Blindsnake evolutionary tree reveals long history on Gondwana

Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic

Background

Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups.

Methods

We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found.

Results

Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.

The colonisation of Madagascar by land-bound vertebrates

Despite discussions extending back almost 160 years, the means by which Madagascar's iconic land vertebrates arrived on the island remains the focus of active debate. Three options have been considered: vicariance, range expansion across land bridges, and dispersal over water. The first assumes that a group (clade/lineage) occupied the island when it was connected with the other Gondwana landmasses in the Mesozoic. Causeways to Africa do not exist today, but have been proposed by some researchers for various times in the Cenozoic. Over-water dispersal could be from rafting on floating vegetation (flotsam) or by swimming/drifting. A recent appraisal of the geological data supported the idea of vicariance, but found nothing to justify the notion of past causeways. Here we review the biological evidence for the mechanisms that explain the origins of 28 of Madagascar's land vertebrate clades [two other lineages (the geckos Geckolepis and Paragehyra) could not be included in the analysis due to phylogenetic uncertainties]. The podocnemid turtles and typhlopoid snakes are conspicuous for they appear to have arisen through a deep-time vicariance event. The two options for the remaining 26 (16 reptile, five land-bound-mammal, and five amphibian), which arrived between the latest Cretaceous and the present, are dispersal across land bridges or over water. As these would produce very different temporal influx patterns, we assembled and analysed published arrival times for each of the groups. For all, a 'colonisation interval' was generated that was bracketed by its 'stem-old' and 'crown-young' tree-node ages; in two instances, the ranges were refined using palaeontological data. The synthesis of these intervals for all clades, which we term a colonisation profile, has a distinctive shape that can be compared, statistically, to various models, including those that assume the arrivals were focused in time. The analysis leads us to reject the various land bridge models (which would show temporal concentrations) and instead supports the idea of dispersal over water (temporally random). Therefore, the biological evidence is now in agreement with the geological evidence, as well as the filtered taxonomic composition of the fauna, in supporting over-water dispersal as the mechanism that explains all but two of Madagascar's land-vertebrate groups.

Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons

Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.

Revealing the cryptic diversity of the widespread and poorly known South American blind snake genus Amerotyphlops (Typhlopidae: Scolecophidia) through integrative taxonomy

Morphological stasis is generally associated with relative constancy in ecological pressures throughout time, producing strong stabilizing selection that retains similar shared morphology. Although climate and vegetation are commonly the main key factors driving diversity and phenotypic diversification in terrestrial vertebrates, fossorial organisms have their morphology mostly defined by their fossorial lifestyle. Among these secretive fossorial organisms, blind snakes of the South American genus Amerotyphlops are considered poorly studied when compared to other taxa. Here, we evaluate the cryptic diversity of Amerotyphlops using phylogenetic and multivariate approaches. We based our phylogenetic analysis on a molecular dataset composed of 12 gene fragments (eight nuclear and four mitochondrial) for 109 species of Typhlopidae. The multivariate analysis was implemented using 36 morphological variables for 377 specimens of Amerotyphlops. Additionally, we contrast our phylogenetic result with the morphological variation found in cranial, external and hemipenial traits. Our phylogenetic results recovered with strong support the following monophyletic groups within Amerotyphlops: (1) a clade formed by A. tasymicris and A. minuisquamus; (2) a clade composed of A. reticulatus; (3) a north-eastern Brazilian clade including A. yonenagae, A. arenensis, A. paucisquamus and A. amoipira; and (4) a clade composed of A. brongersmianus and a complex of cryptic species. Based on these results we describe four new species of Amerotyphlops from north-eastern and south-eastern Brazil, which can be distinguished from the morphologically similar species, A. brongersmianus and A. arenensis.

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.

A new species of Gerrhopilus (family: Gerrhopilidae), with comments on the taxonomic status of Gerrhopilus ater suturalis (Brongersma)

The genus Gerrhopilus is briefly reviewed with a reevaluation of Gerrhopilus ater suturalis and its elevation to full species. In addition, a new species from Sumatra is described based on a single specimen, one of the three species of Gerrhopilus having both an inferior preocular and inferior ocular, and further distinguishable by the supralabial overlap pattern.

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.

