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Since one of the priorities of public policies and conservation projects is biodiversity safeguarding, understanding the richness and distribution of amphibian communities becomes an important tool for defining priority areas for conservation. Herein, we provide a list of amphibians registered in the Estação Ecológica de Murici, state of Alagoas, Brazil, one of the highest priority areas for conservation in the Atlantic Forest. We used data collected over two years of field expeditions together with more than 30 years of information available in herpetological collections. A total of 57 amphibian species were recorded in the study site, two currently considered endangered. This richness represents 10% of all diversity found throughout the Atlantic Forest, and approxiamtely 90% of forest dependent species documented in the northern portion of the biome. The Estação Ecológica de Murici is a key area for biodiversity conservation in the Atlantic Forest and across the planet; therefore, further studies and ongoing monitoring are necessary to guarantee the preservation of its unique biodiversity. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are key molecules in the innate immune defence of vertebrates with rapid action, broad antimicrobial spectrum, and ability to evade pathogen resistance mechanisms. To date, amphibians are the major group of vertebrates from which most AMPs have been characterised, but most studies have focused on the bioactive skin secretions of anurans (frogs and toads). In this study, we have analysed the complete genomes and/or transcriptomes of eight species of caecilian amphibians (order Gymnophiona) and characterised the diversity, molecular evolution, and antimicrobial potential of the AMP repertoire of this order of amphibians. We have identified 477 candidate AMPs within the studied caecilian genome and transcriptome datasets. These candidates are grouped into 29 AMP families, with four corresponding to peptides primarily exhibiting antimicrobial activity and 25 potentially serving as AMPs in a secondary function, either in their entirety or after cleavage. In silico prediction methods were used to identify 62 of those AMPs as peptides with promising antimicrobial activity potential. Signatures of directional selection were detected for five candidate AMPs, which may indicate adaptation to the different selective pressures imposed by evolutionary arms races with specific pathogens. These findings provide encouraging support for the expectation that caecilians, being one of the least-studied groups of vertebrates, and with ~300 million years of separate evolution, are an underexplored resource of great pharmaceutical potential that could help to contest antibiotic resistance and contribute to biomedical advance. [ABSTRACT FROM AUTHOR]

The description of the small Late Triassic temnospondyl Chinlestegophis ushered in a potentially radically new understanding of the origins of the extant amphibian clades. Together with the fragmentary Rileymillerus, Chinlestegophis was argued to link extant caecilians to Permo-Triassic stereospondyl temnospondyls rather than to frogs and salamanders (and through them to amphibamiform temnospondyls or to brachystelechid and lysorophian "lepospondyls"). We critically review the comparative description of Chinlestegophis and phylogenetic analyses of previous studies. Most of the features previously interpreted to be shared by caecilians, Chinlestegophis and/or other stereospondyls have different distributions than scored in the analysis. We also find no evidence for an incipient tentacular sulcus in Chinlestegophis, and note that its vertebrae, unreduced ribs and dermal shoulder girdle are unlike those of any extant amphibians (nor their likely sister group, Albanerpetidae). Furthermore, the original matrices contain misscores accreted over more than a decade that likewise influence the results. Some features are coded as multiple redundant characters: the double toothrow of Chinlestegophis, other stereospondyls, and caecilians is represented as seven characters. Analysis of the unmodified matrix yields much less resolution than originally reported, and tree topology is altered by a small change to the taxon sample (the addition of Albanerpetidae), limited revisions of irreproducible scores, and ordering the most obviously clinal characters; any one of these changes removes Chinlestegophis from Lissamphibia, and confirms it as a stereospondyl. [ABSTRACT FROM AUTHOR]

