The phylogeny of the Casque-headed Treefrogs (Hylidae: Hylinae: Lophyohylini)

Uncovering the rich amphibian fauna of two semideciduous forest fragments in southwestern Bahia, Brazil

Fauna inventories reduce biodiversity knowledge gaps by providing comprehensive data on species distribution, richness, and abundance. Furthermore, they identify undocumented species and enhance understanding of ecosystem dynamics and conservation needs. The richness and abundance of amphibian species were studied in two Semideciduous Seasonal Forest areas in the municipalities of Potiraguá (Serra Azul) and Itarantim (Serra do Mandim) in southwestern Bahia, Brazil. Active visual and acoustic surveys were conducted in 24 forest interior transects, two stream transects, and two permanent ponds investigated in the study area. Opportunistic encounters during team movements were also recorded. The richness was 46 amphibian species distributed in 14 families and 26 genera. Approximately half of the species were shared between the two areas, while 11 species were exclusive to Serra Azul and another nine were found only in Serra do Mandim. Cluster analysis for 42 locations in Atlantic Forest, Caatinga, and Cerrado, in a presence/absence matrix with 216 species, revealed that the composition of the amphibians found in Serra do Mandim and Serra Azul is similar to other sampled locations in the northeastern region of Minas Gerais, close to the study site, which are considered transitional between the Atlantic Forest and the Caatinga. Our results demonstrate that the remaining forest fragments in the region, although small and isolated, still sustain a high richness of amphibians with species restricted to the Atlantic Forest and Bahia, such as Bahiusbilineatus, Ololygonstrigilata, Aplastodiscusweygoldti and Vitreoranaeurygnatha, and others considered typical of the Caatinga, such as Leptodactylustroglodytes and Physalaemuscicada. Additionally, we sampled potential new species, filled occurrence gaps, and expanded the geographical range of Pseudisfusca.

Another new species (and its not over yet) of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of southern Bahia, northeastern Brazil

The genus Phyllodytes, endemic to the Atlantic Forest, stands out for its life cycle being closely associated with bromeliads. Since the 2000s, the number of species in the group has more than doubled and the number is still increasing, a fact proven here with the description of Phyllodytes iuna sp. nov. This species, herein described using morphological and molecular evidence, is endemic to the Atlantic Forest of southern Bahia, in the northern portion of the Atlantic Forest Central Corridor. Phyllodytes iuna differs from both its sister species and most of its congeners by the color pattern on the dorsum and by the presence of a single tubercle in the tibiotarsal region. The genetic distance for a fragment of the 16S gene ranged from 4.4% to 5.0% between Phyllodytes iuna and its sister species (P. brevirostris and P. edelmoi), and from 5.8% to 14.2% with its congeners. The description of a new species of Phyllodytes serves as a reminder that our understanding of the groups diversity is far from complete. Despite the alarming rates of deforestation, the Atlantic Forest continues to hold significant untapped potential for unexplored biodiversity.

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.

Reed bamboos drive skull shape evolution in bush frogs of the Western Ghats, Peninsular India

Reed bamboo is a major ecological and economic resource for many animals, including humans. Nonetheless, the influence of this plant's evolutionary role on the morphology of animal species remains unexplored. Here, we investigated the significance of bamboo habitats as ecological opportunities in shaping the skull morphology of bush frogs (Raorchestes) from the Western Ghats, Peninsular India. We applied a three-dimensional (3D) geometric morphometric approach to capture the skull shape of 55 species of bush frogs. We visualized the skull shape variables in phylomorphospace with principal component analysis and performed phylogenetic generalized least-squares analysis to assess the impact of cranial size (evolutionary allometry) and habitat (bamboo or non-bamboo) on cranial shape. We quantified the morphological disparity between bamboo and non-bamboo bush frogs' skull shape, and employed RRphylo, a phylogenetic ridge regression method, to access the evolutionary rate and rate shifts of skull shape change. The phylomorphospace delineated bamboo and non-bamboo bush frogs. While cranial shape exhibited a significant but smaller association with size, its association with habitat type was non-significant. We detected, however, significant differences in skull shape between the two frog groups, with bamboo frogs showing higher morphological disparity and a remarkable shift in the evolutionary rate of skull shape diversification. These findings underscore the role of reed bamboo in the evolution of skull shape in the radiation of frogs, endemic to the Western Ghats. We demonstrate that the association between the members of two distinct endemic clades (bamboo reeds and bamboo frogs) is the outcome of a deep-time ecological opportunity that dates back to the Miocene.