The status of the anomalepidid snake Liotyphlops albirostris and the revalidation of three taxa based on morphology and ecological niche models

Liotyphlops is a genus of blindsnakes distributed in Central and South America. We reviewed specimens of Liotyphlops albirostris along its current distribution range and, based on morphological data and ecological niche modeling analyses, we restrict the geographical range of L. albirostris and validate three previously described species. In this revision, we describe the morphological variation in the populations from Panamá, Colombia, Ecuador, and Venezuela, and propose a new taxonomic arrangement. We revalidate three previous synonyms of L. albirostris to full species status, while dividing the populations from Colombia in two subspecies-one attributed to a previously recognized species from the Caribbean region, and a new one from the Andean region. The new species differs from L. albirostris from Panamá in cephalic scale arrangements that effectively reduces the previously reported variability of these scales in L. albirostris. We also explore some osteological differences that are congruent with the variation observed. We hope that the recognition of these new species better represents the diversity within Liotyphlops, helping to bring these new species out of their cryptic status so that they will be considered in future conservation efforts.

The herpetological contributions of Richard Thomas

John Paul Richard Thomas is among the living herpetologists to have described the greatest number of new species of amphibians and reptiles, and his contributions to the herpetology of the West Indies, particularly the Greater Antilles, have been exceptional. His academic career followed an unusual path, having established a strong reputation and described 50 new taxa prior to beginning his doctoral studies. His career was strongly influenced by Albert Schwartz and later was characterized by extensive and fruitful collaboration with S. Blair Hedges. Thomas' contributions to the study of blind snakes have been noteworthy. In addition to describing 28 species of scolecophidians he has been a keen observer of blind snake morphology and his 1976 dissertation remains a valuable source of osteological data. We outline some of the highlights of the career of Richard Thomas and provide a bibliography of his scientific works and a listing of the 108 taxa of amphibians and reptiles described by him.

Burrowing in blindsnakes: A preliminary analysis of burrowing forces and consequences for the evolution of morphology

Burrowing is a common behavior in vertebrates. An underground life-style offers many advantages but also poses important challenges including the high energetic cost of burrowing. Scolecophidians are a group of morphologically derived subterranean snakes that show great diversity in form and function. Although it has been suggested that leptotyphlopids and anomalepidids mostly use existing underground passageways, typhlopids are thought to create their own burrows. However, the mechanisms used to create burrows and the associated forces that animals may be able to generate remain unknown. Here, we provide the first data on push forces in scolecophidians and compare them with those in some burrowing alethinophidian snakes. Our results show that typhlopids are capable of generating higher forces for a given size than other snakes. The observed differences are not due to variation in body diameter or length, suggesting fundamental differences in the mechanics of burrowing or the way in which axial muscles are used. Qualitative observations of skull and vertebral shape suggest that the higher forces exerted by typhlopids may have impacted the evolution of their anatomy. Our results provide the basis for future studies exploring the diversity of form and function in this fascinating group of animals. Quantitative comparisons of the cranial and vertebral shape in addition to collecting functional and ecological data on a wider array of species would be particularly important to test the patterns described here.

Digging into blindsnakes' morphology: Description of the skull, lower jaw, and cervical vertebrae of two Amerotyphlops (Hedges et al., 2014) (Serpentes, Typhlopidae) with comments on the typhlopoidean skull morphological diversity

Scolecophidians are small fossorial snakes that exhibit several osteological innovations, most of which driven by their extreme body miniaturization. Considering that data on skull morphology has proven to be relevant in terms of scolecophidian systematics and morphofunctional evolution, herein, we aim to describe in detail the skull, lower jaw, and cervical vertebrae of Amerotyphlops brongersmianus and A. reticulatus. Our results suggest that the investigated osteology of Amerotyphlops resembles several new world typhlopid species, with reduced interspecific variation in the basicranium, lower jaw and cervical vertebrae. Both species exhibit characters states that are typically conserved intragenerically amongst typhlopoids, such as the presence of a single parietal, paired supraoccipitals, and otooccipitals that are in contact medially, and the basioccipital participating in the formation of the foramen magnum. We discuss possible systematically important osteological skull variations among typhlopoids and provide a comprehensive comparison of these taxa based on literature and data gathered herein.