Anurans, along with urodeles and caecilians are the extant representatives of the clade Lissamphibia. Nowadays, lissamphibians are widely distributed in all continents, except Antarctica, but are particularly diversified in South America, where almost 3,000 species are found. This huge biodiversity is directly related to the complex geologic history of South America, which includes key events like the Gondwanan breakup, its isolation during parts of Mesozoic and Cenozoic, the Andean uplift, and the formation of the Panamá isthmus. Here, we present the most comprehensive bibliographic review of fossil lissamphibians from South America to date, covering unpublished (e.g. theses and dissertations) and published data (i.e. peer-reviewed scientific papers, book chapters, monographs, and conferences abstracts). We use a mixed approach, both qualitative (with brief comments on each taxon and specimen) and quantitative (including scientometric parameters). Compared to the latest published reviews with similar scope, our results indicate that approximately 85.4% of the records correspond to specimens new to science or older ones that have been revisited. These materials come from 164 different fossil-bearing localities, spread over eight of the twelve South American countries, and range from the Early Jurassic to the Quaternary. In total, we compile 273 records, mostly anurans (~97.6%), followed by indeterminate caecilians (~1.4%) and urodeles (~1%). Additionally, we discuss issues directly related to those fossil occurrences, such as their temporal and geographic range, as well as the presence of putative biological and taphonomic biases. Finally, we also provide calibration constraints for several anuran taxa. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The diversity and distribution of the amphibians in Rwanda was critically reviewed to provide a reliable species inventory for informed conservation management. The checklist of the amphibian species of Rwanda is based on results of our own fieldwork, historical records compiled from the literature, and examination of voucher specimens in museum collections. A total of 62 species are recorded, and 22 further species listed in field guides and open-access data bases are discussed, identified as erroneous records, and consequently not included in the country list. We provide diagnostic characters of external morphology and the advertisement call for each validated species, and a short synopsis of geographic distribution, altitudinal range, occurrence in the provinces of Rwanda, and habitat preference. We provide keys to all genera, and all taxonomically described species based on morphological characters and additional keys based on features of the advertisement calls. We discuss features of amphibian communities including local community structure and delimitation of altitudinal metacommunities. Based on the IUCN red list assessment and our field surveys, we propose for the first time a national red list of amphibians in Rwanda. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are key molecules in the innate immune defence of vertebrates with rapid action, broad antimicrobial spectrum, and ability to evade pathogen resistance mechanisms. To date, amphibians are the major group of vertebrates from which most AMPs have been characterised, but most studies have focused on the bioactive skin secretions of anurans (frogs and toads). In this study, we have analysed the complete genomes and/or transcriptomes of eight species of caecilian amphibians (order Gymnophiona) and characterised the diversity, molecular evolution, and antimicrobial potential of the AMP repertoire of this order of amphibians. We have identified 477 candidate AMPs within the studied caecilian genome and transcriptome datasets. These candidates are grouped into 29 AMP families, with four corresponding to peptides primarily exhibiting antimicrobial activity and 25 potentially serving as AMPs in a secondary function, either in their entirety or after cleavage. In silico prediction methods were used to identify 62 of those AMPs as peptides with promising antimicrobial activity potential. Signatures of directional selection were detected for five candidate AMPs, which may indicate adaptation to the different selective pressures imposed by evolutionary arms races with specific pathogens. These findings provide encouraging support for the expectation that caecilians, being one of the least-studied groups of vertebrates, and with ~300 million years of separate evolution, are an underexplored resource of great pharmaceutical potential that could help to contest antibiotic resistance and contribute to biomedical advance.

Although the distribution patterns of major amphibian lineages are mainly explained by a Pangean origin with subsequent vicariant diversification, dispersal events have exerted a strong influence on present-day distributions. Long-distance dispersal (LDD) involves movements outside the standard geographic limits and outside the genetic neighbourhood area of individuals. Although considered ‘rare’, LDD is disproportionately important to amphibian populations, species and communities. To understand the role of LDD in shaping current biogeographic patterns in these tetrapods, we reviewed the cases reported in the literature. A systematic bibliographic search was performed to obtain information on how many studies have dealt with LDD in amphibians, which methods they used, which taxa and distances were involved, and when/where events had apparently occurred. In 41 studies, we recovered at least 90 LDD events (3 active, 87 passive) involving at least 56 extant species and 38 genera. Most events (73) involved the colonization of islands, with rafting being suggested as the most conceivable means of overwater passive dispersal for these vertebrates. In this review, we show that LDD events have played an important role in shaping current amphibian biogeographic patterns, especially the occurrence of disjunct distributions and the colonization of islands.

In Colombia, amphibians are a vertebrate group with a high taxonomic richness, and an elevated representativity of species with restricted distributions. In recent years, regional collections have assisted to fill information gaps on the biogeography, intra- and interspecific variation, and systematics of the amphibians of the country. In this work we present the information of 1533 records deposited in the Amphibian Collection of the Museo de Historia Natural of the Universidad de Caldas, represented by 143 species, belonging to 49 genera and 19 families. Most of the records (n = 1194) come from the Department of Caldas, but there are records for 16 additional departments. The most representative order is Anura (n = 1487 records) followed by Caudata (n = 27 records), and Gymnophiona (n = 19 records). The collection houses 152 specimens that have been referenced in 13 national and foreign publications. [ABSTRACT FROM AUTHOR]

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photographs, we surveyed pupil shape across adults of 1294 amphibian species, 74 families and three orders, and additionally for larval stages for all families of frogs and salamanders with a biphasic ontogeny. For amphibians with a biphasic life history, pupil shape changed in many species that occupy distinct habitats before and after metamorphosis. In addition, non-elongated (circular or diamond) constricted pupils were associated with species inhabiting aquatic or underground environments, and elongated pupils (with vertical or horizontal long axes) were more common in species with larger absolute eye sizes. We propose that amphibians provide a valuable group within which to explore the anatomical, physiological, optical and ecological mechanisms underlying the evolution of pupil shape. [ABSTRACT FROM AUTHOR]

The diversity and distribution of the amphibians in Rwanda was critically reviewed to provide a reliable species inventory for informed conservation management. The checklist of the amphibian species of Rwanda is based on results of our own fieldwork, historical records compiled from the literature, and examination of voucher specimens in museum collections. A total of 62 species are recorded, and 22 further species listed in field guides and open-access data bases are discussed, identified as erroneous records, and consequently not included in the country list. We provide diagnostic characters of external morphology and the advertisement call for each validated species, and a short synopsis of geographic distribution, altitudinal range, occurrence in the provinces of Rwanda, and habitat preference. We provide keys to all genera, and all taxonomically described species based on morphological characters and additional keys based on features of the advertisement calls. We discuss features of amphibian communities including local community structure and delimitation of altitudinal metacommunities. Based on the IUCN red list assessment and our field surveys, we propose for the first time a national red list of amphibians in Rwanda.

