The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura, Microhylidae)

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

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

A new high elevation species of Oreophryne Boettger (Anura: Microhylidae) from Sulawesi, Indonesia

We examined the morphology of 50 specimens of Sulawesian Oreophryne and recognize a distinct, undescribed species. Based on morphological data and supported with phylogenetic analysis of the 16S rRNA gene, it is herein described and named as Oreophryne riyantoi sp. nov. The new species is diagnosed by having a combination of rounded snout in dorsal and lateral view, indistinct tympanum, narrow interorbital distance, small hands, small terminal discs on fingers and toes, toes without webbing, short legs, and dorsal surfaces of head, body and limbs irregularly tuberculated in life. It was found in leaf litter on the forest floor in extremely wet primary montane forest on Mount Mekongga at an altitude of 2528 m asl. The forest-dwelling habit of this terrestrial frog is unusual because other terrestrial Oreophryne occuring at high-altitude live in open grassy or fern dominated meadows. Four endemic species of Oreophryne are now known from Sulawesi. However, herpetological research activities, including high elevation surveys and additional taxonomic work, are necessary to achieve a comprehensive understanding of Oreophryne diversity and phylogeography in Sulawesi.

Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process

Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].

Testing Geology with Biology: Plate Tectonics and the Diversification of Microhylid Frogs in the Papuan Region

Studies of the Papuan region have provided fundamental insights into the evolutionary processes generating its exceptional biodiversity, but the influence of geological processes merits further study. Lying at the junction of five tectonic plates, this region has experienced a turbulent geological history that has not only produced towering mountains allowing elevational specialization and island archipelagos with varying degrees of isolation promoting vicariance, but also active margins where land masses have collided and been subsequently rifted apart creating a mosaic of intermixed terranes with vastly different geological histories. Asterophryine frogs are a hyperdiverse clade representing half the world's microhylid diversity (over 360 species) centered on New Guinea and its satellite islands. We show that vicariance facilitated by geological history explains this far and wide distribution of a clade that should have poor dispersal abilities. We recovered a mainland tectonic unit, the East Papua Composite Terrane (EPCT), as the center of origin for Asterophryinae and no fewer than 71 instances of what appear to be long-distance dispersal events, 29 of which are between mainland regions, with 42 from the mainland to the islands, some presently as far as 200 km away from source populations over open ocean. Furthermore, we find strong support for a "Slow and Steady" hypothesis for the formation of the northern margin of New Guinea by many separate accretion events during the Miocene, over other major geological alternatives, consistent with the 20 M year age of the clade and arrival via the EPCT. In addition, the historical biogeography of our frogs strongly supports an affiliation of the Louisiade Archipelago and Woodlark Island with the Owen Stanley Range on the EPCT, and the recent proximity of the large New Britain Island. Our results show that Asterophryinae did not have to repeatedly and independently disperse across large ocean barriers to the offshore islands, against the predictions of island biogeography theory, but that the current distribution can be explained through vicariance and short-distance oceanic dispersal as historical land connections disappeared and islands slowly became separated from each other. We show that islands have a life history, changing in distance from other land masses, with consequent opportunities for dispersal, isolation, and cladogenesis of their biotas. More broadly, we can begin to see how the geological history of the Papuan region can result in the rapid accumulation and staggering number of extant species.

Another giant species of the microhylid frog genus Cophixalus Boettger, 1892 from the mountains of Papua New Guinea and first records of procoracoids in the genus

A new arboreal species of the microhylid genus Cophixalus Boettger, 1892 is described from montane rainforest on Papua New Guinea’s central cordillera. With a male SUL exceeding 44.0 mm, the new species is among the largest members of the genus; the only other Papuan species known to reach this size is C. riparius Zweifel, 1962. The new species differs from C. riparius in a small number of mensural characters and by its distinct advertisement call, a single explosive ‘bark’ uttered singly or in rapid series. In contrast, calls of C. riparius recorded near the type locality are a series of drawn out, rasping croaks. Calls of the two species are analysed and compared. The two species also appear to have different ecologies, with the new species found only high in trees, while C. riparius is often encountered in vegetation on or near the forest floor. Examination of osteological features revealed the presence of cartilaginous procoracoids in both species, representing the first records of procoracoids in the speciose genus Cophixalus. Lack of procoracoids is traditionally considered an important diagnostic character for defining Cophixalus but both species also lack clavicles, a character considered diagnostic for Cophixalus and a key feature distinguishing the genus from the closely related Oreophryne Boettger, 1895. Because preliminary published genetic data indicate that they are nested within Cophixalus, we retain both species in that genus until a comprehensive molecular phylogeny of Cophixalus and related genera, particularly Oreophryne, is completed.

