A Review of the Origin of Snakes

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.

Convergence, divergence, and macroevolutionary constraint as revealed by anatomical network analysis of the squamate skull, with an emphasis on snakes

Traditionally considered the earliest-diverging group of snakes, scolecophidians are central to major evolutionary paradigms regarding squamate feeding mechanisms and the ecological origins of snakes. However, quantitative analyses of these phenomena remain scarce. Herein, we therefore assess skull modularity in squamates via anatomical network analysis, focusing on the interplay between 'microstomy' (small-gaped feeding), fossoriality, and miniaturization in scolecophidians. Our analyses reveal distinctive patterns of jaw connectivity across purported 'microstomatans', thus supporting a more complex scenario of jaw evolution than traditionally portrayed. We also find that fossoriality and miniaturization each define a similar region of topospace (i.e., connectivity-based morphospace), with their combined influence imposing further evolutionary constraint on skull architecture. These results ultimately indicate convergence among scolecophidians, refuting widespread perspectives of these snakes as fundamentally plesiomorphic and morphologically homogeneous. This network-based examination of skull modularity-the first of its kind for snakes, and one of the first to analyze squamates-thus provides key insights into macroevolutionary trends among squamates, with particular implications for snake origins and evolution.

Coordinating tiny limbs and long bodies: Geometric mechanics of lizard terrestrial swimming

Although typically possessing four limbs and short bodies, lizards have evolved diverse morphologies, including elongate trunks with tiny limbs. Such forms are hypothesized to aid locomotion in cluttered/fossorial environments but propulsion mechanisms (e.g., the use of body and/or limbs to interact with substrates) and potential body/limb coordination remain unstudied. Here, we use biological experiments, a geometric theory of locomotion, and robophysical models to investigate body-limb coordination in diverse lizards. Locomotor field studies in short-limbed, elongate lizards (Brachymeles and Lerista) and laboratory studies of fully limbed lizards (Uma scoparia and Sceloporus olivaceus) and a snake (Chionactis occipitalis) reveal that body-wave dynamics can be described by a combination of standing and traveling waves; the ratio of the amplitudes of these components is inversely related to the degree of limb reduction and body elongation. The geometric theory (which replaces laborious calculation with diagrams) helps explain our observations, predicting that the advantage of traveling-wave body undulations (compared with a standing wave) emerges when the dominant thrust-generation mechanism arises from the body rather than the limbs and reveals that such soil-dwelling lizards propel via "terrestrial swimming" like sand-swimming lizards and snakes. We test our hypothesis by inducing the use of traveling waves in stereotyped lizards via modulating the ground-penetration resistance. Study of a limbed/undulatory robophysical model demonstrates that a traveling wave is beneficial when propulsion is generated by body-environment interaction. Our models could be valuable in understanding functional constraints on the evolutionary processes of elongation and limb reduction as well as advancing robot designs.

Ontogeny of the skull of the blind snake Amerotyphlops brongersmianus (Serpentes: Typhlopidae) brings new insights on snake cranial evolution

Blind snakes represent the most basal group of extant snakes and include fossorial species with unusual skeletal traits. Despite their known phylogenetic position, little is known about their ontogeny and what it might reveal about the origin of their skull anatomy. Here we describe for the first time the ontogenetic transformations of the skull of a blind snake, the typhlopid Amerotyphlops brongersmianus, including embryos and postnatal individuals. Furthermore, we provide data on the size changes relative to skull growth of the main elements of the gnathic complex. We observed that the skull of this blind snake undergoes considerable morphological change during late ontogeny. Additionally, we detected delayed development of some traits (closure of the skull roof, opisthotic-exoccipital suture, ossification of the posterior trabeculae) simultaneously with clearly peramorphic traits (development of the crista circumfenestralis, growth of the pterygoid bar). Our analysis suggests that the unique skull anatomy of blind snakes displays plesiomorphic and highly autapomorphic features, as an outcome of heterochronic processes and miniaturization, and is shaped by functional constraints related to a highly specialized feeding mechanism under the selective pressures of a fossorial lifestyle.