We review the use of reproduction technologies (RTs) to support the sustainable management of threatened Caudata (salamanders) and Gymnophiona (caecilian) biodiversity in conservation breeding programs (CBPs) or through biobanking alone. The Caudata include ∼760 species with ∼55% threatened, the Gymnophiona include ∼215 species with an undetermined but substantial number threatened, with 80% of Caudata and 65% of Gymnophiona habitat unprotected. Reproduction technologies include: (1) the exogenous hormonal induction of spermatozoa, eggs, or mating, (2) in vitro fertilisation, (3) intracytoplasmic sperm injection (ICSI), (4) the refrigerated storage of spermatozoa, (5) the cryopreservation of sperm, cell or tissues, (6) cloning, and (7) gonadal tissue or cell transplantation into living amphibians to eventually produce gametes and then individuals. Exogenous hormone regimens have been applied to 11 Caudata species to stimulate mating and to 14 species to enable the collection of spermatozoa or eggs. In vitro fertilisation has been successful in eight species, spermatozoa have been cryopreserved in seven species, and in two species in vitro fertilisation with cryopreserved spermatozoa has resulted in mature reproductive adults. However, the application of RTs to Caudata needs research and development over a broader range of species. Reproduction technologies are only now being developed for Gymnophiona, with many discoveries and pioneering achievement to be made. Species with the potential for repopulation are the focus of the few currently available amphibian CBPs. As Caudata and Gymnophiona eggs or larvae cannot be cryopreserved, and the capacity of CBPs is limited, the perpetuation of the biodiversity of an increasing number of species depends on the development of RTs to recover female individuals from cryopreserved and biobanked cells or tissues. The survival of many salamander and caecilian species requires the targeting and development of biotechnologies to produce offspring from cryopreserved sperm, to lower the costs and increase the reliability of conservation breeding programs. The colonisation of space will also be intimately dependent on the use of cryopreserved biomaterial for terraforming. Cryopreserved sperm has produced mature offspring in salamanders. However, more research and development is needed before the general application of reproduction technologies for salamanders or caecilians. [ABSTRACT FROM AUTHOR]

Modern amphibians have an extraordinary diversity of reproductive modes including varieties of oviparity and viviparity. Oviparous and viviparous caecilian amphibians show high degrees of parental investment including dermato- and uterotrophy. We examined maternal investment and reproductive biology correlations of the aquatic viviparous caecilian amphibian Typhlonectes natans. Litter sizes ranged from two to ten pups, whereas litter masses averaged around 28% of maternal mass and pups reached up to 43% of the female total length. Maternal size was positively related to litter size and to the average pup body size. Although overall fecundity is reduced in viviparous teresomatan caecilian amphibians, as clutch size is decreased in comparison to oviparous ichthyophiid caecilians, a lower fecundity of viviparous taxa is compensated via uterotrophy leading to an increased offspring size and quality. [ABSTRACT FROM AUTHOR]

Abstract Background Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona). Results The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated. Conclusions Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates.

Amphibian reproductive modes (RMs) have been extensively described and applied to amphibian biology studies. However, due to new behavioural observations and past system inconsistencies we found it necessary to review the current classification and redefine the sets of characters which define amphibian RMs. We suggest the use of 11 characters that include phases from egg to early development (including or not including larval stages) and we do not include behavioural aspects that are in general hard to identify, such as parental care, except those related to feeding and incubation. Based on 2,171 amphibian species (roughly a fourth of the species known), we built a dichotomous tree with 74 different possible RMs for amphibians - almost twice the number of the previous classification categories. This system could possibly be applied to other vertebrates as well and therefore facilitate comparisons across different taxa. [ABSTRACT FROM AUTHOR]

