plan, asymmetrical lungs, sensory systems, and digestive adaptations in snakes. We identified some of the genes and regulatory elements that might have shaped the evolution of vision, the skeletal system and diet in blind snakes, and thermoreception in infrared-sensitive snakes. Our study provides insights into the evolution and development of snakes and vertebrates.

The role of timing in the development and evolution of the limb

The term heterochrony was coined to describe changes in the timing of developmental processes relative to an ancestral state. Limb development is a well-suited system to address the contribution of heterochrony to morphological evolution. We illustrate how timing mechanisms have been used to establish the correct pattern of the limb and provide cases where natural variations in timing have led to changes in limb morphology.

Gene expression changes during the evolution of the tetrapod limb

Major changes in the vertebrate anatomy have preceded the conquest of land by the members of this taxon, and continuous changes in limb shape and use have occurred during the later radiation of tetrapods. While the main, conserved mechanisms of limb development have been discerned over the past century using a combination of classical embryological and molecular methods, only recent advances made it possible to identify and study the regulatory changes that have contributed to the evolution of the tetrapod appendage. These advances include the expansion of the model repertoire from traditional genetic model species to non-conventional ones, a proliferation of predictive mathematical models that describe gene interactions, an explosion in genomic data and the development of high-throughput methodologies. These revolutionary innovations make it possible to identify specific mutations that are behind specific transitions in limb evolution. Also, as we continue to apply them to more and more extant species, we can expect to gain a fine-grained view of this evolutionary transition that has been so consequential for our species as well.

The role of spatial heterogeneity in diversity of squamate reptiles in the Atlantic Forest highlands of southeastern Brazil

Spatial heterogeneity of vegetation is considered to be one of the most important factors that can influence species richness in a region and, therefore, an important driver for species diversity. Here, we investigate how squamate diversity varies throughout a heterogeneous area in southeastern Atlantic Forest. Our sampling site corresponded to a mosaic of forest and open fields in Curucutu nucleus, Serra do Mar State Park, São Paulo State, Southeastern Brazil. Species diversity varied throughout the mosaic in terms of species composition and relative abundance, with some species being clearly associated with a particular physiognomy. However, a decrease is observed in species richness in forest, after the rarefaction method is applied, showing that when the abundance effect is excluded, only species composition differed between physiognomies. On the other hand, both space and environmental heterogeneity were associated with diversity and distribution of squamates. Our results emphasize the importance of environmental heterogeneity, as well as the influence of the spatial location of the sample units, in structuring squamate diversity in a highland assemblage from the Atlantic Forest.

Unveiling the elusive: X-rays bring scolecophidian snakes out of the dark

Scolecophidian snakes have long posed challenges for scholars interested in elucidating their anatomy. The importance, and relative paucity, of high-quality anatomical data pertaining to scolecophidians was brought into sharp focus in the late 20^th century as part of a controversy over the phylogeny and ecological origin of snakes. The basal position of scolecophidians in the phylogeny of snakes makes their anatomy, behavior, ecology, and evolution especially important for such considerations. The depauperate fossil record for the group meant that advances in understanding their evolutionary history were necessarily tied to biogeographic distributions and anatomical interpretations of extant taxa. Osteological data, especially data pertaining to the skull and mandible, assumed a dominant role in shaping historical and modern perspectives of the evolution of scolecophidians. Traditional approaches to the exploration of the anatomy of these snakes relied heavily upon serial-sectioned specimens and cleared-and-stained specimens. The application of X-ray computed tomography (CT) to the study of scolecophidians revolutionized our understanding of the osteology of the group, and now, via diffusible iodine-based contrast-enhanced computed tomography (diceCT), is yielding data sets on internal soft anatomical features as well. CT data sets replicate many aspects of traditional anatomical preparations, are readily shared with a global community of scholars, and now are available for unique holotype and other rare specimens. The increasing prevalence and relevance of CT data sets is a strong incentive for the establishment and maintenance of permanent repositories for digital data.