India's biogeographic history through the eyes of blindsnakes- filling the gaps in the global typhlopoid phylogeny

The Indian subcontinent's unique geological history is reflected in the diverse assemblage of its biota. The blindsnake superfamily Typhlopoidea, with its unique mix of ancient as well as younger lineages in Asia, provides an opportunity to understand the various biotic exchange scenarios proposed for the Indian landmass. In this study, we aim to understand the biogeographic origins of the four genera of typhlopoids found in India and to decipher their times and modes of arrival in the subcontinent. Five nuclear markers were sequenced for 12 samples collected from across India, encompassing all four genera under study. Published sequences of typhlopoid genera were compiled and combined with Indian sequences to generate a global dataset. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference methods. Divergence times were estimated using BEAST 1.8.2. Ancestral geographical ranges were estimated using DEC + J, implemented in BioGeoBEARS. Divergence time estimates suggest that Gerrhopilus is an ancient lineage, and the lineage leading to it was present on the Indian landmass since the last 100 million years. The other three genera are more recent dispersals into India, possibly trans-oceanic. Biogeographic reconstructions suggest an East Gondwanan origin for Typhlopoidea, an African origin for Grypotyphlops and an Asian origin for Indotyphlops and Argyrophis. It appears that India harbours a combination of ancient and more recently dispersed lineages of typhlopoids. The genus Gerrhopilus is of Gondwanan origin that likely dispersed out of India into Southeast Asia. The other genera are intrusive elements that dispersed into India from Africa (Grypotyphlops) and Asia (Indotyphlops and possibly Argyrophis) post break-up of Gondwana. Thus, our study provides further evidence on the ability of blindsnakes to undergo long distance trans-oceanic dispersal. Results also suggest an Asian origin for typhlopoids from Australasia, Philippines and Wallacea.

Cretaceous Blind Snake from Brazil Fills Major Gap in Snake Evolution

Blind snakes (Scolecophidia) are minute cryptic snakes that diverged at the base of the evolutionary radiation of modern snakes. They have a scant fossil record, which dates back to the Upper Paleocene-Lower Eocene (∼56 Ma); this late appearance conflicts with molecular evidence, which suggests a much older origin for the group (during the Mesozoic: 160–125 Ma). Here we report a typhlopoid blind snake from the Late Cretaceous of Brazil, Boipeba tayasuensis gen. et sp. nov, which extends the scolecophidian fossil record into the Mesozoic and reduces the fossil gap predicted by molecular data. The new species is estimated to have been over 1 m long, much larger than typical modern scolecophidians (<30 cm). This finding sheds light on the early evolution of blind snakes, supports the hypothesis of a Gondwanan origin for the Typhlopoidea, and indicates that early scolecophidians had large body size, and only later underwent miniaturization.

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Boipeba tayasuensis is the oldest fossil blind snake from the Late Cretaceous of Brazil

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A new phylogenetic analysis places the taxon within living typhlopoids

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Boipeba is estimated to be ∼1 m in length, larger than any living blind snake

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The small body size of extant blind snakes is due to subsequent miniaturization

The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian

Background

Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65–62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles.

Results

Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations.

Conclusions

Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.

Origins of Afrotropical freshwater fishes

The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.

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).

Moving beyond the surface: Comparative head and neck myology of threadsnakes (Epictinae, Leptotyphlopidae, Serpentes), with comments on the 'scolecophidian' muscular system

Studies on the cephalic myology of snakes provide a series of relevant data on their biology and systematics. Despite the great amount of descriptive studies currently available for the group, much of the knowledge remains obscure for most scolecophidian taxa. This study aimed to describe in detail the cephalic (head and neck) myology of members of the tribe Epictinae, Leptotyphlopidae. We provide the first report of the presence of extrinsic ocular muscles, and a double Musculus pterygoideus acessorius in Leptotyphlopidae. A well-developed M. levator anguli oris is exclusive to the subtribes Renina and Epictina, being reduced in Tetracheilostomina species. Both inter- and intraspecific variations are reported for the head and neck muscles, and such results provide additional data and raise an interesting discussion on the neck-trunk boundaries in snakes. We also provide a discussion on the terminology of a few head muscles in Leptoyphlopidae in comparison to the other lineages of ´Scolecophidia´ (Anomalepididae and Typhlopoidea).

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.

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.

Biogeography of worm lizards (Amphisbaenia) driven by end-Cretaceous mass extinction

Worm lizards (Amphisbaenia) are burrowing squamates that live as subterranean predators. Their underground existence should limit dispersal, yet they are widespread throughout the Americas, Europe and Africa. This pattern was traditionally explained by continental drift, but molecular clocks suggest a Cenozoic diversification, long after the break-up of Pangaea, implying dispersal. Here, we describe primitive amphisbaenians from the North American Palaeocene, including the oldest known amphisbaenian, and provide new and older molecular divergence estimates for the clade, showing that worm lizards originated in North America, then radiated and dispersed in the Palaeogene following the Cretaceous-Palaeogene (K-Pg) extinction. This scenario implies at least three trans-oceanic dispersals: from North America to Europe, from North America to Africa and from Africa to South America. Amphisbaenians provide a striking case study in biogeography, suggesting that the role of continental drift in biogeography may be overstated. Instead, these patterns support Darwin and Wallace's hypothesis that the geographical ranges of modern clades result from dispersal, including oceanic rafting. Mass extinctions may facilitate dispersal events by eliminating competitors and predators that would otherwise hinder establishment of dispersing populations, removing biotic barriers to dispersal.

