Insights from Integrative Systematics Reveal Cryptic Diversity in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon Basin

Revisiting current distribution and future habitat suitability models for the endemic Malabar Tree Toad (Pedostibes tuberculosus) using citizen science data

Climate change is one of the major drivers of biodiversity loss. Among vertebrates, amphibians are one of the more sensitive groups to climate change due to their unique ecology, habitat requirements, narrow thermal tolerance and relatively limited dispersal abilities. We projected the influence of climate change on an endemic toad, Malabar Tree Toad (Pedostibes tuberculosus; hereafter MTT) from the Western Ghats biodiversity hotspot, India, for two different shared socio-economic pathways (SSP) using multiple modeling approaches for current and future (2061-2080) scenarios. The data used predominantly comes from a citizen science program, 'Mapping Malabar Tree Toad' which is a part of the Frog Watch citizen science program, India Biodiversity Portal. We also evaluated the availability of suitable habitats for the MTT in Protected Areas (PAs) under the current and future scenarios. Our results show that annual precipitation was the most important bioclimatic variable influencing the distribution of MTT. We used MaxEnt (MEM) and Ensemble (ESM) modeling algorithms. The predicted distribution of MTT with selected environmental layers using MEM was 4556.95 km2 while using ESM was 18,563.76 km2. Overlaying PA boundaries on predicted distribution showed 37 PAs with 32.7% (1491.37 km2) and 44 PAs with 21.9% (4066.25 km2) coverage for MEM and ESM respectively. Among eight future climate scenarios, scenarios with high emissions showed a decreased distribution range from 33.5 to 68.7% of predicted distribution in PAs, while scenarios with low emissions showed an increased distribution range from 1.9 to 111.3% in PAs. PAs from the Central Western Ghats lose most suitable areas with a shift of suitable habitats towards the Southern Western Ghats. This suggests that MTT distribution may be restricted in the future and existing PAs may not be sufficient to conserve their habitats. Restricted and discontinuous distribution along with climate change can limit the dispersal and persistence of MTT populations, thus enhanced surveys of MTT habitats within and outside the PAs of the Western Ghats are an important step in safeguarding the persistence of MTT populations. Overall, our results demonstrate the use of citizen science data and its potential in modeling and understanding the geographic distribution and the calling phenology of an elusive, arboreal, and endemic amphibian species.

A new cryptic species of terrestrial breeding frog of the Pristimantisdanae Group (Anura, Strabomantidae) from montane forests in Ayacucho, Peru

Based on morphological and molecular characters, we describe a new species of terrestrial breeding frog of the Pristimantisdanae Group from montane forests of La Mar Province, Ayacucho Department in southern Peru, at elevations from 1200 to 2000 m a.s.l. The phylogenetic analysis, based on concatenated sequences of gene fragments of 16S rRNA, RAG1, COI and TYR suggests that the new species is a sister taxon of a clade that includes one undescribed species of Pristimantis from Cusco, Pristimantispharangobates and Pristimantisrhabdolaemus. The new species is most similar to P.rhabdolaemus, which differs by lacking scapular tubercules and by its smaller size (17.0-18.6 mm in males [n = 5], 20.8-25.2 mm in females [n = 5] in the new species vs. 22.8-26.3 mm in males [n = 19], 26.0-31.9 mm in females [n = 30] of P.rhabdolaemus). Additionally, we report the prevalence of Batrachochytriumdendrobatidis (Bd) in this species.

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.

Beyond the species name: an analysis of publication trends and biases in taxonomic descriptions of rainfrogs (Amphibia, Strabomantidae, Pristimantis)

