Underestimation of species richness in neotropical frogs revealed by mtDNA analyses

A remarkable new blue Ranitomeya species (Anura: Dendrobatidae) with copper metallic legs from open forests of Juruá River Basin, Amazonia

Poison dart frogs (Dendrobatidae) are known for their aposematic coloration and toxic skin, making them a frequent subject of interest and research. However, descriptions of new species of Ranitomeya were interrupted for more than a decade. The implementation of a RAPELD (Rapid Assessment surveys of Long-Term Ecological Research) module in the Juruá River basin, a highly biodiverse and underexplored region, led to the record of a Ranitomeya species with blue dorsal stripes and coppery limbs. Herein we use morphological, morphometric, advertisement call, natural history, tadpole data and genetic data to describe the new species. Our phylogenetic analysis places the species within the Ranitomeya vanzolinii clade, and all delimitation methods confirmed its status as a new species. The species is characterized by its (i) small size (snout-vent length: males 15.2-17.0 mm, females 14.4-16.9 mm), (ii) dorsum with light sky-blue stripes on a reddish-brown ground, and metallic copper limbs with reddish-brown spots, (iii) ring-shaped granular region on the belly, (iv) toes with poorly developed lateral fringes, (v) later tadpole stages with tooth rows P1 = P2 > P3, P3 of 83-87% of P1, and conspicuous light sky-blue dorsal stripes, and (vi) cricket-like advertisement call consisting of 16-35 notes, call duration of 490-1,005 ms, note duration of 8.2-16.9 ms and dominant frequency of 5,168-6,029 Hz. The discovery of the new species emphasizes the significance of researching under-sampled regions like the Juruá River basin, and the usefulness of using a multidisciplinary approach to reveal new dendrobatid species.

Cryptic biodiversity of freshwater fish species in Bangladesh

Unrecognized cryptic species impede conservation planning and biodiversity assessments. DNA barcoding has tremendously expanded the number of novel and cryptic species in biological science. Despite few sporadic studies, the exact number of freshwater species found in Bangladesh is not known. To assess this biodiversity, we sequenced the COI gene of 124 freshwater specimens, which were gathered from various localities around Bangladesh. Seven cryptic species hidden among the currently studied specimens were identified based on the findings of phylogenetic and species delimitation analyses. The preliminary assessment also encompassed a restricted morphological examination of these cryptic taxa. The appearance of cryptic species, some of them possibly endemic, has been hypothesized. This raises concerns regarding the true diversity and evolutionary history of freshwater species in Bangladesh, which are significantly underrepresented in the current systematic frameworks that do not account for DNA data. Our current study provides baseline data that might aid local ichthyologists in their quest to identify additional new species by combining several variables (morphology and ecology). Further research is warranted to protect the priceless freshwater species in Bangladesh.

An Amazonian hidden gem: a new metallic-colored species of Ranitomeya (Anura, Dendrobatidae) from Juruá River basin forests, Amazonas state, Brazil

The genus Ranitomeya has 16 known species, and the last of them was described 13 years ago. The forests of the Juruá River basin are known for their enormous vertebrate diversity, despite being one of the least sampled regions in the entire Amazonia. Our recent expeditions to the region resulted in the discovery of a Ranitomeya species with blue-green dorsal stripes and quite peculiar behavior. Here, it is described as a new species using morphological, morphometric, advertisement call, natural history, and genetic data. This new species is strongly nested within the R.vanzolinii clade, with interspecific p-distances ranging from 2.94 to 3.91%, and it was confirmed in all the delimitation methods used. It differs from its closest relatives mainly by (i) its size (male SVL 15.4-17.7 mm, n = 8; female SVL 17.3-18.5 mm, n = 5), (ii) its unique color pattern that is metallic pale yellowish green to metallic pale turquoise-green dorsal stripes pattern, limbs metallic chrome with dark carmine spotting), (iii) presence of a conspicuous sulfur yellow spot on the dorsal surface of the thighs, (iv) tadpoles with posterior tooth rows P1 > P2 > P3 in all stages, head translucent brownish and lack of emarginate lateral papillae, and (v) its advertisement call (composed of 21-45 notes, call duration of 647-1,424 ms, note rate of 28-36 notes/s and dominant frequency of 4,996-6,288 Hz).

A taxonomic integrative approach of the anuran species from a Cerrado-Amazonian transitional area in western Tocantins state, Brazil