Unveiling the evolutionary relationships and the high cryptic diversity in Andean rainfrogs (Craugastoridae: Pristimantis myersi group)

Background

Pristimantis is the most diverse genus of terrestrial frogs. Historically, it has been divided into several phenetic groups in order to facilitate species identification. However, in light of phylogenetic analysis, many of these groups have been shown to be non-monophyletic, denoting a high degree of morphological convergence and limited number of diagnostic traits. In this study, we focus on the Pristimantis myersi group, an assemblage of small rainfrogs distributed throughout the Andes of Ecuador and Colombia, whose external morphology is highly conserved, and its species diversity and evolutionary relationships largely unknown.

Methods

We inferred a new phylogenetic hypothesis for the frog genus Pristimantis, including all available sequences of the mtDNA 16S rRNA, as well as new DNA sequences from 175 specimens. Our sampling included 19 of the 24 species currently recognized as part of the Pristimantis myersi group.

Results

Our new evolutionary hypothesis recovered the P. myersi group as non-monophyletic and composed of 16 species. Therefore, we exclude P. albujai, P. bicantus, P. sambalan, and P. nelsongalloi in order to preserve the monophyly of the group. We discovered at least eight candidate species, most of them hidden under the names of P. leoni, P. hectus, P. festae, P. gladiator, and P. ocreatus.

Discussion

Our results reveal the occurrence of a high level of cryptic diversity to the species level within the P. myersi group and highlight the need to redefine some of its species and reassess their conservation status. We suggest that the conservation status of six species within the group need to be re-evaluated because they exhibit smaller distributions than previously thought; these species are: P. festae, P. gladiator, P. hectus, P. leoni, P. ocreatus, and P. pyrrhomerus. Finally, given that the Pristimantis myersi group, as defined in this work, is monophyletic and morphologically diagnosable, and that Trachyphrynus is an available name for the clade containing P. myersi, we implement Trachyphrynus as a formal subgenus name for the Pristimantis myersi group.

Historical biogeography highlights the role of Miocene landscape changes on the diversification of a clade of Amazonian tree frogs

The diversification processes underlying why Amazonia hosts the most species-rich vertebrate fauna on earth remain poorly understood. We studied the spatio-temporal diversification of a tree frog clade distributed throughout Amazonia (Anura: Hylidae: Osteocephalus, Tepuihyla, and Dryaderces) and tested the hypothesis that Miocene mega wetlands located in western and central Amazonia impacted connectivity among major biogeographic areas during extensive periods. We assessed the group’s diversity through DNA-based (16S rRNA) species delimitation to identify Operational Taxonomic Units (OTUs) from 557 individuals. We then selected one terminal for each OTU (n = 50) and assembled a mitogenomic matrix (~14,100 bp; complete for 17 terminals) to reconstruct a Bayesian, time-calibrated phylogeny encompassing nearly all described species. Ancestral area reconstruction indicates that each genus was restricted to one of the major Amazonian biogeographic areas (western Amazonia, Guiana Shield and Brazilian Shield, respectively) between ~10 and 20 Mya, suggesting that they diverged and diversified in isolation during this period around the Pebas mega wetland. After 10 Mya and the transition to the modern configuration of the Amazon River watershed, most speciation within each genus continued to occur within each area. In Osteocephalus, only three species expanded widely across Amazonia (< 6 Mya), and all were pond-breeders. Species with other breeding modes remained mostly restricted to narrow ranges. The spectacular radiation of Osteocephalus was probably driven by climatic stability, habitat diversity and the acquisition of new reproductive modes along the Andean foothills and western Amazonia. Our findings add evidence to the importance of major hydrological changes during the Miocene on biotic diversification in Amazonia.