A New Species of the Genus Microhyla (Amphibia: Anura: Microhylidae) from the Dabie Mountains, China

Species belonging to the genus Microhyla are small-sized frogs that are widely distributed in southern, eastern, and south-eastern Asia. In China, the genus harbors many cryptic species, on two of which—M. beilunensis and M. fanjinshanensis—studies were recently published. In this study, we collected specimens from the Dabie Mountain range, which is at the junction of Anhui, Henan and Hubei Provinces, East China; these specimens belonged to a species previously identified as M. mixtura. Based on phylogenetic analyses, species delimitation analyses, morphological comparisons and advertisement calls comparisons, we found they were significantly different from other known congeners, and thus we describe them as a new species. This study enriches the diversity of Microhylidae, and clarifies the species of the genus Microhyla in the Dabie Mountains.

Resolving the deep phylogeny: Implications for early adaptive radiation, cryptic, and present-day ecological diversity of Papuan microhylid frogs

The microhylid frogs of the New Guinea region are the largest and most ecologically diverse subfamily (Asterophryinae) of one of the largest anuran families in the world and can live in communities of up to 20 species. While there has been recent progress in resolving the phylogenetic relationships of Asterophryinae, significant uncertainties remain, impeding further progress in understanding the evolution of microhabitat use, parental care, and life history variation in this group. In particular, the early divergences at the base of the tree remain unclear; as does the monophyly of some genera; and recent studies have discovered that species with wide geographic distribution are instead cryptic species complexes. In this study, we fortified geographic sampling of the largest previous phylogenetic effort by sequencing an additional 62 taxa and increased data quality and quantity by adding new layers of data vetting and by filling in previously incomplete loci to the five gene dataset (2 mitochondrial, 3 nuclear protein-coding genes) to obtain a dataset that is now 99% complete in over 2400 characters for 233 samples (205 taxa) of Asterophryinae and 3 outgroup taxa, and analyzed microhabitat use data for these taxa from field data and data collected from the literature. Importantly, our sampling includes complete community complements at 19 sites as well as representatives at over 80 sites across New Guinea and its offshore islands. We present a highly resolved molecular phylogeny which, for the first time, has over 95% of nodes supported (84% highly supported) whether using Maximum Likelihood or Bayesian Inference, allowing clarification of all genera (whether monophyletic or clearly not), their sister genera relationships, as well as an age estimate for the Asterophryinae at approximately 20MYA. Early generic diversification occurring between 17 and 12 MYA gave rise to a surprising diversity of about 18 genera as well as the 5 putative microhabitat types. Our tree reveals extensive cryptic diversity calling any widespread taxa into doubt, and clearly demonstrates that complex multispecies communities of Asterophryinae are ecologically diverse, are numerous, and of ancient origin across New Guinea. We discuss the implications of our phylogeny for explaining the explosive diversification of Asterophryinae as the result of adaptive radiation, niche conservatism, and non-adaptive radiation.

A tale of two bellies: systematics of the oval frogs (Anura: Microhylidae: Elachistocleis Parker, 1927)

Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phylogeny of Elachistocleis to date, and explore its genetic diversity using distance-based and tree-based methods for putative species delimitation. Our results show that at least two of the most relevant traditional characters used in the taxonomy of this group (belly pattern and dorsal median white line) carry less phylogenetic information than previously thought. Based on our results, we propose some synonymizations and some candidate new species. This study is a first major step in disentangling the current systematics of Elachistocleis. Yet, a comprehensive review of morphological data is needed before any new species descriptions can be properly made.

FrogCap: A modular sequence capture probe-set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Despite the prevalence of high-throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publicly available FrogCap suite of genomic resources, which is a large collection of ~15,000 markers that unifies previous genetic sequencing efforts. FrogCap is designed to be modular, such that subsets of markers and SNPs can be selected based on the desired phylogenetic scale. FrogCap uses a variety of marker types that include exons and introns, ultraconserved elements, and previously sequenced Sanger markers, which span up to 10,000 bp in alignment lengths; in addition, we demonstrate potential for SNP-based analyses. We tested FrogCap using 121 samples distributed across five phylogenetic scales, comparing probes designed using a consensus- or exemplar genome-based approach. Using the consensus design is more resilient to issues with sensitivity, specificity, and missing data than picking an exemplar genome sequence. We also tested the impact of different bait kit sizes (20,020 vs. 40,040) on depth of coverage and found triple the depth for the 20,020 bait  kit. We observed sequence capture success (i.e., missing data, sequenced markers/bases, marker length, and informative sites) across phylogenetic scales. The incorporation of different marker types is effective for deep phylogenetic relationships and shallow population genetics studies. Having demonstrated FrogCap's utility and modularity, we conclude that these new resources are efficacious for high-throughput sequencing projects across variable timescales.

