ArticlePDF Available

Abstract

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit HI (12S and 16S ribosomal RNA and tRNA(Valine) genes, 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (approximate to 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x ($) over bar = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons.
A preview of the PDF is not available
... Bufonidae is the third largest Anura family (632/630/611 species grouped in 52/53/52 genera, according to [1][2][3] respectively), with a worldwide distribution and extensive presence in the European continent. In the new amphibian taxonomy proposed by Frost [4], the genus Bufo, formerly containing a great number of amphibian species, was reorganized. Most species were moved to other genera and the genus Bufo was restricted to members of the earlier B. bufo group. ...
... Most species were moved to other genera and the genus Bufo was restricted to members of the earlier B. bufo group. In this way, B. viridis and E. calamita, previously included in the genus Bufo, were relocated to other genera [4][5][6], although not without controversy [7,8]. ...
Article
Full-text available
Taxonomy in Bufonidae witnessed notable transformations. Bufotes viridis and Epidalea calamita, previously included in genus Bufo, were relocated in other genera, while the genus Bufo was restricted to members of the earlier Bufo bufo group. On the other hand, Bufo bufo sensu lato now includes four species: Bufo bufo, Bufo spinosus, Bufo verricossissimus and Bufo eichwaldi. In this study, we examined three species of three Bufonidae genera (B. spinosus, B. viridis and E. calamita) by conventional (C-banding and Ag-NOR staining) and molecular (in situ hybridization with probes for telomeric repeats and rDNA loci, and genomic in situ hybridization (GISH)) cytogenetic methods. C-banding patterns are reported for the first time for B. spinosus and E. calamita populations from Iberian Peninsula and for B. viridis from Greece, and reveal several differences with the reported C-banded karyotypes described for other European populations of these species. Silver staining shows size heteromorphisms of the signals at the Nucleolar Organizing Region (NOR). By contrast, FISH with ribosomal probes only reveal size heteromorphism of rDNA sequences in E. calamita, suggesting that the differences observed after silver staining in B. spinosus and B. viridis should be attributed to differences in chromosomal condensation and/or gene activity rather than to differences in the copy number for ribosomal genes. Regarding telomeric repeats, E. calamita is the only species with interstitial telomeric sequences (ITS) located on centromeric regions, probably originated by accumulation of telomeric sequences in the centromeric heterochromatin. Finally, we analyzed the composition and distribution of repetitive sequences by genome in situ hybridization. These experiments reveal the accumulation of repetitive sequences in centromeric regions of the three species, although these sequences are not conserved when species from different genera are compared.
... We also summarize detailed geographic coordinates of each species occurrence, offer insights into their distribution, and reduce knowledge gaps. Moreover, anuran taxonomy has changed greatly during the 21 st century, with large phylogenies and multidata integrative taxonomic reviews enabled by the molecular and digital revolutions (e.g., Frost et al. 2006;Peloso et al. 2014). Thus, to enhance the knowledge regarding the anurans of Amapá, we update and make comments on the taxonomy of several species. ...
Article
Full-text available
We herein present the first annotated anuran checklist for the Brazilian state of Amapá, eastern Amazonia, based on a thorough literature review. We recorded the occurrence of 111 species belonging to 13 anuran families distributed across 48 localities throughout Amapá, within two biomes. Among these species, 62.5% occur exclusively in the Tropical Moist Broadleaf Forest biome, ~8% occur exclusively in the Tropical Savanna biome, and ~29% occur in both. Two species were considered endemic to Amapá and were registered only in the central portion of the state. Regarding the conservation status, only one species (Dendropsophus amicorum) is classified as threatened, assigned to the "critically endangered" category. The other species are categorized as either "least concern" or "data deficient" (85 and 8, respectively), whereas 21 are not evaluated. The current annotated list contributes to the incipient knowledge on anuran species richness in Amapá and, despite the research regarding anuran taxonomy has considerably progressed over the past 20 years, there is still much to do. Our data highlight the need for trained taxonomists to develop research in the state.
... Along with its sister taxon, the also Chilean endemic Telmatobufo, they constitute the clade Calyptocephalellidae. In the recent broadly-sampled, molecular phylogenetic analyses, Calyptocephalellidae resulted the sister-taxon of the Australian Myobatrachoidea in a clade named Australobatrachia, the sister group of all remaining notogaeanurans (sensu Frost et al., 2006;Jetz and Pyron, 2018;Hime et al., 2021). ...
