Frog Genus Research Articles

<p><strong>The <em>Relictus</em> case: it is high time that taxonomists follow the <em>Code</em>’s requirements for nomenclatural availability and validity of new zoological nomina</strong></p>

The new genus-series nomen Relictus, proposed by Sá et al. (2018) for a subgenus of the frog genus Chiasmocleis Méhelÿ, 1904, is unavailable for having been proposed [1] in a paper published online unregistered in Zoobank and [2] without a diagnosis stating in words characters purported to differentiate the taxon. Finally, it is also invalid for being a junior homonym of a generic nomen of fishes. Such mistakes are not new, many other similar ones having been published in the recent years. All taxonomists should give the proper attention to the nomenclatural Rules of the Code when proposing new nomina.

The Influence of Habitat and Phylogeny on the Skin Microbiome of Amphibians in Guatemala and Mexico.

Microbial symbionts are increasingly recognized as playing a critical role in organismal health across a wide range of hosts. Amphibians are unique hosts in that their skin helps to regulate the exchange of water, ions, and gases, and it plays an active role in defense against pathogens through the synthesis of anti-microbial peptides. The microbiome of amphibian skin includes a diverse community of bacteria known to defend against pathogens, including the global pandemic lineage of Batrachochytrium dendrobatidis associated with mass amphibian die-offs. The relative influence of host phylogeny and environment in determining the composition of the amphibian skin microbiome remains poorly understood. We collected skin swabs from montane amphibians in Mexico and Guatemala, focusing on two genera of plethodontid salamanders and one genus of frogs. We used high throughput sequencing to characterize the skin bacterial microbiome and tested the impact of phylogeny and habitat on bacterial diversity. Our results show that phylogenetic history strongly influences the diversity and community structure of the total bacterial microbiome at higher taxonomic levels (between orders), but on lower scales (within genera and species), the effect of habitat predominates. These results add to a growing consensus that habitat exerts a strong effect on microbiome structure and composition, particularly at shallow phylogenetic scales.

Advertisement calls, intraspecific variation and species diagnosis of six Brazilian species of Elachistocleis (Anura: Microhylidae: Gastrophryninae)

We describe for the first time the advertisement calls of three Elachistocleis species (E. surumu, E. magna, E. carvalhoi) and provide additional data on the calls of three other species (E. matogrosso, E. helianneae, E. muiraquitan). Additionally, we evaluate intraspecific variation in morphology and color patterns, and comment on species diagnosis in the genus. The advertisement calls of the six species of Elachistocleis have a stereotyped temporal and spectral structure, which consists of a long sustained multipulsed note with an upsweep in frequency at its onset, followed by a constant frequency along the note. Newly collected Elachistocleis from northern and western Brazil showed intraspecific variation in morphology and coloration that had not been previously reported. Coloration was listed as a diagnostic feature in the original descriptions of the Elachistocleis species evaluated in this study, but color patterns were variable in some species and sometimes did not allow for species differentiation. Our results indicated that the three species with greater degrees of morphological similarity (E. helianneae, E. matogrosso, E. muiraquitan) differed in microtemporal and spectral traits of their calls. Moreover, pulse duration in E. helianneae was very distinct, lasting approximately twice the average pulse duration in calls of the other species studied. Therefore, pulse duration might be an informative trait when assigning specimens to E. helianneae, which is widely distributed across Amazonian lowland forests and in a region of Amazonian savanna. Our results bring novelties on species diagnosis and intraspecific variation in Elachistocleis based on acoustic evidence and morphological/color patterns, and accentuate the importance of taking into consideration multiple lines of evidence as a means for accurate species-level identification in this genus of Neotropical frogs.

