Characterization and Comparison of the Two Mitochondrial Genomes in the Genus Rana

The mitochondrial genome (mitogenome) possesses several invaluable attributes, including limited recombination, maternal inheritance, a fast evolutionary rate, compact size, and relatively conserved gene arrangement, all of which make it particularly useful for applications in phylogenetic reconstruction, population genetics, and evolutionary research. In this study, we aimed to determine the complete mitogenomes of two morphologically similar Rana species (Rana hanluica and Rana longicrus) using next-generation sequencing. The entire circular mitogenome was successfully identified, with a length of 19,395 bp for R. hanluica and 17,833 bp for R. longicrus. The mitogenomes of both species contained 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and one control region; mitogenome size varied predominantly with the length of the control region. The two synonymous codon usages in 13 PCGs showed that T and A were used more frequently than G and C. The ratios of non-synonymous to synonymous substitutions of all 13 PCGs were <1 in the Rana species, indicating that the PCGs were under purifying selection. Finally, phylogenetic relationship analyses suggested that R. hanluica and R. longicrus were classified in the R. japonica group. Our study provides valuable reference material for the taxonomy of the genus Rana.

2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics

Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.

Skeletal description of Pelophylax caralitanus (Anura: Ranidae): Comparison with other ranids

A description of the skeletal development of ranids is scarce despite being well known in the family Ranidae. Herein, the description of several species of two genera representing the family Ranidae from Turkey is studied wherein the larval and adult cranial skeletons of Pelophylax caralitanus are described and compared with that of the water frog (Pelophylax bedriagae) and mountain frog (Rana macrocnemis). The data are based on cleared and double-stained specimens of 20 Gosner developmental Stages (26-46). The first element to ossify in P. caralitanus is the parasphenoid (Stage 30), followed by the exoccipitals (Stage 34) and prootics (Stage 35). The metamorphic climax commences at Stage 42 during which several modifications to the chondrocranium will unfold. In addition, ranids demonstrate remarkable differences between the water (Pelophylax sp.) and mountain (Rana sp.) frog species: (a) the ventromedial bridge between the corpora of the suprarostral cartilage in the larval upper jaw, (b) the number of processes of the central corpus in the hyobranchial skeleton, and (c) the differences in the ossification time and sequence between Pelophylax sp. and Rana sp. A detailed description of the larval osteological features of P. caralitanus conforms to the current phylogenetic position and provides a model for comparison with other ranids.

"Heat waves" experienced during larval life have species-specific consequences on life-history traits and sexual development in anuran amphibians

Extreme temperatures during heat waves can induce mass-mortality events, but can also exert sublethal negative effects by compromising life-history traits and derailing sexual development. Ectothermic animals may, however, also benefit from increased temperatures via enhanced physiological performance and the suppression of cold-adapted pathogens. Therefore, it is crucial to address how the intensity and timing of naturally occurring or human-induced heat waves affect life-history traits and sexual development in amphibians, to predict future effects of climate change and to minimize risks arising from the application of elevated temperature in disease mitigation. We raised agile frog (Rana dalmatina) and common toad (Bufo bufo) tadpoles at 19 °C and exposed them to a simulated heat wave of 28 or 30 °C for six days during one of three ontogenetic periods (early, mid or late larval development). In agile frogs, exposure to 30 °C during early larval development increased mortality. Regardless of timing, all heat-treatments delayed metamorphosis, and exposure to 30 °C decreased body mass at metamorphosis. Furthermore, exposure to 30 °C during any period and to 28 °C late in development caused female-to-male sex reversal, skewing sex ratios strongly towards males. In common toads, high temperature only slightly decreased survival and did not influence phenotypic sex ratio, while it reduced metamorph mass and length of larval development. Juvenile body mass measured 2 months after metamorphosis was not adversely affected by temperature treatments in either species. Our results indicate that heat waves may have devastating effects on amphibian populations, and the severity of these negative consequences, and sensitivity can vary greatly between species and with the timing and intensity of heat. Finally, thermal treatments against cold-adapted pathogens have to be executed with caution, taking into account the thermo-sensitivity of the species and the life stage of animals to be treated.

The complete mitochondrial genome information of Rana uenoi (Amphibia, Anura, Ranidae) and the phylogenetic implication

We determined the complete mitochondrial genome of Rana uenoi (Anura: Ranidae) for the first time. The whole sequences were 17,370 bp and included 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The gene arrangement was completely identical to those observed from other Ranidae species. We used 11 protein-coding genes to examine the phylogenetic placement of this species in the genus Rana. Ranadybowskii was the closest sister species to R. uenoi. The clade of R. uenoi and R. dybowskii formed a cluster with Ranahuarensis, which had a sister relationship with the group of Rana amurensis, Rana coreana, and Rana kunyuensis.

Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships

The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6-trnE-Cytb-D-loop-trnL2 (CUN)-ND5-D-loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.

Complete mitochondrial genome of the American bullfrog in Korea, Lithobates catesbeianus (Anura: Ranidae)

The complete mitochondrial (mt) genome of Lithobates catesbeianus was sequenced and characterized. The circular mt genome was constituted of of 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and a non-coding region (NCR). Phylogenetic analysis based on the full mt genome sequences confirmed that among the genus Lithobates, L. catesbeianus Korea is included in a monophyletic group with L. catesbeianus China, but not with either L. catesbeianus Japan or L. catesbeianus Canada. This is the first completed mt genome from L. catesbeianus Korea, which provide data for further study of phylogeny in Lithobates spp. that have been introduced into a number of different countries originally from North America.

Patterns of fluctuating asymmetry in the limbs of anurans

It has been hypothesized that fluctuating asymmetry (FA) may provide an indication of the functional importance of structures within an organism, with structures that more strongly impact fitness being more symmetric. Based on this idea, we predicted that for tetrapods in which the forelimbs and hindlimbs play an unequal role in locomotion, the less functionally important limb set should display higher levels of FA. We conducted a multispecies test of this hypothesis in anurans (frogs and toads), whose saltatory locomotor mode is powered by the hindlimbs. We also tested whether FA in the forelimbs, which play a more important role during landing, differed between families that differ in the degree of forelimb use in locomotion (Bufonidae vs. Ranidae). We calculated FA from the lengths of humeri and femora measured from disarticulated skeletal specimens of four anuran taxa (Bufonidae: Anaxyrus americanus, Rhinella marina; Ranidae: Lithobates catesbeianus, Lithobates clamitans). Our findings were consistent with the hypothesis that natural selection for increased locomotor performance may influence patterns of FA seen in vertebrate limbs, with all species displaying lower mean FA in the hindlimbs. More subtle functional roles between the forelimbs of bufonids and ranids, however, did not elicit different levels of FA.

Functional variation at an expressed MHC class IIβ locus associates with Ranavirus infection intensity in larval anuran populations

Infectious diseases are causing catastrophic losses to global biodiversity. Iridoviruses in the genus Ranavirus are among the leading causes of amphibian disease-related mortality. Polymorphisms in major histocompatibility complex (MHC) genes are significantly associated with variation in amphibian pathogen susceptibility. MHC genes encode two classes of polymorphic cell-surface molecules that can recognize and bind to diverse pathogen peptides. While MHC class I genes are the classic mediators of viral-acquired immunity, larval amphibians do not express them. Consequently, MHC class II gene diversity may be an important predictor of Ranavirus susceptibility in larval amphibians, the life stage most susceptible to Ranavirus. We surveyed natural populations of larval wood frogs (Rana sylvatica), which are highly susceptible to Ranavirus, across 17 ponds and 2 years in Maryland, USA. We sequenced the peptide-binding region of an expressed MHC class IIβ locus and assessed allelic and genetic diversity. We converted alleles to functional supertypes and determined if supertypes or alleles influenced host responses to Ranavirus. Among 381 sampled individuals, 26% were infected with Ranavirus. We recovered 20 unique MHC class IIβ alleles that fell into two deeply diverged clades and seven supertypes. MHC genotypes were associated with Ranavirus infection intensity, but not prevalence. Specifically, MHC heterozygotes and supertype ST1/ST7 had significantly lower Ranavirus infection intensity compared to homozygotes and other supertypes. We conclude that MHC class IIβ functional genetic variation is an important component of Ranavirus susceptibility. Identifying immunogenetic signatures linked to variation in disease susceptibility can inform mitigation strategies for combatting global amphibian declines.

Distribution of Alaria spp. mesocercariae in waterfrogs

The distribution of Alaria-spp.-mesocercariae within the host is relevant for the examination via Alaria spp. mesocercariae migration technique (AMT) regarding predilection sites and may indicate an interaction between parasite and host. Naturally Alaria-exposed frogs of Pelophylax species (n = 13) were examined for systemic distribution and localization-specific parasite density of Alaria spp. mesocercariae. The frogs were necropsied and their body was divided into the following localizations: inner organs, head, torso, forelimbs, and hind limbs. The localizations were analyzed individually and in toto using Alaria spp. mesocercariae migration technique. Our results showed neither statistical differences concerning the number of mesocercariae in the different localizations nor in respect of the rate of positive localizations. Therefore, an accumulation in a particular predilection site seems unlikely. Further research on a representative sample is necessary before final conclusions can be drawn.

