Global patterns of diversification in the history of modern amphibians

The Angiosperm Terrestrial Revolution buffered ants against extinction

With ~14,000 extant species, ants are ubiquitous and of tremendous ecological importance. They have undergone remarkable diversification throughout their evolutionary history. However, the drivers of their diversity dynamics are not well quantified or understood. Previous phylogenetic analyses have suggested patterns of diversity dynamics associated with the Angiosperm Terrestrial Revolution (ATR), but these studies have overlooked valuable information from the fossil record. To address this gap, we conducted a comprehensive analysis using a large dataset that includes both the ant fossil record (~24,000 individual occurrences) and neontological data (~14,000 occurrences), and tested four hypotheses proposed for ant diversification: co-diversification, competitive extinction, hyper-specialization, and buffered extinction. Taking into account biases in the fossil record, we found three distinct diversification periods (the latest Cretaceous, Eocene, and Oligo-Miocene) and one extinction period (Late Cretaceous). The competitive extinction hypothesis between stem and crown ants is not supported. Instead, we found support for the co-diversification, buffered extinction, and hyper-specialization hypotheses. The environmental changes of the ATR, mediated by the angiosperm radiation, likely played a critical role in buffering ants against extinction and favoring their diversification by providing new ecological niches, such as forest litter and arboreal nesting sites, and additional resources. We also hypothesize that the decline and extinction of stem ants during the Late Cretaceous was due to their hyper-specialized morphology, which limited their ability to expand their dietary niche in changing environments. This study highlights the importance of a holistic approach when studying the interplay between past environments and the evolutionary trajectories of organisms.

Animal models to study cardiac regeneration

Permanent fibrosis and chronic deterioration of heart function in patients after myocardial infarction present a major health-care burden worldwide. In contrast to the restricted potential for cellular and functional regeneration of the adult mammalian heart, a robust capacity for cardiac regeneration is seen during the neonatal period in mammals as well as in the adults of many fish and amphibian species. However, we lack a complete understanding as to why cardiac regeneration takes place more efficiently in some species than in others. The capacity of the heart to regenerate after injury is controlled by a complex network of cellular and molecular mechanisms that form a regulatory landscape, either permitting or restricting regeneration. In this Review, we provide an overview of the diverse array of vertebrates that have been studied for their cardiac regenerative potential and discuss differential heart regeneration outcomes in closely related species. Additionally, we summarize current knowledge about the core mechanisms that regulate cardiac regeneration across vertebrate species.

Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas

Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.

Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species

Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.

The impact of the insecticide acetamiprid on the embryogenesis of the aquatic model organism Xenopus laevis

Acetamiprid (ACT) is used extensively in agriculture worldwide, although data on ACT concentrations in natural water bodies and its impact on aquatic organisms are limited. To study whether ACT influences the embryogenesis of the South African clawed frog Xenopus laevis, embryos were incubated in ACT solutions from 0.01 to 100 mg/L. The low concentrations were chosen on the basis of concentrations already found in nature. ACT treatment leads to shorter embryo lengths, intestine malformation and reduced eye areas. It also affects the cranial cartilage and cardiac development as well as the embryo's mobility. The expression of tissue-specific marker genes is affected as well. Thus, our study suggests that pesticides may lead to an increased mortality of non-target organisms and emphasizes the importance of regular testing for ACT concentrations in nature. Our study provides an overview of ACT effects and can therefore be used as a basis for an ACT risk assessment.

Identification and functional characterization of protein kinase R (PKR) in amphibian Xenopus tropicalis

As one of interferon-induced serine/threonine kinases, the protein kinase R (PKR) plays vital roles in antiviral defense, and functional features of PKR remain largely unknown in amphibians, which suffer from ranaviral diseases in the last few decades. In this study, a PKR gene named Xt-PKR was characterized in the Western clawed frog (Xenopus tropicalis). Xt-PKR gene was widely expressed in different organs/tissues, and was rapidly induced by poly(I:C) in spleen, kidney, and liver. Intriguingly, Xt-PKR could be up-rugulated by the treatment of type I and type III interferons, and the transcript level of Xt-PKR induced by type I interferon was much higher than that of type III interferon. Moreover, overexpression of Xt-PKR can suppress the protein synthesis and ranavirus replication in vitro, and the residue lysine required for the translation inhibition activity in mammalian PKR is conserved in Xt-PKR. The present study represents the first characterization on the functions of amphibian PKR, and reveals considerable functional conservation of PKR in early tetrapods.

Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.