The Brazilian Atlantic Forest holds a major part of the country's amphibian species richness and high rates of endemism. In this study, we conducted surveys using the Rapid Assessment (RA) method to sample the amphibian fauna of the Serra das Torres Natural Monument (MONAST), an Atlantic Forest remnant in southeastern Brazil. We sampled actively with a 6-10-person team to collect standard samples from 09:00 to 12:00 hours for the daytime period, and from 18:00 to 22:00 hours for the crepuscular/nighttime period, with a total of approximately 1,320 hours of sampling effort. We supplemented these data with 720 hours of passive sampling, using pitfall traps with drift fences (30 bucket-days). We recorded 54 amphibian species (two gymnophionans and 52 anurans), and the species richness estimated by the Bootstrap method indicates that a slightly larger number of species (n = 60) may occur in the study area. The most speciose family was Hylidae (n = 21), followed by Brachycephalidae (n = 8). Overall, 25% of the species (n = 13) were recorded only once (singletons) and 15% (n = 8) only twice (doubletons). Most amphibians recorded in this study (71%, n = 37 species) were restricted to the Atlantic Forest biome, two species (Euparkerella robusta and Luetkenotyphlus fredi) are endemic to the Espírito Santo state, and one of them, the leaf litter species, is endemic to the MONAST. Euparkerella robusta is currently listed as Vulnerable by the IUCN and is classified as Critically Endangered in the Espírito Santo State red list, while L. fredi has yet to be evaluated due to its recent description. Thoropa cf. lutzi is currently listed as Endangered (EN) by both the IUCN and in the State list. Nine species are listed as Data Deficient (DD) and populations of 13 species are considered to be declining by the IUCN. We extend the geographical distribution of two anuran species (Hylodes babax and Phasmahyla lisbella) and fill an important gap in the distribution of Siphonops hardyi. Amphibians associated with the forest floor represented 42% of the species richness from MONAST, and 43% of these species inhabit the leaf litter exclusively. Our study revealed that Serra das Torres preserves a considerable diversity of Atlantic Forest amphibians, which reinforces the need for the conservation of this forest remnant. [ABSTRACT FROM AUTHOR]

Abstract Background Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates.

Abstract Background Caecilians (Gymnophiona) are the least speciose extant lissamphibian order, yet living forms capture approximately 250 million years of evolution since their earliest divergences. This long history is reflected in the broad range of skull morphologies exhibited by this largely fossorial, but developmentally diverse, clade. However, this diversity of form makes quantification of caecilian cranial morphology challenging, with highly variable presence or absence of many structures. Consequently, few studies have examined morphological evolution across caecilians. This extensive variation also raises the question of degree of conservation of cranial modules (semi-autonomous subsets of highly-integrated traits) within this clade, allowing us to assess the importance of modular organisation in shaping morphological evolution. We used an intensive surface geometric morphometric approach to quantify cranial morphological variation across all 32 extant caecilian genera. We defined 16 cranial regions using 53 landmarks and 687 curve and 729 surface sliding semilandmarks. With these unprecedented high-dimensional data, we analysed cranial shape and modularity across caecilians assessing phylogenetic, allometric and ecological influences on cranial evolution, as well as investigating the relationships among integration, evolutionary rate, and morphological disparity. Results We found highest support for a ten-module model, with greater integration of the posterior skull. Phylogenetic signal was significant (K mult = 0.87, p < 0.01), but stronger in anterior modules, while allometric influences were also significant (R 2 = 0.16, p < 0.01), but stronger posteriorly. Reproductive strategy and degree of fossoriality were small but significant influences on cranial morphology (R 2 = 0.03–0.05), after phylogenetic (p

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The fish-tetrapod transition (which incorporates the related fin-limb and water-land transitions) is celebrated as one of the most important junctions in vertebrate evolution. Sarcopterygian fishes (the “lobe-fins”) are today represented by lungfishes and coelacanths, but during the Paleozoic they were much more diverse. It was some of these sarcopterygians, a lineage of the tetrapodomorph fishes, that gave rise to tetrapods (terrestrial vertebrates with limbs bearing digits). This spectacular leap took place during the Devonian Period. Due to the nature of preservation, it is the hard parts of an animal’s body that are most likely to fossilize, while soft tissues such as muscular and brain tissues, typically fail to do so. Thus, our understanding of the adaptations of the hard skeletal structures of vertebrates is considerably greater than that of the soft tissue systems. Fortunately, the braincases of early vertebrates are often ossified and thereby have the potential to provide detailed morphological information. However, the correspondence between brain and endocast (an internal mold of the cavity) has historically been considered poor in most “lower” vertebrates and consequently neglected in such studies of brain evolution. Despite this, recent work documenting the spatial relationship in extant basal sarcopterygians (coelacanth, lungfish, axolotl, and salamander) has highlighted that this is not uniformly the case. Herein, we quantify and illustrate the brain-endocast relationship in four additional extant basal tetrapod exemplars: neobatrachian anurans (frogs) Breviceps poweri and Ceratophrys ornata; and gymnophionans (caecilians) Gegeneophis ramaswamii and Rhinatrema bivittatum. We show that anurans and caecilians appear to have brains that fill their endocasts to a similar degree to that of lungfishes and salamanders, but not coelacanth. Ceratophrys has considerably lower correspondence between the brain and endocast in the olfactory tract and mesencephalic regions, while Breviceps has low correspondence along its ventral endocranial margin. The brains of caecilians reflect their endocasts most closely (vol. ∼70%). The telencephalon is tightly fitted within the endocast in all four taxa. Our findings highlight the need to adequately assess the brain-endocast relationship in a broad range of vertebrates, in order to inform neural reconstructions of fossil taxa using the Extant Phylogenetic Bracket approach and future studies of brain evolution.