Picking up the threads: Comparative osteology and associated cartilaginous elements for members of the genus Trilepida Hedges, 2011 (Serpentes, Leptotyphlopidae) with new insights on the Epictinae systematics

The threadsnakes of the family Leptotyphlopidae have been historically neglected in terms of their natural history, ecology, systematics, and morphology. Given the relevance of morphological data for resolving systematic, evolutionary, and functional issues, we aimed to provide a detailed comparative description of osteology and associated cartilaginous elements for members of the genus Trilepida. Data were obtained through high-resolution computed tomography images, cleared and stained specimens, and radiography images of a total of 47 specimens and 12 species. Both cranial and axial osteology characters exhibited a relevant degree of intraspecific variation regarding qualitative and quantitative data associated with skull and vertebrae foramina and the shape of bony sutures and processes. The high representativeness of examined species and specimens allows us to provide a comprehensive discussion on the inter- and intraspecific osteological variation, as well as a compelling osteological diagnosis for the entire genus. Trilepida spp. differ from all Epictinae by the presence of the following combination of characters: paired nasals, fused supraoccipitals (distinct from parietal, prootics, and otooccipitals), a single (fused) parietal without a dorsal fontanelle, and the basioccipital participating in the foramen magnum (except in Trilepida nicefori). Our results reinforce the need for integration of detailed anatomical traits to usually conserved external morphological data to provide accurate diagnostic features for Epictinae. In addition, new phylogenetic hypotheses or even taxonomic re-allocations may broadly benefit from these detailed comparative studies.

New opportunities and challenges of venom-based and bacteria-derived molecules for anticancer targeted therapy

Due to advances in detection and treatment of cancer, especially the rise in the targeted therapy, the five-year relative survival rate of all cancers has increased significantly. However, according to the analysis of the survival rate of cancer patients in 2019, the survival rate of most cancers is still less than five years. Therefore, to combat complex cancer and further improve the 5-year survival rate of cancer patients, it is necessary to develop some new anticancer drugs. Because of the adaptive evolution of toxic species for millions of years, the venom sac is a "treasure bank", which has millions of biomolecules with high affinity and stability awaiting further development. Complete utilization of venom-based and bacteria-derived drugs in the market is still staggering because of incomplete understanding regarding their mode of action. In this review, we focused on the currently identified targets for anticancer effects based on venomous and bacterial biomolecules, such as ion channels, membrane non-receptor molecules, integrins, and other related target molecules. This review will serve as the key for exploring the molecular mechanisms behind the anticancer potential of venom-based and bacteria-derived drugs and will also lay the path for the development of anticancer targeted therapy.

The evolution of the pectoral extrinsic appendicular and infrahyoid musculature in theropods and its functional and behavioral importance

Birds have lost and modified the musculature joining the pectoral girdle to the skull and hyoid, called the pectoral extrinsic appendicular and infrahyoid musculature. These muscles include the levator scapulae, sternomandibularis, sternohyoideus, episternocleidomastoideus, trapezius, and omohyoideus. As non-avian theropod dinosaurs are the closest relatives to birds, it is worth investigating what conditions they may have exhibited to learn when and how these muscles were lost or modified. Using extant phylogenetic bracketing, osteological correlates and non-osteological influences of these muscles are identified and discussed. Compsognathids and basal Maniraptoriformes were found to have been the likeliest transition points of a derived avian condition of losing or modifying these muscles. Increasing needs to control the feather tracts of the neck and shoulder, for insulation, display, or tightening/readjustment of the skin after dynamic neck movements may have been the selective force that drove some of these muscles to be modified into dermo-osseous muscles. The loss and modification of shoulder protractors created a more immobile girdle that would later be advantageous for flight in birds. The loss of the infrahyoid muscles freed the hyolarynx, trachea, and esophagus which may have aided in vocal tract filtering.

Adaptations and evolutionary trajectories of the snake rod and cone photoreceptors

Most vertebrates have duplex retinas, with two classes of photoreceptors, rods and cones. In the group of Snakes, however, distinct patterns of retinal morphology are associated with transitions between diurnal-nocturnal habits and reflect important adaptations of their visual system. Pure-cone, pure-rod and duplex retinas were described in different species, and this variability led Gordon Walls (1934) to formulate the transmutation theory, which suggests that rods and cones are not fixed entities, but can assume transitional states. Three opsin genes are expressed in retinas of most snake species, lws, rh1, and sws1, and recent studies have shown that the rhodopsin gene, rh1, is expressed in pure-cone retinas of diurnal snakes. This expression raised many questions about the nature of transmutation and functional aspects of the rhodopsin in a cone-like photoreceptor. Extreme differences in the retinal architecture of diurnal and nocturnal snakes also highlight the complexity of adaptations of their visual structures, which might have contributed to the adaptive radiation of this group and will be discussed in this review.