Amphibians distribution and habitats in the southwestern region of Saudi Arabia

This study surveyed 205 wetland sites in the Southwestern Saudi Arabia. We found seven species of amphibians (Anura), which belong to four families: Bufonidae; which includes four species, Sclerophrys tihamica; S. Arabica, Duttaphrynus dhufarensis, and Bufotes viridis; Hylidae, represented by only one species, the tree frog Hyla savignyi; Ranidae, which represented by one species, Pelophylax ridibundus and finally the Dicroglossidae, represented by one species, Euphlyctis ehrenbergii. The reasonable amount of rain received in southwest Arabia, and habitat diversity contribute to the relative abundance of amphibians in the region. Five types of wetland habitats were found in the study area. Valley streams, irrigated farms, seasonal ponds, dam reservoir and lagoons of treated sewage water. The current study revealed the wide spread of amphibians in southwestern Saudi Arabia than what had been reported earlier and confirmed the presence of the Bufotes viridis at three new sites in Asir Heights. It also showed the wide spread of S. arabica in all types of habitats in the southwestern region of Saudi Arabia. Habitat degradation was evident in the region, which might lead to species loss.

Eocene Western European endemic genus Thaumastosaurus: new insights into the question "Are the Ranidae known prior to the Oligocene?"

Background

Amphibians, due to their ecophysiological peculiarities, have a physiology dependent on environmental conditions and sensitively respond to their changes. Here, the oldest record of the genus Thaumastosaurus is described, whose fossil record known exclusively from Western Europe is discussed in the scope of the climatic changes of 33.5-40.5 Ma.

Results

In the present paper, the fossil remains of the genus from three localities in Switzerland (11 samples overall) have been studied and referred to the species Thaumastosaurus bottii. Its stratigraphic distribution has been revised and summarised. The studied localities present the stratigraphically oldest and the most eastern occurrences of the genus Thaumastosaurus. Eocene probable ranids (Ranidae indet./Rana sp./? Rana sp.) from Europe could be referred to Thaumastosaurus.

Discussion

Their first occurrence of ranids most likely coincides with a warm phase of the global climate at 40 Ma, as tropical conditions were prevailing in Europe. As a result of the gradual cooling of the global climate, the tropical conditions in Europe were replaced by drier open habitats towards the latest Eocene at 34 Ma, when the latest occurrence of the European endemic genus Thaumastosaurus is known. Taking the fossil record and the climate evolution of that time into account, it can be concluded that Thaumastosaurus represents one of the groups among the vertebrates that disappeared during the large extinction event at the Eo-Oligocene transition, known as the Grande Coupure. The fossil finds of the genus from the studied localities allow to refer the previously suggested Eocene true frogs to the genus Thaumastosaurus, hereby stating the arrival of the true frog family Ranidae by the genus Pelophylax in Europe from the east at the earliest Oligocene.

Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest

Comparative landscape genetics has uncovered high levels of variability in which landscape factors affect connectivity among species and regions. However, the relative importance of species traits versus environmental variation for predicting landscape patterns of connectivity is unresolved. We provide evidence from a landscape genetics study of two sister taxa of frogs, the Oregon spotted frog (Rana pretiosa) and the Columbia spotted frog (Rana luteiventris) in Oregon and Idaho, USA. Rana pretiosa is relatively more dependent on moisture for dispersal than R. luteiventris, so if species traits influence connectivity, we predicted that connectivity among R. pretiosa populations would be more positively associated with moisture than R. luteiventris. However, if environmental differences are important drivers of gene flow, we predicted that connectivity would be more positively related to moisture in arid regions. We tested these predictions using eight microsatellite loci and gravity models in two R. pretiosa regions and four R. luteiventris regions (n = 1,168 frogs). In R. pretiosa, but not R. luteiventris, connectivity was positively related to mean annual precipitation, supporting our first prediction. In contrast, connectivity was not more positively related to moisture in more arid regions. Various temperature metrics were important predictors for both species and in all regions, but the directionality of their effects varied. Therefore, the pattern of variation in drivers of connectivity was consistent with predictions based on species traits rather than on environmental variation.

Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs

Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection.

Transcriptome analyses of immune tissues from three Japanese frogs (genus Rana ) reveals their utility in characterizing major histocompatibility complex class II

Background

In Japan and East Asia, endemic frogs appear to be tolerant or not susceptible to chytridiomycosis, a deadly amphibian disease caused by the chytrid fungus Batrachochytridium dendrobatidis (Bd). Japanese frogs may have evolved mechanisms of immune resistance to pathogens such as Bd. This study characterizes immune genes expressed in various tissues of healthy Japanese Rana frogs.

Results

We generated transcriptome data sets of skin, spleen and blood from three adult Japanese Ranidae frogs (Japanese brown frog Rana japonica, the montane brown frog Rana ornativentris, and Tago’s brown frog Rana tagoi tagoi) as well as whole body of R. japonica and R. ornativentris tadpoles. From this, we identified tissue- and stage-specific differentially expressed genes; in particular, the spleen was most enriched for immune-related genes. A specific immune gene, major histocompatibility complex class IIB (MHC-IIB), was further characterized due to its role in pathogen recognition. We identified a total of 33 MHC-IIB variants from the three focal species (n = 7 individuals each), which displayed evolutionary signatures related to increased MHC variation, including balancing selection. Our supertyping analyses of MHC-IIB variants from Japanese frogs and previously studied frog species identified potential physiochemical properties of MHC-II that may be important for recognizing and binding chytrid-related antigens.

Conclusions

This is one of the first studies to generate transcriptomic resources for Japanese frogs, and contributes to further understanding the immunogenetic factors associated with resistance to infectious diseases in amphibians such as chytridiomycosis. Notably, MHC-IIB supertyping analyses identified unique functional properties of specific MHC-IIB alleles that may partially contribute to Bd resistance, and such properties provide a springboard for future experimental validation.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4404-0) contains supplementary material, which is available to authorized users.

Age, Size, and Growth of the Turkish Endemic Frog Pelophylax Caralitanus (Anura: Ranidae)

Pelophylax caralitanus is a medium-sized frog that is endemic to the upland Lake District of south-central Turkey and currently identified as a threatened species as a result of overharvesting and habitat modification. In this report, demographic data are provided for four major lakeside populations of this species based on a skeletochronological analysis of bone growth in large samples of frogs that were captured and released during 2011 and 2013. Adult males (aged 2-9 years) and females (aged 2-10 years) ranged in size from 66 to 105 mm snout-vent length (SVL) and 65 to 110 mm SVL, respectively, and typically attained sexual maturity in their second (low-elevation sites) or third (high-elevation sites) summer of growth following metamorphosis. The four populations exhibited differences in growth rate and age at sexual maturity, which appeared to reflect differences in the average monthly temperature and length of the growth season rather than elevation per se, that is, warmer temperatures and longer growth seasons resulted in smaller adults. All populations had a similar overall age structure, with approximately equal frequencies of individuals in the five age and size classes following maturity. Anat Rec, 301:1224-1234, 2018. © 2017 Wiley Periodicals, Inc.

Evolutionary dynamics of an expressed MHC class IIβ locus in the Ranidae (Anura) uncovered by genome walking and high-throughput amplicon sequencing

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class IIβ chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a range of anuran taxa.

Sequencing and analysis of the complete mitochondrial genome of Rana amurensis (Anura: Ranidae)

In this study, the complete mitogenome sequence of Rana amurensis (Anura: Ranidae) is determined using long PCR. It is a circular molecule of 20,571 bp in length (GenBank accession no. MF370348). The complete mtDNA sequence of R. amurensis contained 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes (PCGs) and 2 control regions (D-loops). The nucleotide composition was 28.6% A, 26.8% C, 14.0% G and 30.6% T. Mitochondrial genome analyses based on NJ method yield phylogenetic trees, including that 20 reported family Ranidae frogs. These molecular data presented here provide a useful tool for systematic analyses of genus Rana.