Toxicity of the neonicotinoid insecticides thiamethoxam and imidacloprid to tadpoles of three species of South American amphibians and effects of thiamethoxam on the metamorphosis of Rhinella arenarum

The present study examined the acute and chronic toxicity of the neonicotinoid insecticides imidacloprid (IMI) and thiamethoxam (TIA) on the neotropical amphibian species Rhinella arenarum, Rhinella fernandezae and Scinax granulatus. The median lethal concentration after 96 hr exposure (96 hr-LC₅₀) ranged between 11.28 and >71.2 mg/L amongst all species and development stages tested, indicating that these pesticides are not likely to produce acute toxicity in the wild. The subchronic toxicity was also low, with 21 day-LC₅₀ values ranging between 27.15 and >71.2 mg/L. However, tadpoles of Rhinella arenarum exposed to thiamethoxam from stage 27 until completion of metamorphosis presented a significantly lower metamorphic success rate together with a smaller size at metamorphosis, starting from the lowest concentration tested. Although a number of studies previously examined the effects of neonicotinoids on amphibian tadpoles, these investigations focused on the time to metamorphosis and reported a variety of results including retardation, acceleration or lack of effect. Here, data demonstrated that thiamethoxam predominantly impacts metamorphosis through reduction of the transformation success and body weight, rather than by affecting the timings of metamorphosis. By closely monitoring progression of tadpoles through the different stages, impairment of metamorphosis was demonstrated to occur during the transition from stage 39 to 42, suggesting an effect on the thyroid system. An asymmetry in the length of the arms was also observed in metamorphs treated with thiamethoxam. Overall, these results indicate that thiamethoxam, and conceivably other neonicotinoids, have the potential to significantly impair metamorphosis of amphibians and diminish their performance and survival in the wild.

Biogeographic history of Palearctic caudates revealed by a critical appraisal of their fossil record quality and spatio-temporal distribution

The disjunct geographical range of many lineages of caudates points to a complex evolutionary and biogeographic history that cannot be disentangled by only considering the present-day distribution of salamander biodiversity. Here, we provide a critical reappraisal of the published fossil record of caudates from the Palearctic and quantitatively evaluate the quality of the group's fossil record. Stem-Urodela and Karauridae were widespread in the Palearctic in the Middle Jurassic, suggesting an earlier, unsampled diversification for this group. Cryptobranchidae reached Europe no later than the Oligocene, but this clade was subsequently extirpated from this continent, as well as from western and central Asia. The relatively recent appearance of hynobiids in the fossil record (Early Miocene) is most likely an artefact of a taphonomic bias against the preservation of high-mountain, stream-type environments which early members likely inhabited. Salamandroids first appear in Europe, expanding into Asia by the Miocene. The apparently enigmatic and disjunct distribution of extant caudate lineages is therefore explained by a wider past geographical range, as testified by the fossil record, which was fragmented during the late Cenozoic by a combination of tectonic (i.e. the uplift of the Tibetan Plateau) and climatic drivers, resulting in regional extirpations.

Electrophysiological responses to conspecific odorants in Xenopus laevis show potential for chemical signaling

The fully aquatic African clawed frog, Xenopus laevis, has an unusual and highly adapted nose that allows it to separately sample both airborne and waterborne stimuli. The function of the adult water nose has received little study, despite the fact that it is quite likely to receive information about conspecifics through secretions released into the water and could aid the frog in making decisions about social and reproductive behaviors. To assess the potential for chemical communication in this species, we developed an in situ electroolfactogram preparation and tested the olfactory responses of adult males to cloacal fluids and skin secretions from male and female conspecifics. We found robust olfactory responses to all conspecific stimuli, with greatest sensitivity to female cloacal fluids. These results open the door to further testing to identify compounds within cloacal fluids and skin secretions that are driving these responses and examine behavioral responses to those compounds. Understanding the role of chemical communication in social and reproductive behaviors may add to our rich understanding of vocal communication to create a more complete picture of social behavior in this species.