Combined phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae)

The genus Pleurodema comprises 15 species distributed through the Neotropical region, from sea level up to 5000 m.a.s.l. A total-evidence analysis of Pleurodema is provided based on the parsimony criterion. The combined dataset included morphometric, phenotypic, and DNA evidence (34 taxa, 4441 characters). The parsimony analysis yielded one most-parsimonious tree. Pleurodema was recovered as a well-supported clade composed of two major subclades. One subclade has an identical topology to that of previous analyses, the P. brachyops Clade (P. alium, P. borellii, P. brachyops, P. cinereum, P. diplolister, and P. tucumanum). The other subclade includes the remaining nine species of the genus, exhibiting a topology different from that of previous studies. According to the present phylogeny, this second lineage is formed by the P. nebulosum Clade (P. guayapae + P. nebulosum), P. marmoratum, the re-defined P. thaul Clade (P. bufoninum, P. somuncurense, P. thaul) and the P. bibroni Clade (P. bibroni, P. cordobae, P. kriegi). The reproductive modes of Pleurodema represent a unique combination of features within Leiuperinae, including three egg-clutch structures, two types of amplexus, and lack of vocalization. Also, some species of Pleurodema have been considered fossorial, because they are capable of digging with their hind-limbs and remaining in self-made burrows during dry seasons. The evolution of characters associated with reproductive biology and fossoriality is discussed in light of the obtained results.

The phylogeny of Dendropsophini (Anura: Hylidae: Hylinae)

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus.

Diversity and evolution of the extraordinary vocal sacs of casque-headed treefrogs (Anura: Hylidae)

Vocal sacs are among the most conspicuous features of anurans and are particularly striking in casque-headed treefrogs (Hylidae: Hylinae: Lophyohylini) with their wide array of morphologies. In this paper, we assessed the anatomy of vocal sacs in representatives of the Lophyohylini, described eight discrete characters and studied their evolution. We inferred that dorsolateral projections of the vocal sacs were already present during the early evolution of the tribe. Subsequently, they reached surprising volumes in some species, whereas in others they were notably reduced. We inferred between nine and 11 independent events of reduction of the size and lateral projections of the vocal sac, showing unprecedented levels of plasticity for the structure. Moreover, these events were strongly correlated with the colonization of phytotelmata as breeding sites, probably due to their confined space which hampers the inflation of large vocal sacs. Finally, we discuss the evolution of paired lateral vocal sacs in different groups of anurans, and the extent to which the paired and dorsally-projecting lobes of most Trachycephalus differ from those of distantly related taxa. Our findings highlight how variation in internal structure affects the shape of the inflated vocal sac and provides a framework applicable across the Anura.

A new record for the milk frog Trachycephalus coriaceus (ANURA: HYLIDAE) from teles pires river, South Amazonia, Brazil

Herein, we report a new record of the milk frog Trachycephalus coriaceusfor the Brazilian southern Amazonia and provide an updated geographic distribution map. We collected one specimen of T. coriaceuson 8 november 2016, during a nocturnal survey inside a dense ombrophilousforest in the right bank of the Teles Pires River, municipality of Jacareacanga, southern of Pará State. The record of T. coriaceusto Jacareacanga is the first to the State. The disjoint geographic distribution of this species along de Amazonia may just reflect the paucity of amphibian knowledge throughout this biome and the difficulty to detect this species in the field, given its explosive reproductive behavior.

A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil

The known diversity of treefrogs of the genus Phyllodytes has rapidly increased in recent years, currently comprising 14 species. Recent field work in the Atlantic Rainforest of the state of Bahia lead to the discovery of a new large species of Phyllodytes which is herein described based on multiple evidence including morphological, acoustical and genetic data. Phyllodytes sp. nov. is one of the largest species within the genus and presents immaculate yellowish dorsum and limbs. The advertisement call of the species is composed of 7-31 notes (half pulsed/pulsatile-half harmonic) with frequency-modulated harmonics. Phyllodytes sp. nov. has a karyotype of 2n = 22 chromosomes, as also found in other species of the genus. Genetic distance values of the 16S mitochondrial rRNA among Phyllodytes sp. nov. and its congeners range between 6.4 to 10.2%. The description of another new species for this state reinforces the need for further taxonomic work with Phyllodytes in this region that has been revealed as a priority area for research and conservation of this genus.