The rainfrogs of the genus Pristimantis are one of the most diverse groups of vertebrates, with outstanding reproductive modes and strategies driving their success in colonizing new habitats. The rate of Pristimantis species discovered annually has increased continuously during the last 50 years, establishing the remarkable diversity found in this genus. In this paper the specifics of publications describing new species in the group are examined, including authorship, author gender, year, language, journal, scientific collections, and other details. Detailed information on the descriptions of 591 species of Pristimantis published to date (June 2022) were analyzed and extracted. John D. Lynch and William E. Duellman are the most prolific authors, yet Latin American researchers have scaled up and continued the description processes since the 1990s. The most common language used for descriptions is English, followed by Spanish. The great majority of authors have described only one species. The largest proportion of authors who have participated in the descriptions is of Ecuadorian nationality. Ecuador is the country with the highest description rate per year (3.9% growth rate). Only 20% of the contributions have included women and only 2% have featured women as principal authors. 36.8% of the species described are in the Not Evaluated or Data Deficient categories under the IUCN global red list. The importance of enhancing the descriptions in Spanish is emphasized and the inclusion based on equal access to opportunities for female researchers in Pristimantis taxonomy is encouraged. In general, if the current trends in Pristimantis descriptions continue, in ten years, a total of 770 or more species described could be expected.

A new species of rain frog (Anura: Strabomantidae: Pristimantis) from the Guiana Shield and amended diagnosis of P. ockendeni (Boulenger, 1912)

Pristimantis is already the most speciose genus among vertebrates, yet the current number of species remains largely underestimated. A member of the P. unistrigatus species group from the Guiana Shield has been historically misidentified as P. ockendeni, a species described from southern Peru. We combined mitochondrial (16S and COI) and nuclear (RAG1) loci, external morphology, skull osteology (μ-CT scan), vocalization (advertisement and courtship calls), geographic distribution and natural history data to differentiate the Guiana Shield populations from P. ockendeni, and describe them as a new species. The new species is crepuscular and nocturnal and inhabits the understory of unflooded (terra firme) forests in Brazil, Guyana and Suriname. It is phylogenetically related to P. arda­lonychus, P. martiae and undescribed species from Brazilian Amazonia. The new species notably differs from P. ockendeni and its congeners in the P. unistrigatus species group occurring in the Guiana Shield by the combination of the following characters: absence of dentigerous processes of vomers, presence of vocal slits in males, body size (SVL 16.2–20.7 mm in males and 21.4–25.7 mm in females), advertisement call (call with 4–6 notes, call duration of 158–371 ms and dominant frequency of 3,466–4,521 Hz) and translucent groin coloration in life. To facilitate the recognition and description of cryptic species previously hidden under the name P. ockendeni, we provide an amended diagnosis of this taxon based on external morphology and advertisement call of specimens recently collected nearby the type locality and additional localities in southwestern Amazonia.

Six new species of Pristimantis (Anura: Strabomantidae) from Llanganates National Park and Sangay National Park in Amazonian cloud forests of Ecuador

We describe six new species of rainfrogs of the genus Pristimantis (Strabomantidae) from Amazonian cloud forests in Ecuador. We also present a phylogeny showing the relationships of the new species. The phylogeny is based on mitochondrial genes 16S rRNA (16S), 12 rRNA (12S), NADH-ubiquinone oxidoreductase chain 1 (ND1) and the nuclear gene recombination-activating 1 (RAG1). We also describe the osteology of two of the new species using high-resolution x-ray computed tomography. The new species belong to two clades. The first clade is sister to the subgenus Huicundomantis and includes P. tamia sp. nov., P. miktos, and P. mallii. Pristimantis tamia sp. nov. is morphologically similar to P. miktos, P. mallii, P. martiae, and P. incomptus, but differs from them by lacking vocal slits and tympanic membrane and by having light greenish blue iris. Based in our results we expand the subgenus Huicundomantis to include the P. miktos species group. The second clade is remarkable by being highly divergent and consisting exclusively of new species: P. anaiae sp. nov., P. glendae sp. nov., P. kunam sp. nov., P. resistencia sp. nov., and P. venegasi sp. nov. The new species resemble P. roni, P. yanezi, P. llanganati, P. katoptroides, P. verecundus, and P. mutabilis but can be distinguished from them by lacking vocal slits and tympanic membrane and by having large dark round areas with thin clear borders in the sacral region. All six new species occur in the eastern slopes of the Ecuadorian Andes and are known from a single locality in Llanganates or Sangay National Park. We recommend assigning all of them to the Data Deficient (DD) Red List category. Based in our high-resolution x-ray tomographies, we report the presence of structures that appear to be intercalary elements. This would be the first report of such structures in Terrarana.