A New Miocene-Divergent Lineage of Old World Racer Snake from India

A distinctive early Miocene-divergent lineage of Old world racer snakes is described as a new genus and species based on three specimens collected from the western Indian state of Gujarat. Wallaceophis gen. et. gujaratenesis sp. nov. is a members of a clade of old world racers. The monotypic genus represents a distinct lineage among old world racers is recovered as a sister taxa to Lytorhynchus based on ~3047bp of combined nuclear (cmos) and mitochondrial molecular data (cytb, ND4, 12s, 16s). The snake is distinct morphologically in having a unique dorsal scale reduction formula not reported from any known colubrid snake genus. Uncorrected pairwise sequence divergence for nuclear gene cmos between Wallaceophis gen. et. gujaratenesis sp. nov. other members of the clade containing old world racers and whip snake is 21–36%.

Systematics of the Madagascar Anelosimus spiders: remarkable local richness and endemism, and dual colonization from the Americas

Despite the alarming rates of deforestation and forest fragmentation, Madagascar still harbors extraordinary biodiversity. However, in many arthropod groups, such as spiders, this biodiversity remains mostly unexplored and undescribed. The first subsocial Madagascan species of the theridiid spider genus Anelosimus were described in 2005 when six new species were found to coexist in the Périnet forest fragment within Andasibe-Mantadia NP. However, this discovery was based only on a few specimens and the extent of this Madagascan radiation has remained unknown. We here report on a thorough survey of >350 colonies from Périnet, and three pilot surveys into additional Madagascar forests (Ambohitantely, Ranamofana, and Montagne d'Ambre). The morphological, molecular and natural history data from these surveys facilitated a revised taxonomy and phylogenetic hypothesis of Madagascan Anelosimus. This subsocial clade currently comprises six previously known (Anelosimusandasibe Agnarsson & Kuntner, 2005, Anelosimusmay Agnarsson, 2005, Anelosimusnazariani Agnarsson & Kuntner, 2005, Anelosimussallee Agnarsson & Kuntner, 2005, Anelosimussalut Agnarsson & Kuntner, 2005, Anelosimusvondrona Agnarsson & Kuntner, 2005) and 10 new species: Anelosimusata sp. n., Anelosimusbuffoni sp. n., Anelosimusdarwini sp. n., Anelosimushookeri sp. n., Anelosimushuxleyi sp. n., Anelosimuslamarcki sp. n., Anelosimusmoramora sp. n., Anelosimustita sp. n., Anelosimustorfi sp. n., Anelosimuswallacei sp. n.. With the exception of Anelosimusmay and Anelosimusvondrona, all other species appear to be single forest endemics. While additional sampling is necessary, these data imply a much higher local richness and endemism in Madagascan forests than in any other comparable area globally. The phylogenetic results establish a sister clade relationship between the subsocial Anelosimus in Madagascar and the American 'eximius group', and between the solitary Anelosimusdecaryi on Madagascar and a solitary American clade. These findings imply duplicate colonizations from America, an otherwise rare biogeographical pattern, calling for more detailed investigation of Anelosimus biogeography.

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.

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.

Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus, Gekkota)

The region between the Asian and Australian continental plates (Wallacea) demarcates the transition between two differentiated regional biotas. Despite this striking pattern, some terrestrial lineages have successfully traversed the marine barriers of Wallacea and subsequently diversified in newly colonized regions. The hypothesis that these dispersals between biogeographic realms are correlated with detectable shifts in evolutionary trajectory has however rarely been tested. Here, we analyse the evolution of body size in a widespread and exceptionally diverse group of gekkotan lizards (Cyrtodactylus), and show that a clade that has dispersed eastwards and radiated in the Australopapuan region appears to have significantly expanded its body size 'envelope' and repeatedly evolved gigantism. This pattern suggests that the biotic composition of the proto-Papuan Archipelago provided a permissive environment in which new colonists were released from evolutionary constraints operating to the west of Wallacea.

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

BACKGROUND

The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata.

RESULTS

The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy.

CONCLUSIONS

We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.