Phenotypic and life-history diversification in Amazonian frogs despite past introgressions

The advent of genomics in phylogenetics and population genetics strengthened the perception that conflicts among gene trees are frequent and often due to introgression. However, hybridization occurs mostly among species that exhibit little phenotypic differentiation. A recent study delineating species in Anomaloglossus, a frog genus endemic to the Guiana Shield, identified an intriguing pattern in the A. baeobatrachus species complex. This complex occurs in French Guiana and Amapá (Brazil) and comprises two sympatric phenotypes contrasting not only in body size, habitat, and advertisement call, but also in larval development mode (endotrophic vs exotrophic tadpoles). However, molecular and phenotypic divergences are, in some cases, incongruent, i.e specimens sharing mtDNA haplotypes are phenotypically distinct, suggesting a complex evolutionary history. Therefore, we genotyped 106 Anomaloglossus individuals using ddRADseq to test whether this phenotype/genotype incongruence was a product of phenotypic plasticity, incomplete lineage sorting, multiple speciation events, or admixture. Based on more than 16,000 SNPs, phylogenetic and population genetic approaches demonstrated that exotrophic populations are paraphyletic. Species tree and admixture analyses revealed a strikingly reticulate pattern, suggesting multiple historical introgression events. The evolutionary history of one exotrophic population in northern French Guiana is particularly compelling given that it received genetic material from exotrophic ancestors but shows very strong genetic affinity with the nearby endotrophic populations. This suggests strong selection on larval development and mating call after secondary contact and hybridization. The case of A. baeobatrachus represents a striking example of introgression among lineages that are phenotypically distinct, even in their larval development mode, and highlights how high-resolution genomic data can unravel unexpectedly complex evolutionary scenarios.

A new species of the odorous frog genus Odorrana (Amphibia, Anura, Ranidae) from southwestern China.

The genus Odorrana is widely distributed in the mountains of East and Southeastern Asia. An increasing number of new species in the genus have been recognized especially in the last decade. Phylogenetic studies of the O. schmackeri species complex with wide distributional range also revealed several cryptic species. Here, we describe a new species in the species complex from Guizhou Province of China. Phylogenetic analyses based on mitochondrial DNA indicated the new species as a monophyly clustered into the Odorrana clade and sister to O. schmackeri, and nuclear DNA also indicated it as an independent lineage separated from its related species. Morphologically, the new species can be distinguished from its congeners based on a combination of the following characters: (1) having smaller body size in males (snout-vent length (SVL) <43.3 mm); (2) head longer than wide; (3) dorsolateral folds absent; (4) tympanum of males large and distinct, tympanum diameter twice as long as width of distal phalanx of finger III; (5) two metacarpal tubercles; (6) relative finger lengths: II < I < IV < III; (7) tibiotarsal articulation reaching to the level between eye to nostril when leg stretched forward; (8) disks on digits with circum-marginal grooves; (9) toes fully webbed to disks; (10) the first subarticular tubercle on fingers weak; (11) having white pectoral spinules, paired subgular vocal sacs located at corners of throat, light yellow nuptial pad on the first finger in males.

Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical Pristimantis leaf litter frogs

The Neotropical leaf litter frog genus Pristimantis is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in Pristimantis. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 Pristimantis presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of Pristimantis at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in Pristimantis phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within Pristimantis. Diversification rates decrease towards the present following a density-dependent pattern for Pristimantis overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of Pristimantis and thus contributed to the origins of evolutionary independent phylogenetic clusters.

Advertisement calls and DNA sequences reveal a new species of Scinax (Anura: Hylidae) on the Pacific lowlands of Ecuador.

Scinax is a speciose genus of Neotropical hylid frogs. We describe a new species from western Ecuador (elevations between 0 and 1207 m) using morphology, vocalizations, and DNA sequences. We also present a new phylogeny for Scinax based on mitochondrial DNA genes 12S rRNA, Cytochrome Oxidase sub-unit I, Cytochrome B, 16S rRNA, NADH dehydrogenase subunit 1, and adjacent tRNAs. The new species, Scinax tsachila sp. nov. was previously confused with S. quinquefasciatus, a morphologically similar sympatric species. They differ by having markedly different advisement calls, distinct skin texture in the dorsum, and different bone coloration. The new species is sister to S. elaeochroa, a species that differs in advertisement call and color pattern. We provide an updated species account for Scinax quinquefasciatus and a redescription of its holotype.