Gymnophiona, popularly known as caecilians, the most poorly known major taxon of extant amphibians, are elongate and limbless tetrapods, with compact ossified skulls and reduced eyes, mainly adapted to fossorial life as adults. Caecilians are poorly represented in the fossil record, but despite the scarcity of fossil specimens described (only four named taxa, in addition to indeterminate fragmentary material), their fossils play a key role in our knowledge of the origin and evolution of Lissamphibia, as well as contribute directly to a better understanding of the phylogeny, taxonomy and biogeography of extant gymnophionan taxa. These records are scattered throughout geological time (from the Jurassic to the sub-Recent) and space (North and South America and Africa). Here, we revisit the caecilian fossil record, providing a brief description of all known extinct taxa described so far, along with general remarks about their impact on systematics, time range, and geographical distribution of the clade, as well as prospects for future research. Possible calibration constraints based on the caecilian fossil record are provided. [ABSTRACT FROM AUTHOR]

Background: Gene expression profiles can provide insights into the molecular machinery behind tissue functions and, in turn, can further our understanding of environmental responses, and developmental and evolutionary processes. During vertebrate evolution, the skin has played a crucial role, displaying a wide diversity of essential functions. To unravel the molecular basis of skin specialisations and adaptations, we compared gene expression in the skin with eight other tissues in a phylogenetically and ecologically diverse species sample of one of the most neglected vertebrate groups, the caecilian amphibians (order Gymnophiona). Results: The skin of the five studied caecilian species showed a distinct gene expression profile reflecting its developmental origin and showing similarities to other epithelial tissues. We identified 59 sequences with conserved enhanced expression in the skin that might be associated with caecilian dermal specialisations. Some of the up-regulated genes shared expression patterns with human skin and potentially are involved in skin functions across vertebrates. Variation trends in gene expression were detected between mid and posterior body skin suggesting different functions between body regions. Several candidate biologically active peptides were also annotated. Conclusions: Our study provides the first atlas of differentially expressed sequences in caecilian tissues and a baseline to explore the molecular basis of the skin functions in caecilian amphibians, and more broadly in vertebrates. [ABSTRACT FROM AUTHOR]

Monospecific and bispecific genera are of particular interest in studies of taxonomic diversity and speciation evolution. Here, the distribution patterns of mono- and bispecific amphibians worldwide are investigated, with some discussion of on the conservation implications also presented. Based on an online database search (available from the American Museum of Natural History, New York), we found that the mean number of mono- and bispecific genera was similar among zoogeographic regions, with a total of 120 mono- (95 Anura, 17 Caudata, 8 Gymnophiona) and 65 bispecific (48 Anura, 10 Caudata, 7 Gymnophiona) genera. Out of 73 known amphibian families worldwide, only 35.6% of them do not contain any mono- or bispecific genera. The frequency of mono- or bispecific genera by family was not significantly different among Anura, Caudata and Gymnophiona. There was a general tendency for the number of mono- and bispecific genera of amphibians to be positively correlated with the total number of genera in that family. In Anura, there was a preponderance of mono-specific genera in Afrotropical and Neotropical regions. Concerning bispecific genera, there was a clear preponderance in the Neotropical region for anurans. There was a positive correlation between the number of threatened genera (according to the IUCN Red List) in both the mono- and bispecific groups and the relative number of species in each taxon, thus showing that taxonomical speciosity clearly influences the frequency of occurrence of mono- and bispecific taxa in each family and order. In this regard, Anura dominated in both the number of worldwide described mono- and bispecific taxa as well as in that of the threatened ones according to IUCN Red List. [ABSTRACT FROM AUTHOR]

Aim: Species distributions are one of the most important ways to understand how communities interact through macroecological relationships. The functional abilities of a species, such as its plasticity in various environments, can determine its distribution, species richness and beta diversity patterns. In this study, we evaluate how functional traits influence the distribution of amphibians, and hypothesize which functional traits explain the current pattern of amphibian species composition. Location: Atlantic Forest, Brazil. Taxon: Amphibia (Anura and Gymnophiona) Methods: Using potential distributions of Brazilian amphibians from Atlantic Forest based on their functional traits, we analysed the influence of biotic and abiotic factors on species richness, endemism (with permutation multivariate analysis) and beta diversity components (i.e. total, turnover and nestedness dissimilarities). Results: Environmental variables explained 59.5% of species richness, whereas functional traits explained 15.8% of species distribution (geographical species range) for Anuran and 88.8% for Gymnophiona. Body size had the strongest correlation with species distribution. Results showed that species with medium to large body size, and species that are adapted to living in open areas tended to disperse from west to east direction. Current forest changes directly affected beta diversity patterns (i.e. most species adapted to novel environments increase their ranges). Beta diversity partitioning between humid and dry forests showed decreased nestedness and increased turnover by increasing altitude in the south‐eastern region of the Atlantic Forest. Main Conclusions: Our study shows that functional traits directly influence the ability of the species to disperse. With the alterations of the natural environment, species more apt to these alterations have dispersed or increased their distribution, which consequently changes community structure. As a result, there are nested species distribution patterns and homogenization of amphibian species composition throughout the Brazilian Atlantic Forest. [ABSTRACT FROM AUTHOR]