Total evidence and sensitivity phylogenetic analyses of egg-brooding frogs (Anura: Hemiphractidae)

We study the phylogenetic relationships of egg-brooding frogs, a group of 118 neotropical species, unique among anurans by having embryos with large bell-shaped gills and females carrying their eggs on the dorsum, exposed or inside a pouch. We assembled a total evidence dataset of published and newly generated data containing 51 phenotypic characters and DNA sequences of 20 loci for 143 hemiphractids and 127 outgroup terminals. We performed six analytical strategies combining different optimality criteria (parsimony and maximum likelihood), alignment methods (tree- and similarity-alignment), and three different indel coding schemes (fifth character state, unknown nucleotide, and presence/absence characters matrix). Furthermore, we analyzed a subset of the total evidence dataset to evaluate the impact of phenotypic characters on hemiphractid phylogenetic relationships. Our main results include: (i) monophyly of Hemiphractidae and its six genera for all our analyses, novel relationships among hemiphractid genera, and non-monophyly of Hemiphractinae according to our preferred phylogenetic hypothesis; (ii) non-monophyly of current supraspecific taxonomies of Gastrotheca, an updated taxonomy is provided; (iii) previous differences among studies were mainly caused by differences in analytical factors, not by differences in character/taxon sampling; (iv) optimality criteria, alignment method, and indel coding caused differences among optimal topologies, in that order of degree; (v) in most cases, parsimony analyses are more sensitive to the addition of phenotypic data than maximum likelihood analyses; (vi) adding phenotypic data resulted in an increase of shared clades for most analyses.

A closer look at pupil diversity and evolution in frogs and toads

The eyes of frogs and toads (Anura) are among their most fascinating features. Although several pupil shapes have been described, the diversity, evolution, and functional role of the pupil in anurans have received little attention. Studying photographs of more than 3200 species, we surveyed pupil diversity, described their morphological variation, tested correlation with adult habits and diel activity, and discuss major evolutionary patterns considering iris anatomy and visual ecology. Our results indicate that the pupil in anurans is a highly plastic structure, with seven main pupil shapes that evolved at least 116 times during the history of the group. We found no significant correlation between pupil shape, adult habits, and diel activity, with the exception of the circular pupil and aquatic habits. The vertical pupil arose at least in the most-recent common ancestor of Anura + Caudata, and this morphology is present in most early-diverging anuran clades. Subsequently, a horizontal pupil, a very uncommon shape in vertebrates, evolved in most neobatrachian frogs. This shape evolved into most other known pupil shapes, but it persisted in a large number of species with diverse life histories, habits, and diel activity patterns, demonstrating a remarkable functional and ecological versatility.

A new species of Micryletta Dubois, 1987 (Anura, Microhylidae) from Yunnan Province, China

A new species of the genus Micryletta Dubois, 1987 is described from Yunnan Province, China, based on morphological and molecular analyses. The most obvious differences between the new species and other species of this genus are small body size, unique coloration, and relatively longer hind limbs. In 16S rRNA gene sequences, the new species is diverged from all other congeners by 3.1%–8.0%.

Description of six new species of Xenorhina Peters, 1863 from southern Papua New Guinea (Amphibia, Anura, Microhylidae)

We describe six new species of the microhylid frog genus Xenorhina from the southern slopes of Papua New Guinea’s central cordillera and adjacent lowlands, based on a combination of morphological (including osteology) and bioacoustic features. All of the new species are fossorial or terrestrial inhabitants of tropical rainforest habitats and belong to a group of Xenorhina having a single, enlarged odontoid spike on each vomeropalatine bone. Advertisement calls and habitat preferences are described for each species, one of which is amongst the smallest hitherto members of the genus. Description of these six species brings the total number of Xenorhina known to 40 and emphasises the importance of the high-rainfall belt that extends along the southern flanks of New Guinea’s central cordillera as a hotspot of Melanesian amphibian diversity.

Rampant tooth loss across 200 million years of frog evolution

Teeth are present in most clades of vertebrates but have been lost completely several times in actinopterygian fishes and amniotes. Using phenotypic data collected from over 500 genera via micro-computed tomography, we provide the first rigorous assessment of the evolutionary history of dentition across all major lineages of amphibians. We demonstrate that dentition is invariably present in caecilians and salamanders, but teeth have been lost completely more than 20 times in frogs, a much higher occurrence of edentulism than in any other vertebrate group. The repeated loss of teeth in anurans is associated with a specialized diet of small invertebrate prey as well as shortening of the lower jaw, but it is not correlated with a reduction in body size. Frogs provide an unparalleled opportunity for investigating the molecular and developmental mechanisms of convergent tooth loss on a large phylogenetic scale.

Two new cryptic species of Microhyla Tschudi, 1838 (Amphibia, Anura, Microhylidae) related to the M. heymonsi group from central Vietnam

The Microhyla heymonsi species complex from central Vietnam was examined, and based upon morphological and molecular evidence, two new species are described. The discovery of Microhyla daklakensis sp. nov. and Microhyla ninhthuanensis sp. nov. brings the total number of known species in the genus to 46 and the species number of Microhyla in Vietnam to 13. The Truong Son Range harbors the highest diversity of the genus Microhyla with 11 recorded species so far. However, this apparent micro-endemic diversity is at risk because of habitat loss by deforestation, which highlights the necessity of further research leading to improved conservation measures.

Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes

Target enrichment is a term that encompasses multiple related approaches where desired genomic regions are captured by molecular baits, leaving behind redundant or non-target regions in the genome, followed by amplification and next-generation sequencing of those captured regions. A molecular bait set was developed based on 426 single-copy, oomycete-specific orthologs and 3 barcoding genes. The bait set was tested on 27 oomycete samples (belonging to the Saprolegniales, Albuginales, and Peronosporales) derived from live and herbarium specimens, as well as control samples of true fungi and plants. Results show that (i) our method greatly enriches for the targeted orthologs on oomycete samples, but insignificantly on fungal and plant samples; (ii) an average of 263 out of 429 orthologs (61%) were recovered from oomycete live and herbarium specimens; (iii) sequencing roughly 100 000 read pairs per sample is sufficient for optimal ortholog recovery while maintaining low sequencing costs; and (iv) the expected relationships were recovered by phylogenetic analysis from the data generated. This is the first report of an oomycete-specific target enrichment method with broad potential applications for evolutionary and taxonomic studies. A key benefit of our target enrichment method is that it allows researchers to easily unlock the vast and unexplored oomycete genomic diversity stored in natural history collections.

Genetic diversity of the Pegu Rice Frog, Microhyla berdmorei (Anura: Microhylidae) based on mitochondrial DNA

The Pegu Rice Frog, Microhyla berdmorei is distributed across ten Asian countries. However, the DNA barcoding information (COI gene) is restricted to only Southeast Asian countries. Here, we sampled a specimen of M. berdmorei in Mizoram state, northeast India to allow the genetic diversity of the species across its range. We generated both COI and 16S ribosomal RNA sequences of the studied species to check the population genetic diversity. The Bayesian analyses clearly discriminate M. berdmorei from its sister species Microhyla pulchra. The present datasets of M. berdmorei also revealed 11 and 19 haplotypes with high uncorrected pairwise genetic distances in COI (3.8-11.8%) and 16S rRNA (0-4.6%) gene, respectively. Owing to the high intra-species genetic distances and different haplotypes with sufficient mutational steps in both mitochondrial genes, this study affirms the existence of M. berdmorei species complex or cryptic diversity within its range distribution in South and Southeast Asia.

Impact of the Miocene orogenesis on Kaloula spp. radiation and implication of local refugia on genetic diversification

The phylogeography of the Kaloula genus in East Asia is still poorly understood. One of the difficulties is the absence of fossils to corroborate molecular dating estimates. Here, we examined the mitochondrial structure of Kaloula spp. in East Asia and focused on the impact of glaciations on the northernmost species: Kaloula borealis. We determined the phylogenetic relationships, molecular dating, and genetic connectivity assessments within the genus from 1211 bp of concatenated mitochondrial 12S and 16S. The relaxed clock analyses reveal the emergence of Kaloula spp. common ancestor in East and Southeast Asia between the Eocene and Oligocene, c. 38.47 Ma (24.69-53.65). The genetic diversification of lineages then increased on the East Asian Mainland during the Lower Miocene, c. 20.10 (8.73-30.65), most likely originating from the vicariance and radiation triggered by the orogeny of the Qinghai-Tibetan Plateau. Later, the dispersal towards the North East Asian Mainland during the Upper Miocene drove the population diversification of K. borealis c. 9.01 Ma (3.66-15.29). Finally, the central mainland population became isolated following orogenesis events and diverged into K. rugifera during the Pliocene, c. 3.06 Ma (0.02-10.90). The combination of population genetic and barrier analyses revealed a significant genetic isolation between populations of Kaloula spp. matching with the massive Qinling-Daba Mountain chain located in south-central China. Finally, we highlight a young divergence within the Eastern Mainland population of K. borealis, possibly attributed to refugia in south eastern China from which populations later expanded.

Consequences of parallel miniaturisation in Microhylinae (Anura, Microhylidae), with the description of a new genus of diminutive South East Asian frogs

The genus Microhyla Tschudi, 1838 includes 52 species and is one of the most diverse genera of the family Microhylidae, being the most species-rich taxon of the Asian subfamily Microhylinae. The recent, rapid description of numerous new species of Microhyla with complex phylogenetic relationships has made the taxonomy of the group especially challenging. Several recent phylogenetic studies suggested paraphyly of Microhyla with respect to Glyphoglossus Günther, 1869, and revealed three major phylogenetic lineages of mid-Eocene origin within this assemblage. However, comprehensive works assessing morphological variation among and within these lineages are absent. In the present study we investigate the generic taxonomy of Microhyla–Glyphoglossus assemblage based on a new phylogeny including 57 species, comparative morphological analysis of skeletons from cleared-and-stained specimens for 23 species, and detailed descriptions of generalized osteology based on volume-rendered micro-CT scans for five species–altogether representing all major lineages within the group. The results confirm three highly divergent and well-supported clades that correspond with external and osteological morphological characteristics, as well as respective geographic distribution. Accordingly, acknowledging ancient divergence between these lineages and their significant morphological differentiation, we propose to consider these three lineages as distinct genera: Microhylasensu stricto, Glyphoglossus, and a newly described genus, Nanohylagen. nov.