Middle Jurassic fossils document an early stage in salamander evolution

Salamanders are an important group of living amphibians and model organisms for understanding locomotion, development, regeneration, feeding, and toxicity in tetrapods. However, their origin and early radiation remain poorly understood, with early fossil stem-salamanders so far represented by larval or incompletely known taxa. This poor record also limits understanding of the origin of Lissamphibia (i.e., frogs, salamanders, and caecilians). We report fossils from the Middle Jurassic of Scotland representing almost the entire skeleton of the enigmatic stem-salamander Marmorerpeton. We use computed tomography to visualize high-resolution three-dimensional anatomy, describing morphologies that were poorly characterized in early salamanders, including the braincase, scapulocoracoid, and lower jaw. We use these data in the context of a phylogenetic analysis intended to resolve the relationships of early and stem-salamanders, including representation of important outgroups alongside data from high-resolution imaging of extant species. Marmorerpeton is united with Karaurus, Kokartus, and others from the Middle Jurassic-Lower Cretaceous of Asia, providing evidence for an early radiation of robustly built neotenous stem-salamanders. These taxa display morphological specializations similar to the extant cryptobranchid "giant" salamanders. Our analysis also demonstrates stem-group affinities for a larger sample of Jurassic species than previously recognized, highlighting an unappreciated diversity of stem-salamanders and cautioning against the use of single species (e.g., Karaurus) as exemplars for stem-salamander anatomy. These phylogenetic findings, combined with knowledge of the near-complete skeletal anatomy of Mamorerpeton, advance our understanding of evolutionary changes on the salamander stem-lineage and provide important data on early salamanders and the origins of Batrachia and Lissamphibia.

A new genus and species of frog from the Kem Kem (Morocco), the second neobatrachian from Cretaceous Africa

Neobatrachia, a clade representing the majority of extant anuran diversity, is thought to have emerged and diversified during the Cretaceous. Most of the early diversification of neobatrachians occurred in southern Gondwana, especially the regions that are today South America and Africa. Whereas five extinct neobatrachians have been described from the Cretaceous of South America in the last decade, only one is known from Africa. This difference in the known extinct diversity is linked to the lack of well-preserved specimens, understudy of fragmentary remains, and lack of known Cretaceous sites in Africa. Study of fragmentary anuran remains from Africa could allow for the identification of previously unknown neobatrachians, allowing for a better understanding of their early diversification. We reanalysed several previously described anuran specimens from the well-known Kem Kem beds, including using CT-scanning. Through our osteological study, we determined that several cranial bones and vertebrae represent a new hyperossified taxon for which we provide a formal description. Comparison to other hyperossified anurans revealed similarities and affinity of this new taxon with the neobatrachians Beelzebufo (extinct) and Ceratophrys (extant). Phylogenetic analyses supported this affinity, placing the new taxon within Neobatrachia in an unresolved clade of Ceratophryidae. This taxon is the oldest neobatrachian from Africa, and reveals that neobatrachians were already widespread throughout southern Gondwana during the earliest Late Cretaceous.

Distinct Amphibian Elevational and Seasonal Phylogenetic Structures Are Determined by Microhabitat Variables in Temperate Montane Streams

Simple Summary

Phylogenetic structure can be used to understand various ecological patterns. The main objective of the present study was to understand the elevational and seasonal amphibian phylogenetic structures in temperate montane streams. This study was conducted in 13 streams located in lowland and highland sites of Tianping mountain, China, in April, June, August, and October 2017, separately. We found that the elevational spatial patterns were not significantly different, but the seasonal temporal patterns differed significantly for amphibian phylogenetic structures, associated with the variation of microhabitat variables.

Abstract

Phylogenetic structure is a key facet of biodiversity, reflecting the evolutionary history of species, and thus can be used to understand various ecological patterns. Although amphibian phylogenetic structures have been tested across space and time separately, simultaneous quantifications are still needed. In the present study, amphibians in streams of Tianping mountain, China, were selected as the model to investigate their elevational spatial and seasonal temporal patterns of phylogenetic diversity. Specifically, 13 streams located in lowland and highland sites were sampled for amphibians and measured for microhabitat variables in April, June, August, and October 2017, separately. Four phylogenetic structural indices, including Faith’s PD, standardized effect size (SES) of Faith’s PD, mean pairwise phylogenetic distance index (MPD), and SES.MPD, were calculated. Our results revealed that amphibian phylogenetic patterns were not significantly different between lowland and highland sites, but differed significantly between four seasons, associated with distinct community assembly rules (phylogenetically overdispersed vs. phylogenetically clustered). Importantly, these patterns were strongly determined by microhabitat variables such as rock cover, water temperature, and water depth. Our results provide fundamental knowledge to better protect amphibian diversity. Both elevational and seasonal variations are important to understanding the general patterns of amphibian community assembly rules.