Sex Chromosome Differentiation in the Frog Genus Pseudis Involves Satellite DNA and Chromosome Rearrangements.

The genus Pseudis comprises six frogs of the family Hylidae and only P. tocantins had heteromorphic sex chromosomes detected by classical cytogenetics. In this species, the W chromosome is larger than the Z chromosome and has a large heterochromatic block located between the centromere and the nucleolus organizer region (NOR) in the long arm. This large heterochromatic band is enriched for the PcP190 satellite DNA (satDNA), whereas the Z chromosome bears a smaller C-band adjacent to the centromere in the long arm that is not detected by PcP190 probes. To assess sex chromosome differentiation in the genus Pseudis, we investigated the PcP190 satDNA in P. bolbodactyla, P. cardosoi, P. minuta, and P. paradoxa and in one species of Lysapsus, which is the sister genus of Pseudis. PcP190 sequences were isolated, sequenced, and the diversity of this class of satDNA was analyzed. To evaluate whether sex-related variations in PcP190 satDNA were present, we used in situ hybridization (for P. bolbodactyla, P. paradoxa, P. cardosoi, and P. minuta) and Southern blotting analysis (for all species). We found a low level of sex chromosome heteromorphism in P. bolbodactyla, as a PcP190 cluster was detected in the short arm of one of the homologs of pair 7 exclusively in females. In P. paradoxa, P. minuta, and P. cardosoi, PcP190 satDNA is not sex-related, although a cluster of PcP190 sequences could be recognized in the NOR-bearing chromosomes 7 of P. paradoxa and P. minuta and their homologous chromosome 5 of P. cardosoi. By tracking cytogenetic data in a species tree, we may hypothesize that the positioning of the PcP190 site adjacently to the NOR (as observed in the long arm of the W chromosome of P. tocantins) is a derived condition with respect to the location of the PcP190 site apart from the NOR, in the short arm of the NOR-bearing chromosomes 7 (as present in P. bolbodactyla, P. paradoxa, and P. minuta) or 5 (as present in P. cardosoi) and we discuss about the emergence of PcP190 satDNA as a sex-related trait.

Two New Species of the GenusLeptobrachella(Amphibia: Anura: Megophryidae) from Kalimantan, Indonesia

Two new species of the dwarf litter frog genus Leptobrachella are described from North and Central Kalimantan, Indonesian part of the Borneo Island. Leptobrachella fusca n. sp. from Bulungan Regency, differs from all congeneric species in the following combination of characters: body small (SVL: 16.3 mm in a male); dorsum uniformly dark brown; sides of body without marking; a series of elongate ventrolateral glands present on flank; ventrum darkly pigmented except for throat and posterior portion; lineae masculinae invisible through ventral skin in preservative; and toe webs rudimentary. Leptobrachella bondangensis n. sp. from Gunung (=Mt.) Bondang of Murung Raya Regency, is distinct in possessing the following combination of characters: body large as this genus (SVL: 17.8 mm in a male); dorsum grayish brown; sides of body without dark blotches; a sparse series of rounded ventrolateral glands present on flunk; ventrum pale gray with dark mottles; lineae masculinae invisible through ventral skin in preservative; and toe webs rudimentary.

Phylogenomics of montane frogs of the Brazilian Atlantic Forest is consistent with isolation in sky islands followed by climatic stability