Cytotoxic peptides with insulin-releasing activities from skin secretions of the Italian stream frog Rana italica (Ranidae)

Peptidomic analysis of norepinephrine-stimulated skin secretions from Italian stream frog Rana italica led to the purification and characterization of two host-defense peptides differing by a single amino acid residue belonging to the brevinin-1 family (brevinin-1ITa and -1ITb), a peptide belonging to the temporin family (temporin-ITa) and a component identified as prokineticin Bv8. The secretions contained relatively high concentrations of the methionine-sulphoxide forms of brevinin-1ITa and -1ITb suggesting that these peptides may have a role as antioxidants in the skin of this montane frog. Brevinin-1ITa (IVPFLLGMVPKLVCLITKKC) displayed potent cytotoxicity against non-small cell lung adenocarcinoma A549 cells (LC₅₀  = 18 μM), breast adenocarcinoma MDA-MB-231 cells (LC₅₀  = 8 μM) and colorectal adenocarcinoma HT-29 cells (LC₅₀  = 18 μM), but the peptide was also strongly hemolytic against mouse erythrocytes (LC₅₀  = 7 μM). Temporin-ITa (VFLGAIAQALTSLLGKL.NH₂ ) was between three and fivefold less potent against these cells. Brevinin-1ITa inhibited growth of both Gram-positive Staphylococcus epidermidis and Gram-negative Escherichia coli as well as a strain of the opportunist yeast pathogen Candida parapsilosis, whereas temporin-ITa was active only against S. epidermidis and C. parapsilosis. Both peptides stimulated the release of insulin from BRIN-BD11 clonal β-cells at concentrations ≥1 nM, but brevinin-1ITa was cytotoxic to the cells at concentrations ≥3 μM. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources

We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies. Altogether, we obtained 292 putatively sex-linked RAD loci, 98% of which point to male heterogamety. We could map 15 of them to the Xenopus tropicalis genome, all but one on chromosome pair 1, which seems regularly co-opted for sex determination among amphibians. The most efficient mapping strategy was a three-step hierarchical approach, where R. arvalis reads were first mapped to a low-coverage genome of Rana temporaria (17 My divergence), then the R. temporaria scaffolds to the Nanorana parkeri genome (90 My divergence), and finally the N. parkeri scaffolds to the X. tropicalis genome (210 My). We validated our conclusions with PCR primers amplifying part of Dmrt1, a candidate sex determination gene mapping to chromosome 1: a sex-diagnostic allele was present in all 30 males but in none of the 21 females. Our approach is likely to be productive in many situations where biological samples and/or genomic resources are limited.

Patterns of Cranial Development in Larval Rana macrocnemis: Chondrocranial Size and Shape Relationship With Pelophylax bedriagae (Anura: Ranidae)

Notwithstanding the abundance of amphibians, there are few descriptions about ranid cranial development. Herein, larval chondrocranial development of Uludağ frog, Rana macrocnemis (Boulenger, 1885), is described on cleared and double-stained specimens. Descriptions are related with the ontogeny of the chondrocranium and osteogenesis of the cranial skeleton. The larval chondrocranial development of R. macrocnemis is compared to those of Rana and Pelophylax larvae (Pelophylax bedriagae, Rana pipiens, R. palustris, R. sphenocephala, R. catesbeiana, R. clamitans and R. sylvatica). In R. macrocnemis, the first bones to ossify are the parasphenoid and exoccipital (Stage 33), followed by the frontoparietal and prootic (stages 35 and 40, respectively). The major reconstruction of the chondrocranium begins at Stage 41. The ossification sequence of R. macrocnemis is distinguished from other ranids. Adult cranial osteology of R. macrocnemis is compared to that of P. bedriagae. Osteologically, R. macrocnemis is different from P. bedriagae by the shape and size of the vomer and number of teeth. Additionally, geometric morphometric methods are used to analyze chondrocranial size and shape changes of ranid larva of R. macrocnemis and P. bedriagae. Anat Rec, 299:711-721, 2016. © 2016 Wiley Periodicals, Inc.

Environmental constraints and call evolution in torrent-dwelling frogs

Although acoustic signals are important for communication in many taxa, signal propagation is affected by environmental properties. Strong environmental constraints should drive call evolution, favoring signals with greater transmission distance and content integrity in a given calling habitat. Yet, few empirical studies have verified this prediction, possibly due to a shortcoming in habitat characterization, which is often too broad. Here we assess the potential impact of environmental constraints on the evolution of advertisement call in four groups of torrent-dwelling frogs in the family Ranidae. We reconstruct the evolution of calling site preferences, both broadly categorized and at a finer scale, onto a phylogenetic tree for 148 species with five markers (∼3600 bp). We test models of evolution for six call traits for 79 species with regard to the reconstructed history of calling site preferences and estimate their ancestral states. We find that in spite of existing morphological constraints, vocalizations of torrent-dwelling species are most probably constrained by the acoustic specificities of torrent habitats and particularly their high level of ambient noise. We also show that a fine-scale characterization of calling sites allows a better perception of the impact of environmental constraints on call evolution.