Caecilians (order Gymnophiona) are apodan, snake-like amphibians, usually with fossorial habits, constituting one of the most unknown groups of terrestrial vertebrates. As in orders Anura (frogs, tree frogs and toads) and Caudata (salamanders and newts), the caecilian skin is rich in mucous glands, responsible for body lubrication, and poison glands, producing varied toxins used in defence against predators and microorganisms. Whereas in anurans and caudatans skin gland morphology has been well studied, caecilian poison glands remain poorly elucidated. Here we characterised the skin gland morphology of the caecilian Siphonops annulatus, emphasising the poison glands in comparison to those of anurans and salamanders. We showed that S. annulatus glands are similar to those of salamanders, consisting of several syncytial compartments full of granules composed of protein material but showing some differentiated apical compartments containing mucus. An unusual structure resembling a mucous gland is frequently observed in lateral/apical position, apparently connected to the main duct. We conclude that the morphology of skin poison glands in caecilians is more similar to salamander glands when compared to anuran glands that show a much-simplified structure.

The desire to own a pet amphibian is growing, and with it a growth in amphibian trade and in negative impacts on native populations, including disease transmission and invasive amphibian populations. We know very little about how or why people choose amphibians as pets, but amphibian owners share large numbers of videos on freely accessible platforms, such as YouTube. We aimed to use videos of captive amphibians to determine which species are kept, their life-history stage and the types of videos uploaded. We watched and categorized 1,162 videos by video type, type of amphibian behavior and amphibian taxonomy (superfamily, family, and species). We used data on the amphibian trade from the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), on conservation status from the International Union for Conservation of Nature (IUCN) red list, and on potential environmental impact from published Environmental Impact Classification of Alien Taxa (EICAT) records, to determine potential conflicts of owning pet amphibians. We recorded 173 captive species in 847 videos with a taxonomic overrepresentation of salamandroids and pipoids, and an underrepresentation of ranoids and plethodontoids. When compared to videos of wild amphibian species, videos of captive animals featured disproportionate amounts of adults feeding, being handled and moving. The videos watched had a smaller proportion of threatened amphibian species, but a higher proportion of invasive species, than would be expected by chance, with the proportion present in CITES appendices (18%) being non-significant. We suggest that such data can be used to profile potential pets for trade and attempt to avoid conflicts with threatened and highly impacting alien species.

Current biodiversity patterns of Neotropical amphibians are the result of their functional and phylogenetic relationships. Understanding the associations between ecological similarity and phylogenetic relatedness among species can provide a convincing statement on the role of evolutionary history in the filling of the niche space. Here, we assessed the ancestral character states of amphibian ecological traits and their evolutionary history in the Atlantic Forest Hotspot. We used 12 genes (11,906 bp) to reconstruct a phylogeny for 207 amphibian species and related it to eight ecological traits regarding their morphology, life-history and behavioural features. We revealed that closely related species can have similar ecological traits, suggesting that these traits are driven by phylogenetic history. Despite the high endemism rate of Atlantic Forest amphibians, our findings heavily rely on good studies on complete amphibian phylogenetic lineages to overcome potential biogeographical constraints. Using mechanisms of adaptive evolution in the context of phylogenetic diversification, we suggest that closely related species have different phylogenetic signals and ecological traits can evolve without relatedness. [ABSTRACT FROM AUTHOR]

Body size shapes ecological interactions across and within species, ultimately influencing the evolution of large‐scale biodiversity patterns. Therefore, macroecological studies of body size provide a link between spatial variation in selection regimes and the evolution of animal assemblages through space. Multiple hypotheses have been formulated to explain the evolution of spatial gradients of animal body size, predominantly driven by thermal (Bergmann's rule), humidity ('water conservation hypothesis') and resource constraints ('resource rule', 'seasonality rule') on physiological homeostasis. However, while integrative tests of all four hypotheses combined are needed, the focus of such empirical efforts needs to move beyond the traditional endotherm–ectotherm dichotomy, to instead interrogate the role that variation in lifestyles within major lineages (e.g. classes) play in creating neglected scenarios of selection via analyses of largely overlooked environment–body size interactions. Here, we test all four rules above using a global database spanning 99% of modern species of an entire Order of legless, predominantly underground‐dwelling amphibians (Gymnophiona, or caecilians). We found a consistent effect of increasing precipitation (and resource abundance) on body size reductions (supporting the water conservation hypothesis), while Bergmann's, the seasonality and resource rules are rejected. We argue that subterranean lifestyles minimize the effects of aboveground selection agents, making humidity a dominant selection pressure – aridity promotes larger body sizes that reduce risk of evaporative dehydration, while smaller sizes occur in wetter environments where dehydration constraints are relaxed. We discuss the links between these principles with the physiological constraints that may have influenced the tropically‐restricted global radiation of caecilians. [ABSTRACT FROM AUTHOR]