Due to their complexity environments, ecotonal areas harbor high levels of biodiversity. The Cerrado is geographically situated among other Brazilian biomes and exhibits extensive transitional areas with neighboring biomes. The state of Tocantins, in northern Brazil, has a vast transitional area between the Cerrado and Amazonia in the North and West. Despite the remarkable richness revealed in recent studies, the anuran fauna of Tocantins is likely underestimated, as several municipalities have knowledge gaps, particularly those located in these Cerrado-Amazonia transitional areas. Here, we improve the knowledge of amphibians' diversity in a Cerrado-Amazonia transitional area in western Tocantins state using integrative taxonomy. We conducted four field expeditions in the Caseara municipality, totaling 50 days of fieldwork. We performed diurnal and nocturnal active surveys and installed pitfall traps along an environmental gradient, ranging from typical Cerrado habitats to typical Amazon habitats. We combined morphology, bioacoustic, and mtDNA to improve the identification of the collected specimens. In total, we collected 738 vouchers assigned to 42 species belonging to seven families. We also present morphometric data for 38 of the recorded species (n = 609), acoustic data for 19 species, and 21 new 16S mtDNA sequences for seven species. These new data were essential to identify 38 of the 42 recorded species at the species level, including interesting new records for species like Allobates crombiei and Scinax similis. Four recorded species remained with an undefined status: Boana sp. (gr. semilineata), Adenomera sp. (aff. hylaedactyla), Physalaemus sp. (gr. cuvieri), and Proceratophrys sp. (cf. ararype). We encourage the use of similar approaches in species inventories to ensure taxonomic accuracy and to provide reliable data for conservation policies.

Three new species of torrent treefrogs (Anura, Hylidae) of the Hyloscirtusbogotensis group from the eastern Andean slopes and the biogeographic history of the genus

The Hyloscirtusbogotensis group contains 17 species of treefrogs from the tropical Andes and Central America. A taxonomic review of the Amazonian clades of this group is presented based on DNA sequences of nuclear and mitochondrial DNA and a preliminary phylogenomic analysis of ultraconserved elements, as well as morphological, bioacoustic, and environmental characters. Additionally, the role of the Andes in the diversification of the genus Hyloscirtus is explored by reconstructing their ancestral basin (Amazon, Pacific, Caribbean). Our integrative analysis indicates the existence of eight undescribed candidate species within the group. Three of those species are described, previously masked within H.albopunctulatus, H.phyllognathus, and H.torrenticola. A lectotype is also designated for Hylaalbopunctulata. The new evidence suggests that neither Hyloscirtusphyllognathus nor H.torrenticola occur in Ecuador. The new species, H.elbakyanae sp. nov., H.dispersus sp. nov., and Hyloscirtusmaycu sp. nov. differ from other members of the group in bioacoustics and external morphology. The most useful diagnostic characters among species were advertisement calls. In contrast, skin coloration is highly variable intraspecifically and, as a result, of low diagnostic value. High variation in color is partly a result of phenotypic plasticity. Our biogeographic reconstructions indicate that the Andean barrier influenced the diversification of Hyloscirtus. Since the early Oligocene, there have been only four colonization events across de Andes, between the Pacific and Amazon basins. Two of those events occurred more than 14 Mya, when most of the tropical Andes were below 3000 m. Species in the highland H.larinopygion group are younger, suggesting recent diversification as high montane forests and paramo habitats emerged.

Delimiting Species-Prospects and Challenges for DNA Barcoding

Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals, the challenge is particularly acute within the arthropods, which comprise approximately 85% of all described animals, with approximately 1 million described species. The true number of arthropod species is estimated to be in excess of 10 million species. This estimate is likely to be revised upward in the light of global DNA barcode sequencing initiatives that are cataloguing unprecedented levels of cryptic or overlooked diversity. The scale of diversity that is being recovered with barcode sequencing places further strain on a taxonomic system confronted by ever-limited global taxonomic capacity to verify and describe new species. It is predicted that the number of novel operational taxonomic units delimited by barcode sequencing is likely to eclipse the number of species described by Linnean taxonomy by as early as 2029. Unless addressed, this may see an increasing proportion of arthropod species falling outside of protective legislative frameworks as a consequence of their lack of formal description. Confronted with this challenge, there is increasing, but controversial, acceptance of species delimitation and species description based on barcode sequence clustering thresholds. In response to the evolving controversy surrounding this issue, it is both timely and important to identify and clarify prospects and challenges for DNA barcoding, with a specific focus on species delimitation to address important shortfalls and impediments in biodiversity research.

Discovery and description of a deeply divergent frog lineage of the genus Minervarya Dubois, Ohler & Biju, 2001 (Anura: Dicroglossidae) from the basaltic plateau of the northern Western Ghats, Maharashtra, India

A new species of dicroglossid frog Minervarya ghatiborealis sp. nov. is described from the Mahabaleshwar region of the northern Western Ghats, India, based on multiple axis of evidences like morphological, acoustics, genetic datasets, and geographical isolation. The new species is phenotypically distinct from its congeners by a combination of morphological characters: body large, robust, with SVL 55.0-59.1 mm (n = 5) in adult males and SVL 67.1 mm (n = 1) in adult female; sub-elliptical snout; rudimentary webbing; dorsal skin glandular with highly ridged folds. Phylogenetically, the new species exhibits sister relationship to the clade containing Minervarya goemchi, M. mysorensis and M. brevipalmata. Genetic distance between the new species and the members of its sister clade varies from 6.5% to 7.2% for DNA sequences of the mitochondrial 16S rRNA gene. For the nuclear-encoded Tyrosinase gene genetic distance between the new species and its syntopic, large-bodied, congener M. goemchi is 1.4%. Additionally, an advertisement call description is provided to differentiate the new species from its congeners. The importance of the Mahabaleshwar plateau and altitudinal preferences of large-sized Minervarya frogs in the northern Western Ghats are discussed.