Differential locomotor and predatory strategies of Gondwanan and derived Laurasian dromaeosaurids (Dinosauria, Theropoda, Paraves): Inferences from morphometric and comparative anatomical studies

Tetrapod limbs morphology is a reliable proxy of locomotor capacities. Beyond this, other aspects of life habits, such as predation abilities, can also be relevant to determine main morphofunctional appendicular properties, which ultimately reflect a compromise between different factors of the biological role. Dromaeosauridae is a dinosaur clade belonging to Theropoda, a group of bipedal predators. Dromaeosaurids represent an interesting study case, in which the hindlimbs have been proposed to be involved in both locomotion and predation activity. A peculiar feature characterizing all dromaeosaurids is a modified second pedal digit, which is typically related to predation. This theropod group is closely related to birds and diversified during the Cretaceous Period, mainly in the Northern Hemisphere (Laurasia). However, a subclade of dromaeosaurids, the Unenlagiinae, was recently recognized for Gondwana. Nevertheless, there are morphological differences between derived Laurasian dromaeosaurids (eudromaeosaurs) and unenlagiines. Such differences are observed in the proportions between hindlimb bones and in the presence of a subarctometatarsalian condition in unenlagiines, which is mainly characterized by a proximally constricted metatarsal III. To evaluate the function of these divergent morphologies, we conducted morphometric analyses and comparisons of qualitative morphological aspects, encompassing unenlagiines, other dromaeosaurids, as well as taxa from other theropod groups, including extant birds. The former approach consisted of two phylogenetic principal component analyses, one based on the main measurements of the hindlimb, and the other focused on the lengths of the pedal phalanges. The first analysis drew the unenlagiines close to taxa with long tibiae, as well as long and slender metatarsi. Instead, eudromaeosaurs are closer to taxa with shorter tibiae, and shorter and wider metatarsi. The second analysis showed that eudromaeosaurs and unenlagiines have similar phalangeal proportions, including the elongation of distal phalanges. However, the shorter second phalanx of the pedal digit II of eudromaeosaurs could have increased the force generated by this digit, which was the main predatory tool of the autopodium. This, together with a shorter and wider metatarsus, and a marked hinge-like morphology of the articular surfaces of metatarsals and phalanges, possibly allowed eudromaeosaurs to exert a great gripping strength and hunt large prey. Conversely, the longer and slender subarctometatarsus, and less well-marked hinge joints of unenlagiines possibly gave them greater cursorial capacities. Additionally, the longer second phalanx of digit II allowed unenlagiines fast movements of this digit to hunt smaller and elusive prey. Thus, the distinctive morphological evolutionary pathways of these two dromaeosaurid clades seem to have been influenced by the particular locomotor and predatory specializations that characterized each of these lineages.

Discovery of the oldest South American fossil lizard illustrates the cosmopolitanism of early South American squamates

Squamates have an extremely long evolutionary history with a fossil record that extends into the Middle Triassic. However, most of our knowledge of their early evolutionary history is derived from Laurasian records. Therefore, fundamental questions regarding the early evolution of squamates in the Southern Hemisphere, such as the origins of the extremely diverse and endemic South American fauna, remain unanswered. Here, we describe a new lizard species that represents the oldest fossil squamate from South America, demonstrating that squamates were present on that continent at least 20 million years earlier than previously recorded. The new species represents the first occurrence of the extinct squamate family Paramacellodidae in South America and displays an unusual limb morphology. Finally, our findings suggest early South American squamates were part of a much broader distribution of their respective clades, in sharp contrast to the high levels of endemicity characteristic of modern faunas.