Eye-Transcriptome and Genome-Wide Sequencing for Scolecophidia: Implications for Inferring the Visual System of the Ancestral Snake

Molecular genetic data have recently been incorporated in attempts to reconstruct the ecology of the ancestral snake, though this has been limited by a paucity of data for one of the two main extant snake taxa, the highly fossorial Scolecophidia. Here we present and analyze vision genes from the first eye-transcriptomic and genome-wide data for Scolecophidia, for Anilios bicolor, and A. bituberculatus, respectively. We also present immunohistochemistry data for retinal anatomy and visual opsin-gene expression in Anilios. Analyzed in the context of 19 lepidosaurian genomes and 12 eye transcriptomes, the new genome-wide and transcriptomic data provide evidence for a much more reduced visual system in Anilios than in non-scolecophidian (=alethinophidian) snakes and in lizards. In Anilios, there is no evidence of the presence of 7 of the 12 genes associated with alethinophidian photopic (cone) phototransduction. This indicates extensive gene loss and many of these candidate gene losses occur also in highly fossorial mammals with reduced vision. Although recent phylogenetic studies have found evidence for scolecophidian paraphyly, the loss in Anilios of visual genes that are present in alethinophidians implies that the ancestral snake had a better-developed visual system than is known for any extant scolecophidian.

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.

Insights into skull evolution in fossorial snakes, as revealed by the cranial morphology of Atractaspis irregularis (Serpentes: Colubroidea)

Comparative osteological analyses of extant organisms provide key insight into major evolutionary transitions and phylogenetic hypotheses. This is especially true for snakes, given their unique morphology relative to other squamates and the persistent controversy regarding their evolutionary origins. However, the osteology of several major snake groups remains undescribed, thus hindering efforts to accurately reconstruct the phylogeny of snakes. One such group is the Atractaspididae, a family of fossorial colubroids. We herein present the first detailed description of the atractaspidid skull, based on fully segmented micro-computed tomography (micro-CT) scans of Atractaspis irregularis. The skull of Atractaspis presents a highly unique morphology influenced by both fossoriality and paedomorphosis. This paedomorphosis is especially evident in the jaws, palate, and suspensorium, the major elements associated with macrostomy (large-gaped feeding in snakes). Comparison to scolecophidians-a group of blind, fossorial, miniaturized snakes-in turn sheds light on current hypotheses of snake phylogeny. Features of both the naso-frontal joint and the morphofunctional system related to macrostomy refute the traditional notion that scolecophidians are fundamentally different from alethinophidians (all other extant snakes). Instead, these features support the controversial hypothesis of scolecophidians as "regressed alethinophidians," in contrast to their traditional placement as the earliest-diverging snake lineage. We propose that Atractaspis and scolecophidians fall along a morphological continuum, characterized by differing degrees of paedomorphosis. Altogether, a combination of heterochrony and miniaturization provides a mechanism for the derivation of the scolecophidian skull from an ancestral fossorial alethinophidian morphotype, exemplified by the nonminiaturized and less extreme paedomorph Atractaspis.

Locomotion and palaeoclimate explain the re-evolution of quadrupedal body form in Brachymeles lizards

Evolutionary reversals, including re-evolution of lost structures, are commonly found in phylogenetic studies. However, we lack an understanding of how these reversals happen mechanistically. A snake-like body form has evolved many times in vertebrates, and occasionally a quadrupedal form has re-evolved, including in Brachymeles lizards. We use body form and locomotion data for species ranging from snake-like to quadrupedal to address how a quadrupedal form could re-evolve. We show that large, quadrupedal species are faster at burying and surface locomotion than snake-like species, indicating a lack of expected performance trade-off between these modes of locomotion. Species with limbs use them while burying, suggesting that limbs are useful for burying in wet, packed substrates. Palaeoclimatological data suggest that Brachymeles originally evolved a snake-like form under a drier climate probably with looser soil in which it was easier to dig. The quadrupedal clade evolved as the climate became humid, where limbs and large size facilitated fossorial locomotion in packed soils.