Article
Calyptocephalella is nowadays only represented by the emblematic Chilean Helmeted Water Toad C. gayi, restricted to water bodies of Central Chile. Numerous fossil remains from latest Cretaceous to Miocene sedimentary rocks at the east of Los Andes have been attributed to this genus and several extinct Calyptocephalella species were erected. The relationships of these taxa, including the monophyly of the genus and the validity of some species, are however still unresolved. Here, we described a fossil anuran from the late Miocene of the northern Argentine Patagonia, which we attributed to a new extinct species of Calyptocephalella after analyzing the osteology and shared characters of all presumed species of the genus. These characters, whose co-occurrence seems to be exclusive of Calyptocephalella, include ornamented skull, extensive nasal processes contacting maxillae, broad nasal-frontoparietal contact, occipital artery enclosed by bone, maxilla contributing to the orbital margin and contacting squamosal, squamosal zygomatic and otic rami forming a continuous plate, scapula with a well-developed anterior lamina, and high iliac dorsal crest. The new species is differentiable in the proportion of the maxillary partes, triangular maxillary postorbital process, narrow maxillary contribution to the orbital margin; an oblique frontoparietal-squamosal suture. We also analyzed the putative morphological and ecological diversity of Calyptocephalella along the geological record, from which this fossil is nowadays the youngest and northernmost record east of Los Andes. We concluded that Calyptocephalella would be a successful lineage that inhabited Patagonia since, probably, the latest Cretaceous and during most of the Cenozoic, whose diversification might be related with the environmental changes that took place in southern South America during the these times, and from which C. gayi is only a vestigial representative.
... Two host species have not been sequenced for both genes. Instead, the missing genes were taken from phylogenetically closely related species, as per the classification proposed by [40]. Previous analysis showed that the replacement of these genes does not impact the phylogenetic position of taxa in this dataset [38]. ...
Article
Full-text available
Today parasites comprise a huge proportion of living biodiversity and play a major role in shaping community structure. Given their ecological significance, parasite extinctions could result in massive cascading effects across ecosystems. It is therefore crucial that we have a way of estimating their extinction risk. Attempts to do this have often relied on information about host extinction risk, without explicitly incorporating information about the parasites. However, assuming an identical risk may be misleading. Here, we apply a novel metric to estimate the cophylogenetic extinction rate, Ec, of parasites with their hosts. This metric incorporates information about the evolutionary history of parasites and hosts that can be estimated using event-based cophylogenetic methods. To explore this metric, we investigated the use of different cophylogenetic methods to inform the Ec rate, based on the analysis of polystome parasites and their anuran hosts. We show using both parsimony- and model-based approaches that different methods can have a large effect on extinction risk estimation. Further, we demonstrate that model-based approaches offer greater potential to provide insights into cophylogenetic history and extinction risk.
... In the past few decades the phylogenetic relationship between R. rhodopus and R. bipunctatus has attracted considerable controversy. For example, Inger et al. and Frost suggest that R. rhodopus is a synonym of R. bipunctatus 16,17 , but subsequently Bordoloi et al. consider R. rhodopus as a valid species 18 . Moreover, the phylogenetic relationships among R. bipunctatus, R. rhodopus and R. reinwardtii have also been disputed. ...
Article
Full-text available
Classification of the genus Rhacophorus has been problematic. In particular there has been considerable controversy surrounding the phylogenetic relationships among Rhacophorus rhodopus, R. bipunctatus, and R. reinwardtii. To examine the relationship among these Rhacophorus species, we assembled the complete mitochondrial genome sequence of R. rhodopus. The R. rhodopus genome is 15,789 bp in length with 12 protein-coding genes (PCGs) (losing ND5), two ribosomal genes, 22 transfer RNA genes, and a control region (D-loop). Base composition of the overall sequence was 60.86% for A + T content and 39.14% for C + G content. Most of the PCGs used ATG as a start codon, except for the COX I gene, which used the ATA start codon. COX I and ND6 used AGG and ATP8 stop codons respectively, while ND3 and ND4L used the TAA stop codon. For the remaining seven genes, the stop codons was incomplete. In addition, both 5' and 3' of the control areas had distinct repeating regions. Based on three datasets and two methods (Bayesian inference (BI) and maximum likelihood (ML)), we reconstructed three phylogenetic trees to explore the taxonomic status of the species and the phylogenetic relationship among R. rhodopus, R. bipunctatus and R. reinwardtii. Our results indicated that these three species are non-monophyletic; thus, the phylogenetic relationship among them is complex and difficult to determine. Further, R. rhodopus is divided into three lineages from different parts of China. The two Rhacophorus samples showed very close phylogenetic relationship with R. rhodopus. Our results add to the mitochondrial genome database of amphibians and will help to disentangle the phylogenetic relationships within the Rhacophoridae.