Abstract Despite encompassing a relatively small geographical area, montane regions harbor disproportionately high levels of species diversity and endemism. Yet, relatively little is known about the evolutionary mechanisms ultimately leading to montane diversity. In this study, we use target capture of ultraconserved elements to investigate the phylogenetic relationships and diversification patterns of Melanophryniscus (Bufonidae) and Brachycephalus (Brachycephalidae), two frog genera that occur in sky islands of the southern Atlantic Forest of Brazil. Specifically, we test whether diversification of montane species in these genera can be explained by a single climatic shift leading to isolation in sky islands, followed by relative climatic stability that maintained populations in allopatry. In both genera, the topologies inferred using concatenation and coalescent-based methods were concordant and had strong nodal support, except for a few recent splits. These recent splits tended to be supported by more informative loci (those with higher average bootstrap support), suggesting that, while individual trees may be well resolved, the relationships they recover are being obscured by non-informative data. Divergence dating of a combined dataset using both genera is consistent with concordant timing of their diversification. These results support the scenario of diversification-by-isolation in sky islands, and suggest that allopatry due to climatic gradients in montane regions are an important mechanism for generating species diversity and endemism in these regions.

The mitochondrial genomes of five frog species of the Neotropical genus Ischnocnema (Anura: Brachycephaloidea: Brachycephalidae)

We report the mitogenomes for five species of the Ischnocnema guentheri series, being the first described for this genus of brachycephalid frogs. We assembled mitogenomes from anchored hybrid enrichment data and recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for all species. The general structure agrees with most previously sequenced neobatrachians, with two exceptions: the origin of replication of L-strand (OL) was found between tRNA-A and tRNA-N, and the position of tRNA-L and tRNA-T, which are dispersed in the control region. We provide a phylogenetic tree with outgroups, which is consistent with previous phylogenetic hypotheses.

Molecular phylogeny of Ischnocnema (Anura: Brachycephalidae) with the redefinition of its series and the description of two new species

We present a new phylogenetic hypothesis for Ischnocnema, a Neotropical brachycephaloid genus of ground-dwelling direct-developing frogs. We performed Bayesian inference, maximum likelihood, and maximum parsimony analyses using two nuclear (RAG1 and Tyr) and three mitochondrial genes (12S rRNA, tRNA-Val, and 16S rRNA) in a matrix comprising more than 80% of the described species. We recover Ischnocnema nanahallux outside the Ischnocnema parva series, and it is now unassigned to any species series, nor are Ischnocnema manezinho and Ischnocnema sambaqui. We propose the Ischnocnema venancioi species series to comprise Ischnocnema venancioi, Ischnocnema hoehnei, and two new species described herein (Ischnocnema parnaso sp. nov. and Ischnocnema colibri sp. nov.). Furthermore, we designate a lectotype for I. venancioi. The nuptial pad present in males is an important character in the genus, and having a large, conspicuous, and glandular-appearing nuptial pad seems to be a synapomorphy for the clade composed of the I. parva, Ischnocnema guentheri, and the newly proposed I. venancioi series.

Anomaloglossus meansi sp. n., a new Pantepui species of the Anomaloglossus beebei group (Anura, Aromobatidae).

Recent extinctions and drastic population declines have been documented in the Guiana Shield endemic frog genus Anomaloglossus, hence the importance to resolve its alpha-taxonomy. Based on molecular phylogenies, the literature has long reported the occurrence of an undescribed species in the Pakaraima Mountains of Guyana in the Pantepui region. We here describe this new taxon and demonstrate that in addition to divergence at the molecular level the new species differs from congeners by a unique combination of morphological characters, notably a small size (maximum SVL in males 18.86 mm, maximum SVL in females 21.26 mm), Finger I = Finger II when fingers adpressed, Finger III swollen in breeding males, fringes on fingers absent, toes basally webbed but lacking fringes, in life presence of a thin dorsolateral stripe from tip of snout to tip of urostyle, and a black throat in preserved males (immaculate cream in females). Virtually nothing is known about the ecology of the new species. We suggest the new species to be considered as Data Deficient according to IUCN standards.