Evolution of fossorial locomotion in the transition from tetrapod to snake-like in lizards

Dramatic evolutionary transitions in morphology are often assumed to be adaptive in a new habitat. However, these assumptions are rarely tested because such tests require intermediate forms, which are often extinct. In vertebrates, the evolution of an elongate, limbless body is generally hypothesized to facilitate locomotion in fossorial and/or cluttered habitats. However, these hypotheses remain untested because few studies examine the locomotion of species ranging in body form from tetrapod to snake-like. Here, we address these functional hypotheses by testing whether trade-offs exist between locomotion in surface, fossorial and cluttered habitats in Australian Lerista lizards, which include multiple intermediate forms. We found that snake-like species penetrated sand substrates faster than more lizard-like species, representing the first direct support of the adaptation to fossoriality hypothesis. By contrast, body form did not affect surface locomotion or locomotion through cluttered leaf litter. Furthermore, all species with hindlimbs used them during both fossorial and surface locomotion. We found no evidence of a trade-off between fossorial and surface locomotion. This may be either because Lerista employed kinematic strategies that took advantage of both axial- and limb-based propulsion. This may have led to the differential occupation of their habitat, facilitating diversification of intermediate forms.

Interrogating Genomic-Scale Data for Squamata (Lizards, Snakes, and Amphisbaenians) Shows no Support for Key Traditional Morphological Relationships

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, and amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS), phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously well-supported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a few undesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata. We comment on the origins and diversification of Squamata throughout the Mesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Cranial ontogeny of Thamnophis radix (Serpentes: Colubroidea) with a re-evaluation of current paradigms of snake skull evolution

Accurate knowledge of skeletal ontogeny in extant organisms is crucial in understanding important morpho-functional systems and in enabling inferences of the ontogenetic stage of fossil specimens. However, detailed knowledge of skeletal ontogeny is lacking for most squamates, including snakes. Very few studies have discussed postnatal development in snakes, with none incorporating data from all three major ontogenetic stages-embryonic, juvenile and adult. Here, we provide the first analysis encompassing these three ontogenetic stages for any squamate, using the first complete micro-computed tomography (micro-CT)-based segmentations of any non-adult snake, based on fresh specimens of Thamnophis radix. The most significant ontogenetic changes involve the feeding apparatus, with major elongation of the tooth-bearing elements and jaw suspensorium causing a posterior shift in the jaw articulation. This shift enables macrostomy (large-gaped feeding in snakes) and occurs in T. radix via a different developmental trajectory than in most other macrostomatans, indicating that the evolution of macrostomy is more complex than previously thought. The braincase of T. radix is also evolutionarily unique among derived snakes in lacking a crista circumfenestralis, a phenomenon considered herein to represent paedomorphic retention of the embryonic condition. We thus present numerous important challenges to current paradigms regarding snake cranial evolution.

Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes)

Caenophidian snakes include the file snake genus Acrochordus and advanced colubroidean snakes that radiated mainly during the Neogene. Although caenophidian snakes are a well-supported clade, their inferred affinities, based either on molecular or morphological data, remain poorly known or controversial. Here, we provide an expanded molecular phylogenetic analysis of Caenophidia and use three non-parametric measures of support-Shimodaira-Hasegawa-Like test (SHL), Felsentein (FBP) and transfer (TBE) bootstrap measures-to evaluate the robustness of each clade in the molecular tree. That very different alternative support values are common suggests that results based on only one support value should be viewed with caution. Using a scheme to combine support values, we find 20.9% of the 1265 clades comprising the inferred caenophidian tree are unambiguously supported by both SHL and FBP values, while almost 37% are unsupported or ambiguously supported, revealing the substantial extent of phylogenetic problems within Caenophidia. Combined FBP/TBE support values show similar results, while SHL/TBE result in slightly higher combined values. We consider key morphological attributes of colubroidean cranial, vertebral and hemipenial anatomy and provide additional morphological evidence supporting the clades Colubroides, Colubriformes, and Endoglyptodonta. We review and revise the relevant caenophidian fossil record and provide a time-calibrated tree derived from our molecular data to discuss the main cladogenetic events that resulted in present-day patterns of caenophidian diversification. Our results suggest that all extant families of Colubroidea and Elapoidea composing the present-day endoglyptodont fauna originated rapidly within the early Oligocene-between approximately 33 and 28 Mya-following the major terrestrial faunal turnover known as the "Grande Coupure" and associated with the overall climate shift at the Eocene-Oligocene boundary. Our results further suggest that the caenophidian radiation originated within the Caenozoic, with the divergence between Colubroides and Acrochordidae occurring in the early Eocene, at ~ 56 Mya.

Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry

The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole-genome and targeted capture sequencing data. We used these data to analyze gene loss and shifts in selection pressures in phototransduction genes that may be associated with snake evolutionary origins and photoreceptor transmutation. We identified the surprising loss of rhodopsin kinase (GRK1), despite a low degree of gene loss overall and a lack of relaxed selection early during snake evolution. These results provide some of the first evolutionary genomic corroboration for a dim-light ancestor that lacks strong fossorial adaptations. Our results also indicate that snakes with photoreceptor transmutation experienced significantly different selection pressures from other reptiles. Significant positive selection was found primarily in cone-specific genes, but not rod-specific genes, contrary to our expectations. These results reveal potential molecular adaptations associated with photoreceptor transmutation and also highlight unappreciated functional differences between rod- and cone-specific phototransduction proteins. This intriguing example of snake visual system evolution illustrates how the underlying molecular components of a complex system can be reshaped in response to changing selection pressures.

The bizarre skull of Xenotyphlops sheds light on synapomorphies of Typhlopoidea

The emerging picture of non-monophyly of scolecophidian snakes is increasingly indicative that fossorial lifestyle, myrmecophagous diet, and miniaturisation are powerful drivers of morphological evolution in squamate skulls. We provide a detailed description of the skull of Xenotyphlops grandidieri, with reference to the skulls of other scolecophidian snakes. The skull, which shows dramatic ventral inflection of the snout complex, is remarkably bizarre, and the mouth opening is more ventrally oriented than in other typhlopoids. The eyes are strongly reduced, and the enlarged and rather flat anterior head shield is covered in numerous sensillae. We put forward several potential explanations for the evolution of these unusual modifications. On the other hand, Xenotyphlops shares numerous synapomorphies with other typhlopoid snakes, including the highly specialized jaw mechanism. We argue that the key differences between the jaw mechanisms of Leptotyphlopidae, Anomalepididae, and Typhlopoidea provide compelling evidence for a strong role of convergence in the evolution of the scolecophidian bauplan, and these clades therefore cannot be interpreted as representative of ancestral anatomy or ecology among snakes.

Fossil snakes (Squamata, Serpentes) from the tar pits of Venezuela: taxonomic, palaeoenvironmental, and palaeobiogeographical implications for the North of South America during the Cenozoic/Quaternary boundary

Background

Tar seep deposits in South America historically are well-known for their rich record of fossil mammals, contrasting with only a few formal reports of reptile remains. Here we report a new snake fauna recovered from two tar pits from Venezuela. The fossil remains come from two localities: (a) El Breal de Orocual, which comprises an inactive tar seep estimated to be Plio/Pleistocene in age; and (b) Mene de Inciarte, an active surface asphalt deposit with an absolute age dating to the late Pleistocene.

Methods

The taxonomic identity of all specimens was assessed via consultation of the relevant literature and comparison with extant specimens. The taxonomic assignments are supported by detailed anatomical description.

Results

The Mene de Inciarte snake fauna comprises vertebral remains identified as the genus Epicrates sp. (Boidae), indeterminate viperids, and several isolated vertebrae attributable to "Colubridae" (Colubroidea, sensu Zaher et al., 2009). Amongst the vertebral assemblage at El Breal de Orocual, one specimen is assigned to the genus Corallus sp. (Boidae), another to cf. Micrurus (Elapidae), and several others to "Colubrids" (Colubroides, sensu Zaher et al., 2009) and the Viperidae family.