The identity of Rhinella mirandaribeiroi (Gallardo, 1965) (Anura: Bufonidae) and its diagnosis in relation to Rhinella granulosa (Spix, 1824)

The Rhinella granulosa group is composed of 13 species widely distributed in South America and Panama. The richness of the group may be poorly characterized due to limited characterizations caused by a lack of topotype data. This is the case for Rhinella mirandaribeiroi, which lacks topotypical (from Marajó Island, Pará state, Brazil) characterization in terms of acoustics and molecular data, as well as interpopulation variation, considering specimens from the Cerrado, including its junior synonym Bufo granulosus lutzi (Pirapora, Minas Gerais state, Brazil). At the same time, morphological and acoustic differences seem scarce and subtle compared to R. granulosa, a sister species with contiguous distribution areas. Therefore, an integrative taxonomic approach arises as necessary to assess the status of these species and differentiate them. Here, we present morphological data from recently collected topotypes of R. mirandaribeiroi, as well as acoustic and genetic data from this population. We found acoustic, molecular, and morphological evidence that B. g. lutzi and individuals distributed in the Cerrado belong to the same species of R. mirandaribeiroi, maintaining its condition of synonym. We also found that R. granulosa and R. mirandaribeiroi exhibit a conserved phenotype (morphology and acoustics) and that the presence/absence of a clear vertebral line is not a diagnostic character for both named species. However, R. granulosa and R. mirandaribeiroi show a significant genetic distance and therefore should be maintained as valid species until a better understanding of the distribution of both species is achieved.

Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data

The Craugastor podiciferus Species Group contains eleven species of terraranan frogs distributed from eastern Honduras to eastern Panama. All species have remarkable color pattern polymorphisms, which may contribute to potential taxonomic problems. We performed exhaustive sampling throughout the geographic distribution of the group to evaluate the phylogenetic relationships and biogeographic history of all named species based on two mitochondrial markers and nuclear ddRAD loci. We also implemented various species delimitation methods to test for the presence of unconfirmed candidate species within the group. Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. Species delimitation was discordant between the mitochondrial and nuclear datasets and among analytical methods. Adopting a conservative approach, we propose that the C. podiciferus species group contains at least 12 unconfirmed candidate species. Ancestral area reconstruction showed that the group originated and diversified in the highlands of the Talamancan montane forest ecoregion of Costa Rica and western Panama.

A comprehensive molecular phylogeny of the genus Sylvirana (Anura: Ranidae) highlights unrecognized diversity, revised classification and historical biogeography

The genus Sylvirana includes 12 species widely distributed in South China and Southeast Asia. The phylogenetic relationships and species diversity for Sylvirana and allied genera remain unresolved and controversial due to insufficient data and incomplete taxon sampling. Using a combined dataset of mitochondrial genes (16S and COI) and 101 nuclear genes obtained through the amplicon sequence capture approach, we generated the most comprehensive phylogenetic analysis for the genus Sylvirana to date, inferring diversity, phylogenetic relationships, and historical biogeography with unprecedented levels of taxon and geographic sampling. Our results conservatively reveal six undescribed species, mostly distributed in peninsular Indochina. Phylogenetic analyses strongly support the non-monophyly of Sylvirana with respect to Pterorana. Additionally, phylogenetic results place Sylvirana guentheri and Pelophylax lateralis into genus Humerana, supporting the inclusion of Hylarana latouchii, Papurana milleti, and Hylarana attigua within Pterorana + Sylvirana. The long-disputed species of Hylarana bannanica (previously Sylvirana) cluster with genus Papurana. Because the results of multiple non-monophyletic genera create taxonomic confusion, we suggest relegating all genera to subgenus rank of Hylarana. Sylvirana is a junior synonym of the Pterorana. Biogeographically, we trace the origin of Pterorana to Southeast Asia during the early Miocene, with subsequent dispersal thereafter. Our study shows that climatic changes may have profoundly influenced the diversification of Pterorana during the Miocene.

Taxonomic assessment of the Bolitoglossa (Eladinea) subgenus (Caudata: Plethodontidae) with the description of two new species from the Cordillera de Talamanca, Costa Rica

Isthmian Central America boasts a diverse array of salamanders, with a total of 72 species spanning three genera. Among these, a subset of the subgenus Bolitoglossa (Eladinea), stands out as particularly rare within the Cordillera de Talamanca. Many of its species have been discovered since 2009, with the majority documented from fewer than five specimens. In our endeavor to elucidate the taxonomy of this species group, we conducted fieldwork at Tapantí and the summits of Utyum, Echandi, and Fábregas, aiming to locate specimens. Our efforts have led to the expansion of the distributional range and the elucidation of the known body size of Bolitoglossa bramei, while Bolitoglossa robinsoni underwent redefinition. Furthermore, we describe two additional species herein, including a miniature salamander from Cerro Utyum and another salamander of moderate size from Valle del Silencio. As result of this study, the Bolitoglossa diminuta species group is now recognized to encompass seven species, all confined within the limits of the Cordillera de Talamanca.