Concentration of current-use pesticides in frogs from the Pampa region and correlation of a mixture toxicity index with biological effects

Contamination with current-use pesticides is frequently mentioned as a key factor in global amphibian declines although a limited number of studies have examined the mixture of pesticides accumulated by free-living frogs. This study examined the presence of 46 different pesticide residues in the muscle and kidney tissues of two frog species living in close association with row crops in the Pampa region of Argentina: The terrestrial Leptodactylus latinasus and the semi-aquatic Leptodactylus latrans. A total of 20 different pesticides were identified in frog tissues; chlorpyrifos-methyl, pirimiphos-methyl and acetochlor being the most frequently detected molecules. Overall, one or more pesticide residues (up to 12 in a single frog) were detected in 40-57 % of L. latrans. L. latinasus was found to present more pesticide detections than L. latrans. Interestingly, frog sampled in a natural reserve where no pesticides are applied presented an equivalent frequency of detections as frogs living near a crop. In L. latrans, the calculation of a pesticide toxicity index (PTI) permitted to highlight the existence of a strong positive correlation between PTI and liver GSH contents of females whereas, in males, PTI was negatively correlated with the perimeter of testicular seminiferous tubules. Males also presented near significant negative correlations between PTI and both body condition and the scaled fat index. These results indicate that frogs inhabiting agricultural regions are exposed to a complex and diffuse contamination by pesticide mixtures which is likely responsible for a number of biological effects that may be relevant at the population level.

Fire-prone Rhamnaceae with South African affinities in Cretaceous Myanmar amber

The rapid Cretaceous diversification of flowering plants remains Darwin's 'abominable mystery' despite numerous fossil flowers discovered in recent years. Wildfires were frequent in the Cretaceous and many such early flower fossils are represented by charcoalified fragments, lacking complete delicate structures and surface textures, making their similarity to living forms difficult to discern. Furthermore, scarcity of information about the ecology of early angiosperms makes it difficult to test hypotheses about the drivers of their diversification, including the role of fire in shaping flowering plant evolution. We report the discovery of two exquisitely preserved fossil flower species, one identical to the inflorescences of the extant crown-eudicot genus Phylica and the other recovered as a sister group to Phylica, both preserved as inclusions together with burned plant remains in Cretaceous amber from northern Myanmar (~99 million years ago). These specialized flower species, named Phylica piloburmensis sp. nov. and Eophylica priscastellata gen. et sp. nov., exhibit traits identical to those of modern taxa in fire-prone ecosystems such as the fynbos of South Africa, and provide evidence of fire adaptation in angiosperms.

An exceptionally well-preserved herbaceous eudicot from the Early Cretaceous (late Aptian-early Albian) of Northwest China

A fossil eudicot, Gansufructus saligna gen. et sp. nov., is reported from the Early Cretaceous (late Aptian-early Albian) of the Gansu Province, Northwest China, based on numerous well-preserved axes with attached leaves and infructescences. The leaves are alternate, short petiolate and linear-lanceolate with low rank pinnate to reticulate venation. The infructescences are loose panicles bearing fruits in different stages of maturity, each containing four partly free carpels borne in a whorled arrangement. Each carpel has three to five seeds borne along its ventral margin. The nature of the leaves and axes indicates a terrestrial, herbaceous habit. In general organization, Gansufructus is closely similar to the fruit-bearing axes of Sinocarpus decussatus from the Early Cretaceous Jehol Biota, as well as other more or less contemporaneous angiosperms from the Far East, which together provide evidence of diverse eudicot angiosperms of low stature colonizing areas close to environments of deposition.

Endoparasite community structure of an anuran assemblage in the Caatinga, Northeastern Neotropical Region

Amphibians are a widespread Chordata taxon and are important for maintaining the balance of both terrestrial and aquatic ecosystems. Brazil has a rich amphibian fauna; however, little is known about the role of their ecology and phylogenetic relationships during the assembly processes of associated endoparasite communities. Herein, we describe an endoparasite community in an anuran assemblage in the Caatinga, a unique biome of dry forests in north-eastern Brazil. We studied endoparasite diversity, as well as the effects of body length, body mass, body volume and sex on parasite abundance. We also investigated the influence of ecological and historical factors and anuran microhabitat use on endoparasite composition. We analysed individuals from 13 anuran species distributed across five families: Odontophrynidae (Proceratophrys cristiceps); Leptodactylidae (Leptodactylus fuscus, Leptodactylus vastus, Leptodactylus macrosternum, Leptodactylus troglodytes and Physalaemus cuvieri); Hylidae (Pithecopus gonzagai, Scinax x-signatus, Boana raniceps and Dendropsophus nanus); Bufonidae (Rhinella diptycha and Rhinella granulosa); and Microhylidae (Dermatonotus muelleri). We found nine species of endoparasites, including seven nematodes (Aplectana membranosa, Cosmocerca sp., Oswaldocruzia mazzai, Raillietnema spectans, Rhabdias fuelleborni, Schrankiana sp. and Physaloptera sp.), one species of Trematoda (Glypthelmins pseudium) and one non-identified cestode. There was no significant relationship between endoparasite abundance and host body length, body mass, body volume and sex. A phylogenetic principal component analysis showed that ecological factors had a greater influence on endoparasite assemblage than historical factors. Similarly, our results showed that ecological factors had a greater influence on anuran microhabitat use compared to historical factors, which contributed to the generalist characteristics presented by most of the sampled endoparasite species.