Species diversity and biogeography of an ancient frog clade from the Guiana Shield (Anura: Microhylidae: Adelastes, Otophryne, Synapturanus) exhibiting spectacular phenotypic diversification

The outstanding biodiversity of the Guiana Shield has raised many questions about its origins and evolution. Frogs of the genera Adelastes, Otophryne and Synapturanus form an ancient lineage distributed mostly across this region. These genera display strikingly disparate morphologies and life-history traits. Notably, Synapturanus is conspicuously adapted to fossoriality and is the only genus within this group to have dispersed further into Amazonia. Moreover, morphological differences among Synapturanus species suggest different degrees of fossoriality that might be linked to their biogeographical history. Through integrative analysis of genetic, morphometric and acoustic data, we delimited 25 species in this clade, representing a fourfold increase. We found that the entire clade started to diversify ~55 Mya and Synapturanus ~30 Mya. Members of this genus probably dispersed three times out of the Guiana Shield both before and after the Pebas system, a wetland ecosystem occupying most of Western Amazonia during the Miocene. Using a three-dimensional osteological dataset, we characterized a high morphological disparity across the three genera. Within Synapturanus, we further characterized distinct phenotypes that emerged concomitantly with dispersals during the Miocene and possibly represent adaptations to different habitats, such as soils with different physical properties.

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

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

A New Species of Micryletta (Amphibia: Anura) from Sumatra, Indonesia

Micryletta inornata is a complex species that is widely distributed from Sumatra to mainland Asia, including the Thai-Malay Peninsula and Indochina. Recently, this species was confirmed to be endemic to regions near the type locality in Sumatra, and the populations from other regions were suggested to be different species. We examined phenotypic and genotypic characters of the Sumatran populations and found an unnamed lineage in addition to the true M. inornata. The newly found lineage can be distinguished from M. inornata and other congeners by both molecular and morphological traits and has been named Micryletta sumatrana sp. nov. The new species is characterized by having a small body size, golden brown dorsum with scattered dark spots, dark brown ventrum with diffuse cream mottling, dark brown lateral head with cream spots on lips and the tympanum region extending to the axilla, and tibiotarsal articulation reaching to the front of the eye. We discuss the taxonomic status of so-called M. inornata occurring outside of its type locality, especially of M. inornata lineata.

The rise and fall of globins in the amphibia

The globin gene repertoire of gnathostome vertebrates is dictated by differential retention and loss of nine paralogous genes: androglobin, neuroglobin, globin X, cytoglobin, globin Y, myoglobin, globin E, and the α- and β-globins. We report the globin gene repertoire of three orders of modern amphibians: Anura, Caudata, and Gymnophiona. Combining phylogenetic and conserved synteny analysis, we show that myoglobin and globin E were lost only in the Batrachia clade, but retained in Gymnophiona. The major amphibian groups also retained different paralogous copies of globin X. None of the amphibian presented α^D-globin gene. Nevertheless, two clades of β-globins are present in all amphibians, indicating that the amphibian ancestor possessed two paralogous proto β-globins. We also show that orthologs of the gene coding for the monomeric hemoglobin found in the heart of Rana catesbeiana are present in Neobatrachia and Pelobatoidea species we analyzed. We suggest that these genes might perform myoglobin- and globin E-related functions. We conclude that the repertoire of globin genes in amphibians is dictated by both retention and loss of the paralogous genes cited above and the rise of a new globin gene through co-option of an α-globin, possibly facilitated by a prior event of transposition.

A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae)

Frogs of the genus Microhyla include some of the world's smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla-Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene-early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla-Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15-33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.

B, P. Karthik, Babu Rao, S. Babu. Catalogue of herpetological specimens from peninsular India at the Sálim Ali Centre for Ornithology & Natural History (SACON), India

We list the herpetological voucher specimens in the holdings of the Sálim Ali Centre for Ornithology & Natural History (SACON), a wildlife research institute in India.  Most of the collections are the fruition of fieldwork by SACON’s herpetologist and a coauthor of this work—late Dr. Subramanian Bhupathy (1963–2014).  Taxonomically, the collection represents 125 species, comprising 29 amphibian species belonging to eight families and 96 reptilian species belonging to 17 families.  Geographically, the material in this collection originates from the Western Ghats, the Eastern Ghats, the Deccan Plateau, and the Coromandel Coast, comprehensively covering all ecoregions of peninsular India.  A total of 15 taxa (three amphibians, 12 reptiles) remain to be fully identified and are provisionally referred to most-resembling taxa, with cf. prefix.  All the specimens in this collection are non-types as on date.              

