Comparative transcriptomic analysis delineates adaptation strategies of Rana kukunoris toward cold stress on the Qinghai-Tibet Plateau.

BACKGROUND: Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter. RESULTS: Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing technology. A total of 10,062 unigenes of R. kukunoris were obtained, and 9,924 coding sequences (CDS) were successfully annotated. Our examination of the mRNA response to whole body freezing and recover in the frogs revealed key genes concerning underlying antifreeze proteins and cryoprotectants (glucose and urea). Functional pathway analyses revealed differential regulated pathways of ribosome, energy supply, and protein metabolism which displayed a freeze-induced response and damage recover. Genes related to energy supply in the muscle of winter frogs were up-regulated compared with the muscle of spring frogs. The liver of hibernating frogs maintained modest levels of protein synthesis in the winter. In contrast, the liver underwent intensive high levels of protein synthesis and lipid catabolism to produce substantial quantity of fresh proteins and energy in spring. Differences between hibernation and spring were smaller than that between tissues, yet the physiological traits of hibernation were nevertheless passed down to active state in spring. CONCLUSIONS: Based on our comparative transcriptomic analyses, we revealed the likely adaptive mechanisms of R. kukunoris. Ultimately, our study expands genetic resources for the freezing-tolerant frogs.

A hundred-year-old mystery-the reproductive mode and larval morphology of the enigmatic frog genus Allophryne (Amphibia; Anura; Allophrynidae).

Frogs of the Allophrynidae are an enigmatic family from South America. To date, published information is lacking regarding this group's reproductive biology and larval morphology. Here, we provide the first detailed description of the reproductive mode, developmental mode, and tadpole morphology for Allophryne ruthveni. We developed a captive breeding and rearing protocol for this species and then conducted a series of observations to describe aspects of its reproductive biology. In captivity, this species exhibits aquatic oviposition, where single eggs are laid ungrouped within a simple jelly capsule and are scattered free in the water column before sinking to develop on benthic substrates. We did not observe parental care nor any parental interactions with eggs post-fertilization. Tadpoles are characterized by an oval body, anteroventral oral disc, a labial tooth row formula of 2(2)/3, and a dextral vent tube. The buccopharyngeal cavity is marked by the presence of two pairs of infralabial papilla and four lingual papillae. Cranial morphology is characterized by the presence of the commissura quadratoorbital. This species possesses an additional slip of the m. rectus cervicis and of the m. levator arcuum branchialium III. We discuss our results in comparison with glassfrogs (Centrolenidae).

Ontogenetic Expression of Aquaporins in the Kidney and Urinary Bladder of the Japanese Tree Frog, Dryophytes japonicus.

For adult anuran amphibians, the kidney and urinary bladder play important osmoregulatory roles through water reabsorption. In the present study, we have examined ontogenetic expression of aquaporins, i.e., AQP2, AQPamU (AQP6ub, AQPa2U), and AQP3, in these organs using the Japanese tree frog, Dryophytes japonicus. Immunohistochemistry using the metamorphosing larvae at stages 40-43 localized AQP2 protein to the collecting ducts in the dorsal zone of the mesonephric kidney. At prometamorphic stages 40 and 41, labelling of AQP2 protein was observed in the apical/ subapical regions of the collecting duct cells. At climax stages 42 and 43, labels for AQP2 and AQP3 became observed in the apical/subapical regions and basolateral membrane of the collecting duct cells, respectively, as seen in the adults. As for the urinary bladder, immuno-positive labels for AQPamU were localized to the apical/subapical regions of granular cells in the mucosal epithelium at stages 40-43. On the other hand, AQP3 immunoreactivity was hardly observed in the urinary bladder at stage 40, and weakly appeared in many granular cells at stage 41. Thereafter, labels for AQP3 became evident along the basolateral membrane of granular cells at stages 42 and 43, together with AQPamU in the apical/subapical regions. These results suggest that the kidney and urinary bladder might be capable of water reabsorption, via AQP2, AQPamU, and AQP3, at stage 42, contributing to the acclimation of the tree frogs to terrestrial environments.

Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments.

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.

Vocal repertoire of Microhyla nilphamariensis from Delhi and comparison with closely related M. ornata populations from the western coast of India and Sri Lanka.

Advertisement calls in frogs have evolved to be species-specific signals of recognition and are therefore considered an essential component of integrative taxonomic approaches to identify species and delineate their distribution range. The species rich genus Microhyla is a particularly challenging group for species identification, discovery and conservation management due to the small size, conserved morphology and wide distribution of its members, necessitating the need for a thorough description of their vocalization. In this study, we provide quantitative description of the vocal behaviour of Microhyla nilphamariensis, a widely distributed south Asian species, from Delhi, India, based on call recordings of 18 individuals and assessment of 21 call properties. Based on the properties measured acrossed 360 calls, we find that a typical advertisement call of M. nilphamariensis lasts for 393.5 ±  57.5 ms, has 17 pulses on average and produce pulses at rate of 39 pulses/s. The overall call dominant frequency was found to be 2.8 KHz and the call spectrum consisted of two dominant frequency peaks centered at 1.6 KHz and 3.6 KHz, ranging between 1.5-4.1 KHz. Apart from its typical advertisement call, our study also reveals the presence of three 'rare' call types, previously unreported in this species. We describe variability in call properties and discuss their relation to body size and temperature. We found that overall dominant frequency 1 (spectral property) was found to be correlated with body size, while first pulse period (temporal property) was found to be correlated with temperature. Further, we compare the vocal repertoire of M. nilphamariensis with that of the congener Microhyla ornata from the western coast of India and Sri Lanka and also compare the call properties of these two populations of M. ornata to investigate intra-specific call variation. We find statistically significant differentiation in their acoustic repertoire in both cases. Based on 18 call properties (out of 20), individuals of each locality clearly segregate on PCA factor plane forming separate groups. Discriminant function analysis (DFA) using PCA factors shows 100% classification success with individuals of each locality getting classified to a discrete group. This confirms significant acoustic differentiation between these species as well as between geographically distant conspecifics. The data generated in this study will be useful for comparative bioacoustic analysis of Microhyla species and can be utilized to monitor populations and devise conservation management plan for threatened species in this group.

Back to the water: Tongue morphology associated to contrasting lifestyles in two Andean frogs of the genus Telmatobius.

The evolution of the tongue in tetrapods is associated with feeding in the terrestrial environment. This study analyzes the tongue morphology of two closely related frog species, Telmatobius oxycephalus and T. rubigo, which exhibit contrasting feeding mechanisms. Telmatobius oxycephalus, a semi-aquatic species, relies on its tongue to capture terrestrial prey whereas T. rubigo, a secondarily aquatic species, uses suction feeding not involving the tongue. Through anatomical, histological and scanning electron microscopy analyses, we revealed remarkable differences in tongue morphology between these species. Telmatobius oxycephalus exhibits a well-developed tongue whose dorsal epithelium has numerous and slender filiform papillae. The epithelial cells of the papillae are protruded and have a complex array of microridges. In contrast, T. rubigo possesses a reduced tongue with flat and less numerous filiform papillae. The epithelial cells are completely flat and lack microridges. These findings highlight the remarkable adaptability of lingual morphology in Telmatobius to respond to the contrasting ecological niches and prey capture mechanisms. This study sheds light on the relationship between tongue shape and the different functional demands, contributing to our understanding of the evolution of prey capture mechanisms in amphibians.

Rice straw ash and amphibian health: A deep dive into microbiota changes and potential ecological consequences.