Geology and paleontology of the Upper Cretaceous Kem Kem Group of eastern Morocco

The geological and paleoenvironmental setting and the vertebrate taxonomy of the fossiliferous, Cenomanian-age deltaic sediments in eastern Morocco, generally referred to as the "Kem Kem beds", are reviewed. These strata are recognized here as the Kem Kem Group, which is composed of the lower Gara Sbaa and upper Douira formations. Both formations have yielded a similar fossil vertebrate assemblage of predominantly isolated elements pertaining to cartilaginous and bony fishes, turtles, crocodyliforms, pterosaurs, and dinosaurs, as well as invertebrate, plant, and trace fossils. These fossils, now in collections around the world, are reviewed and tabulated. The Kem Kem vertebrate fauna is biased toward large-bodied carnivores including at least four large-bodied non-avian theropods (an abelisaurid, Spinosaurus, Carcharodontosaurus, and Deltadromeus), several large-bodied pterosaurs, and several large crocodyliforms. No comparable modern terrestrial ecosystem exists with similar bias toward large-bodied carnivores. The Kem Kem vertebrate assemblage, currently the best documented association just prior to the onset of the Cenomanian-Turonian marine transgression, captures the taxonomic diversity of a widespread northern African fauna better than any other contemporary assemblage from elsewhere in Africa.

New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake body plan

Snakes represent one of the most dramatic examples of the evolutionary versatility of the vertebrate body plan, including body elongation, limb loss, and skull kinesis. However, understanding the earliest steps toward the acquisition of these remarkable adaptations is hampered by the very limited fossil record of early snakes. Here, we shed light on the acquisition of the snake body plan using micro-computed tomography scans of the first three-dimensionally preserved skulls of the legged snake Najash and a new phylogenetic hypothesis. These findings elucidate the initial sequence of bone loss that gave origin to the modern snake skull. Morphological and molecular analyses including the new cranial data provide robust support for an extensive basal radiation of early snakes with hindlimbs and pelves, demonstrating that this intermediate morphology was not merely a transient phase between limbed and limbless body plans.

The homologies and evolutionary reduction of the pelvis and hindlimbs in snakes, with the first report of ossified pelvic vestiges in an anomalepidid (Liotyphlops beui)

We report the first example of ossified pelvic vestiges in an anomalepidid snake, Liotyplophs beui, and provide a review of the diversity of limb and pelvic elements within Serpentes. We trace the evolution, homology and reduction of the pelvic elements and hindlimbs from the oldest known snakes through to living forms. Evolutionary analysis of the pelvic and limb data shows that the most recent common ancestor of all living snakes (Serpentes) most probably retained all three pelvic elements and rudimentary hindlimbs (femoral spurs). Subsequently, there have been multiple losses of ossified pelvic and hindlimb elements and regaining of ossified pelvic elements. Reduction of the pelvis has followed different routes in the two primary groups of living snakes (scolecophidians and alethinophidians). The single remaining rod-like element in some scolecophidians is the ischium, whereas the single remaining rod-like element in many basal alethinophidians is the pubis. Notably, many basal alethinophidians share a distinctive configuration of cloacal spur (claw), femur and a sizeable pubis, which is likely to be related functionally to the widespread use of the hindlimbs in mating and courtship, rather than the usual representation of the bones as non-functional vestiges.

The evolution of the axial skeleton intercentrum system in snakes revealed by new data from the Cretaceous snakes Dinilysia and Najash

Snakes are an extremely modified and long-lived clade of lizards that have either lost or highly altered many of the synapomorphies that would clearly link them to their closest sister-group among squamates. We focus here on one postcranial morphological complex, the intercentrum system which in most non-ophidian squamates is limited to the cervical and caudal regions. The Cervical Intercentrum System (CeIS) is composed of a single intercentral element that sometimes articulates with a ventral projection (hypapophyses) of the centrum; the Caudal Intercentrum System (CaIS) is formed by an intercentral element, the haemal arch/chevron bone, and paired ventral projections of the centrum, the haemapophyses. In modern snakes, the intercentrum element of the CeIS is considered lost or fused to the hypaphophysis, and the chevron bone in CaIS is considered lost. Here, we describe new specimens of the early snake Dinilysia patagonica, and reinterpret previously known specimens of Dinilysia and Najash rionegrina, that do not show the expected snake morphology. The anatomy of these fossil taxa unambiguously shows that free cervical and caudal intercentra attached to distinct downgrowths (hypapophyses and haemapophyses) of the centra, are present in basal fossil snakes, and agrees with the proposed loss of post atlas-axis intercentra in later evolving snakes.