Aim: Abiotic factors such as global temperature or continental fragmentation may favour speciation through the ecological and geographical isolation of lineages, but macroevolutionary quantifications of such effect with both fossil and phylogenetic data are rarely performed. Here, we propose to use biogeographical estimations and palaeo‐environmental diversification models to estimate whether and how palaeotemperature and the sequential break‐ups of Pangaea, Gondwana and Laurasia have affected the diversification of amphibians through time. Location: Global. Methods: Using a time‐calibrated phylogeny for 3,309 amphibian species and a genus‐level fossil record, we estimated the diversification rates of the group with birth–death models allowing rates to depend on the temporal variations of the environment. We used estimates of global palaeotemperature and an index of continental fragmentation through time to test the association between speciation and/or extinction rates and past temperature and fragmentation. We also estimated the biogeographical history based on a time‐stratified parametric model informed by the global palaeogeography. We inferred whether vicariance or dispersal events explained the ancient and current geographical distribution of amphibians. Results: The diversification analyses on the whole amphibians showed that temperature‐dependent models are better supported than tectonic‐dependent, time‐dependent and constant‐rate models for both the fossil and phylogenetic data. The best‐fitting temperature‐dependent model indicated a positive dependence of both speciation and extinction rates with the temperature through time. Biogeographical analyses indicated a Pangaean origin for amphibians and also showed that allopatric speciation (vicariance) explained important phases of the evolution of geographical ranges in the Mesozoic. Main conclusions: Our results support that palaeotemperatures have positively impacted amphibian diversification. Our study provides additional insights into how to quantify the effect of the landmass fragmentation on the diversification processes and shows with biogeographical reconstruction that continental fragmentation is linked to allopatric speciation in the early history of the clade. [ABSTRACT FROM AUTHOR]

Climate refuges have been used by several species over historical climate change. Ectothermic species often display good models for climate change studies because they are highly sensitive to temperature. Analysis of species loss with ecosystem and evolutionary values helps to understand environmental processes and climate change consequences. We determined the functional and phylogenetic diversity of amphibians in the Atlantic Forest hotspot, using multiple models representing present and future conditions. Through a novel approach, we predict species' threat status by 2080, following the IUCN's criterion B1. Our results estimate a drastic reduction in species richness, ecosystem functioning and evolutionary history at low latitudes and altitudes. We show that species will tend to disperse to the areas with milder temperatures (i.e., high latitudes/altitudes). Some of these areas are the same climate refuges that have been suggested for the Late Pleistocene. We highlight that 60% of amphibians can become threatened under predicted-future conditions. This work advances the knowledge on climate refuges for amphibian ecology and evolution, supporting complementary tools for conservation strategies. [ABSTRACT FROM AUTHOR]

RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians. [ABSTRACT FROM AUTHOR]

In March and April 2018 we surveyed amphibians and reptiles in two Proposed Protected Areas (PPAs) in Liberia. In the Krahn-Bassa Proposed Protected Area (KBPPA) in eastern Liberia 36 species of amphibians and 13 species of reptiles were recorded. In the Foya Proposed Protected Area (FPPA) in western Liberia 39 species of amphibians and 10 species of reptiles were recorded. The encountered herpetological communities in both sites were typical for West African rainforests. However, some species indicated disturbances, in particular at the edges of the study areas, the surrounding villages and plantations, and old artisanal gold mining sites within forests. Of particular conservation interest was the discovery of a high percentage of typical rainforest specialists with ranges restricted to the western part of the Upper Guinea rainforest biodiversity hotspot. Outstanding discoveries in KBPPA were two new species of puddle frogs, and the first country record for the arboreal, parachuting lizard Holaspis guentheri. Remarkable records in FPPA comprise a new species of stiletto snake, a new puddle frog and records of various frog species typically breeding in undisturbed rainforest streams, such as Odontobatrachus natator and Conraua alleni. Both study areas comprise an important proportion of the remaining rainforests in the Upper Guinea forest zone. The new discoveries indicate that within this biogeographic area, southeastern and western Liberian rainforest may still hold various undiscovered species and species of conservation concern. Further surveys in KBPPA and FPPA and nearby forests should clarify the distribution and conservation status of the new taxa. This study also emphasizes that the western part of the Liberian forests comprise, at least partly, a herpetofauna which differs from that of the East of the country. The recorded threatened amphibian species are all specialized on relatively undisturbed rainforests and they all have only small geographic ranges. The remaining parts of undisturbed or little disturbed forests thus have high importance for the long-term survival of these species. In conclusion, the study areas have a high conservation potential and should be urgently protected from any further forest loss, degradation, and uncontrolled hunting. [ABSTRACT FROM AUTHOR]