Rice straw is burned as a result of agricultural practices and technical limitations, generating significant volumes of ash that might have environmental and ecological consequences; however, the effects on organisms have not been researched. Amphibians depend on their gut and skin microbiomes. Ash exposure may cause inflammation and changes in microbial diversity and function in frogs' skin and gut microbiota due to its chemical composition and physical presence, but the implications remain unclear. Rana dybowskii were exposed to five aqueous extracts of ashes (AEA) concentrations for 30 days to study survival, metal concentrations, and microbial diversity, analyzing the microbiota of the cutaneous and gut microbiota using Illumina sequencing. Dominant elements in ash: K > Ca > Mg > Na > Al > Fe. In AEA, K > Na > Ca > Mg > As > Cu. Increased AEA concentrations significantly reduced frog survival. Skin microbiota alpha diversity varied significantly among all treatment groups, but not gut microbiota. Skin microbiota differed significantly across treatments via Bray-Curtis and weighted UniFrac; gut microbiota was only affected by Bray-Curtis. Skin microbiota varied significantly with AEA levels in Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes, while the gut microbiota's dominant phyla, Firmicutes, Bacteroidetes, and Proteobacteria, remained consistent across all groups. Lastly, the functional prediction showed that the skin microbiota had big differences in how it worked and looked, which were linked to different health and environmental adaptation pathways. The gut microbiota, on the other hand, had smaller differences. In conclusion, AEA exposure affects R. dybowskii survival and skin microbiota diversity, indicating potential health and ecological impacts, with less effect on gut microbiota.

Multiple Transitions between Y Chromosome and Autosome in Tago's Brown Frog Species Complex.

Sex chromosome turnover is the transition between sex chromosomes and autosomes. Although many cases have been reported in poikilothermic vertebrates, their evolutionary causes and genetic mechanisms remain unclear. In this study, we report multiple transitions between the Y chromosome and autosome in the Japanese Tago's brown frog complex. Using chromosome banding and molecular analyses (sex-linked and autosomal single nucleotide polymorphisms, SNPs, from the nuclear genome), we investigated the frogs of geographic populations ranging from northern to southern Japan of two species, Rana tagoi and Rana sakuraii (2n = 26). Particularly, the Chiba populations of East Japan and Akita populations of North Japan in R. tagoi have been, for the first time, investigated here. As a result, we identified three different sex chromosomes, namely chromosomes 3, 7, and 13, in the populations of the two species. Furthermore, we found that the transition between the Y chromosome (chromosome 7) and autosome was repeated through hybridization between two or three different populations belonging to the two species, followed by restricted chromosome introgression. These dynamic sex chromosome turnovers represent the first such findings in vertebrates and imply that speciation associated with inter- or intraspecific hybridization plays an important role in sex chromosome turnover in frogs.

Strategy for the Identification of Host-Defense Peptides in Frog Skin Secretions with Therapeutic Potential as Antidiabetic Agents.

Several amphibian peptides that were first identified on the basis of their antimicrobial or cytotoxic properties have subsequently shown potential for development into agents for the treatment of patients with Type 2 diabetes. A strategy is presented for the isolation and characterization of such peptides that are present in norepinephrine-stimulated skin secretions from a range of frog species. The methodology involves (1) fractionation of the secretions by reversed-phase HPLC, (2) identification of fractions containing components that stimulate the rate of release of insulin from BRIN-BD11 clonal ß-cells without simultaneously stimulating the release of lactate dehydrogenase, (3) identification of active peptides in the fractions in the mass range 1-6 kDa by MALDI-ToF mass spectrometry, (4) purification of the peptides to near homogeneity by further reversed-phase HPLC on various column matrices, and (5) structural characterization by automated Edman degradation. The effect of synthetic replicates of the active peptides on glucose homeostasis in vivo may be evaluated in appropriate animal models of Type 2 diabetes such as db/db mice and mice fed a high fat diet to produce obesity, glucose intolerance, and insulin resistance.

Prey capture kinematics of horned frogs (Anura: Ceratophryidae).