Leaving no stone unturned: three additional new species of Atractus ground snakes (Serpentes, Colubridae) from Ecuador discovered using a biogeographical approach

The genus Atractus includes 146 species of cryptozoic snakes occurring from Panama to northeastern Argentina. Here, a molecular phylogeny of this genus is presented, which encompasses 29% (= 42; six are included here for the first time) of the species currently recognized. Morphological and phylogenetic support is found for three new species of ground snakes, which are described here based on their unique combination of molecular, meristic, and color pattern characteristics. The name A.arangoi Prado, 1939 is revalidated for a Colombian snake species previously subsumed under A.major Boulenger, 1894 based on new material collected in Ecuador. Reidentifications are provided for Atractus voucher specimens and sequences deposited in GenBank. With these changes, the number of Atractus reported in Ecuador increases from 27 to 31 species. Finally, attention is given to the importance of using a biogeographical framework that includes molecular data and a comprehensive geographic sampling when proposing species limits in complex taxonomic groups.

Rediscovery, redescription and identity of Pristimantis nebulosus (Henle, 1992), and description of a new terrestrial-breeding frog from montane rainforests of central Peru (Anura, Strabomantidae)

The taxonomic status of the strabomantid frog species Pristimantis nebulosus (Henle, 1992), originating from the southern Cordillera Azul in central Peru, is investigated based on examination of the holotype and its comparison with freshly collected topotypic material. Following current standards, we provide a redescription of the holotype. It is in a rather poor state and exhibits certain damages and preservation artifacts, conditions that have hampered an allocation of this nominal taxon to any known living population of Pristimantis in the past. Our detailed specimen-to-specimen comparison provided morphological evidence for the conspecifity of the holotype and freshly collected topotypes. Molecular phylogenetic analysis, based on the mitochondrial 16S gene fragment places P. nebulosus in the P. conspicillatus species group, being closely related to P. bipunctatus and an undescribed candidate species from the Cordillera de Carpish. From both, P. nebulosus differs by considerable divergence in the 16S gene (p-distance 4.1–6.2%). Based on the specimens available, we provide an updated diagnosis for P. nebulosus, compare it to other species in the P. conspicillatus group and describe its advertisement call. In addition, we describe and name the closely related candidate species from the Cordillera de Carpish. It is sister to P. bipunctatus and P. nebulosus, but differs from both mainly by its tuberculate dorsal skin (versus shagreen) and divergence in the 16S gene (3.3–4.1%). We briefly discuss cryptic species diversity in the P. conspicillatus and P. danae species groups and provide justification for the description of a singleton species.

A new rainfrog of the genus Pristimantis (Anura, Brachycephaloidea) from central and eastern Panama

Substantial molecular and morphological character differences lead us to the description of a new species of the genus Pristimantis from the cloud forest of Cerro Chucantí, Maje Mountains, Darien Province, as well as from several other mountain ranges in eastern and central Panama. Pristimantis gretathunbergaesp. nov. is a sister species to the allopatric P. erythropleura-penelopus group from northern Colombia with a mtDNA sequence divergence of > 4.4% at 16S and > 14.6% at COI. Its closest congener in sympatry is P. cruentus that differs by a large sequence divergence of > 9.6% in 16S mtDNA and 19.0% at COI, and from which it differs also by ventral and groin coloration, unusually prominent black eyes, a contrasting light upper lip, commonly a single conical to spine-like tubercle on the upper eyelid, and a larger head. While the habitat continuity at most sites in eastern Panama is moderate, habitats in central Panama are severely fragmented. Cerro Chucantí and the surrounding Maje Mountains are highly threatened by rapid deforestation and replaced by plantations and cattle pastures. Thus, investigations on the ecology of the new species and its population status, especially at the type locality, are highly recommended. As a flagship species, this new frog can help to preserve the Chucantí cloud forest including several recently described species known only from this isolated area in eastern Panama.