Morphology of the Cutaneous Poison and Mucous Glands in Amphibians with Particular Emphasis on Caecilians (Siphonops annulatus)

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.

Biology of primordial germ cells in vertebrates with emphasis in urodeles amphibians

Primordial germ cells (PGCs) are highly specialized cells that play a relevant role in the maintenance and evolution of the species, since they create new combinations of genetic information between the organisms. Amphibians are a class of amniote vertebrates that are divided into three subclasses, the anurans (frogs and toads), the urodeles (salamanders and newts), and the gymnophiones (caecilians). The study of PGCs in amphibians has been addressed in more detail in anurans while little is known about the biology of this cell lineage in urodeles. Studies in some urodeles species have suggested that PGCs are of mesodermal origin, specifying in the lateral plate mesoderm at the late gastrula stage. With classical experiments it shown that, there is an induction of mesoderm, therefore most likely urodeles PGCs develop from unspecialized mesodermal tissue that responds to extracellular signals. However, some fundamental biological processes of PGCs such as the analysis of their specification, arrival, and colonization to the gonads, and their maintenance and differentiation into mature and fertile gametes remain to be elucidated. Therefore, knowledge about the biology of PGCs is of great importance to ensure the perpetuation of urodeles amphibians, as some species are in danger of becoming extinct.

Syamili, A.F. Katakath, U.S. Amal, M.S. Abhin, A. Devarajan, S. Sajitha, T. Arun, J. Jobin. Database of amphibian vouchers and records available at the Kerala Agricultural University Natural History Museum in Thrissur and an updated checklist of amphibians of Kerala, India

The amphibian database of the Centre for Wildlife Studies of Kerala Agricultural University has the data that are either available as voucher specimens with the Kerala Agricultural University Natural History Museum (KAUNHM) or as photo vouchers and other opportunistic records from Kerala part of the southern Western Ghats between 2008 and 2020. This repository holds information on 91 species of amphibians belonging to 10 families, of which 87% are endemic to the Western Ghats and 34% are classified under the IUCN Red List threatened categories.  This study highlights the significance of such digital databases that can serve as an immense source of regional biodiversity data, and therefore, biodiversity monitoring and conservation. 

A new genus of fossil frog (Anura) from lower Cretaceous deposits in South America

The frog clade Neobatrachia or "advanced frogs" represents more than 95% of the diversity within Anura. The neobatrachian fossil record is incomplete due to the small size and fragile nature of their bones but provides some clues on the time and rate of the current diversification of modern-day amphibians. The Crato Formation (Aptian) of northeastern Brazil is known for the presence of, at least, five species of neobatrachian fossils. Herein, we describe a well-preserved fossil that represents a new neobatrachian taxon from the Crato Formation (Cretaceous) in the Araripe Basin, northeastern Brazil, and perform phylogenetic analysis to assess its higher-level relationships. The new specimen is an almost complete and articulated skeleton with soft tissue preservation. Phylogenetic analysis recovered the specimen nested in the clade Hyloidea and our results highlight the remarkable value of the Crato Formation as a Laggerstätte.

Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)

One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.

Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development

Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.

Global Diversity and Geographic Distributions of Padina Species (Dictyotales, Phaeophyceae): New Insights Based on Molecular and Morphological Analyses

The taxonomic status and species diversity of the brown algal genus Padina (Dictyotales, Phaeophyceae) was assessed based on DNA sequences and the morpho-anatomy of specimens collected worldwide, especially from tropical and subtropical western Pacific regions. Phylogenetic analyses using chloroplast rbcL and mitochondrial cox3 gene sequences demonstrated four distinct clades for newly collected samples with high bootstrap support. Each species clade possesses a suite of morphological features that are not shared by any known species of Padina. These are P. imbricata sp. nov., Padina lutea sp. nov., P. moffittianoides sp. nov., and P. nitida sp. nov. The occurrence of these and other species of Padina clearly points to an elevated diversity of the genus in tropical/subtropical waters of the western Pacific. Phylogenetic analyses provided new insights into biogeographic characteristics of the genus, with many species in the Pacific Ocean showing shared/overlapping distributions, whereas species from the Mediterranean/Atlantic and/or the Indian Ocean tend to be confined to particular regions. Consideration has also been given to the evolutionary time frame of the genus Padina based on molecular time trees: a time tree of the concatenated data set (rbcL + cox3) revealed the estimated divergence time in the mid-Cretaceous, whereas those of cox3 and rbcL showed older estimates pointing to the periods of mid-Jurassic and Early Cretaceous, respectively.