Combining citizen science, phylogenetics, and bioacoustics to inform taxonomy and conservation of the Near Threatened Proceratophrys paviotii (Anura, Odontophrynidae)

Herein, basel on novel data gathered by citizens scientists and specialists, we contribute to the improvement of scientific knowledge and conservation of the Near Threatened Proceratophrys paviotii in order to: 1) test for the first time the phylogenetic position and a species delimitation of P. paviotii through a molecular approach; 2) describe a larger sample of its advertisement call to properly encompass the species intraspecific variation; 3) describe for the first time the P. paviotii release call; and 4) provide novel insights on the species conservation status. Our 16S tree confidently grouped P. paviotii with P. cururu, P. renalis, and P. laticeps. The average sequence divergence between P. paviotii and its congeners ranged from 2.2% (P. laticeps) to 9.1% (P. redacta). Advertisement calls consisted of a single note with duration of 0.26-0.58 s, 17-41 pulses emitted at rate of 54.19-77.49 pulses/s and peak frequency of 775.19-947.46 Hz. Release calls consisted of a single note with duration of 0.04-0.43 s, 2-13 pulses emitted at rate of 21.17-81.58 pulses/s and peak frequency of 689.1-1,722.6 Hz. Additionally, our study strongly supports the notion that Citizen Science approaches can yield invaluable information concerning species' geographic distribution and conservation.

Lost in space and time: robust demography and enhanced resilience buffer adverse environmental effects in a highly isolated and sedentary pre-pleistocene landscape vertebrate

BACKGROUND

Few animal populations have been studied under the framework of the OCBIL theory, which addresses the ecology and evolution of biodiversity on old climatically buffered infertile landscapes. Available genetic data challenge the low connectivity and high genetic differentiation predicted for isolated tepui-summit vertebrate communities, suggesting potential dispersal among summits. However, the OCBIL theory posits reduced dispersibility, enhanced resilience to habitat fragmentation and inbreeding due to small populations. We tested these hypotheses by conducting the first analytic evaluation of the spatial ecology and population biology of a tepui-summit vertebrate at multiple spatial scales.

RESULTS

We used harmonic radar tracking (100 individuals/448 points of contact) and capture-mark-recapture data (596 individuals captured/52 recaptured) to reveal the temporal niche, microhabitat use, population size, and dispersal abilities of the tepui-summit endemic toad Oreophrynella quelchii on Roraima-tepui. Abundance was determined using a closed population model incorporating sources of variation in capture probability. We tested the relative influence of biotic and abiotic variables on distances moved through model selection. Our data indicate that the population size of O. quelchii is remarkably large (ca. 12 million individuals), with strong seasonal demographic fluctuations. Ecology and observed limited spatial movements challenge the likelihood of active dispersal among tepui tops in this species. Our results are counter to those predicted by the available genetic data but support two hypotheses of the OCBIL theory: reduced dispersibility and enhanced resilience. However, they do not support the expectation of a small refugial population size.

CONCLUSION

We postulate that the insular, hostile tepui-summit environment tends to produce robust demographic populations, likely to buffer stochastic adverse environmental effects, rather than diversity, as observed in much younger post-Pleistocene Neotropical landscapes. Our results draw attention to the value of faunal studies using an OCBIL framework to better understand the ecology and evolution of this unique biota worldwide.

A new species of Neblinaphryne (Anura: Brachycephaloidea: Neblinaphrynidae) from Serra do Imeri, Amazonas state, Brazil

The highlands of the Guiana Shield (Pantepui) in northern South America harbor a unique fauna and flora. However, this diversity remains poorly documented, as many Pantepui massifs remain little explored or unexplored, mainly because their access is very challenging. Considering amphibians, 11 genera are endemic or sub-endemic to Pantepui, and one of them, Neblinaphryne, is monospecific and was recently described from the Neblina massif, at the border between Brazil and Venezuela. We recently undertook an expedition in the nearby, previously uninventoried Imeri massif and discovered a new species of this genus. We describe this new species herein as Neblinaphryne imeri sp. nov., combining molecular, external morphological, acoustic, osteological and myological data. The new species shares with the other Neblinaphryne species (N. mayeri) minuscule septomaxillae and pointed terminal phalanges, confirming the morphological diagnostic characters of the genus. Nevertheless, the new species can promptly be distinguished from N. mayeri by having the head wider than long, a distinct color pattern, and prominent tubercles on the eyelid and humeral region, as well as osteological and genetic differences. These two species are likely endemic to their respective massifs, providing a striking new example of speciation by isolation within Pantepui, which was possibly mediated by climate and elevation, as previously hypothesized for many other lineages endemic to this region.