Estimating Effects of Species Interactions on Populations of Endangered Species

Global change causes community composition to change considerably through time, with ever-new combinations of interacting species. To study the consequences of newly established species interactions, one available source of data could be observational surveys from biodiversity monitoring. However, approaches using observational data would need to account for niche differences between species and for imperfect detection of individuals. To estimate population sizes of interacting species, we extended N-mixture models that were developed to estimate true population sizes in single species. Simulations revealed that our model is able to disentangle direct effects of dominant on subordinate species from indirect effects of dominant species on detection probability of subordinate species. For illustration, we applied our model to data from a Swiss amphibian monitoring program and showed that sizes of expanding water frog populations were negatively related to population sizes of endangered yellow-bellied toads and common midwife toads and partly of natterjack toads. Unlike other studies that analyzed presence and absence of species, our model suggests that the spread of water frogs in Central Europe is one of the reasons for the decline of endangered toad species. Thus, studying population impacts of dominant species on population sizes of endangered species using data from biodiversity monitoring programs should help to inform conservation policy and to decide whether competing species should be subject to population management.

The complete mitochondrial genome of the Odorrana schmackeri (Anura, Ranidae)

The complete mitochondrial genome of O. schmackeri has been sequenced and characterized in this study. The mitogenome is a circular molecule of 18610 bp in length, containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 21 transfer RNA (tRNA) genes and a non-coding D-loop region (control region). Its gene arrangements are identical to the typical neobatrachian-type except for the loss of tRNA^His gene. Our data provide a useful resource for the phylogenetic studies of genus Odorrana.

The complete mitochondrial genome sequence of the Dark-spotted frog Pelophylax nigromaculatus (Amphibia, Anura, Ranidae)

The dark-spotted frog (Pelophylax nigromaculatus) belongs to Ranidae. This species is known from the Russian Far East, central, northern and north-eastern China, the Democratic People's Republic of Korea, the Republic of Korea, and Japan. In this study, the complete mitochondrial genome of P. nigromaculatus was sequenced. The mitogenome was 17 567 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the P. nigromaculatus is 29.2% A, 27.4% T, 28.4% C, and 15.0% G. Phylogenetic analysis showed P. nigromaculatus was closely related to P. plancyi and P. chosenicus. The complete mitogenome of P. nigromaculatus can provide important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.

The complete mitogenome of Amolops loloensis and related phylogenetic relationship among Ranidae

Rufous-spotted Torrent Frog (Amolops loloensis) is a vulnerable species, which belongs to the family Ranidae and is distributed in high-gradient streams of Sichuan and Yunnan, China. In this study, we first determined the complete mitochondrial DNA sequence of A. loloensis (GenBank accession no. KT750963). The mitogenome sequence of A. loloensis was 18 926 bp in size. It contained 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and a D-loop region. Amolops loloensis shared the same gene arrangement pattern with A. mantzorum. The O_L structures of A. loloensis and A. mantzorum were both located at the upstream of trnA-trnN, while the O_L structures of A. ricketti and A. wuyiensis were both located at the downstream of trnA-trnN. It is of great interest to discuss the gene rearrangement mechanisms in the following study.

The complete mitochondrial genome of the Rana huanrensis (Anura: Ranidae)

We first determined complete mitochondrial genomes of R. huanrensis (Anura: Ranidae). The complete mtDNA sequence is 19 253 bp in length, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and one displacement loop. The start/stop codons of protein-coding genes are similar to which of R. chensinensis. D-loop region of R. huanrensis is 3448 bp in size, contains many tandem repeat units. The phylogenetic trees of 18 species from Ranidae were reconstructed by BI and ML analyses. The result indicated that R. huanrensis is the most closely related species with other Rana species. The molecular data are expected to provide a useful tool for population genetics studies of this species and further phylogenetic analyses of Ranidae.

The complete mitochondrial genome of Lithobates sylvaticus (Anura: Ranidae)

The complete mitochondrial genome of Lithobates sylvaticus (Anura: Ranidae) was sequenced. The genome is a circular molecule of 17,343 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a large non-coding region. The gene order and mitochondrial genome information of L. sylvaticus is similar to most other frogs. The overall AT content of L. sylvaticus mitochondrial DNA is 59.3%. In BI and MLtrees, we found L. sylvaticus is a sister clade to L. catesbeianus. The monophyly of Lithobates, Rana, Odorrana, Glandirana, Pelophylax, and Amolops is well supported, but the paraphyly of Babina is supported.