Imperfect isolation: factors and filters shaping Madagascar's extant vertebrate fauna

Analyses of phylogenetic topology and estimates of divergence timing have facilitated a reconstruction of Madagascar's colonization events by vertebrate animals, but that information alone does not reveal the major factors shaping the island's biogeographic history. Here, we examine profiles of Malagasy vertebrate clades through time within the context of the island's paleogeographical evolution to determine how particular events influenced the arrival of the island's extant groups. First we compare vertebrate profiles on Madagascar before and after selected events; then we compare tetrapod profiles on Madagascar to contemporary tetrapod compositions globally. We show that changes from the Mesozoic to the Cenozoic in the proportions of Madagascar's tetrapod clades (particularly its increase in the representation of birds and mammals) are tied to changes in their relative proportions elsewhere on the globe. Differences in the representation of vertebrate classes from the Mesozoic to the Cenozoic reflect the effects of extinction (i.e., the non-random susceptibility of the different vertebrate clades to purported catastrophic global events 65 million years ago), and new evolutionary opportunities for a subset of vertebrates with the relatively high potential for transoceanic dispersal potential. In comparison, changes in vertebrate class representation during the Cenozoic are minor. Despite the fact that the island's isolation has resulted in high vertebrate endemism and a unique and taxonomically imbalanced extant vertebrate assemblage (both hailed as testimony to its long isolation), that isolation was never complete. Indeed, Madagascar's extant tetrapod fauna owes more to colonization during the Cenozoic than to earlier arrivals. Madagascar's unusual vertebrate assemblage needs to be understood with reference to the basal character of clades originating prior to the K-T extinction, as well as to the differential transoceanic dispersal advantage of other, more recently arriving clades. Thus, the composition of Madagascar's endemic vertebrate assemblage itself provides evidence of the island's paleogeographic history.

Phylogenetic position, origin and biogeography of Palearctic and Socotran blind-snakes (Serpentes: Typhlopidae)

The majority of the family Typhlopidae occurs in the Neotropic, Australasian, Indo-Malayan and Afrotropic ecoregions. They show a restricted distribution in the western Palearctic, where they include few native species, i.e. Rhinotyphlops simoni, R. episcopus and Typhlops vermicularis. A unique species among typhlopids is T. socotranus, found in Socotra, one of the most endemic-rich archipelagoes. In this study we determine the phylogenetic position of the above mentioned species and discuss their systematics, origin and biogeography. For this purpose we use three protein-coding nuclear markers (AMEL-amelogenin, BDNF-brain-derived neurotrophic factor and NT3-neurotrophin 3) to construct a time-calibrated phylogeny of the family Typhlopidae. Our results show that T. socotranus is a sister-species to T. vermicularis, while R. simoni and R. episcopus are sister-species to each other and are found within the African clade of the family, although they are geographically distributed in west Asia. Additionally we discuss several hypotheses on their origin, as well as the occurence of typhlopids in Eurasia.

Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka

Snake diversity in the island of Sri Lanka is extremely high, hosting at least 89 inland (i.e., non-marine) snake species, of which at least 49 are endemic. This includes the endemic genera Aspidura, Balanophis, Cercaspis, Haplocercus, and Pseudotyphlops, which are of uncertain phylogenetic affinity. We present phylogenetic evidence from nuclear and mitochondrial loci showing the relationships of 40 snake species from Sri Lanka (22 endemics) to the remaining global snake fauna. To determine the phylogenetic placement of these species, we create a molecular dataset containing 10 genes for all global snake genera, while also sampling all available species for genera with endemic species occurring in Sri Lanka. Our sampling comprises five mitochondrial genes (12S, 16S, cyt-b, ND2, and ND4) and five nuclear genes (BDNF, c-mos, NT3 RAG-1, and RAG-2), for a total of up to 9582bp per taxon. We find that the five endemic genera represent portions of four independent colonizations of Sri Lanka, with Cercaspis nested within Colubrinae, Balanophis in Natricinae, Pseudotyphlops in Uropeltidae, and that Aspidura+Haplocercus represents a distinct, ancient lineage within Natricinae. We synonymize two endemic genera that render other genera paraphyletic (Haplocercus with Aspidura, and Cercaspis with Lycodon), and discover that further endemic radiations may be present on the island, including a new taxon from the blindsnake family Typhlopidae, suggesting a large endemic radiation. Despite its small size relative to other islands such as New Guinea, Borneo, and Madagascar, Sri Lanka has one of the most phylogenetically diverse island snake faunas in the world, and more research is needed to characterize the island's biodiversity, with numerous undescribed species in multiple lineages.