A new species of direct-developing frog of the genus Eleutherodactylus (Anura: Eleutherodactylidae) from Tamaulipas, Mexico

The number of species of the subgenus Syrrhophus, genus Eleutherodactylus has increased rapidly in the last eight years, due to recent taxonomic studies. This subgenus of direct-developing frogs is well represented in Mexico, which harbors more than 90% of the species richness reported for the subgenus. In this study, we describe one new species, Eleutherodactylus (Syrrhophus) coelum sp. nov. from the El Cielo Biosphere Reserve in Tamaulipas, Mexico, based on morphological and molecular data. The new species, which was previously assigned to E. cystignathoides, differs from its congeners mainly by its small size and by having the tips of Finger III and IV expanded to twice the width of the narrowest part of these fingers. Phylogenetic analyses recovered a well-supported relationship of the new species as the sister group to an undescribed taxon from San Luis Potosí. This analysis also indicates there are more lineages wating for description.

Deep divergences among inconspicuously colored clades of Epipedobates poison frogs

Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ∼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation of this text is available in the supplementary materials.

Multiple contact zones and karyotypic evolution in a neotropical frog species complex

Previous studies of DNA sequence and karyotypic data have revealed high genetic diversity in the Physalaemus cuvieri - Physalaemus ephippifer species complex-a group of small leptodactylid frogs in South America. To date, seven major genetic lineages have been recognized in this group, with species delimitation tests supporting four to seven of them as valid species. Among these, only P. ephippifer shows heteromorphic sex chromosomes, but the implications of cytogenetic divergence for the evolution of this group are unknown. We analyzed karyotypic, mitochondrial DNA, and 3RAD genomic data to characterize a putative contact zone between P. ephippifer and P. cuvieri Lineage 1, finding evidence for admixture and karyotypic evolution. We also describe preliminary evidence for admixture between two other members of this species complex-Lineage 1 and Lineage 3 of P. cuvieri. Our study sheds new light on evolutionary relationships in the P. cuvieri - P. ephippifer species complex, suggesting an important role of karyotypic divergence in its evolutionary history and underscoring the importance of hybridization as a mechanism of sex chromosome evolution in amphibians.

Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species

The area around the Malagasy village of Andasibe, which includes Analamazaotra-Mantadia National Park as well as other protected areas, is characterized by very species-rich and well-studied communities of animals and plants, but new species are still regularly discovered. Three species of phytotelmic frogs of the subgenus Pandanusicola in the genus Guibemantis are known from this area, G. flavobrunneus, G. liber, and G. pulcher. Further Pandanusicola frogs from this area have been provisionally assigned to G. bicalcaratus or G. albolineatus, pending detailed taxonomic review. During preliminary exploration of the ecology of these specialized frogs that live and reproduce in the leaf axils of Pandanus screw pines, we noticed the syntopic presence of two differently colored and differently sized Pandanusicola in Andasibe that could not be unambiguously assigned to any known species. A genetic screening revealed that these correspond to yet two further species in the area. Based on our data, seven species of Pandanusicola occur in Andasibe and nearby forests: (1) G. liber, the only non-phytotelmic species of the subgenus in the region; (2) G. flavobrunneus which is the largest species and characterized by a diagnostic yellowish brown dorsal pattern; (3) G. pulcher, characterized by translucent-green color with purplish brown spotting not observed in any other species in the area; (4) G. methueni, a brownish species usually lacking contrasted dorsolateral bands that differs from the other species in the area by emitting a characteristic trill-like advertisement call series (rather than clicks or chirps) and according to our data is widespread along Madagascars east coast; as well as three new species: (5) G. ambakoana sp. nov., a brownish species, typically with contrasted incomplete light dorsolateral bands and with single click-like advertisement calls; (6) G. vakoa sp. nov., a species that is equally brownish but lacks contrasted light dorsolateral bands and that has single click-like advertisement calls of very short duration; and (7) G. rianasoa sp. nov., a species that is smaller sized and has less distinct femoral glands than all the others, and emits a short series of soft chirp-like advertisement calls. All these species are genetically highly distinct, with >5% uncorrected pairwise distances in the mitochondrial 16S rRNA gene, and lack of haplotype sharing in two nuclear-encoded genes. The co-occurrence of seven Pandanusicola frogs in a relatively small geographic area is unprecedented in Madagascar and calls for in-depth studies of a possible differentiation in habitat use and life history.

DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy

Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.

Integrated phylogenetic analyses reveal the evolutionary, biogeographic, and diversification history of Asian warty treefrog genus Theloderma (Anura, Rhacophoridae)

Asian warty treefrogs, genus Theloderma, are morphologically variable arboreal frogs endemic to Southeast Asia and Southern China. However, integrated systematic studies are lacking, and knowledge of the genus in terms of diversity, origin, and historical diversification remains limited. To address these knowledge gaps, we used three mitochondrial and five nuclear gene fragments to reconstruct the Theloderma phylogeny, estimate divergence times, and examine the biogeography of the genus. Phylogenetic and species delimitation analyses suggest that the genus Theloderma comprises three major clades corresponding to two subgenera and seven species groups, and mPTP identified at least 12 putative cryptic species, suggesting that species diversity has been underestimated. Biogeographic analyses indicated that most recent common ancestor of Theloderma originated in the Indochina Peninsula during the Middle Oligocene (ca. 27.77 Ma) and the splitting of Clade A to C occurred in the Late Oligocene (ca. 23.55-25.57 Ma). Current biogeographic patterns result from two distinct processes: in situ diversification in the Indochina Peninsula and dispersal in multiple areas, namely southward dispersal to the Malay Peninsula and Borneo, northeastward dispersal to Southern China, northward dispersal to the Himalayas, and dispersal from Southern China to the Indochina Peninsula. Ancestral character reconstruction suggests that the ancestor of Theloderma may have possessed a small body size, rough dorsal skin, and absence of vomerine teeth and hand webbing, and that these four characters have undergone multiple evolutions. Principal component analysis based on eight bioclimatic variables did not clearly distinguish the three major clades of Theloderma, suggesting that species in these clades may occupy similar climatic ecological niches. Our research highlights the importance of orogeny and paleoclimatic changes, in shaping amphibian biodiversity in mountain ecosystems.