Ontogenetic Change of Signal Brightness in the Foot-Flagging Frog Species Staurois parvus and Staurois guttatus

Adult individuals of several anuran species exhibit conspicuous visual displays during intraspecific communication. While signal properties in adults have been subject to an increasing number of studies, little is known about the variation of visual signals in juveniles and during ontogenetic changes. Foot-flagging signals of the Bornean frogs Staurois guttatus and S. parvus were observed in juveniles a few days after metamorphosis. We investigated color parameters of foot webbings and body coloration of individuals bred at the Vienna Zoo, and their relation to age and body size using spectrophotometry. Our results indicate that the brightness of foot webbings of S. guttatus and S. parvus increased with increasing age. Additionally, we compared the results with measurements of adult individuals from a population in Brunei and discuss possible differences related to diet and age as well as the habitat use of juveniles and adults. We suggest that the ontogenetic increase in foot-webbing brightness enhances visual conspicuousness and the signal-to-noise ratio of the visual signal with sexual maturity and potentially functions as cue to the age of the signaler.

DNA barcoding and molecular phylogeny in Ranidae

The family Ranidae has the widest distribution compared with other frog family. The phylogeny of the Ranidae is still a matter of dispute. In the present study, we analyzed the COI barcodes of 29 species from six genera belonging to the family Ranidae. Twenty-seven species (93.10% of all the species) were correctly identified by their DNA barcodes. Pelophylax lessonae and Pelophylax ridibundus shared the same one barcode sequence. Kimura two-parameter distances were calculated between barcodes. Pair-wise comparisons among-species were distributed from 0.16% (between Pelophylax lessonae and Pelophylax esculenta) to 29.13% (between Rana warszewitschii and Rana dybowskii). The average genetic distance between species was 28 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree, which grouped all the genera into two divergent clades. The results indicated that some currently recognized genera of Ranidae may not be monophyletic. COI gene data supported the hypothesis of polyphyly for Rana, Amolops, Babina, and Hylarana. DNA barcoding is an effective molecular tool for Ranidae species identification and phylogenetic inference.

Identification and characterization of major histocompatibility complex class IIB alleles from three species of European ranid frogs

Immune genes of the major histocompatibility complex (MHC) are among the most polymorphic genes in the vertebrate genome. Due to their polymorphic nature, they are often used to assess the adaptive genetic variability of natural populations. This study describes the first molecular characterization of 13 partial MHC class IIB sequences from three European ranid frogs. The utility of previously published primers was expanded by using them to successfully amplify eight exon 2 alleles from Rana arvalis.We also designed a novel primer set that successfully amplified exon 2 from Pelophylax kurtmuelleri. Pelophylax lessonae was also designed as part of this study. Results indicate the presence of one or two class IIB loci in these three species. In R. arvalis, significant evidence of positive selection acting on MHC antigen binding sites was found. Many European ranid populations are experiencing disease-related declines; the newly developed primers can, therefore, be used for further population analyses of native frogs.

The complete mitochondrial genome of Amolops wuyiensis (Anura: Ranidae)

In the organisms, mitochondrial DNA plays an important role in the evolutionary studies, which can serve as a powerful molecular marker. Amolops wuyiensis, belongs to the family Ranidae that is known to occur in southeast China. The complete mitochondrial genome of A. wuyiensis was sequenced (17,797 bp in length, GenBank accession number KM386618). Similar to the typical mtDNA of amphibians, the complete mtDNA sequence of A. wuyiensis contained 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes and 1 control region. The nucleotide composition was 25.9% A, 33.8% T, 28.0% C and 12.3% G.

The complete mitochondrial genome of Glandirana tientaiensis (Ranidae, Anura)

The Tiantai frog (Glandirana tientaiensis) is an endemic to China, which has been listed as an endangered species in IUCN Red List of Threatened Species. In this study, the complete nucleotide sequence of the mitochondrial genome of G. tientaiensis is determined. The circle genome is 17,681 bp and consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region. Comparing with the typical mtDNA of species in the family Ranidae, no distinctive rearrangement of mtDNA genes was found. Yet a obvious feature on the use of codon were observed, that 8 of 13 protein-conding genes ended with a single stop nucleotide T except for COI, ATPase 8, ND4L, ND6 and Cyt b.