The Pristimantis trachyblepharis species group, a clade of miniaturized frogs: description of four new species and insights into the evolution of body size in the genus

Species richness in the genus Pristimantis is underestimated due to the existence of morphologically cryptic species. This is worsened by the low sampling effort and the lack of studies using genetic markers. Here, we use molecular and morphological data to determine the phylogenetic relationships of a clade of Pristimantis distributed throughout montane tropical forests in the eastern Andes, from central Ecuador to northern Perú. We name this clade the Pristimantis trachyblepharis species group. Our results show that it comprises nine species, of which four are formally described and five are new. Four of these undescribed species are formally described here. The group is composed of miniaturized species, such as Pristimantis nanus sp. nov., currently the smallest known species of the genus and the smallest vertebrate in Ecuador. As a first approach to understanding the evolutionary origin and implications of body-size reduction in Pristimantis, we here study the phylogenetic signal and evolutionary trends of body size within the genus. We also provide the first record of P. aquilonaris in Ecuador and we show, for the first time, the phylogenetic position of P. albujai, P. aquilonaris, P. minimus and P. trachyblepharis, which are also members of the P. trachyblepharis species group.

A new cryptic species of the Pristimantis lacrimosus group (Anura, Strabomantidae) from the eastern slopes of the Ecuadorian Andes

With 566 species, the neotropical genus Pristimantis is the most speciose vertebrate genus. As a result of its striking diversity, taxonomic reviews remain a challenge. Herein, we present an updated phylogeny of the Pristimantis lacrimosus group and describe a new species from Llanganates and Sangay National Parks. We also report, for the first time, the phylogenetic position of Pristimantis degener, P. eugeniae, P. katoptroides, and P. petersi. Based on our phylogeny, we add two species to the Pristimantis lacrimosus group. Through the integration of molecular and bioacoustic evidence, we describe a new species which was hidden under “Pristimantis petersi”. Pristimantis petersioidessp. nov. is most closely related to Pristimantis petersi and an undescribed species from Peru. It can be distinguished from P. petersi by its advertisement call and large genetic differences (uncorrected p-genetic distances 7.9% to 8.4% for gene 16S). Moreover, the new species and P. petersi are not sister species. We suggest assigning the new species to the Endangered Red List category because it has a small distribution range with deforestation as result of agriculture and other anthropogenic influences.

Filling Linnean shortfalls increases endemicity patterns: conservation and biogeographical implications for the extreme case of Liolaemus (Liolaemidae, Squamata) species

Linnean shortfalls, or the discrepancy between formally described species and the number of existing species, imply noteworthy biodiversity conservation constraints. The case of Argentinian reptiles is unique in this context. The genus Liolaemus represents ~60% of the Argentine reptile fauna and has a current species description rate of 3.25 spp./year, leading to a significant increase in the number of known species. Filling Linnean shortfalls within this genus has revealed an extraordinary recent evolutionary radiation that strongly modifies the spatial accumulation patterns of richness and endemism, mainly in the Patagonian steppe and Monte ecoregions of Argentina. Thus, while 40 years ago none of the studied species was considered endemic at the ecoregional level, today the genus represents an essential element to define the southernmost terrestrial ecoregions of the world. Furthermore, the remarkable decrease in the average extent of occurrence (EOO) of Liolaemus species implies an increased extinction risk in light of threats caused by humans. Based on the thresholds for the IUCN Red List B1 criteria, and 11 well-studied clades of Liolaemus, we show that, while in 1980 87% of the described species would not qualify as threatened based on EOO, today 80% of the species have an EOO smaller than 20 000 km2. Therefore, they may qualify as threatened based on the B1 EOO thresholds, which demonstrates the importance of the recent increase of knowledge regarding the taxonomy, systematics and genetics of the group.

Red List assessment of amphibian species of Ecuador: A multidimensional approach for their conservation