Two new species of Leptobrachella Smith 1925 (Amphibia: Megophryidae) from Cao Bang Province, Vietnam

Two new species, Leptobrachella phiaoacensis sp. nov. and Leptobrachella phiadenensis sp. nov., are described from Phia Oac-Phia Den National Park, Cao Bang Province, Vietnam based on genetic divergence and morphological differences. Leptobrachella phiaoacensis sp. nov. is characterized by a combination of the following characters: size medium (27.833.3 mm in five adult males and 31.541.8 mm in five adult females); head longer than wide; tympanum distinct; dorsal skin shagreened with fine tubercles; toes webbing rudimentary, with narrow lateral fringes; supratympanic fold edged by a distinct black line; the presence of a dark brown triangle in interorbital region and a W-shaped marking in scapular region; belly from pinkish white to white with dark brown specking on belly periphery; iris bicolored copper in upper part, fading to silvery grey in lower part. Leptobrachella phiadenensis sp. nov. is distinguished from its congeners by a combination of the following morphological characters: size medium (27.628.6 mm in two adult females); head wider than long; tympanum distinct; skin on dorsal head and body rough with warts, tubercles and dermal ridges; toes webbing rudimentary, with narrow dermal fringes; supratympanic fold orange; dorsal surface of head and body with some large dark brown markings, a dark brown triangle in interorbital region, edged in white; flank light brown with some dark flecks; belly white with dark specking on outer margins; iris bicolored, copper in upper part, fading to silvery grey in lower part. In terms of genetic distance, the two new species differ from each other and other congeners for which comparable sequences are available by at least 3.7% (16S rRNA gene). Recognition of these new species brings the total number of known species in the genus Leptobrachella from Vietnam to 34.

A new species of Pandanus-dwelling frog from northern Madagascar related to Guibemantis pulcher

Populations of phytotelmic frogs from northern Madagascar assigned to Guibemantis (Pandanusicola) pulcher are known to differ genetically from populations further south in the eastern rainforest belt of the island, but to date, their status has not been analyzed in depth. We combined molecular genetic data with an examination of color pattern to clarify the taxonomy of these frogs. DNA sequences of both mitochondrial and nuclear-encoded genes were consistently differentiated between the northern populations and those occurring further south. Uncorrected pairwise distance in the 16S rRNA gene was 3.7‒4.3% and thus at a level usually characterizing distinct frog species in Madagascar. Furthermore, the northern specimens were characterized by more and smaller purplish-brown spots on their green dorsal surface, and a less distinct brown patch on the flanks. Although fully conclusive evidence for the species status of the northern lineage from bioacoustic differences, sympatric occurrence or narrow hybrid zone is currently lacking, such species-level distinctness is currently the most likely hypothesis. We therefore name the northern populations as Guibemantis (Pandanusicola) pulcherrimus sp. nov. The new species is known from Makira (type locality) and Bemanevika, and specimens morphologically assignable to this taxon have also been recorded from Masoala, Marojejy and Anjanaharibe-Sud.

Two new species of Allobates of the trilineatus clade (Anura: Aromobatidae) from the Eastern Guiana Shield

The actual diversity of anurans occurring in Amazonia remains only partly described. This is notably the case of the species of the genus Allobates despite a fast rate of species description in this genus during the last decade. This increasing taxonomic effort has been particularly facilitated by the availability of DNA sequences throughout the region. These data suggest for instance the existence of three lineages in the Guiana Shield that may correspond to unnamed species. We examined morphology and calls of these putative species and compared them to related nominal species, which confirmed that two of these lineages not only differ genetically but also morphologically and bioacoustically. These two species are thus named and described herein. Allobates vicinus sp. nov. from northern Suriname forms a clade with another candidate species from southern Suriname and Northern Pará, (Brazil) and with A. granti that occurs in French Guiana. Allobates ripicolus sp. nov. occurs throughout the eastern Guiana Shield and is nested within the A. tapajos complex which otherwise occurs in southeastern Amazonia and comprises A. tapajos and A. kamilae, along with three additional candidate species.

Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest

Background

The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex.

Methods

We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations.

Results

Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.