Abstract. The amphibian fauna of the state of Rio de Janeiro, in southeatern Brazil, is characterized by high species richness and rates of endemism, and is still insufficiently known. A first list of amphibian species with occurrence in the state was published in 2004 and reported 166 taxa, but since then many new records, descriptions of new taxa, and revalidations and synonymizations of species have consistently improved the knowledge about the state’s amphibian biodiversity. Thus, a review and update of that list was deemed necessary. We herein present an updated and commented list of amphibian species occurring in the state of Rio de Janeiro based on a survey of the literature. We recorded the occurrence of a total of 201 species of amphibians (197 anurans and four caecilians) in Rio de Janeiro, with 54 of them (ca. 27%) considered to be endemic of the state. Our study presents an increase in species richness of 21% since the publication of the previous list, indicating a consistent advance in knowledge of the composition of the amphibian fauna in the state. In spite of its relatively small territorial extension (total area ca. 43,800 km²), the state of Rio de Janeiro contains nearly 20% of the amphibian species known to occur in Brazil and around 40% of those occurring in the Atlantic Forest biome. Thus, that state constitutes an important reservoir of amphibian biodiversity in the Atlantic Forest biome and in Brazil, as a whole.

Here, we describe the anatomy of the female reproductive system of the aquatic, viviparous caecilian Typhlonectes natans. We conducted our research on two adult females using light microscopy and reflected our results with the available literature data on the anatomy of the reproductive systems of caecilian amphibians. The female reproductive system of T. natans consisted of longitudinal, paired ovaries incorporated with fat bodies, paired oviducts and the cloaca. The ovaries were arranged in segmental mannered germinal nests and the oocytes were in various stages of development. Ovulated, postvitellogenic oocytes were present in the oviducts of both females. The wall of the oviduct consisted of three layers: the mucous membrane, layers of muscles and serous membrane. The presence of wedge-like cells, not previously reported in the mucous membrane of the caecilian oviduct is postulated. Although the females possessed ovulated eggs, no sperm were detected in any part of the oviducts leaving the question of eventual female sperm storage in Typhlonectes natans open.

Introduction. Typhlonectes compressicauda is a viviparous gymnophionan amphibian living in tropical areas of South America. This lengthened amphibian is submitted to seasonal variations characterized by the rainy season (from January to June) and the dry season (from July to December). The mineral homeostasis in amphibians is partly ensured by the neurohormones arginine-vasotocin (AVT), and mesotocin (MST). These two hormones were localized in the hypothalamus, and their receptors, mesotocin receptors (MTR) and vasotocin receptors (VTR2) in the kidney. The aim of the study was to better understand the physiology of the hydromineral regulation of the studied species. Material and methods. The specimens of T. compressicauda male and female adult were divided into 6 groups: males in the rainy season, males in the dry season, females pregnant in the rainy season, females pregnant in the dry season, females not pregnant in the rainy season, females not pregnant in the dry season. We studied the expression of hormones (AVT, MST) and their receptors (MTR, VTR2) in the hypothalamus and the kidney, respectively, by immunohistochemical and histological techniques. We also studied the expression of aquaporin-2 (AQP2), a water-channel protein in the kidney. Results. We found that the MST (diuretic hormone) and its receptor were more intensively expressed during the rainy season, whereas the period of maximal AVT (anti-diuretic hormone) and VTR2 expression was the dry season. A quantitative analysis showed significant differences in the number of labeled cells in the hypothalamus depending on the seasonal variation. The expression of AQP2 was observed in renal tubules during both seasons with an increased intensity during the dry season. Conclusion. The expression of the MST/AVT in brain, their receptors MTRs/VTR2, and AQP2 in kidney changed in T. compressicauda according to the seasonal variations. A direct relationship between the seasonal cycle and reproduction cycle was demonstrated in this species. [ABSTRACT FROM AUTHOR]

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-naukpyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii). [ABSTRACT FROM AUTHOR]

An inventory of the amphibians of the Reserva Ecológica Michelin - REM in southern Bahia, Brazil is presented. Sixty-nine species were recorded during a ten-year sampling period. Amphibians were distributed in two orders (Gymnophiona and Anura), belonging to twelve families [Aromobatidae (1), Bufonidae (3), Centrolenidae (1), Craugastoridae (5), Eleutherodactylidae (3), Hemiphractidae (2), Hylidae (34), Phyllomedusidae (5) Leptodactylidae (7), Microhylidae (4), Odontophrynidae (3) and Caeciliidae (1)]. Fifty per cent of the reproductive modes known for Atlantic forest anurans were recorded. While no threatened species were found at REM, six species are classified as data deficient (DD) by the Brazilian Red List of threatened species and deserve additional attention. Phasmahyla timbo and Vitreorana eurygnatha are listed as endangered in Bahia according to the list of threatened species of the state. Despite a higher diversity of amphibians in the Atlantic forest having been reported for mountainous regions, our results revealed that amphibian richness for lowland forests is also high. [ABSTRACT FROM AUTHOR]