Conclusions

These new records provide valuable insight into the diversity of snakes in the north of South America during the Neogene/Quaternary boundary. The snake fauna of El Breal de Orocual and Mene de Inciarte demonstrates the presence of Boidae, Viperidae, "colubrids", and the oldest South American record of Elapidae. The presence of Corallus, Epicrates, and viperids corroborates the mosaic palaeoenvironmental conditions of El Breal de Orocual. The presence of Colubroides within both deposits sheds light on the palaeobiogeographical pattern of caenophidians snake colonization of South America and is consistent with the hypothesis of two episodes of dispersion of Colubroides to the continent.

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.

Postnatal ontogeny and the evolution of macrostomy in snakes

Macrostomy is the anatomical feature present in macrostomatan snakes that permits the ingestion of entire prey with high cross-sectional area. It depends on several anatomical traits in the skeleton and soft tissues, of which the elongation of gnathic complex and backward rotation of the quadrate represent crucial skeletal requirements. Here, the relevance of postnatal development of these skull structures and their relationship with macrohabitat and diet are explored. Contrary to the condition present in lizards and basal snakes that occupy underground macrohabitats, elements of the gnathic complex of most macrostomatan snakes that exploit surface macrohabitats display conspicuous elongation during postnatal growth, relative to the rest of the skull, as well as further backward rotation of the quadrate bone. Remarkably, several clades of small cryptozoic macrostomatans reverse these postnatal transformations and return to a diet based on prey with low cross-sectional area such as annelids, insects or elongated vertebrates, thus resembling the condition present in underground basal snakes. Dietary ontogenetic shift observed in most macrostomatan snakes is directly linked with this ontogenetic trajectory, indicating that this shift is acquired progressively as the gnathic complex elongates and the quadrate rotates backward during postnatal ontogeny. The numerous independent events of reversion in the gnathic complex and prey type choice observed in underground macrostomatans and the presence of skeletal requirements for macrostomy in extinct non-macrostomatan species reinforce the possibility that basal snakes represent underground survivors of clades that had the skeletal requirements for macrostomy. Taken together, the data presented here suggest that macrostomy has been shaped during multiple episodes of occupation of underground and surface macrohabitats throughout the evolution of snakes.

A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

BACKGROUND

With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61).

RESULTS

Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades.

CONCLUSION

Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes.

Patterns of postnatal ontogeny of the skull and lower jaw of snakes as revealed by micro-CT scan data and three-dimensional geometric morphometrics

We compared the head skeleton (skull and lower jaw) of juvenile and adult specimens of five snake species [Anilios (=Ramphotyphlops) bicolor, Cylindrophis ruffus, Aspidites melanocephalus, Acrochordus arafurae, and Notechis scutatus] and two lizard outgroups (Ctenophorus decresii, Varanus gilleni). All major ontogenetic changes observed were documented both qualitatively and quantitatively. Qualitative comparisons were based on high-resolution micro-CT scanning of the specimens, and detailed quantitative analyses were performed using three-dimensional geometric morphometrics. Two sets of landmarks were used, one for accurate representation of the intraspecific transformations of each skull and jaw configuration, and the other for comparison between taxa. Our results document the ontogenetic elaboration of crests and processes for muscle attachment (especially for cervical and adductor muscles); negative allometry in the braincase of all taxa; approximately isometric growth of the snout of all taxa except Varanus and Anilios (positively allometric); and positive allometry in the quadrates of the macrostomatan snakes Aspidites, Acrochordus and Notechis, but also, surprisingly, in the iguanian lizard Ctenophorus. Ontogenetic trajectories from principal component analysis provide evidence for paedomorphosis in Anilios and peramorphosis in Acrochordus. Some primitive (lizard-like) features are described for the first time in the juvenile Cylindrophis. Two distinct developmental trajectories for the achievement of the macrostomatan (large-gaped) condition in adult snakes are documented, driven either by positive allometry of supratemporal and quadrate (in pythons), or of quadrate alone (in sampled caenophidians); this is consistent with hypothesised homoplasy in this adaptive complex. Certain traits (e.g. shape of coronoid process, marginal tooth counts) are more stable throughout postnatal ontogeny than others (e.g. basisphenoid keel), with implications for their reliability as phylogenetic characters.