Article
The paper contains data on sexual size dimorphism of Bufotes sitibundus Pallas, 1771 with samples from the “Greater Caucasus”, “Lankaran” and “Absheron” territories of Azerbaijan. The 139 adult specimens (62♂ and 77♀) from 3 populations were collected. They were released after morphometric measurements and pattern morphs analysis. The data were processed in the STATISTICA Stat Soft 10 program. Reliability of differences was estimated using Independent Sample t-test. Statistical analysis of morphological features showed that there are differences in different features between males and females in different populations. In each of the populations studied, the femur (FmL) and tibia (TbL) were longer in males than in females. Investigation of the pattern polymorphism in 126 specimens has shown that dorsal pattern with spots separated by short distance between them is dominant in 2 studied populations (“Absheron” and “Lankaran”). There were not found any differences between males and females according to pattern charcteristcs.
Article
The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present, a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MY. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.
Article
Full-text available
The highly differentiated anuran larvae make them an interesting and complementary source of information to understand anuran evolution. Among neotropical foam‐nesting frogs, the available information on tadpole morphology for the subfamily Leiuperinae remains largely incomplete and variably reported among genera; in the monophyletic genus Engystomops it is still incipient. Herein, we summarize available information on larval morphology for five of the nine known species of Engystomops, three of them for the first time, reporting external morphology, buccopharyngeal cavity, and skeleton. The tadpoles of the genus have an overall generalized morphology and many traits are conserved across species. Nevertheless, many characters are systematically informative and some are diagnostic for some species, as the paravertebral gland in E. petersi and the dorsally directed spiracle in E. puyango. Other characters provide support for some subclades within the genus. Moreover, some traits, such as the direction of the vent tube, supports the close relationship between Engystomops and Physalaemus, whereas other support the existence of these two as distinct genera, such as the overall shape of the lateral ridge papillae and the presence of a processus pseudopterygoideus. This article is protected by copyright. All rights reserved.
Chapter
Full-text available
Unisexual Ambystoma phylogeny and lampbrush chromosomes
Thesis
One-hundred and five microhylid species, which represent 56 genera in all ten subfamilies, were examined for external morphology, myology, and osteology in order to determine the phylogenetic relationships among these species and between microhylids and other frog families. Phylogenetic relationships were analyzed using cladistic methodology, and 28 outgroup taxa, which represent ten frog families, were used to root the hypothesis. Variation is reported in many morphological characters that had been considered constant among microhyloid frogs. New morphological characters that are useful in microhylid systematics are described and discussed. One-hundred-twenty equally parsimonious cladograms, each with a consistency index of 0.089, are found using 133 taxa and 188 characters. The low consistency index of the phylogenetic hypothesis proposed in this study reflects the high levels of convergences and reversals of morphological characters in microhylid evolution. More than two thirds of the characters show character state reversals. This suggests that reversal is more important in microhylid evolution than convergence. Such plasticity of morphological character evolution in microhylids can probably be attributed to heterochrony, as indicated by the short or absent larval stage found in many microhylids. The microhyloid phylogeny proposed in this study also offers an explanation for the origin of scoptanuran tadpoles through neoteny. The monophyletic Microhyloidea delimited in this study includes two monophyletic taxa: Brevicipitidae and Microhylidae. Hemisus and Rhinophrynus form a clade that is the sister taxon of brevicipitines in Brevicipitidae. Within Microhylidae, only two subfamilies are now recognized: Cophylinae and Microhylinae. The most parsimonious explanation for the distribution of monophyletic microhylid lineages in South America, Madagascar, and Southeast Asia is through vicariance. Microhyloids are hypothesized to have existed in Gondwanaland before its breakup prior to or during the early Jurassic. This study shows that the topology of the cladogram and the nature of the synapomorphies of microhyloid taxa can be affected by the choice of outgroup as well as ingroup taxa employed. In order to minimize the assumptions that are associated with cladistic analyses, selection of outgroup taxa should not be bounded by the present classification, because doing so emphasizes stability rather than phylogenetic precision.
Article
Rana psaltes n sp has been confused with R. adenopleura, but the 2 differ in several morphological and ecological features; R. psaltes constructs a small mud nest and lays a few eggs in it.-from Author