The complete mitochondrial genome of Amolops ricketti (Amphidia, Anura, Ranidae)

The complete mitochondrial genome from the South China torrent frog Amolops ricketti was determined. This mitogenome was 17,771 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region (CR). All the protein-coding genes in A. ricketti were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

When a clonal genome finds its way back to a sexual species: evidence from ongoing but rare introgression in the hybridogenetic water frog complex

Besides several exceptions, asexual metazoans are usually viewed as ephemeral sinks for genomes, which become 'frozen' in clonal lineages after their emergence from ancestral sexual species. Here, we investigated whether and at what rate the asexuals are able to introgress their genomes back into the parental sexual population, thus more or less importantly affecting the gene pools of sexual species. We focused on hybridogenetic hybrids of western Palaearctic water frogs (Pelophylax esculentus), which originate through hybridization between P. ridibundus and P. lessonae, but transmit only clonal ridibundus genome into their gametes. Although usually mating with P. lessonae, P. esculentus may upon mating with P. ridibundus or another hybrid produce sexually reproducing P. ridibundus offspring with the introgressed ex-clonal genome. We compared the rate of nuclear amplified fragment length polymorphism (AFLP) and mitochondrial introgression in two types of populations, that is, those where P. ridibundus occurs in isolation and those where it lives with the hybridogens. Although significant differentiation (Φpt) between sexual and clonal ridibundus genomes suggested limited gene flow between sexuals and hybridogens, a non-negligible (~5%) proportion of P. ridibundus bore introgressed mtDNA and AFLP markers. Whereas transfer of mtDNA was exclusively unidirectional, introgression of nuclear markers was bidirectional. The proportion of introgressed P. ridibundus was highest in syntopic populations with P. esculentus, proving an ongoing and site-specific interspecific genetic transfer mediated by hybridogenetic hybrids. It turns out that asexual hybrids are not just a sink for genes of sexual species, but may significantly influence the genetic architecture of their sexual counterparts.

Complete mitochondrial genomes of two brown frogs, Rana dybowskii and Rana cf. chensinensis (Anura: Ranidae)

We first determined complete mitochondrial genomes of Rana dybowskii and Rana cf. chensinensis (Anura: Ranidae). The mitogenomic lengths of R. dybowskii and R. cf. chensinensis were 18,864 and 18,808 bp, respectively. The two mitogenomes have similar gene compositions including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. Rana dybowskii and R. cf. chensinensis mitogenomes displayed same gene order arrangements and similar base compositions with an A + T bias. Mitogenomic data of the two species contributed to provide molecular marker for their conservative genetics and clarified their phylogenetic position under mitogenome-based phylogeny of the genus Rana.

Complete mitochondrial genome of a brown frog, Rana kunyuensis (Anura: Ranidae)

The first complete mitochondrial genome (mitogenome) of Rana sensu stricto (sensu Frost, 2013) was determined using Rana kunyuensis as a representative species. The mitogenome was 22,255 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and duplicated control regions. The mitogenome of R. kunyuensis showed novel gene order arrangement with a translocation of tRNA(Leu)((CUN)) and ND5 in comparison with published anuran mitogenomes to date. This mitogenome should contribute to understand the evolution of anuran mitochondrial gene order arrangements.

Molecular phylogeny and diversification of the genus Odorrana (Amphibia, Anura, Ranidae) inferred from two mitochondrial genes

A diversity of hypotheses have been proposed for phylogenetic relationships and taxonomy within the genus Odorrana, and great progress has been made over the past several decades. However, there is still some controversy concerning relationships among Odorrana species. Here, we used many paratypes and topotypes and utilized 1.81 kb of mitochondrial sequence data to generate a phylogeny for approximately 4/5 of Odorrana species, and Odorrana haplotypes form a strongly supported monophyletic group relative to the other genera sampled. The deepest phylogenetic divergences within Odorrana separate 3 lineages whose interrelationships are not recovered with strong support. These lineages include the ancestral lineage of O. chapaensis, the ancestral lineage of a strongly supported clade comprising many western species, and the ancestral lineage of a strongly supported clade comprising all other Odorrana sampled. Within the latter clade, the first phylogenetic split separates O. ishikawae from a well-supported clade comprising its other species. These divergences likely occurred in the middle Miocene, approximately 12-15 million years ago. Separation of the ancestral lineage of Odorrana from its closest relative, Babina in our study, likely occurred in the early Miocene or possibly late Oligocene. Rates of lineage accumulation remained high from the middle Miocene through the Pleistocene.