Horned frogs, members of the Ceratophryidae family, encompass a group of anurans varying in size and behavior, yet unified by morphological and behavioral traits enabling them to adopt a megalophagous diet (i.e., large prey feeding). Although the group has been the focus of numerous studies, our understanding of its feeding behavior remains limited. In this study, we characterize the feeding mechanism in five species representing the three extant genera of ceratophryid anurans, both in terrestrial and aquatic environments. We also explore the ability of Chacophrys pierottii to adjust feeding behavior based on prey type. Our findings show that all species are capable of wide mouth opening, displaying an asymmetric feeding cycle. While tongue usage is the primary method for capturing prey on land, ceratophryids may use their forelimbs to manipulate prey into their mouths, exhibiting different behavioral patterns. C. pierottii shows modulation of its feeding kinematics and is also capable of some modulation of its feeding in response to prey properties.

Importance of the receiver's height for transmission studies in acoustic ecology.

In animal communication, the sound pressure level (SPL) of the acoustic signals has been studied in relation to various biological functions. Previous research reported that senders and receivers benefit from being at elevated positions. However, sometimes, researchers find contradictory results. Using a transmission experiment, we measured SPL of two acoustic stimuli: (i) white noise, and (ii) advertisement calls of the Iberian tree frog (Hyla molleri) at two different heights above ground level (0.05 and 0.75 m) and from six distances (1, 2, 4, 8, 16, and 32 m) from a loudspeaker. Calls of the Iberian tree frog have two spectral peaks centred at the frequencies of ca. 1 and 2 kHz. As expected, SPL decreased with distance, but following a distinct attenuation pattern across height above the ground and frequency. Our findings show that the ground effect may critically alter frequency attenuation and, therefore, signal composition and discrimination at the listener's location, even at low heights above the ground. We suggest that recording devices should be positioned at the same height that natural listeners are usually located in nature, to facilitate the replication and comparison of experiments in the field of acoustic ecology and, also, bioacoustics.

A new species of the Scinax cruentomma group (Anura: Hylidae) from the Ucayali River basin of Loreto, Peru.

We describe a new species of the Scinax cruentomma species group, with a red streak in the iris and a weakly bilobate vocal sac. It is known from oligotrophic soils in the sedimentary basin of the Ucayali River near Jenaro Herrera (province of Requena, Peru) and Ro Blanco (buffer zone of the Matses Indigenous territory and reserve). The new species can be distinguished from the other species of the S. cruentomma group by its small snout-vent length, body and iris color patterns, weakly bilobate vocal sac, myological characters, and the number of notes and pulses of the advertisement call. It is morphologically most similar to S. strussmannae, from which the advertisement call, nostril, canthus rostralis, and loreal region can distinguish it.

Systematic assessment of the brown tree frog (Anura: Pelodryadidae: Litoria ewingii) reveals two endemic species in South Australia.

The brown tree frog (Litoria ewingii) is a relatively widespread, commonly encountered pelodryadid frog from south-eastern Australia, known for its characteristic whistling call. The distribution of Litoria ewingii spans over more than 350,000 km2, encompassing a range of moist temperate habitats, and is fragmented by well-known biogeographic barriers. A preliminary analysis of mitochondrial DNA sequences revealed evidence for deep phylogenetic structure between some of these fragmented populations. In this study, we sought to re-evaluate the systematics and taxonomy of Litoria ewingii sensu lato by analysing variation in nuclear and mitochondrial DNA, adult morphology and male advertisement calls throughout the species range. Our analyses reveal two additional, deeply divergent and allopatric lineages in South Australia. We herein re-describe Litoria ewingii from Tasmania, southern New South Wales, Victoria and south-eastern South Australia, resurrect the name Litoria calliscelis for a species occurring in the Mount Lofty Ranges and Fleurieu Peninsula in South Australia, and describe a new species, Litoria sibilus sp. nov., endemic to Kangaroo Island.