A new stump-toed frog from the transitional forests of NW Madagascar (Anura, Microhylidae, Cophylinae, Stumpffia)

A new species of the miniaturised microhylid frog genus Stumpffia, from north-western Madagascar, is described. Stumpffiafroschauerisp. nov. differs from all other described Stumpffia species in colouration and morphology and is genetically divergent (≥ 7% uncorrected p-distance to all other nominal species of the genus) in a fragment of the mitochondrial 16S rRNA gene and in a segment of the nuclear Rag-1 gene. The new species is reliably known only from a few specimens collected in the Sahamalaza (and surroundings) region. Its known distribution is limited to three forest patches severely threatened by fire, drought and high levels of forest clearance, thus suggesting a classification of “Critically Endangered” according to IUCN Red List criteria.

Frogs of the genus Platypelis from the Sorata massif in northern Madagascar: description of a new species and reports of range extensions

We describe a new species of arboreal microhylid frog, genus Platypelis, from northeastern Madagascar and report the expansion of distribution ranges of two other species. Platypelis laetussp. nov. is small to medium-sized (24.3–25.6 mm snout-vent length) compared to other Platypelis, exhibits a greenish colored throat and was found in bamboo forest of the Sorata Massif. Its advertisement call consists of a single short tonal note repeated at regular intervals in long call series. Based on DNA sequences of a fragment of the mitochondrial 16S rRNA gene, the new species was placed in a clade with Platypelis olgae from the Tsaratanana Massif, and with two other, unconfirmed candidate species from the Sorata Massif and from Andravory, herein named Platypelis sp. Ca12 and Ca13. Molecular divergences among these lineages were substantial, amounting to 7.6‒8.1% uncorrected 16S p-distance to the closest nominal species, P. olgae, from which the new species is also distinguished by a lack of allele sharing in the nuclear RAG-1 gene. We also provide new records of Platypelis alticola and P. tsaratananaensis from the Sorata Massif, supported by molecular analysis. This confirms a wider distribution of these two species that previously were considered to be endemic to the Tsaratanana Massif. However, their populations in Sorata were characterized by a certain degree of genetic differentiation from Tsaratanana populations suggesting they require more detailed taxonomic assessment.

Analysis of ultraconserved elements supports African origins of narrow-mouthed frogs

Narrow-mouthed frogs (Anura: Microhylidae) are globally distributed and molecular data suggest the rapid evolution of multiple subfamilies shortly after their origin. Despite recent progress, several subfamilial relationships remain unexplored using phylogenomic data. We analysed 1,796 nuclear ultraconserved elements, a total matrix of 400,664 nucleotides, from representatives of most microhylid subfamilies. Summary method species-tree and maximum likelihood analyses unambiguously supported Hoplophryninae as the earliest diverging microhylid and confirm Chaperininae as a junior synonym of Microhylinae. Given the emerging consensus that subfamilies from mainland Africa diverged early, microhylids have likely occupied the continent for more than 66 million years.

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

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

Shared response to changes in drainage basin: Phylogeography of the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Anura: Microhylidae)

AIM

With the late Cenozoic uplift of the Qinghai-Tibetan Plateau (QTP), drainage of the southeastern edge of the QTP changed significantly. However, the impact of this dramatic change on the geographical distribution and genetic diversity of endemic organisms is still poorly understood. Here, we examined the geographical patterns of genetic variation in the Yunnan small narrow-mouthed frog, Glyphoglossus yunnanensis (Microhylidae), and two alternative hypotheses were tested: That is, the geographical distribution of genetic variation was determined by either the contemporary drainage basin or historical drainage basins.

LOCATION

The Mountains of southwest China.

MATERIALS AND METHODS

Analyses were based on 417 specimens collected from across the distribution of the species. We reconstructed the genealogy (Bayesian and maximum parsimony methods) and assessed demographic history based on DNA sequencing data from mitochondrial and nuclear markers. We also mapped the genetic diversity and estimated the divergence times by a relaxed clock model.

RESULTS

The species has maintained a relatively stable population size without recent population expansion. Four major maternal lineages were identified with good support, one representing a possible cryptic species and the other three showing further subdivision. The distribution of these deeply differentiated lineages/sublineages corresponded well to geographical regions. The secondary contact zones and phylogeographic breaks in distinct lineages of G. yunnanensis were almost concordant with those of Nanorana yunnanensis.

MAIN CONCLUSIONS

Lineage division conformed to the hypothesis of drainage system evolution, that is, the phylogeographic pattern of G. yunnanensis was shaped by historical drainage patterns. Concordance in phylogeographic patterns may suggest a shared response to common hydrogeological history and also might indicate that there was more contribution of the drainage history than ecological or life-history traits in structuring genetic variation between these two disparate codistributed taxa G. yunnanensis and N. yunnanensis.