Quantification and evolution of mitochondrial genome rearrangement in Amphibians

BACKGROUND

Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution.

RESULTS

Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation.

CONCLUSION

It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].

Molecular and functional characterization of interferon regulatory factor 1 (IRF1) in amphibian Xenopus tropicalis

Interferon regulatory factor 1 (IRF1) is an important regulator in controlling the transcription of type I interferon genes, and its functions have been well-characterized in mammals, birds and fish. However, little information is available regarding the function of amphibian IRF1. In this study, an IRF1 gene homolog named as Xt-IRF1 was identified in the Western clawed frog (Xenopus tropicalis), an amphibian model specie widely used for comparative immunology research. Xt-IRF1 and IRF1 in other vertebrates possess similar genomic structure and flanking genes, and were grouped together to form a separate clade in phylogenetic tree. In addition, Xt-IRF1 gene was constitutively expressed in all tissues examined, with the highest expression level observed in spleen, and was inducible after poly(I:C) stimulation. Importantly, the expression of Xt-IRF1 was markedly induced by recombinant type I interferon, and Xt-IRF1 induced a strong activation of both IFNβ and ISRE promoters. The present study opens the door to investigate the roles of IRF1 in amphibians, and thus contributes to a better understanding of the functional evolution of IRFs in lower tetrapods.

The struggle to equilibrate outer and inner milieus: Renal evolution revisited

The journey of life, from primordial protoplasm to a complex vertebrate form, is a tale of survival against incessant alterations in climate, surface topography, food chain, and chemistry of the external environment. Kidneys present with an ensemble embodiment of the adaptations devised by diverse life-forms to cope with such challenges and maintain a chemical equilibrium of water and solutes, both in and outside the body. This minireview revisits renal evolution utilizing the classic: From Fish to Philosopher; the story of our internal environment, by Prof. Homer W. Smith (1895-1962) as a template. Prof. Smith's views exemplified the invention of glomeruli, or its abolishment, as a mechanism to filter water. Moreover, with the need to preserve water, as in reptiles, the loop of Henle was introduced to concentrate urine. When compared to smaller mammals, the larger ones, albeit having loops of Henle of similar lengths, demonstrated a distinct packing of the nephrons in kidneys. Moreover, the renal portal system degenerated in mammals, while still present in other vertebrates. This account will present with a critique of the current concepts of renal evolution while examining how various other factors, including the ones that we know more about now, such as genetic factors, synchronize to achieve renal development. Finally, it will try to assess the validity of ideas laid by Prof. Smith with the knowledge that we possess now, and understand the complex architecture that evolution has imprinted on the kidneys during its struggle to survive over epochs.

Phylomitogenomics provides new perspectives on the Euphasmatodea radiation (Insecta: Phasmatodea)

Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics. We performed a divergence time analysis leveraging ten fossil specimens representative of most polyneopteran lineages: the time tree obtained supports an older radiation of the clade with respect to previous hypotheses. Euphasmatodea diversification is inferred to have started ~ 187 million years ago, suggesting that the Triassic-Jurassic mass extinction and the breakup of Pangea could have contributed to the process. We also investigated Euphasmatodea mitogenomes patterns of dN, dS and dN/dS ratio throughout our time-tree, trying to characterize the selective regime which may have shaped the clade evolution.

Functional differences of three CXCL10 homologues in the giant spiny frog Quasipaa spinosa

Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in acting as a bridge between the innate and adaptive immune responses. In this study, we identified three CXC motif chemokine 10 (CXCL10) homologues (QsCXCL10-1, QsCXCL10-2 and QsCXCL10-3) from giant spiny frog Quasipaa spinosa. All three deduced QsCXCL10 proteins contained four conserved cysteine residues as found in other known CXC chemokines. Phylogenetic analysis showed that QsCXCL10-1, 2, 3 and other CXCL10s in amphibian were grouped together to form a separate clade. These three QsCXCL10s were highly expressed in spleen and blood. Upon infection with Staphylococcus aureus or Aeromonas hydrophila, the expressions of QsCXCL10s were markedly increased in spleen and blood during biotic stresses. Meanwhile, the QsCXCL10s transcription in liver could also be up-regulated under abiotic stresses such as cold and heat stresses. The recombinant proteins of frog CXCL10 homologues were produced and purified in E. coli and possessed similar but differential bioactivities. Both rCXCL10-1 and rCXCL10-2 had strong effects on the up-regulation of pro-inflammatory cytokines (TNF-α, IL-1β and IL-8) in vivo, whereas rCXCL10-3 induced a weak expression of these cytokines. Moreover, the rCXCL10-1 and rCXCL10-2 could strongly promote splenocyte proliferation and induce lymphocytes migration, while rCXCL10-3 had limited effects on these biological processes. All three frog chemokines triggered their functional activities by engaging CXC motif chemokine receptor 3 (CXCR3). Taken together, these results revealed that the three QsCXCL10s had similar but differential functional activities in mediating immune responses and host defenses, which might contribute to a better understanding of the functional evolution of CXCL10 in vertebrates.

Morphological Evidence for an Oral Venom System in Caecilian Amphibians

Amphibians are known for their skin rich in glands containing toxins employed in passive chemical defense against predators, different from, for example, snakes that have active chemical defense, injecting their venom into the prey. Caecilians (Amphibia, Gymnophiona) are snake-shaped animals with fossorial habits, considered one of the least known vertebrate groups. We show here that amphibian caecilians, including species from the basal groups, besides having cutaneous poisonous glands as other amphibians do, possess specific glands at the base of the teeth that produce enzymes commonly found in venoms. Our analysis of the origin of these glands shows that they originate from the same tissue that gives rise to teeth, similar to the venom glands in reptiles. We speculate that caecilians might have independently developed mechanisms of production and injection of toxins early in their evolutionary history.

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Amphibian caecilians have tooth-related glands in both upper and lower jaws

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The glands have the same origin of reptile venom glands

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The secretion contains proteins with enzymatic activities commonly found in venoms

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Caecilians might have developed the ability to inject oral toxins early in evolution

Recent accelerated diversification in rosids occurred outside the tropics

Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.

Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini), based on complete mitochondrial genome analysis. Next-generation sequencing (NGS) of genomic DNA was used to obtain 16 new mitogenomes of Darevskia. These, along with 35 sequences downloaded from GenBank: genera Darevskia, Zootoca, Podarcis, Phoenicolacerta, Takydromus, Lacerta, and Eremias-were used in the analysis. All four analytical methods (Bayesian Inference, BI; Maximum Likelihood, ML; Maximum Parsimony, MP; and Neighbor-Joining, NJ) showed almost congruent intra-generic topologies for Darevskia and other lizard genera. However, ML and NJ methods on one side, and BI and MP methods on the other harvested conflicting phylogenies. The ML/NJ topology supports earlier published separation of Darevskia into three mitochondrial clades (Murphy, Fu, Macculloch, Darevsky, and Kupinova, 2000), but BI and MP topologies support that the basal branching occurred between D. parvula from the western Lesser Caucasus and the rest of Darevskia. All topologies altered the phylogenetic position of some individual species, including D. daghestanica, D. derjugini, and D. chlorogaster. Reanalysis after excluding four saturated genes from the data set, and excluding genus Eremias gives fully convergent topologies. The most basal branching for true lizards was between Far Eastern Takydromus and the Western Eurasian genera (BI). Comparing phylogenetic performance of individual genes relative to whole mitogenome data, concatenated 16S RNA (the least saturated gene in our analyses) and Cytochrome b genes generate a robust phylogeny that is fully congruent with that based on the complete mitogenome.

Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids

PREMISE

Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results.

METHODS

We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR).

RESULTS

We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa.

CONCLUSIONS

We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.

Biomarker and hematological fieldwork with amphibians: is it necessary to sample all night?

