Caecilians comprise a relatively small (~220 species) group (Gymnophiona) of snake-like or worm-like, mostly tropical amphibians. Most adult caecilians are fossorial, although some species may live in aquatic or semi-aquatic environments, either as larvae or adults. Caecilians exhibit numerous morphological features traditionally interpreted as adaptations to their specialized ecologies, such as a compact and well-ossified skull and an elongated body lacking both girdles and limbs. Caecilian vertebrae differ substantially from those of other amphibians in having amphicoelous centra, well-developed basapophyseal processes, pronounced posterosagittal processes and hypapophyseal keels, and low and flat neural arches. However, caecilian postcranial osteology has received little attention, and the vast majority of the species remain unstudied. Consequently, the variation in the vertebral morphology among caecilians is still unknown or poorly documented. Inconsistencies in the anatomical terminology used by different authors are potentially confusing and may hamper understanding of homologies. Here we present an overview of caecilian postcranial osteology, define the main structural features, including many not previously described, and propose a standardized nomenclature.

Myriapods, a diverse group of terrestrial arthropods, comprise four main subgroups: Chilopoda (centipedes), Diplopoda (millipedes), Pauropoda, and Symphyla. Recent phylogenomic studies affirm Myriapoda's monophyly and the monophyletic status of each subgroup but differ in their relationships. To investigate these relationships further, we reanalyzed a transcriptomic dataset of 59 species across 292 single-copy protein-coding genes. Departing from conventional methods, we employed a novel approach that relies on information from polarized quartets (i.e., sets of four orthologous sequences, with one being an outgroup) to evaluate molecular phylogenies. This Hennigian analysis reduces misleading phylogenetic signals in molecular data caused by convergence, plesiomorphy, and rate heterogeneity across sites and across lineages. Our findings reveal that some species, especially those with long root-to-tip distances, disproportionately contribute misleading signals. Analyses using conventional likelihood-based phylogenetic methods suggest that Chilopoda and Diplopoda are sister taxa. By contrast, analyses incorporating novel filters designed to minimize conflict among phylogenetically confounding signals support the monophyly of Progoneata, aligning with morphological evidence. Simulations validate the reliability of our approach, demonstrating its potential to resolve myriapod evolutionary relationships and highlight uncertainty.

We describe a new species of the rhinatrematid caecilian genus Rhinatrema Dum & eacute;ril & Bibron, 1841 from Guyana based on a single specimen previously confused with the type species of Rhinatrema, R. bivittatum (Gu & eacute;rin-M & eacute;neville, 1838), and the more recently described Guyanese endemic R. shiv Gower, Wilkinson, Sherratt & Kok, 2010. The new species is distinctive in external morphology (a substantial pale dorsal head spot, no substantial pale dorsal tail spot), cranial osteology (many more inner than outer mandibular teeth) and mitochondrial DNA sequence data. We propose revised morphological diagnoses for the constituent genera as part of a brief systematic overview of the Rhinatrematidae Nussbaum, 1977, provide a key to the species of Rhinatrema, and present improved images of the cranial osteology of R. shiv.

Eleven specimens of striped species of the Asian caecilian amphibian genus Ichthyophis from peninsular India are present in the collections of London's Natural History Museum. The most recently collected specimen of these was recently reported upon. We reassessed the other specimens that were accessioned in the period 1874-1955. We identified four species, I. beddomei, I. kodaguensis, I. longicephalus and I. tricolor, with five specimens reidentified from previous catalogue entries. Morphological data and photographs are presented. These specimens provide insights into the taxonomic history of Ichthyophis in India, especially G.A. Boulenger's synonymy of I. beddomei with I. glutinosus, and E.H. Taylor's resurrection of that species and elevation of I. tricolor from a ‘variety’ to full species. The material also includes, as far as is known, the earliest collected specimens of I. kodaguensis (accessioned 1882) and I. longicephalus (accessioned 1874), species described in 2007 and 1986, respectively. One specimen of I. tricolor from the Nilgiri hills proves this species is not restricted to the southernmost Western Ghats, south of the Palakkad (Palghat) Gap biogeographic barrier.