Pectoral myology of limb-reduced worm lizards (Squamata, Amphisbaenia) suggests decoupling of the musculoskeletal system during the evolution of body elongation

Background

The evolution of elongated body forms in tetrapods has a strong influence on the musculoskeletal system, including the reduction of pelvic and pectoral girdles, as well as the limbs. However, despite extensive research in this area it still remains unknown how muscles within and around bony girdles are affected by these reductions. Here we investigate this issue using fossorial amphisbaenian reptiles, or worm lizards, as a model system, which show substantial variation in the degree of reductions of girdles and limbs. Using iodine-based contrast-enhanced computed tomography (diceCT), we analyze the composition of the shoulder muscles of the main clades of Amphisbaenia and their outgroups relative to the pectoral skeleton.

Results

All investigated amphisbaenian taxa retain the full set of 17 shoulder muscles, independent of the degree of limb and girdle reductions, whereas in some cases muscles are fused to complexes or changed in morphology relative to the ancestral condition. Bipes is the only taxon that retains forelimbs and an almost complete pectoral girdle. All other amphisbaenian families show more variation concerning the completeness of the pectoral girdle having reduced or absent girdle elements. Rhineura, which undergoes the most severe bone reductions, differs from all other taxa in possessing elongated muscle strands instead of discrete shoulder muscles. In all investigated amphisbaenians, the shoulder muscle agglomerate is shortened and shifted anteriorly relative to the ancestral position as seen in the outgroups.

Conclusions

Our results show that pectoral muscle anatomy does not necessarily correspond to the loss or reduction of bones, indicating a decoupling of the musculoskeletal system. Muscle attachment sites change from bones to non-skeletal areas, such as surrounding muscles, skin or connective tissue, whereas muscle origins themselves remain in the same region where the pectoral bones were ancestrally located. Our findings indicate a high degree of developmental autonomy within the musculoskeletal system, we predict that the observed evolutionary rearrangements of amphisbaenian shoulder muscles were driven by functional demands rather than by developmental constraints. Nevertheless, worm lizards display a spatial offset of both pectoral bones and muscles relative to the ancestral position, indicating severe developmental modifications of the amphisbaenian body axis.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1303-1) contains supplementary material, which is available to authorized users.

A mid-Cretaceous embryonic-to-neonate snake in amber from Myanmar

We present the first known fossilized snake embryo/neonate preserved in early Late Cretaceous (Early Cenomanian) amber from Myanmar, which at the time, was an island arc including terranes from Austral Gondwana. This unique and very tiny snake fossil is an articulated postcranial skeleton, which includes posterior precloacal, cloacal, and caudal vertebrae, and details of squamation and body shape; a second specimen preserves a fragment of shed skin interpreted as a snake. Important details of skeletal ontogeny, including the stage at which snake zygosphene-zygantral joints began to form along with the neural arch lamina, are preserved. The vertebrae show similarities to those of fossil Gondwanan snakes, suggesting a dispersal route of Gondwanan faunas to Laurasia. Finally, the new species is the first Mesozoic snake to be found in a forested environment, indicating greater ecological diversity among early snakes than previously thought.

Postcranial skeletal anatomy of the holotype and referred specimens of Buitreraptor gonzalezorum Makovicky, Apesteguía and Agnolín 2005 (Theropoda, Dromaeosauridae), from the Late Cretaceous of Patagonia

Here we provide a detailed description of the postcranial skeleton of the holotype and referred specimens of Buitreraptor gonzalezorum. This taxon was recovered as an unenlagiine dromaeosaurid in several recent phylogenetic studies and is the best represented Gondwanan dromaeosaurid discovered to date. It was preliminarily described in a brief article, but a detailed account of its osteology is emerging in recent works. The holotype is the most complete specimen yet found, so an exhaustive description of it provides much valuable anatomical information. The holotype and referred specimens preserve the axial skeleton, pectoral and pelvic girdles, and both fore- and hindlimbs. Diagnostic postcranial characters of this taxon include: anterior cervical centra exceeding the posterior limit of neural arch; eighth and ninth cervical vertebral centra with lateroventral tubercles; pneumatic foramina only in anteriormost dorsals; middle and posterior caudal centra with a complex of shallow ridges on lateral surfaces; pneumatic furcula with two pneumatic foramina on the ventral surface; scapular blade transversely expanded at mid-length; well-projected flexor process on distal end of the humerus; dorsal rim of the ilium laterally everted; and concave dorsal rim of the postacetabular iliac blade. A paleohistological study of limb bones shows that the holotype represents an earlier ontogenetic stage than one of the referred specimens (MPCA 238), which correlates with the fusion of the last sacral vertebra to the rest of the sacrum in MPCA 238. A revised phylogenetic analysis recovered Buitreraptor as an unenlagiine dromaeosaurid, in agreement with previous works. The phylogenetic implications of the unenlagiine synapomorphies and other characters, such as the specialized pedal digit II and the distal ginglymus on metatarsal II, are discussed within the evolutionary framework of Paraves.