Ecuador is one of the most biodiverse countries in the world, but faces severe pressures and threats to its natural ecosystems. Numerous species have declined and require to be objectively evaluated and quantified, as a step towards the development of conservation strategies. Herein, we present an updated National Red List Assessment for amphibian species of Ecuador, with one of the most detailed and complete coverages for any Ecuadorian taxonomic group to date. Based on standardized methodologies that integrate taxonomic work, spatial analyses, and ecological niche modeling, we assessed the extinction risk and identified the main threats for all Ecuadorian native amphibians (635 species), using the IUCN Red List Categories and Criteria. Our evaluation reveals that 57% (363 species) are categorized as Threatened, 12% (78 species) as Near Threatened, 4% (26 species) as Data Deficient, and 27% (168 species) as Least Concern. Our assessment almost doubles the number of threatened species in comparison with previous evaluations. In addition to habitat loss, the expansion of the agricultural/cattle raising frontier and other anthropogenic threats (roads, human settlements, and mining/oil activities) amplify the incidence of other pressures as relevant predictors of ecological integrity. Potential synergic effects with climate change and emergent diseases (apparently responsible for the sudden declines), had particular importance amongst the threats sustained by Ecuadorian amphibians. Most threatened species are distributed in montane forests and paramo habitats of the Andes, with nearly 10% of them occurring outside the National System of Protected Areas of the Ecuadorian government. Based on our results, we recommend the following actions: (i) An increase of the National System of Protected Areas to include threatened species. (ii) Supporting the ex/in-situ conservation programs to protect species considered like Critically Endangered and Endangered. (iii) Focalizing research efforts towards the description of new species, as well as species currently categorized as Data Deficient (DD) that may turn out to be threatened. The implementation of the described actions is challenging, but urgent, given the current conservation crisis faced by amphibians.

Three new species of frogs of the genus Pristimantis (Anura, Strabomantidae) with a redefinition of the P. lacrimosus species group

A new phylogeny for the Pristimantis lacrimosus species group is presented, its species content reviewed, and three new species described from the eastern slopes of the Ecuadorian Andes. Our phylogeny includes, for the first time, samples of P. aureolineatus, P. bromeliaceus, and P. lacrimosus. The morphology of hyperdistal subarticular tubercles is also assessed among 21 species of Pristimantis. The P. lacrimosus species group is composed of 36 species distributed in the Chocó, Guiana, and Amazon regions of tropical South America with a single species reaching Central America. Ancestral area reconstruction indicates that, despite its high diversity in the Amazon region, the P. lacrimosus group originated in the Pacific basin, Chocó region of Ecuador and Colombia. Pristimantis amaguanae sp. nov. is most closely related to P. bromeliaceus. It differs from P. bromeliaceus by being smaller, having transversal dark bands in the hindlimbs (absent or faint in P. bromeliaceus) and the absence of discoidal fold (present in P. bromeliaceus). Pristimantis nankints sp. nov. and P. romeroae sp. nov. are part of a clade of predominantly light-green frogs that includes P. acuminatus, P. enigmaticus, P. limoncochensis, and P. omeviridis. Pristimantis nankints sp. nov. and P. romeroae sp. nov. can be distinguished from all of them by the presence of a dark dorsolateral stripe that borders a light green band on a green background. Hyperdistal tubercles are present in all examined species of the P. lacrimosus species group and its sister clade. Species with hyperdistal tubercles are characterized by having relatively long terminal phalanges and narrow T-shaped expansion at the end of the terminal phalange. We discuss the phylogenetic distribution of these characters and their potential diagnostic significance.

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.

Four new species of Pristimantis Jiménez de la Espada, 1870 (Anura: Craugastoridae) in the eastern Amazon