Lost in time: Unraveling the identity of Vitreorana parvula (Boulenger, 1895) (Anura: Centrolenidae).

Vitreorana parvula was the first glassfrog described for the Atlantic Forest. The species, however, has become a taxonomic puzzle as the only known individual is the lectotype from the 19th century, which is not particularly well-preserved or accompanied by a detailed original description. To solve this problem, we collected topotypic specimens, as well as advertisement calls, tissue samples, and natural history data, and compared them to other Vitreorana species. Our results show clear morphological, acoustic, and genetic differences between V. parvula and other species of Vitreorana, except for V. uranoscopa. Following our results, we consider V. uranoscopa as a junior synonym of V. parvula and redescribe the species based on topotypic material, while summarizing relevant variation from across its distribution.

Discovery and description of a new species of burrowing frog Sphaerotheca Gnther, 1859 (Anura: Dicroglossidae) from the suburban landscapes of Bengaluru, India.

Recent resolution of prevailing taxonomic ambiguities in the genus Sphaerotheca and new species discoveries from urban/suburban landscapes highlight the need for attention to non-forested habitats for amphibian conservation. In this paper, we review the status of the members of the genus Sphaerotheca and justify the synonymy of Sphaerotheca magadha as a junior synonym of Sphaerotheca swani. The prospects of resurrection of Sphaerotheca swani (herein preliminarily referred to as Sphaerotheca cf. breviceps [swani]) are discussed. In addition, we describe a new species Sphaerotheca varshaabhu sp. nov. from the suburban region of Bengaluru, India. We employ an integrative taxonomic approach to characterize the new species using molecular phylogeny, genetic distance, morphological characters, and geographical isolation as lines of evidence. We also provide a description of vocal repertoire of Sphaerotheca varshaabhu sp. nov. and provide comparative bioacoustics data for four species. This previously undescribed species from the suburban areas of Bengaluru described herein as Sphaerotheca varshaabhu sp. nov. forms a genetically divergent lineage and its genetic distance varied from 3.6% to 12.2% for 16S rRNA with respect to other species of Sphaerotheca. Our phylogenetic analysis for the genus including the new species confirms the synonymy of one recently described species, resulting in 10 valid species in the genus Sphaerotheca. These results emphasize the need for utilizing an integrative taxonomic approach for uncovering hidden diversity of suburban areas. Given these recent discoveries, we advocate for more robust surveys in human dominated areas, so that these amphibians may receive more attention.

Female frogs communicate with males through blinking.

Blinking is a behavior unique to animal taxa with motile eyelids, such as most amphibians and reptiles as well as all birds and mammals1. Eyelid movement has physiological functions, such as lubricating the cornea and washing away dust, but its potential signaling functions are not well understood1,2. The use of eyeblinks as a social signal is currently thought to be restricted to some primates, especially humans and their companion animals, but has not been verified in other taxa1,3,4. Here, through field observation and experiments, we demonstrate that female concave-eared torrent frogs (Odorrana tormota), which inhabit noisy streams, use eyeblinks to communicate with males to urge them to initiate amplexus for mating. Our findings reveal that eyeblinks may serve as a social signal in non-primate species.

Piecing the barcoding puzzle of Palearctic water frogs (Pelophylax) sheds light on amphibian biogeography and global invasions.