Osteology and Cartilaginous Elements of Trilepida salgueiroi (Amaral, 1954) (Scolecophidia: Leptotyphlopidae)

Morphological and anatomical studies on the Leptotyphlopidae have increased in the past 10 years, providing important data on the systematics of this group, mainly focused on the skull and lower jaw morphology. However, most studies are based on a single specimen, rarely combining more than one single method of assessing morphological information. Therefore, several data on postcranial morphology, sexual dimorphism, and ontogenetic and intraspecific variation of leptotyphlopids remain poorly understood. Herein, we provide a detailed description of the cranial and postcranial skeleton of Trilepida salgueiroi based on more than 20 specimens (including males, females and juveniles), as well as a description of osteology and cartilaginous elements through the use of combined methodologies such as X-ray scanning, high resolution CT-scanning, and clearing and staining of articulated and disarticulated specimens. We also provide data on the presence/absence of dimorphic and intraspecific variation of the observed characters. The presence of a statolithic mass in the cavum vestibuli differs from the pattern found in other scolecophidians. A correlation of dorsal vertebrae with ventral and subcaudal scales was found (1:1), as well as total number of vertebrae with middorsal scales (1:1), thoracolumbar vertebrae and ventral scales (1:1), and a higher number of caudal vertebra with subcaudal scales (1.23:1). Intraspecific variation was found in several elements of the skull, lower jaw, pelvic girdle and vertebral number, but no evidence of sexual dimorphism was found in any of the species characters analysed. The homologies of several elements are discussed, although still remaining poorly understood and unknown.

Visual system evolution and the nature of the ancestral snake

The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this, we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497 nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e. they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2 and SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic.

Locomotor benefits of being a slender and slick sand swimmer

Squamates classified as 'subarenaceous' possess the ability to move long distances within dry sand; body elongation among sand and soil burrowers has been hypothesized to enhance subsurface performance. Using X-ray imaging, we performed the first kinematic investigation of the subsurface locomotion of the long, slender shovel-nosed snake (Chionactis occipitalis) and compared its biomechanics with those of the shorter, limbed sandfish lizard (Scincus scincus). The sandfish was previously shown to maximize swimming speed and minimize the mechanical cost of transport during burial. Our measurements revealed that the snake also swims through sand by propagating traveling waves down the body, head to tail. Unlike the sandfish, the snake nearly followed its own tracks, thus swimming in an approximate tube of self-fluidized granular media. We measured deviations from tube movement by introducing a parameter, the local slip angle, βs, which measures the angle between the direction of movement of each segment and body orientation. The average βs was smaller for the snake than for the sandfish; granular resistive force theory (RFT) revealed that the curvature utilized by each animal optimized its performance. The snake benefits from its slender body shape (and increased vertebral number), which allows propagation of a higher number of optimal curvature body undulations. The snake's low skin friction also increases performance. The agreement between experiment and RFT combined with the relatively simple properties of the granular 'frictional fluid' make subarenaceous swimming an attractive system to study functional morphology and bauplan evolution.

Relict endemism of extant Rhineuridae (Amphisbaenia): testing for phylogenetic niche conservatism in the fossil record