Eleven specimens of striped species of the Asian caecilian amphibian genus Ichthyophis from peninsular India are present in the collections of London's Natural History Museum. The most recently collected specimen of these was recently reported upon. We reassessed the other specimens that were accessioned in the period 1874-1955. We identified four species, I. beddomei, I. kodaguensis, I. longicephalus and I. tricolor, with five specimens reidentified from previous catalogue entries. Morphological data and photographs are presented. These specimens provide insights into the taxonomic history of Ichthyophis in India, especially G.A. Boulenger's synonymy of I. beddomei with I. glutinosus, and E.H. Taylor's resurrection of that species and elevation of I. tricolor from a 'variety' to full species. The material also includes, as far as is known, the earliest collected specimens of I. kodaguensis (accessioned 1882) and I. longicephalus (accessioned 1874), species described in 2007 and 1986, respectively. One specimen of I. tricolor from the Nilgiri hills proves this species is not restricted to the southernmost Western Ghats, south of the Palakkad (Palghat) Gap biogeographic barrier.

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands. These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

The lissamphibian clade Gymnophiona includes approximately 220 recognized modern species known by the English vernacular as caecilians and characterized by their elongated and annulated bodies, without girdles or limbs. Fossils of caecilians are particularly rare and mostly limited to isolated vertebrae. Until now, only four bona fide Gymnophionomorpha species have been named based on fossils. Only one of these (Apodops pricei) is a crown-group caecilian, but its affinities with modern caecilians are uncertain because the material is limited to one damaged vertebra and is currently lost. Here we describe a new genus and species of caecilian from the Oligocene Tremembe Formation, Brazil, based on a partially preserved fossil skeleton (including elements of the skull and postcranium) that is damaged but still partly articulated. We investigated the fossil caecilian's anatomy using high-resolution microcomputed tomography, and then compared it to the osteology of modern species. We interpret the fossil as a member of Typhlonectidae, a family of caecilians well known for their aquatic and semi-aquatic lifestyles. This new record represents the first record for caecilians from the Oligocene and also the first fossil species confidently assigned to an extant caecilian family.

We describe two new caecilian species of the genus Caecilia (Gymnophiona: Caeciliidae) from the wet tropical Choco Forest, north-western Ecuador. We applied an integrative taxonomic approach, taking into consideration external morphology, osteology from intensive ct-scanning, and molecular phylogenetic analyses. The two new species were compared to all other Caecilia species, known to occur west of the Ecuadorian and Colombian Andes. The new taxa can be distinguished by their external morphological characters, as well as by their osteology, genetic divergence, and phylogenetic relationships. The two new species, although morphologically quite different, were closely related. Caecilia tesoro sp. n. is a large-bodied, robust species with a unique colour pattern in larger individuals. In contrast, Caecilia truncata sp. n. is a smaller caeciliid and sister to medium-sized C. volcani, a species known from Panama. Morphologically, C. truncata sp. n. is best recognized by a very truncated snout shape. As know from many previously recognized neotropical caeciliids, both new species are likely endemic to small ranges, here the humid tropical lowland to mid-altitude forests of western Ecuador. Both new species seem to tolerate some degree of habitat degradation. Our new findings support to intensify research and conservation activities in one of South America's most diverse but severely endangered biomes. We also present, for the first time, some clues of the phylogenetic position of elongated C. nigricans and C. leucocephala. Caecilia nigricans was sister to a clade composed of one Oscaecilia and ten species of Caecilia. This topology rendered the genus Caecilia paraphyletic relative to Oscaecilia.

In limbless fossorial vertebrates such as caecilians (Gymnophiona), head‐first burrowing imposes severe constraints on the morphology and overall size of the head. As such, caecilians developed a unique jaw‐closing system involving the large and well‐developed m. interhyoideus posterior , which is positioned in such a way that it does not significantly increase head diameter. Caecilians also possess unique muscles among amphibians. Understanding the diversity in the architecture and size of the cranial muscles may provide insights into how a typical amphibian system was adapted for a head‐first burrowing lifestyle. In this study, we use dissection and non‐destructive contrast‐enhanced micro‐computed tomography (μCT) scanning to describe and compare the cranial musculature of 13 species of caecilians. Our results show that the general organization of the head musculature is rather constant across extant caecilians. However, the early‐diverging Rhinatrema bivittatum mainly relies on the ‘ancestral’ amphibian jaw‐closing mechanism dominated by the m. adductores mandibulae , whereas other caecilians switched to the use of the derived dual jaw‐closing mechanism involving the additional recruitment of the m. interhyoideus posterior . Additionally, the aquatic Typhlonectes show a greater investment in hyoid musculature than terrestrial caecilians, which is likely related to greater demands for ventilating their large lungs, and perhaps also an increased use of suction feeding. In addition to three‐dimensional interactive models, our study provides the required quantitative data to permit the generation of accurate biomechanical models allowing the testing of further functional hypotheses.