The ecological origins of snakes as revealed by skull evolution

The ecological origin of snakes remains amongst the most controversial topics in evolution, with three competing hypotheses: fossorial; marine; or terrestrial. Here we use a geometric morphometric approach integrating ecological, phylogenetic, paleontological, and developmental data for building models of skull shape and size evolution and developmental rate changes in squamates. Our large-scale data reveal that whereas the most recent common ancestor of crown snakes had a small skull with a shape undeniably adapted for fossoriality, all snakes plus their sister group derive from a surface-terrestrial form with non-fossorial behavior, thus redirecting the debate toward an underexplored evolutionary scenario. Our comprehensive heterochrony analyses further indicate that snakes later evolved novel craniofacial specializations through global acceleration of skull development. These results highlight the importance of the interplay between natural selection and developmental processes in snake origin and diversification, leading first to invasion of a new habitat and then to subsequent ecological radiations.

Burrowing with a kinetic snout in a snake (Elapidae: Aspidelaps scutatus)

Of the few elongate, fossorial vertebrates that have been examined for their burrowing mechanics, all were found to use an akinetic, reinforced skull to push into the soil, powered mostly by trunk muscles. Reinforced skulls were considered essential for head-first burrowing. In contrast, I found that the skull of the fossorial shield-nosed cobra (Aspidelaps scutatus) is not reinforced and retains the kinetic potential typical of many non-fossorial snakes. Aspidelaps scutatus burrows using a greatly enlarged rostral scale that is attached to a kinetic snout that is independently mobile with respect to the rest of the skull. Two mechanisms of burrowing are used: (1) anteriorly directed head thrusts from a loosely bent body that is anchored against the walls of the tunnel by friction, and (2) side-to-side shovelling using the head and rostral scale. The premaxilla, to which the rostral scale is attached, lacks any direct muscle attachments. Rostral scale movements are powered by, first, retractions of the palato-pterygoid bar, mediated by a ligament that connects the anterior end of the palatine to the transverse process of the premaxilla and, second, by contraction of a previously undescribed muscle slip of the m. retractor pterygoidei that inserts on the skin at the edge of the rostral scale. In derived snakes, palatomaxillary movements are highly conserved and power prey capture and transport behaviors. Aspidelaps scutatus has co-opted those mechanisms for the unrelated function of burrowing without compromising the original feeding functions, showing the potential for evolution of functional innovations in highly conserved systems.

Genomic regression of claw keratin, taste receptor and light-associated genes provides insights into biology and evolutionary origins of snakes

Regressive evolution of anatomical traits often corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The evolutionary origins of snakes involved the regression of a number of anatomical traits, including limbs, taste buds and the visual system, and by analyzing serpent genomes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins are pseudogenized/deleted in snake genomes, providing additional evidence of claw-specificity. The second hypothesis is that snakes lack taste buds, an issue complicated by conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least one gustatory channel. The final hypothesis addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light-associated functions in snakes, demonstrating a pattern of gene loss similar to other dim light-adapted clades. Molecular dating estimates suggest that dim light adaptation preceded the loss of limbs, providing some bearing on interpretations of the ecological origins of snakes.

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.

Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution.

Snakes have many characteristics that distinguish them from their relatives. Here, Yin et al. sequence the genome of the five-pacer viper, Deinagkistrodon acutus, and use comparative genomic analyses to elucidate the evolution of transposable elements, developmental genes and sex chromosomes in snakes.