In the context of the global amphibian crisis, biomonitoring constitutes a valuable assessment tool to provide critical up to date information on the status and health of amphibians worldwide. The aim of the current study was to evaluate the possible confounding effects of sex, size, and time since capture on enzymatic biomarkers and hematologic parameters of the South American frog Leptodactylus latrans. Frogs were collected by hand between 9 pm and 12 am on two consecutive nights. On the first night, captured frogs were transported for 2 h by car to laboratory installations, maintained overnight in plastic containers, and blood and tissue sampled on the next morning. In contrast, frogs collected on the second night were blood and tissue sampled in the field, immediately after the capture period. Hematological parameters were analyzed, and enzymatic activities of catalase, cholinesterase (ChE), and glutathione S-transferase (GST) were determined in the plasma, liver, kidney, and muscle. A sex difference was observed only for total white blood cell counts (WBC), females exhibiting significantly greater values than males. The packed cell volume (PCV), mean corpuscular hemoglobin concentration (MCHC), WBC, and muscle ChE activity were significantly correlated with snout-vent length (SVL). The correlation was inversed in the case of MCHC, WBC, and muscle ChE, while the correlation was positive between PCV and SVL. Most examined parameters presented similar values when frogs were sampled at night following capture or the next morning. Total red blood cells (RBCs) count, and plasma enzymatic activities of ChE and GST were the only parameters that presented significantly increased values in morning samplings compared with night samplings. Overall, the current study indicates that it is best to sample the frogs as soon as possible after capture if hematologic or plasmatic biomarkers are examined. Nevertheless, it is possible to sample on the next morning if tissular biomarkers are employed.

Toxicity to Rhinella arenarum tadpoles (Anura, Bufonidae) of herbicide mixtures commonly used to treat fallow containing resistant weeds: glyphosate-dicamba and glyphosate-flurochloridone

Glyphosate (GLY)-dicamba (DIC) and GLY-flurochloridone (FLC) are herbicide mixtures which are widely used for treating fallow containing glyphosate resistant weeds. The aim of this study was to evaluate the acute toxic effects and the prevailing interactions on stage 36 tadpoles of the anuran species Rhinella arenarum when exposed to equitoxic and non-equitoxic combinations of these herbicide combinations. Experiments were realized using the following combinations of commercial formulations: 48% GLY-based Credit® + 57.71% DIC-based Banvel® and 48% GLY-based Credit® + 25% FLC-based Twin Pack Gold®. GLY-DIC and GLY-FLC equitoxic mixtures were assayed mixing each constituent with an equivalent individual toxicity able to induce the same lethality effect. After 96 h of exposure, GLY-DIC and GLY-FLC equitoxic mixtures presented toxic unit 50 values (TU50 96h) of 1.74 (confidence interval: 1.58-1.92) and 1.54 (confidence interval: 1.46-1.62) respectively, indicating the presence of a weak antagonistic interaction as TU values were greater than 1. For their part, most non-equitoxic combinations of GLY-DIC and GLY-FLC tested did not significantly differ from additivity, the only exception being when DIC and FLC were fixed at 0.33 TUs, where a weak antagonism was observed. Overall, results indicate that the toxicity of both GLY-DIC and GLY-FLC mixtures to R. arenarum tadpoles vary from additive to slightly antagonistic, depending on the proportion of constituting herbicide formulations present in the mixture.

A New Family of Diverse Skin Peptides from the Microhylid Frog Genus Phrynomantis

A wide range of frogs produce skin poisons composed of bioactive peptides for defence against pathogens, parasites and predators. While several frog families have been thoroughly screened for skin-secreted peptides, others, like the Microhylidae, have remained mostly unexplored. Previous studies of microhylids found no evidence of peptide secretion, suggesting that this defence adaptation was evolutionarily lost. We conducted transcriptome analyses of the skins of Phrynomantis bifasciatus and Phrynomantis microps, two African microhylid species long suspected to be poisonous. Our analyses reveal 17 evolutionary related transcripts that diversified from to those of cytolytic peptides found in other frog families. The 19 peptides predicted to be processed from these transcripts, named phrynomantins, show a striking structural diversity that is distinct from any previously identified frog skin peptide. Functional analyses of five phrynomantins confirm the loss of a cytolytic function and the absence of insecticidal or proinflammatory activity, suggesting that they represent an evolutionary transition to a new, yet unknown function. Our study shows that peptides have been retained in the defence poison of at least one microhylid lineage and encourages research on similarly understudied taxa to further elucidate the diversity and evolution of skin defence molecules.

Sexual Dichromatism Drives Diversification within a Major Radiation of African Amphibians

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales.

The MHC Class Ia Genes in Chenfu's Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Simple Summary

Amphibians, the first terrestrial vertebrates, provide materials for adaptive evolutionary studies, such as the evolution of the major histocompatibility complex (MHC). To date, various MHC evolutionary mechanisms have been identified in frogs, but more research is needed to determine the evolutionary mechanisms of the frog MHC. The main purpose of this study was to evaluate polymorphisms in the MHC class Ia genes of the Chenfu’s Treefrog. The MHC class Ia genes of the Chenfu’s Treefrog have high polymorphism. The mechanisms responsible for the formation of the polymorphisms include gene duplication, recombination, and selection.

Abstract

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.