Predatory innovations impose reciprocal selection pressures upon prey. The evolution of snake venom alpha-neurotoxins has triggered the corresponding evolution of resistance in the post-synaptic nicotinic acetylcholine receptors of prey in a complex chemical arms race. All other things being equal, animals like caecilians (an Order of legless amphibians) are quite vulnerable to predation by fossorial elapid snakes and their powerful alpha-neurotoxic venoms; thus, they are under strong selective pressure. Here, we sequenced the nicotinic acetylcholine receptor alpha-1 subunit of 37 caecilian species, representing all currently known families of caecilians from across the Americas, Africa, and Asia, including species endemic to the Seychelles. Three types of resistance were identified: (1) steric hindrance from N-glycosylated asparagines; (2) secondary structural changes due to the replacement of proline by another amino acid; and (3) electrostatic charge repulsion of the positively charged neurotoxins, through the introduction of a positively charged amino acid into the toxin-binding site. We demonstrated that resistance to alpha-neurotoxins convergently evolved at least fifteen times across the caecilian tree (three times in Africa, seven times in the Americas, and five times in Asia). Additionally, as several species were shown to possess multiple resistance modifications acting synergistically, caecilians must have undergone at least 20 separate events involving the origin of toxin resistance. On the other hand, resistance in non-caecilian amphibians was found to be limited to five origins. Together, the mutations underlying resistance in caecilians constitute a robust signature of positive selection which strongly correlates with elapid presence through both space (sympatry with caecilian-eating elapids) and time (Cenozoic radiation of elapids). Our study demonstrates the extent of convergent evolution that can be expected when a single widespread predatory adaptation triggers parallel evolutionary arms races at a global scale.

Oral and other cephalic glands have been surveyed by several studies with distinct purposes. Despite the wide diversity and medical relevance of the New World coral snakes, studies focusing on understanding the biological roles of the glands within this group are still scarce. Specifically, the venom glands of some coral snakes were previously investigated but all other cephalic glands remain uncharacterized. In this sense, performing morphological and molecular analysis of these glands may help better understand their biological role. Here, we studied the morphology of the venom, infralabial, rictal, and harderian glands of thirteen species of Micrurus and Micruroides euryxanthus. We also performed a molecular characterization of these glands from selected species of Micrurus using transcriptomic and proteomic approaches. We described substantial morphological variation in the cephalic glands of New World coral snakes and structural evidence for protein-secreting cells in the inferior rictal glands. Our molecular analysis revealed that the venom glands, as expected, are majorly devoted to toxin production, however, the infralabial and inferior rictal glands also expressed some toxin genes at low to medium levels, despite the marked morphological differences. On the other hand, the harderian glands were dominated by the expression of lipocalins, but do not produce toxins. Our integrative analysis, including the prediction of biological processes and pathways, helped decipher some important traits of cephalic glands and better understand their biology.

We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons being the most abundant. We identify 1,150 orthogroups that are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception, and immunity amongst others. We discover that caecilian genomes are missing the zone of polarizing activity regulatorysequence (ZRS) enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus, revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.

Records of biodiversity over time are important resources for assessing conservation priorities. However, such baseline data are missing for regions of key biodiversity importance. The Eastern Arc Mountains of Tanzania are known for their species richness and endemism, but not all mountain blocks have received the same attention. The Ukaguru Mountains, for example, have only infrequently been surveyed by herpetologists, with the first known herpetological survey in 1990. Here we compile and quantify all amphibian survey efforts in the Ukaguru Mountains in the past 30 years, publish an updated species list and comment on the health of amphibian populations and their habitat. We report on fourteen described species of amphibians, with potentially three additional species awaiting formal description. Of these seventeen lineages, seven are endemic to the Ukaguru Mountains. Although total species numbers remain low, compared with other Eastern Arc Mountains, surveys frequently recorded new species for the Ukaguru Mountains and for science. Worryingly, however, endemics, such as the monotypic bufonid Churamiti maridadi, have not been recorded in the past fifteen years. Our analyses show the region is becoming warmer and drier and is experiencing an alarming rate of deforestation. We find that over the past 30 years, dense forest cover inside the boundaries of the forest reserves has reduced by 8.4%.