Evolutionary Developmental Biology (Evo-Devo) Research in Latin America

Famous for its blind cavefish and Darwin's finches, Latin America is home to some of the richest biodiversity hotspots of our planet. The Latin American fauna and flora inspired and captivated naturalists from the nineteenth and twentieth centuries, including such notable pioneers such as Fritz Müller, Florentino Ameghino, and Léon Croizat who made a significant contribution to the study of embryology and evolutionary thinking. But, what are the historical and present contributions of the Latin American scientific community to Evo-Devo? Here, we provide the first comprehensive overview of the Evo-Devo laboratories based in Latin America and describe current lines of research based on endemic species, focusing on body plans and patterning, systematics, physiology, computational modeling approaches, ecology, and domestication. Literature searches reveal that Evo-Devo in Latin America is still in its early days; while showing encouraging indicators of productivity, it has not stabilized yet, because it relies on few and sparsely distributed laboratories. Coping with the rapid changes in national scientific policies and contributing to solve social and health issues specific to each region are among the main challenges faced by Latin American researchers. The 2015 inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology played a pivotal role in bringing together Latin American researchers eager to initiate and consolidate regional and worldwide collaborative networks. Such networks will undoubtedly advance research on the extremely high genetic and phenotypic biodiversity of Latin America, bound to be an almost infinite source of amazement and fascinating findings for the Evo-Devo community.

An enigmatic aquatic snake from the Cenomanian of Northern South America

We report the first record of a snake from the Cretaceous of northern South America. The remains come from the La Luna Formation (La Aguada Member, Cenomanian of Venezuela) and consist of several vertebrae, which belong to the precloacal region of the vertebral column. Comparisons to extant and extinct snakes show that the remains represent a new taxon, Lunaophis aquaticus gen. et sp nov. An aquatic mode of life is supported by the ventral position of the ribs, indicating a laterally compressed body. The systematic relationships of this new taxon are difficult to determine due to the scarcity of fossil material; it is, however, a representative of an early lineage of snakes that exploited tropical marine pelagic environments, as reflected by the depositional conditions of the La Aguada Member. Lunaophis is also the first aquatic snake from the Cenomanian found outside of the African and European Tethyan and Boreal Zones.

The burrowing origin of modern snakes

Modern snakes probably originated as habitat specialists, but it controversial unclear whether they were ancestrally terrestrial burrowers or marine swimmers. We used x-ray virtual models of the inner ear to predict the habit of Dinilysia patagonica, a stem snake closely related to the origin of modern snakes. Previous work has shown that modern snakes perceive substrate vibrations via their inner ear. Our data show that D. patagonica and modern burrowing squamates share a unique spherical vestibule in the inner ear, as compared with swimmers and habitat generalists. We built predictive models for snake habit based on their vestibular shape, which estimated D. patagonica and the hypothetical ancestor of crown snakes as burrowers with high probabilities. This study provides an extensive comparative data set to test fossoriality quantitatively in stem snakes, and it shows that burrowing was predominant in the lineages leading to modern crown snakes.

A stem acrodontan lizard in the Cretaceous of Brazil revises early lizard evolution in Gondwana

Iguanians are one of the most diverse groups of extant lizards (>1,700 species) with acrodontan iguanians dominating in the Old World, and non-acrodontans in the New World. A new lizard species presented herein is the first acrodontan from South America, indicating acrodontans radiated throughout Gondwana much earlier than previously thought, and that some of the first South American lizards were more closely related to their counterparts in Africa and Asia than to the modern fauna of South America. This suggests both groups of iguanians achieved a worldwide distribution before the final breakup of Pangaea. At some point, non-acrodontans replaced acrodontans and became the only iguanians in the Americas, contrary to what happened on most of the Old World. This discovery also expands the diversity of Cretaceous lizards in South America, which with recent findings, suggests sphenodontians were not the dominant lepidosaurs in that continent as previously hypothesized.

Iguanians are a diverse group of lizards. Here, the authors report an acrodontan iguanian from the Late Cretaceous of Brazil, which suggests that this group achieved a global distribution during the Mesozoic but was replaced by non-acrodontans in the Americas.