A new species of Andean frog of the genus Phrynopus (Anura: Strabomantidae) from southeastern Peru

The Cordillera de los Andes is one of the most important regions for biodiversity. Among amphibians, many endemic species of terrestrial-breeding frogs have recently been discovered. Herein we describe Phrynopus sancristobali from the Andes of southeastern Peru based on molecular and morphological data. The new species is known from the ecotone between humid puna and montane forest at 3910 m a.s.l. on the left side of the Apurímac Valley in the Department of Ayacucho. The new species differs from congeners by having dorsum bearing pustules and light brown with dark brown reticulations surrounding the areolas, and coloration consisting of flanks golden brown with gray or dark brown marks, palms pale orange, soles deep orange, toes IV and V dark brown in dorsal and ventral view, belly cream to yellow with gray to light brown marks, and groin and throat deep orange. The snout-vent length (SVL) is 20.7 and 22.2 in two females, and 19.5 mm in one male. According to our phylogeny inferred using Maximum Likelihood with a concatenated dataset of three mitochondrial and two nuclear genes, P. sancristobali is sister taxon of P. apumantarum, recently described from Department Huancavelica. Our description extends the known geographic range of Phrynopus 73 km to the south, and P. sancristobali is the only species in the genus known to occur south of the Mantaro River, whose deep valley is hypothesized to be a biogeographic barrier for high-Andean organisms. The discovery of P. sancristobali confirms the high levels of endemism and beta diversity of Phrynopus in the moist puna grasslands and montane forests of the high Andes of Peru, and suggests that further work will reveal the presence of additional species in southern Peru.

A synoptic review of the Amphibians of Iran: bibliography, taxonomy, synonymy, distribution, conservation status, and identification key to the eggs, larvae, and adults

This study provides an illustrated account, a comprehensive update of the systematics, and a bibliography of the 15 species of anurans in five families, eight genera; and of the six species of urodeles in two families, four genera in Iran. Bufonidae, with eight species, is the most diverse family; Salamandridae has five species and Ranidae has four species. This study also presents updated identification keys for the eggs, larvae, and metamorphosed amphibians of Iran. We designated specimen NMW 19855.1 as neotype of Pelophylax persicus (Schneider, 1799) comb. nov.. Along with distribution maps obtained from all the reliable localities and museum specimens known at this time, the modelled habitat of species, and for the first time, the National Red List of amphibians based on the IUCN red list categories and criteria. Based on our evaluation we propose to categorize Bufo eichwaldi, Paradactylodon persicus, Neurergus derjugini, and N. kaiseri as Vulnerable at National Red List, and to move Bufotes (Calliopersa) luristanicus, B. (C.) surdus, Firouzophrynus olivaceus, and Rana pseudodalmatina from the category of Least Concern (LC) to Near Threatened (NT). The National Red List of amphibians that we propose has significant implications for endangered species management and conservation. Forty-one percent of amphibian species in Iran are endemic to the country, and more than forty percent of the Iranian amphibians are at risk of extinction. Zagros Mountain forest and Hyrcaniain forests have more than 80% (i.e. 18 species) of the diversity of Iranian amphibians. A considerable amount of scientific literature published on Iranian amphibians in Persian language is not easily accessible to researchers outside Iran. This monograph attempts to remedy the situation and provides broader access to international herpetology. We recognize that taxonomy is always in a state of flux, and the names and synonymies used here reflect our current view.

Purification and Biological Properties of Raniseptins-3 and -6, Two Antimicrobial Peptides from Boana raniceps (Cope, 1862) Skin Secretion

The number of multidrug-resistant pathogenic microorganisms has been growing in recent years, most of which is due to the inappropriate use of the commercial antibiotics that are currently available. The dissemination of antimicrobial resistance represents a serious global public health problem. Thus, it is necessary to search for and develop new drugs that can act as antimicrobial agents. Antimicrobial peptides are a promising alternative for the development of new therapeutic drugs. Anurans' skin glands are a rich source of broad-spectrum antimicrobial compounds and hylids, a large and diverse family of tree frogs, are known as an important source of antimicrobial peptides. In the present study, two novel antimicrobial peptides, named Raniseptins-3 and -6, were isolated from Boana raniceps skin secretion and their structural and biological properties were evaluated. Raniseptins-3 and -6 are cationic, rich in hydrophobic residues, and adopt an α-helix conformation in the presence of SDS (35 mM). Both peptides are active against Gram-negative bacteria and Gram-positive pathogens, with low hemolytic activity at therapeutic concentrations. No activity was observed for yeasts, but the peptides are highly cytotoxic against B16F10 murine melanoma cells and NIH3T3 mouse fibroblast cells. None of the tested compounds showed improvement trends in the MTT and LDH parameters of MHV-3 infected cells at the concentrations tested.

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

LAY SUMMARY

- What factors are common among bird species with cryptic diversity in Panama? What role do geography, ecology, phylogeographic history, and other factors play in generating bird diversity?- 19% of widely-sampled bird species form two or more distinct DNA barcode clades, suggesting widespread unrecognized diversity.- Traits associated with reduced dispersal ability, such as use of forest understory, high territoriality, low hand-wing index, and insectivory, were more common in taxa with cryptic diversity. Filogeografía comparada revela amplia diversidad críptica causada por la ecología en las aves de Panamá.