The Pristimantis genus (Anura: Craugastoridae) is the most diverse among all vertebrates with 531 described species. The highest diversity occurs in Ecuador (215 species), followed by Colombia (202), Peru (139), Venezuela (60), Brazil (30), Bolivia (17), Guyana (6) Suriname and French Guiana (5). The genus is divided into 11 species groups. Of these, the P. conspicillatus group (containing 34 species), distributed in extreme southeastern Costa Rica, Isla Taboga (Panama), northern South America (from Colombia to eastern Guyana), south Bolivia, and is the best represented in Brazil (16 species). The main characteristics of this group are the tympanic membrane and tympanic annulus distinct (except in P. johannesdei); dorsum smooth or shagreen; dorsal lateral fold present or absent; usually smooth belly, but may be weakly granular in some species; toe V slightly larger than the toe III. Most of the taxonomic inconsistencies in species of Pristimantis could be due to its much conserved morphology and the lack of comprehensive taxonomic evaluations. Thus, an ongoing challenge for taxonomists dealing with the Pristimantis genus is the ubiquitous abundance of cryptic species. In this context, accurate species delimitation should integrate evidences of morphological, molecular, bioacoustics and ecological data, among others. Based on an integrative taxonomy perspective, we utilize morphological, molecular (mtDNA) and bioacoustic evidence to describe four new species of the Pristimantis conspicillatus group from the eastern Amazon basin. Pristimantis giorgiisp. nov. is known from the Xingu/Tocantins interfluve and can be distinguished from the other Pristimantis species of the region by presenting discoidal fold, dorsolateral fold absent, vocalization composed of three to four notes and genetic distance of 7.7% (16S) and 14.8% (COI) from P. latro, the sister and sympatric species with respect P. giorgiisp. nov.. Pristimantis pictussp. nov. is known to the northern Mato Grosso state, Brazil, and can be distinguished from the other species of Pristimantis by presenting the posterior surface of the thigh with light yellow patches on a brown background, also extending to the inguinal region, vocalization consisting of four to five notes and a genetic distance of 11.6% (16S) and 19.7% (COI) from P. pluviansp. nov., which occurs in sympatry. Pristimantis pluviansp. nov. is known to the northern Mato Grosso state, Brazil, and may be distinguished from the other Pristimantis species by having a posterior surface of the thigh reddish and vocalization composed of two notes. Pristimantis moasp. nov. is known to the northern Tocantins state and southwestern Maranhão state. This species can be distinguished from the other Pristimantis species by possessing slightly perceptible canthal stripe, external thigh surface with dark yellow spots on brown background, vocalization consisting of three to five notes and genetic distance of 2.3–11.7 (16S) and 10.5–23.1 (COI) for the new Pristimantis species of this study.

Biogeographical, ecological, and phylogenetic analyses clarifying the evolutionary history of Calibrachoa in South American grasslands

Calibrachoa is a charismatic South American genus of Solanaceae, closely related to Petunia, which encompasses approximately 30 species. Studies that were based solely on plastid molecular markers indicated the monophyly of the genus and distributed its species in two subgenera; to date no phylogeny has included a broad morphological variants and nuclear markers. Here, we present a phylogenetic analysis based on eight plastid and eight nuclear markers that cover the most extensive geographic distribution for the genus. We use this phylogeny to infer the biogeographic history of the genus and to understand the primary drivers for species diversification. Our results yield a fully supported tree where monophyly is confirmed to genus and subgenera. The species of Stimomphis subgenus that were previously considered uncertain, here emerge in four highly supported clades. The hypothesis of niche conservatism is confirmed, and adaptive radiation explains the species diversification. The lowlands are the most likely ancestral area of the genus, subgenera, and two clades of Stimomphis subgenus. Our results constitute an excellent starting point for further evolutionary and taxonomic studies and explain several uncertain evolutionary relationships in the group and the evolution of their distribution.

Extensive Cryptic Diversity Within the Physalaemus cuvieri-Physalaemus ephippifer Species Complex (Amphibia, Anura) Revealed by Cytogenetic, Mitochondrial, and Genomic Markers

Previous cytogenetic and phylogenetic analyses showed a high variability in the frog taxa Physalaemus cuvieri and Physalaemus ephippifer and suggested the presence of undescribed diversity in this species complex. Here, by 1) adding specimens from the Brazilian Amazon region, 2) employing sequence-based species delimitation approaches, and 3) including RADseq-style markers, we demonstrate that the diversity in the P. cuvieri-P. ephippifer species complex is even greater than previously suspected. Specimens from Viruá and Western Pará, located at the Guiana Amazonian area of endemism, were recovered as distinct from all previously identified lineages by the phylogenetic analyses based on mitochondrial DNA and RAD markers, a PCA from RAD data, and cytogenetic analysis. The sequence-based species delimitation analyses supported the recognition of one or two undescribed species among these Amazonian specimens and also supported the recognition of at least three other species in the P. cuvieri-P. ephippifer species complex. These new results reinforce the need for a comprehensive taxonomic revision.