EVOLUTION. A four-legged snake from the Early Cretaceous of Gondwana

Snakes are a remarkably diverse and successful group today, but their evolutionary origins are obscure. The discovery of snakes with two legs has shed light on the transition from lizards to snakes, but no snake has been described with four limbs, and the ecology of early snakes is poorly known. We describe a four-limbed snake from the Early Cretaceous (Aptian) Crato Formation of Brazil. The snake has a serpentiform body plan with an elongate trunk, short tail, and large ventral scales suggesting characteristic serpentine locomotion, yet retains small prehensile limbs. Skull and body proportions as well as reduced neural spines indicate fossorial adaptation, suggesting that snakes evolved from burrowing rather than marine ancestors. Hooked teeth, an intramandibular joint, a flexible spine capable of constricting prey, and the presence of vertebrate remains in the guts indicate that this species preyed on vertebrates and that snakes made the transition to carnivory early in their history. The structure of the limbs suggests that they were adapted for grasping, either to seize prey or as claspers during mating. Together with a diverse fauna of basal snakes from the Cretaceous of South America, Africa, and India, this snake suggests that crown Serpentes originated in Gondwana.

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

Background

The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new ‘tip-dating’ and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes.

Results

Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group – approximated by the Coniophis node – is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K-Pg) mass extinction, clarifying the pattern and timing of the extant snake radiation. Although the snake crown-group most likely arose on the supercontinent of Gondwana, our results suggest the possibility that the snake total-group originated on Laurasia.

Conclusions

Our study provides new insights into when, where, and how snakes originated, and presents the most complete picture of the early evolution of snakes to date. More broadly, we demonstrate the striking influence of including fossils and phenotypic data in combined analyses aimed at both phylogenetic topology inference and ancestral state reconstruction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0358-5) contains supplementary material, which is available to authorized users.

The oldest known snakes from the Middle Jurassic-Lower Cretaceous provide insights on snake evolution

The previous oldest known fossil snakes date from ~100 million year old sediments (Upper Cretaceous) and are both morphologically and phylogenetically diverse, indicating that snakes underwent a much earlier origin and adaptive radiation. We report here on snake fossils that extend the record backwards in time by an additional ~70 million years (Middle Jurassic-Lower Cretaceous). These ancient snakes share features with fossil and modern snakes (for example, recurved teeth with labial and lingual carinae, long toothed suborbital ramus of maxillae) and with lizards (for example, pronounced subdental shelf/gutter). The paleobiogeography of these early snakes is diverse and complex, suggesting that snakes had undergone habitat differentiation and geographic radiation by the mid-Jurassic. Phylogenetic analysis of squamates recovers these early snakes in a basal polytomy with other fossil and modern snakes, where Najash rionegrina is sister to this clade. Ingroup analysis finds them in a basal position to all other snakes including Najash.

The earliest colubroid-dominated snake fauna from Africa: perspectives from the Late Oligocene Nsungwe Formation of southwestern Tanzania

The extant snake fauna has its roots in faunal upheaval occurring across the Paleogene-Neogene transition. On northern continents, this turnover is well established by the late early Miocene. However, this transition is poorly documented on southern landmasses, particularly on continental Africa, where no late Paleogene terrestrial snake assemblages are documented south of the equator. Here we describe a newly discovered snake fauna from the Late Oligocene Nsungwe Formation in the Rukwa Rift Basin of Tanzania. The fauna is small but diverse with eight identifiable morphotypes, comprised of three booids and five colubroids. This fauna includes Rukwanyoka holmani gen. et sp. nov., the oldest boid known from mainland Africa. It also provides the oldest fossil evidence for the African colubroid clade Elapidae. Colubroids dominate the fauna, comprising more than 75% of the recovered material. This is likely tied to local aridification and/or seasonality and mirrors the pattern of overturn in later snake faunas inhabiting the emerging grassland environments of Europe and North America. The early emergence of colubroid dominance in the Rukwa Rift Basin relative to northern continents suggests that the pattern of overturn that resulted in extant faunas happened in a more complex fashion on continental Africa than was previously realized, with African colubroids becoming at least locally important in the late Paleogene, either ahead of or as a consequence of the invasion of colubrids. The early occurrence of elapid snakes in the latest Oligocene of Africa suggests the clade rapidly spread from Asia to Africa, or arose in Africa, before invading Europe.