Caecilians are predominantly burrowing, elongate, limbless amphibians that have been relatively poorly studied. Although it has been suggested that the sturdy and compact skulls of caecilians are an adaptation to their head-first burrowing habits, no clear relationship between skull shape and burrowing performance appears to exist. However, the external forces encountered during burrowing are transmitted by the skull to the vertebral column, and, as such, may impact vertebral shape. Additionally, the muscles that generate the burrowing forces attach onto the vertebral column and consequently may impact vertebral shape that way as well. Here, we explored the relationships between vertebral shape and maximal in vivo push forces in 13 species of caecilian amphibians. Our results show that the shape of the two most anterior vertebrae, as well as the shape of the vertebrae at 90% of the total body length, is not correlated with peak push forces. Conversely, the shape of the third vertebrae, and the vertebrae at 20% and 60% of the total body length, does show a relationship to push forces measured in vivo. Whether these relationships are indirect (external forces constraining shape variation) or direct (muscle forces constraining shape variation) remains unclear and will require quantitative studies of the axial musculature. Importantly, our data suggest that mid-body vertebrae may potentially be used as proxies to infer burrowing capacity in fossil representatives.

Striking asymmetries of species richness characterise the tree of life, and understanding their causes is a major research agenda in evolutionary biology. Genome duplications have been proposed as one mechanism by which lineages acquire greater potential for rapid genetic evolution following the relaxation of pleiotropic constraints. This enhanced evolvability might facilitate faster rates of morphological change and speciation. We provide a comprehensive test of the empirical association between polyploidy – a marker of genome duplication – and species richness in 356 pairs of extant polyploid and non-polyploid sister clades. Comparing sister clades controls for divergence time and many ecological and morphological properties of groups. Clades with inferred basal genome duplications have significantly higher species diversity than their sister clades, both for the whole dataset, major groups of animals and plants within it and at the genus and family levels. Genome duplications therefore offer one possible, widespread cause of heterogeneities in species richness.

Caecilians are elongate, limbless and annulated amphibians that, as far as is known, all have an at least partly fossorial lifestyle. It has been suggested that elongate limbless vertebrates show little morphological differentiation throughout the postcranial skeleton. However, relatively few studies have explored the axial skeleton in limbless tetrapods. In this study, we used μCT data and three‐dimensional geometric morphometrics to explore regional differences in vertebral shape across a broad range of caecilian species. Our results highlight substantial differences in vertebral shape along the axial skeleton, with anterior vertebrae being short and bulky, whereas posterior vertebrae are more elongated. This study shows that despite being limbless, elongate tetrapods such as caecilians still show regional heterogeneity in the shape of individual vertebrae along the vertebral column. Further studies are needed, however, to understand the possible causes and functional consequences of the observed variation in vertebral shape in caecilians.

Maintaining Gymnophiona in captivity provides opportunities to study the behaviour and life-history of this poorly known Order, and to investigate and provide species-appropriate welfare guidelines, which are currently lacking. This study focuses on the terrestrial caecilian Herpele squalostoma to investigate its sensitivity to disturbances associated with routine husbandry needed for monitoring and maintaining adequate wellbeing in captivity. Fossorial caecilians gradually pollute their environment in captivity with waste products, and substrate must be replaced at intervals; doing so disturbs the animals directly and via destruction of burrow networks. As inappetence is frequently associated with stress in amphibians, the percentage consumption of offered food types, river shrimp (Palaemon varians) and brown crickets (Gryllus assimilis), was measured as an indicator of putative stress following three routine substrate changes up to 297 days post-substrate change. Mean daily variation in substrate temperatures were also recorded in order to account for environmental influences on food consumption, along with nitrogenous waste in tank substrate prior to a substrate change and fresh top soil in order to understand the trade-off between dealing with waste accumulation and disturbing animals. We found a significant negative effect of substrate disturbance on food intake, but no significant effect of prey type. Variations in daily soil temperatures did not have a significant effect on food intake, but mean substrate temperature did. Additionally, substrate nitrogenous waste testing indicated little difference between fresh and tank substrate. In conclusion, this study provides a basis from which to develop further welfare assessment for this and other rarely kept and rarely observed terrestrial caecilian species.