Systematics of Huicundomantis, a new subgenus of Pristimantis (Anura, Strabomantidae) with extraordinary cryptic diversity and eleven new species

Pristimantis is the most diverse genus of tetrapods comprising 532 described species. It contains a large number of morphologically cryptic species that are being discovered with the assistance of genetic evidence. We use molecular, morphological, bioacoustic, and environmental data to assess the phylogenetic relationships and determine the species within an Andean clade of Pristimantis, which is distributed from central Ecuador to northern Peru. We assign to this clade the name Huicundomantis and propose it as a subgenus. Our results show that Huicundomantis is composed of two large clades which we name as the P.phoxocephalus species group and the P.cryptomelas species group. Huicundomantis is composed of 28 species of which 12 have been described and 16 are new. We describe 11 of these undescribed species. The most effective characters to discriminate among species are DNA sequences, qualitative morphology, and advertisement calls. Morphometric and environmental characters are not very useful to define species limits. We clarify the identity of P.riveti and show that populations from southern Ecuador traditionally ascribed to P.riveti are a new species, P.lutzaesp. nov. We also show that P.prometeii is a junior synonym of P.hampatusami. The current diversity and geographic distribution of Huicundomantis are consistent with a model of allopatric speciation. All species have a restricted distribution range (less than 4330 km²) and are assigned to the Red List categories Data Deficient or threatened with extinction. We provide new reasons to increase conservation efforts for these species and their habitat. Taking our results into account, Pristimantis species richness in Ecuador increases from 211 to 221 species, and the number of species endemic to Ecuador from 119 to 129.

Species delimitation of the Dermacentor ticks based on phylogenetic clustering and niche modeling

Three species belonging to the genus Dermacentor (Acari: Ixodidae), D. marginatus, D. nuttalli and D. silvarum are well known as vectors for a great variety of infection pathogens. All three of them are host ticks, which are very similar in morphology characteristics, life cycle, seasonal variation and ecological conditions, making it difficult to distinguish the three species. In the present study, these three species were delimitated based on molecular data and ecological niche. The molecular analysis showed that the three species can be distinguished by COI and ITS2 sequences. We created future potential distribution maps for the three species under climate changes with MaxEnt, which highlighted the different levels of the suitable habitats for each tick species. In addition, niche comparisons among the three species in Dermacentor were conducted, and the analysis suggested that niche overlap was relatively high with D. nuttalli and D. silvarum compared to the other species pairs, which was consistent with the molecular data. Niche equivalency and similarity test confirmed that these Dermacentor species were closely related but distinct species. In conclusion, delimitation of these three species within Dermacentor was supported by molecular phylogeny and quantitative ecological space. This study will provide deep insights into the biology, ecology, and diversification processes within Dermacentor species, and for the development of effective control for ticks.

Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)

The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.

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.

Species limits within the widespread Amazonian treefrog Dendropsophus parviceps with descriptions of two new species (Anura, Hylidae)

The genus Dendropsophus is one of the most speciose among Neotropical anurans and its number of described species is increasing. Herein, molecular, morphological, and bioacoustic evidence are combined to assess species limits within D. parviceps, a widely distributed species in the Amazon Basin. Phylogenetic relationships were assessed using 3040 bp sequences of mitochondrial DNA, genes 12S, ND1, and CO1. The phylogeny shows three well-supported clades. Bioacoustic and morphological divergence is congruent with those clades demonstrating that Dendropsophus parviceps is a species complex. Dendropsophus parvicepssensu stricto occurs in the Amazon basin of Ecuador, northern Peru, southern Colombia and northwestern Brazil. It is sister to two previously undescribed species, D. kubrickisp. n. from central Peru and D. kamagarinisp. n. from southern Peru, northeastern Bolivia, and northwestern Brazil. Genetic distances (uncorrected p, gene 12S) between D. parviceps and the new species is 3 to 4%. Dendropsophus kamagarinisp. n. can be distinguished from D. parviceps by having a prominent conical tubercle on the distal edge of the upper eyelid (tubercle absent in D. parviceps). Dendropsophus kubrickisp. n. differs from D. parviceps by having scattered low tubercles on the upper eyelids (smooth in D. parviceps). Dendropsophus parviceps and both new species differ from all their congeners by their small size (adult maximum SVL = 28.39 mm in females, 22.73 mm in males) and by having a bright orange blotch on the hidden areas of the shanks and under arms. The advertisement call of the two new species has lower dominant frequency relative to D. parviceps. Probable speciation modes are discussed. Available evidence indicates that ecological speciation along an elevation gradient is unlikely in this species complex.