Rhineurid amphisbaenians are represented by a rich Cenozoic fossil record in North America, but today conisist of a single living species restricted to the Florida Peninsula. Such relict endemism may be the result of phylogenetic niche conservatism (PNC), the retention of ancestral traits preventing expansion into new environments. Most tests of PNC derive ancestral niche preferences from species' extant ecologies, while ignoring valuable paleontological information. To test if PNC contributes to the restricted distribution of modern Rhineura floridana, we compare the species' current environmental preferences (temperature, precipitation and soil) to paleoenvironmental data from the rhineurid fossil record. We find no evidence of PNC in modern R. floridana, as it also occurred in Florida during drier glacial periods. Ancient rhineurids also exhibit tolerance to changing climates, having undergone a shift from subtropical-humid to semi-arid savanna conditions during the Eocene-Oligocene transition. However, rhineurids nearly disappear from North America after the middle Miocene, potentially due to the onset of prolonged freezing temperatures following the mid-Miocene Climatic Optimum. This physiological limit of environmental tolerances could be interpreted as PNC for the entire family, but also characterizes much of Amphisbaenia, emphasizing the relevance of the temporal as well as phylogenetic scale at which PNC is investigated.

The evolutionary history of the development of the pelvic fin/hindlimb

The arms and legs of man are evolutionarily derived from the paired fins of primitive jawed fish. Few evolutionary changes have attracted as much attention as the origin of tetrapod limbs from the paired fins of ancestral fish. The hindlimbs of tetrapods are derived from the pelvic fins of ancestral fish. These evolutionary origins can be seen in the examination of shared gene and protein expression patterns during the development of pelvic fins and tetrapod hindlimbs. The pelvic fins of fish express key limb positioning, limb bud induction and limb outgrowth genes in a similar manner to that seen in hindlimb development of higher vertebrates. We are now at a point where many of the key players in the development of pelvic fins and vertebrate hindlimbs have been identified and we can now readily examine and compare mechanisms between species. This is yielding fascinating insights into how the developmental programme has altered during evolution and how that relates to anatomical change. The role of pelvic fins has also drastically changed over evolutionary history, from playing a minor role during swimming to developing into robust weight-bearing limbs. In addition, the pelvic fins/hindlimbs have been lost repeatedly in diverse species over evolutionary time. Here we review the evolution of pelvic fins and hindlimbs within the context of the changes in anatomical structure and the molecular mechanisms involved.

Comparative skull morphology of uropeltid snakes (Alethinophidia: Uropeltidae) with special reference to disarticulated elements and variation

Uropeltids form a diverse clade of highly derived, fossorial snakes that, because of their phylogenetic position among other alethinophidian lineages, may play a key role in understanding the early evolution of cranial morphology in snakes. We include detailed osteological descriptions of crania and mandibles for eight uropeltid species from three nominal genera (Uropeltis, Rhinophis, and Brachyophidium) and emphasize disarticulated elements and the impact of intraspecific variation on previously proposed morphological characters used for phylogenetic analysis. Preliminary analysis of phylogenetic relationships strongly supports a clade composed exclusively of species of Plectrurus, Uropeltis, and Rhinophis. However, monophyly of each of those genera and Melanophidium is not upheld. There is moderate support that Sri Lankan species (e.g., Rhinophis and Uropeltis melanogaster) are monophyletic with respect to Indian uropeltids. Previously proposed characters that are phylogenetically informative include the shape of the nasals, length of the occipital condyle, level of development of the posteroventral process of the dentary, and participation of the parietal in the optic foramen. Additionally, thirty new features that may be systematically informative are identified and described, but were not verified for their utility. Such verification must await availability of additional disarticulated cranial material from a larger sample of taxa. All characters require further testing through increased focus on sources and patterns of intraspecific variation, inclusion of broader taxonomic samples in comparative studies, and exploration of skeletal development, sexual dimorphism, and biogeographic patterns. Additionally, trends in the relative enlargement of the sensory capsules, reduction in cranial ossification and dentition, fusion of elements, and the appearance of novel morphological conditions, such as the structure and location of the suspensorium, may be related to fossoriality and miniaturization in some uropeltid taxa, and may complicate analysis of relationships within Uropeltidae and among alethinophidian snakes.