Palearctic water frogs (genus Pelophylax) are an outstanding model in ecology and evolution, being widespread, speciose, either threatened or threatening to other species through biological invasions, and capable of siring hybrid offspring that escape the rules of sexual reproduction. Despite half a century of genetic research and hundreds of publications, the diversity, systematics and biogeography of Pelophylax still remain highly confusing, in no small part due to a lack of correspondence between studies. To provide a comprehensive overview, we gathered >13,000 sequences of barcoding genes from >1700 native and introduced localities and built multigene mitochondrial (~17 kb) and nuclear (~10 kb) phylogenies. We mapped all currently recognized taxa and their phylogeographic lineages (>40) to get a grasp on taxonomic issues, cyto-nuclear discordances, the genetic makeup of hybridogenetic hybrids, and the origins of introduced populations. Competing hypotheses for the molecular calibration were evaluated through plausibility tests, implementing a new approach relying on predictions from the anuran speciation continuum. Based on our timetree, we propose a new biogeographic paradigm for the Palearctic since the Paleogene, notably by attributing a prominent role to the dynamics of the Paratethys, a vast paleo-sea that extended over most of Europe. Furthermore, our results show that distinct marsh frog lineages from Eastern Europe, the Balkans, the Near East, and Central Asia (P. ridibundus ssp.) are naturally capable of inducing hybridogenesis with pool frogs (P. lessonae). We identified 14 alien lineages (mostly of P. ridibundus) over ~20 areas of invasions, especially in Western Europe, with genetic signatures disproportionally pointing to the Balkans and Anatolia as the regions of origins, in line with exporting records of the frog leg industry and the stocks of pet sellers. Pelophylax thus emerges as one of the most invasive amphibians worldwide, and deserves much higher conservation concern than currently given by the authorities fighting biological invasions.

Minimal zoonotic risk of cryptosporidiosis and giardiasis from frogs and reptiles.

The zoonotic potential of the protist parasites Cryptosporidium spp. and Giardia duodenalis in amphibians and reptiles raises public health concerns due to their growing popularity as pets. This review examines the prevalence and diversity of these parasites in wild and captive amphibians and reptiles to better understand the zoonotic risk. Research on Giardia in both groups is limited, and zoonotic forms of Cryptosporidium or Giardia have not been reported in amphibians. Host-adapted Cryptosporidium species dominate in reptiles, albeit some reptiles have been found to carry zoonotic (C. hominis and C. parvum) and rodent-associated (C. tyzzeri, C. muris and C. andersoni) species, primarily through mechanical carriage. Similarly, the limited reports of Giardia duodenalis (assemblages A, B and E) in reptiles may also be due to mechanical carriage. Thus, the available evidence indicates minimal zoonotic risk associated with these organisms in wild and captive frogs and reptiles. The exact transmission routes for these infections within reptile populations remain poorly understood, particularly regarding the importance of mechanical carriage. Although the risk appears minimal, continued research and surveillance efforts are necessary to gain a more comprehensive understanding of the transmission dynamics and ultimately improve our ability to safeguard human and animal health.

Developmental programming by prenatal sounds: insights into possible mechanisms.

In recent years, the impact of prenatal sound on development, notably for programming individual phenotypes for postnatal conditions, has increasingly been revealed. However, the mechanisms through which sound affects physiology and development remain mostly unexplored. Here, I gather evidence from neurobiology, developmental biology, cellular biology and bioacoustics to identify the most plausible modes of action of sound on developing embryos. First, revealing often-unsuspected plasticity, I discuss how prenatal sound may shape auditory system development and determine individuals' later capacity to receive acoustic information. I also consider the impact of hormones, including thyroid hormones, glucocorticoids and androgen, on auditory plasticity. Second, I review what is known about sound transduction to other - non-auditory - brain regions, and its potential to input on classical developmental programming pathways. Namely, the auditory pathway has direct anatomical and functional connectivity to the hippocampus, amygdala and/or hypothalamus, in mammals, birds and anurans. Sound can thus trigger both immediate and delayed responses in these limbic regions, which are specific to the acoustic stimulus and its biological relevance. Third, beyond the brain, I briefly consider the possibility for sound to directly affect cellular functioning, based on evidence in earless organisms (e.g. plants) and cell cultures. Together, the multi-disciplinary evidence gathered here shows that the brain is wired to allow multiple physiological and developmental effects of sound. Overall, there are many unexplored, but possible, pathways for sound to impact even primitive or immature organisms. Throughout, I identify the most promising research avenues for unravelling the processes of acoustic developmental programming.