A new yellow-toed Platypelis species (Anura, Microhylidae, Cophylinae) from the Maroantsetra region, northeastern Madagascar

We describe a new species of arboreal narrow-mouthed frog, genus Platypelis, from Ambodivoangy near Maroantsetra in northeastern Madagascar. The new species, Platypelisandosp. nov., is characterised by small body size (under 19 mm), a generally rather slender body, yellowish finger and toe tips, and a dark brown dorsal chevron. Its advertisement call is a single, moderately long, high-pitched whistle repeated at regular intervals. It is the sister species of P.ravus from Marojejy National Park, but differs from that species by considerable pairwise genetic distances (7.9%) in a fragment of the mitochondrial 16S rRNA gene, and also in bioacoustic and morphological features, especially the absence of yellow on the posterior abdomen. It is also surprisingly similar in external appearance to Cophylaoccultans and C.maharipeo, to which it is not, however, closely related; these species are most easily discerned based on their calls. Platypelisandosp. nov. joins the ranks of several species recently described from Ambodivoangy with close affiliations to species in the nearby Marojejy National Park, that are still divergent at species level. The species qualifies as Critically Endangered according to the IUCN Red List criteria, in line with other species recently assessed from this area, but we urge that more research be conducted in the nearby forests to extend the range of this and other species known only from Ambodivoangy.

Novel morphological structures in frogs: vocal sac diversity and evolution in Microhylidae (Amphibia: Anura)

Vocal sacs are present in most species of frogs and are the product of the interaction of three elements: the gular skin, the superficial submandibular musculature and an internal mucosa derived from the buccal floor. In this paper, we surveyed the structural diversity in the vocal sac of microhylids and related families in 109 exemplar species, including 11 of the 13 currently recognized subfamilies. We defined five characters related to anatomical and histological properties of the m. interhyoideus, as well as the relationship of this muscle and the vocal sac internal mucosa. We describe a vocal sac configuration characterized by highly abundant elastic fibres in association with muscle fibres, a very unusual structure in animal tissues. We discuss the evolution of novel structures in a phylogenetic context and identify new synapomorphies for Microhylidae and internal clades. Furthermore, we comment on the functional implications that these features have in vocal sac inflation.

A new species of Micryletta frog (Microhylidae) from Northeast India

We describe a new species of frog in the microhylid genus Micryletta Dubois, 1987 from Northeast India based on molecular and morphological evidence. The new species, formally described as Micryletta aishani sp. nov., is phenotypically distinct from other congeners by a suite of morphological characters such as brown to reddish-brown dorsum; dorsal skin shagreened with minute spinules; snout shape nearly truncate in dorsal and ventral view; a prominent dark streak extending from tip of the snout up to the lower abdomen; ash-grey mottling along the margins of upper and lower lip extending up to the flanks, limb margins and dorsal surfaces of hand and foot; tibiotarsal articulation reaching up to the level of armpits; absence of outer metatarsal tubercles; and absence of webbing between toes. Phylogenetic relationships within the genus are inferred based on mitochondrial data and the new taxon is found to differ from all the recognised Micryletta species by 3.5-5.9% divergence in the mitochondrial 16S rRNA. The new species was found in the states of Assam, Manipur, and Tripura, from low to moderate elevation (30-800 m asl) regions lying south of River Brahmaputra and encompassing the Indo-Burma Biodiversity Hotspot. The discovery validates the presence of genus Micryletta in Northeast India based on genetic evidence, consequently confirming the extension of its geographical range, westwards from Southeast Asia up to Northeast India. Further, for nomenclatural stability of two previously known species, Microhyla inornata (= Micryletta inornata) and Microhyla steinegeri (= Micryletta steinegeri), lectotypes are designated along with detailed descriptions.

Morphological and ecological convergence at the lower size limit for vertebrates highlighted by five new miniaturised microhylid frog species from three different Madagascan genera

Miniaturised frogs form a fascinating but poorly understood amphibian ecomorph and have been exceptionally prone to taxonomic underestimation. The subfamily Cophylinae (family Microhylidae), endemic to Madagascar, has a particularly large diversity of miniaturised species which have historically been attributed to the single genus Stumpffia largely based on their small size. Recent phylogenetic work has revealed that several independent lineages of cophyline microhylids evolved towards highly miniaturised body sizes, achieving adult snout-vent lengths under 16 mm. Here, we describe five new species belonging to three clades that independently miniaturised and that are all genetically highly divergent from their relatives: (i) a new genus (Mini gen. nov.) with three new species from southern Madagascar, (ii) one species of Rhombophryne, and (iii) one species of Anodonthyla. Mini mum sp. nov. from Manombo in eastern Madagascar is one of the smallest frogs in the world, reaching an adult body size of 9.7 mm in males and 11.3 mm in females. Mini scule sp. nov. from Sainte Luce in southeastern Madagascar is slightly larger and has maxillary teeth. Mini ature sp. nov. from Andohahela in southeast Madagascar is larger than its congeners but is similar in build. Rhombophryne proportionalis sp. nov. from Tsaratanana in northern Madagascar is unique among Madagascar's miniaturised frogs in being a proportional dwarf, exhibiting far less advanced signs of paedomorphism than other species of similar size. Anodonthyla eximia sp. nov. from Ranomafana in eastern Madagascar is distinctly smaller than any of its congeners and is secondarily terrestrial, providing evidence that miniaturisation and terrestriality may be evolutionarily linked. The evolution of body size in Madagascar's microhylids has been more dynamic than previously understood, and future studies will hopefully shed light on the interplay between ecology and evolution of these remarkably diverse frogs.