Feeding habits of the bromeligenous treefrog Phyllodytes edelmoi Peixoto, Caramaschi & Freire, 2003 (Anura: Hylidae) from the State of Alagoas, Northeastern Brazil

The hylid frog genus Phyllodytes comprised 12 species distributed in eastern Brazil and known to strictly inhabit inside bromeliads. In this study, we explore the feeding habits of P. edelmoi and test the prey selectivity of the species by comparing the prey items in the stomachs contents with the availability of preys in bromeliads. Our results show that P. edelmoi consumes high amounts of ants along the year, and therefore it could be considered an “ant specialist” species. This specialist feeding behaviour could be considered a synapomorphy of the genus Phyllodytes .

Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia.

The frog genus Leptopelis is composed of ~50 species that occur across sub-Saharan Africa. The majority of these frogs are typically arboreal; however, a few species have evolved a fossorial lifestyle. Most species inhabit lowland forests, but a few species have adapted to high elevations. Five species of Leptopelis occupy the Ethiopian highlands and provide a good opportunity to study the evolutionary transition from an arboreal to a fossorial lifestyle, as well as the diversification in this biodiversity hot spot. We sequenced 14 nuclear and three mitochondrial genes, and generated thousands of SNPs from ddRAD sequencing to study the evolutionary relationships of Ethiopian Leptopelis. The five species of highland Leptopelis form a monophyletic group, which diversified during the late Miocene and Pliocene. We found strong population structure in the fossorial species L.gramineus, with levels of genetic differentiation between populations similar to those found between arboreal species. This could indicate that L.gramineus is a complex of cryptic species. We propose that after the original colonization of the Ethiopian highlands by the ancestor of the L.gramineus group, episodes of vicariance fragmented the ancestral populations of this group. We also report the re-evolution of arboreality in L.susanae, which evolved from a fossorial ancestor, a rare ecological switch in frogs that had previously been reported only once.

Resolution of the types and type localities of some early nominal species of the Australian myobatrachid frog genus Pseudophryne Fitzinger, 1843.

The types and type localities of Bombinator australis Gray, 1835, Pseudophryne bibronii Günther, 1859, and Phryniscus albifrons Duméril, Bibron Duméril, 1854, are defined. The nominal type locality for B. australis, Swan River, is considered to be in error. The source of the specimen, Joseph Wright, owned property in the Swan River colony in Western Australia, but later resided in Sydney, the latter locality within the known range of the species. We designate a specimen in the Museum National d'Histoire Naturelle, Paris as lectotype of Pseudophryne bibronii, restricting the type locality of both species to Parramatta, near Sydney, based on the published statements of the collector, François Péron. The holotype of Phryniscus albifrons, a species defined by a painting of a specimen, was likely to have been collected by Jules Verreaux, but the only extant Pseudophryne obtained from Verreaux does not match the type illustration. Verreaux is renowned for the numerous errors in the localities associated with his specimens, and the locality for this specimen, Moreton Bay, Queensland, is likely to be another such error. Resolution of these issues facilitates ongoing taxonomic work on the genus using genetic and morphological data.

Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae)

Southeast Asia and southern China (SEA-SC) harbor a highly diverse and endemic flora and fauna that is under increasing threat. An understanding of the biogeographical history and drivers of this diversity is lacking, especially in some of the most diverse and threatened groups. The Asian leaf-litter frog genus Leptolalax Dubois 1980 is a forest-dependent genus distributed throughout SEA-SC, making it an ideal study group to examine specific biogeographic hypotheses. In addition, the diversity of this genus remains poorly understood, and the phylogenetic relationships among species of Leptolalax and closely related Leptobrachella Smith 1928 remain unclear. Herein, we evaluate species-level diversity based on 48 of the 53 described species from throughout the distribution of Leptolalax. Molecular analyses reveal many undescribed species, mostly in southern China and Indochina. Our well-resolved phylogeny based on multiple nuclear DNA markers shows that Leptolalax is not monophyletic with respect to Leptobrachella and, thus, we assign the former to being a junior synonym of the latter. Similarly, analyses reject monophyly of the two subgenera of Leptolalax. The diversification pattern of the group is complex, involving a high degree of sympatry and prevalence of microendemic species. Northern Sundaland (Borneo) and eastern Indochina (Vietnam) appear to have played pivotal roles as geographical centers of diversification, and paleoclimatic changes and tectonic movements seem to have driven the major divergence of clades. Analyses fail to reject an “upstream” colonization hypothesis, and, thus, the genus appears to have originated in Sundaland and then colonized mainland Asia. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns in the genus.