The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs

Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence. We found low genetic divergence (2.6% in the 16S gene) despite substantial differences in color and acoustic signals. While chemical defense is inferred to have evolved in the ancestor of Epipedobates, aposematic coloration evolved at least twice or was lost once in Epipedobates, suggesting that it is evolutionarily labile. We inferred at least one event of introgression between two cryptically colored species with adjacent ranges (E. boulengeri and E. machalilla). We also find evidence for peripheral isolation resulting in phenotypic divergence and potential speciation of the aposematic E. tricolor from the non-aposematic E. machalilla. However, we were unable to estimate a well-supported species tree or delimit species using multispecies coalescent models. We attribute this failure to factors associated with recent speciation including mitochondrial introgression, incomplete lineage sorting, and too few informative molecular characters. We suggest that species delimitation within young aposematic lineages such as Epipedobates will require genome-level molecular studies. We caution against relying solely on DNA barcoding for species delimitation or identification and highlight the value of phenotypic divergence and natural history in delimiting species.

High Species Richness of Scinax Treefrogs (Hylidae) in a Threatened Amazonian Landscape Revealed by an Integrative Approach

Rising habitat loss is one of the main drivers of the global amphibian decline. Nevertheless, knowledge of amphibian diversity needed for effective habitat protection is still highly inadequate in remote tropical regions, the greater part of the Amazonia. In this study we integrated molecular, morphological and bioacoustic evidence to evaluate the species richness of the treefrogs genus Scinax over a 1000 km transect across rainforest of the Purus-Madeira interfluve, and along the east bank of the upper Madeira river, Brazilian Amazonia. Analysis revealed that 82% of the regional species richness of Scinax is still undescribed; two nominal species, seven confirmed candidate species, two unconfirmed candidate species, and one deep conspecific lineage were detected in the study area. DNA barcoding based analysis of the 16s rRNA gene indicates possible existence of three discrete species groups within the genus Scinax, in addition to the already-known S. rostratus species Group. Quantifying and characterizing the number of undescribed Scinax taxa on a regional scale, we provide a framework for future taxonomic study in Amazonia. These findings indicate that the level to which Amazonian anura species richness has been underestimated is far greater than expected. Consequently, special attention should be paid both to taxonomic studies and protection of the still-neglected Amazonian Scinax treefrogs.

A new species of frog of the genus Pristimantis from Tingo María National Park, Huánuco Department, central Peru (Anura, Craugastoridae)

A new species of Craugastoridae frog encountered from 1000-1700 m in elevation in the premontane forests of the Peruvian central Andes is described. The new species is similar in appearance to many other species of Pristimantis, but is easily distinguishable from these species by having bright red coloration on the groin, posterior surface of thighs, and shanks. The new species is only known for two localities 27 km apart in the Huánuco Region.

A new species of Pristimantis (Amphibia, Anura, Craugastoridae) from the foothills of the Andes in Manu National Park, southeastern Peru

We describe a new species of Pristimantis from the humid sub-montane forest of the Región Cusco in Peru. Pristimantispluvialissp. n. was collected in the Kosñipata and Entoro valleys at elevations from 740 to 1110 m a.s.l., near the borders of Manu National Park and within the Huachiperi Haramba Queros Conservation Concession. The new species can be distinguished from other members of the genus Pristimantis by its rostral tubercle, smooth dorsal skin, and by its advertisement call. Pristimantislacrimosus and Pristimantiswaoranii superficially most resemble the new species, but Pristimantispluvialissp. n. differs from both species by having a rostral tubercle (absent in Pristimantiswaoranii and variable in Pristimantislacrimosus) and larger size, from Pristimantislacrimosus by its call emitted at a lower frequency, and from Pristimantiswaoranii for its dorsal coloration with dark markings. Two other species have partially overlapping distributions and resemble the new species, Pristimantismendax and Pristimantisolivaceus, but they produce advertisement calls with much higher dominant frequencies than the advertisement call of the new species. Furthermore, Pristimantismendax differs from the new species by lacking a rostral tubercle and by having a sigmoid inner tarsal fold, whereas Pristimantisolivaceus differs by being smaller and by having dorsal skin shagreen with scattered tubercles. The new species has snout-vent length of 21.8–26.9 mm in males (n = 12) and 28.8 mm in a single female.