Eocene lizard from Germany reveals amphisbaenian origins

Amphisbaenia is a speciose clade of fossorial lizards characterized by a snake-like body and a strongly reinforced skull adapted for head-first burrowing. The evolutionary origins of amphisbaenians are controversial, with molecular data uniting them with lacertids, a clade of Old World terrestrial lizards, whereas morphology supports a grouping with snakes and other limbless squamates. Reports of fossil stem amphisbaenians have been falsified, and no fossils have previously tested these competing phylogenetic hypotheses or shed light on ancestral amphisbaenian ecology. Here we report the discovery of a new lacertid-like lizard from the Eocene Messel locality of Germany that provides the first morphological evidence for lacertid-amphisbaenian monophyly on the basis of a reinforced, akinetic skull roof and braincase, supporting the view that body elongation and limblessness in amphisbaenians and snakes evolved independently. Morphometric analysis of body shape and ecology in squamates indicates that the postcranial anatomy of the new taxon is most consistent with opportunistically burrowing habits, which in combination with cranial reinforcement indicates that head-first burrowing evolved before body elongation and may have been a crucial first step in the evolution of amphisbaenian fossoriality.

Controversial snake relationships supported by reproductive anatomy

Since the advent of molecular character sets in phylogenetic systematics our understanding of the evolutionary history of snakes has changed considerably. In some cases the novel topologies reconstructed from molecular datasets have left researchers puzzled, as no morphological feature seems to support the new relationships found. This is the case for 'Amerophidia'sensu Vidal et al. (2007; Biology of the Boas and Pythons, Eagle Mountain: Eagle Mountain Publishing; Aniliidae+ Tropidophiidae), a grouping of the Red Pipesnakes and Neotropical Dwarf Boas. We contend that in some cases the apparent lack of historical morphological support for the molecular phylogenies is due to our poor understanding of the organisms as a whole, and not the complete lack of morphological support for controversial clades. For example, we found novel evidence from reproductive anatomy that demonstrates a unique association of the oviducts and cloaca in Amerophidia. Whereas in all other female squamates the oviducts communicate directly with the cloaca, the oviducts of Aniliidae and Tropidophiidae communicate with diverticuli of the cloaca. At present this is the only unambiguous synapomorphy for the Amerophidia. We feel that confirmation of controversial molecular relationships will revolve around the investigation of non-traditional morphological characters such as reproductive anatomy.

The molecular evolutionary tree of lizards, snakes, and amphisbaenians

Squamate reptiles (lizards, snakes, amphisbaenians) number approximately 8200 living species and are a major component of the world's terrestrial vertebrate diversity. Recent molecular phylogenies based on protein-coding nuclear genes have challenged the classical, morphology-based concept of squamate relationships, requiring new classifications, and drawing new evolutionary and biogeographic hypotheses. Even the key and long-held concept of a dichotomy between iguanians (approximately 1470 sp.) and scleroglossans (all other squamates) has been refuted because molecular trees place iguanians in a highly nested position. Together with snakes and anguimorphs, iguanians form a clade--Toxicofera--characterized by the presence of toxin secreting oral glands and demonstrating a single early origin of venom in squamates. Consequently, neither the varanid lizards nor burrowing lineages such as amphisbaenians or dibamid lizards are the closest relative of snakes. The squamate timetree shows that most major groups diversified in the Jurassic and Cretaceous, 200-66 million years (Myr) ago. In contrast, five of the six families of amphisbaenians arose during the early Cenozoic, approximately 60-40 Myr ago, and oceanic dispersal on floating islands apparently played a significant role in their distribution on both sides of the Atlantic Ocean. Among snakes, molecular data support the basic division between the small fossorial scolecophidians (approximately 370 sp.) and the alethinophidians (all other snakes, approximately 2700 sp.). They show that the alethinophidians were primitively macrostomatan and that this condition was secondarily lost by burrowing lineages. The diversification of alethinophidians resulted from a mid-Cretaceous vicariant event, the separation of South America from Africa, giving rise to Amerophidia (aniliids and tropidophiids) and Afrophidia (all other alethinophidians). Finally, molecular phylogenies have made it possible to draw a detailed evolutionary history of venom among advanced snakes (Caenophidia), a key functional innovation underlying their radiation (approximately 2500 sp.).