A New Bromeligenous Species of Fritziana Mello-Leitão, 1937 (Amphibia: Anura: Hemiphractidae) from High Elevations in the Serra Dos Órgãos, Rio de Janeiro, Brazil

Abstract Fritziana is a genus of phytotelm-dwelling frogs that inhabits bamboo and bromeliads in the southern and southeastern portions of the Brazilian Atlantic Forest. Currently, five species are known, but the existence of undescribed species has been acknowledged. Here, we conducted a species-delimitation analysis of Fritziana using deoxyribonucleic acid sequences comprising two fragments of a mitochondrial gene (16S). The species delimitation analysis (with 16S) with Bayesian inference and maximum parsimony supported the recognition of a new species as an exclusive lineage, sister to all other Fritziana species. Bioacoustic and morphological evidence also support this finding. The new species occurs from 1166 to 2146 m above sea level and inhabits bromeliads from the National Park of Serra dos Orgaos, in the municipality of Teresopolis, state of Rio de Janeiro, Brazil. Compared with its congeners, the new species has nostrils narrowly separated, diameter of tympanum equal to or larger than diameter o...

Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java

Geological and climatological processes can drive the synchronous diversification of co-distributed species. The islands of Sumatra and Java have experienced complex geological and climatological histories, including extensive sea-level changes and the formation of valleys between northern, central, and southern components of the Barisan Mountain Range, which may have promoted diversification of their resident species. We investigate diversification on these islands using 13 species of the parachuting frog genus Rhacophorus. We use both mitochondrial and nuclear sequence data, along with genome-wide SNPs to estimate phylogenetic structure and divergence times, and to test for synchronous diversification. We find support for synchronous divergence among sister-species pairs from Sumatra and Java ∼9 Ma, as well as of populations of four co-distributed taxa on Sumatra ∼5.6 Ma. We found that sister species diverged in allopatry on Sumatra and conclude that divergence on Sumatra and Java was affected by sea-level fluctuations that promoted isolation in allopatry.

A striking new genus and species of cave-dwelling frog (Amphibia: Anura: Microhylidae: Asterophryinae) from Thailand.

We report on a discovery of Siamophryne troglodytes Gen. et sp. nov., a new troglophilous genus and species of microhylid frog from a limestone cave in the tropical forests of western Thailand. To assess its phylogenetic relationships we studied the 12S rRNA–16S rRNA mtDNA fragment with final alignment comprising up to 2,591 bp for 56 microhylid species. Morphological characterization of the new genus is based on examination of external morphology and analysis of osteological characteristics using microCT-scanning. Phylogenetic analyses place the new genus into the mainly Australasian subfamily Asterophryinae as a sister taxon to the genus Gastrophrynoides, the only member of the subfamily known from Sundaland. The new genus markedly differs from all other Asterophryinae members by a number of diagnostic morphological characters and demonstrates significant mtDNA sequence divergence. We provide a preliminary description of a tadpole of the new genus. Thus, it represents the only asterophryine taxon with documented free-living larval stage and troglophilous life style. Our work demonstrates that S. troglodytes Gen. et sp. nov. represents an old lineage of the initial radiation of Asterophryinae which took place in the mainland Southeast Asia. Our results strongly support the “out of Indo-Eurasia” biogeographic scenario for this group of frogs. To date, the new frog is only known from a single limestone cave system in Sai Yok District of Kanchanaburi Province of Thailand; its habitat is affected by illegal bat guano mining and other human activities. As such, S. troglodytes Gen. et sp. nov. is likely to be at high risk of habitat loss. Considering high ecological specialization and a small known range of the new taxon, we propose a IUCN Red List status of endangered for it.