New microhylid frog genus from Peninsular India with Southeast Asian affinity suggests multiple Cenozoic biotic exchanges between India and Eurasia

Anurans in Peninsular India exhibit close biogeographical links with Gondwana as well as Laurasia, often explainable by the geological history of the Indian subcontinent; its breakup from Gondwanan landmasses followed by long isolation that resulted in diversification of endemic lineages, and subsequent land connections with Asia that enabled dispersal of widespread groups. Although widely distributed, the frog subfamily Microhylinae mostly comprises of geographically restricted genera found either in Southeast and East Asia or Peninsular India and Sri Lanka. Here we report a previously unknown microhylid from the Western Ghats in Peninsular India with closest relatives found over 2,000 km away in Southeast Asia. Based on integrated evidence from mitochondrial and nuclear DNA, adult and tadpole morphology, hand musculature, male advertisement call, and geographical distance, we recognize this enigmatic frog as a distinct new species and genus endemic to the Western Ghats. The discovery of Mysticellus franki gen. et sp. nov. and its close evolutionary relationship with the Southeast Asian genus Micryletta also provide insights on the biogeography of Microhylinae. Genus-level divergences within the subfamily suggest multiple Cenozoic biotic exchange events between India and Eurasia, particularly through postulated Eocene land bridges via Southeast Asia prior to accretion of the two landmasses.

A new limestone-dwelling species of Micryletta (Amphibia: Anura: Microhylidae) from northern Vietnam

We report on a new species of the genus Micryletta from limestone karst areas in northern Vietnam, which is described on the basis of molecular and morphological evidence. Micryletta nigromaculata sp. nov. is restricted to narrow areas of subtropical forests covering karst massifs in Cat Ba National Park (Hai Phong Province) and Cuc Phuong National Park (Ninh Binh Province) at elevations of 90-150 m a.s.l. In the phylogenetic analyses, the new species is unambiguously positioned as a sister lineage to all remaining species of Micryletta. We also discuss genealogical relationships and taxonomic problems within the genus Micryletta, provide molecular evidence for the validity of M. erythropoda and discuss the taxonomic status of M. steinegeri. We suggest the new species should be considered as Endangered (B1ab(iii), EN) following the IUCN's Red List categories. A discussion on herpetofaunal diversity and conservation in threatened limestone karst massifs in Southeast Asia is provided.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

High-throughput sequencing has fundamentally changed how molecular phylogenetic data sets are assembled, and phylogenomic data sets commonly contain 50- to 100-fold more loci than those generated using traditional Sanger sequencing-based approaches. Here, we demonstrate a new approach for building phylogenomic data sets using single-tube, highly multiplexed amplicon sequencing, which we name HiMAP (highly multiplexed amplicon-based phylogenomics) and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and postsequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously and requires minimal hands-on time at the bench (<1/2 day), and data analysis can be accomplished without the need for read mapping or assembly. We demonstrate this approach by sequencing 878 amplicons in single reactions for 82 species of tephritid fruit flies across seven genera (384 individuals), including some of the most economically important agricultural insect pests. The resulting filtered data set (>150,000-bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting data set provides into relationships of this diverse insect group.

A distinctive new frog species (Anura, Mantellidae) supports the biogeographic linkage of two montane rainforest massifs in northern Madagascar

We describe a new species of the genusGephyromantis, subgenusVatomantis (Mantellidae, Mantellinae), from moderately high elevation (1164–1394 m a.s.l.) on the Marojejy, Sorata, and Andravory Massifs in northern Madagascar. The new species, Gephyromantis (Vatomantis) lomorinasp. n.is highly distinct from all other species, and was immediately recognisable as an undescribed taxon upon its discovery. It is characterised by a granular, mottled black and green skin, reddish eyes, paired subgular vocal sacs of partly white colour, bulbous femoral glands present only in males and consisting of three large granules, white ventral spotting, and a unique, amplitude-modulated advertisement call consisting of a series of 24–29 rapid, quiet notes at a dominant frequency of 5124–5512 Hz. Genetically the species is also strongly distinct from its congeners, with uncorrected pairwise distances ≥10 % in a fragment of the mitochondrial 16S rRNA gene to all other nominalGephyromantisspecies. A molecular phylogeny based on 16S sequences places it in a clade with species of the subgeneraLaurentomantisandVatomantis, and we assign it to the latter subgenus based on its morphological resemblance to members ofVatomantis. We discuss the biogeography of reptiles and amphibians across the massifs of northern Madagascar, the evidence for a strong link between Marojejy and Sorata, and the role of elevation in determining community sharing across this landscape.