RESUMEN

Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos. Palabras clave: biodiversidad tropical, biogeografía, códigos de barras, dispersión, especies crípticas.

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

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.

Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).

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.

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.

An unexpected new red-bellied Stumpffia (Microhylidae) from forest fragments in central Madagascar highlights remaining cryptic diversity

The Madagascan endemic subfamily Cophylinae in the family Microhylidae, is an example of a taxonomic group for which much is still to be discovered. Indeed, the cophyline frogs present a large portion of Madagascar's cryptic and microendemic amphibian diversity, yet they remain understudied. A new red-bellied species of the microhylid frog genus Stumpffia is described from the central plateau of Madagascar. Visual encounter surveys in Ambohitantely and Anjozorobe in 2019 and 2020 identified this previously unknown Stumpffia species, which closely resembles Stumpffiakibomena known from Andasibe in the east. Stumpffialynnae sp. nov. adds another species to the red-bellied species complex, differing from S.kibomena by genetic differentiation in the mitochondrial 16S rRNA gene (3.6-3.9%) and distinct nuclear RAG1 haplotypes, as well as strongly by its advertisement call. The new species is known from across Ambohitantely Special Reserve and Anjozorobe Angavo protected area, but is known only from one complete specimen and eight individual tissue samples. Based on the rarity of the species, the small number of locations in which it has been found, and its disappearing forest habitat, its IUCN Red List classification is suggested as "Endangered". This species is the first Stumpffia described from Madagascar's central plateau, highlighting the importance of conserving the remnant forest fragments in this area and the ongoing need to survey and protect this threatened habitat type.

Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians

Background

The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths.

Results

Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content.

Conclusions

Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01994-y.

DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest

Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.

An integrative approach reveals high species diversity in the primitively segmented spider genus

Accurate species delimitation is crucial for our understanding of evolution, biodiversity and conservation. However, morphology-based species delimitation alone appears to be prone to taxonomic errors and ineffective for taxa with high interspecific morphological homogeneity or intraspecific morphological variations, as is the case for mesothele and mygalomorph spiders. Combined molecular–morphology species delimitation has shown great potential to delimit species boundaries in such ancient lineages. In the present study, molecular and morphological evidence were integrated to delimit species of the primitively segmented spider genus Songthela Ono, 2000. The cytochrome c oxidase subunit I gene (COI) was sequenced for 192 novel specimens belonging to 12 putative morphospecies. The evolutionary relationships within Songthela and the 12-morphospecies hypothesis were tested in two steps – species discovery and species validation – using four single-locus species delimitation approaches. All species delimitation analyses supported the 12-species hypothesis. Phylogenetic analyses yielded three major clades in Songthela, which are consistent with morphology. Accordingly, we assigned 19 known and 11 new species (S. aokoulong, sp. nov., S. bispina, sp. nov., S. dapo, sp. nov., S. huayanxi, sp. nov., S. lianhe, sp. nov., S. lingshang, sp. nov., S. multidentata, sp. nov., S. tianmen, sp. nov., S. unispina, sp. nov., S. xiujian, sp. nov., S. zizhu, sp. nov.) of Songthela to three species-groups: the bispina-group, the multidentata-group and the unispina-group. Another new species, S. zimugang, sp. nov., is not included in any species groups, but forms a sister lineage to the bispina- and unispina-groups. These results elucidate a high species diversity of Songthela in a small area and demonstrate that integrating morphology with COI-based species delimitation is fast and cost-effective in delimiting species boundaries. http://zoobank.org/urn:lsid:zoobank.org:pub:AF0F5B31-AFAF-4861-9844-445AE8678B67

A needle in a haystack: Integrative taxonomy reveals the existence of a new small species of fossorial frog (Anura, Microhylidae, Synapturanus) from the vast lower Putumayo basin, Peru

We describe a new species of microhylid frog of the genus Synapturanus from the lower Putumayo basin in Loreto, Perú. Specimens inhabited the soils of stunted pole forests growing on peat. The new species is distinguished from other species of Synapturanus through morphology, genetics, and acoustic characteristics. This species differs from most nominal congeners by having a head flat in lateral view (vs convex in the rest of species), a characteristic only shared by S. rabus and S. salseri. The new species can be distinguished from S. rabus and S. salseri by a combination of morphological characters and by having an advertisement call with a note length of 0.05–0.06 seconds (vs 0.03 seconds in S. rabus) and a dominant frequency ranging from 1.73 to 1.81 kHz (vs 1.10–1.47 kHz in S. salseri). Principal component analyses of 12 morphological characters and three acoustic variables further support differences between the new species and its described and undescribed congeners.

Distribution extension of Leptobrachella eos (Ohler, Wollenberg, Grosjean, Hendrix, Vences, Ziegler & Dubois, 2011): first record from Thailand

We report the first country record of Leptobrachella eos (Ohler, Wollenberg, Grosjean, Hendrix, Vences, Ziegler & Dubois, 2011) from Thailand, based on one specimen collected from Chom poo Phuka nature trail, Bo Kluea District. Morphologically, the specimen displayed good agreement with the original descriptions provided for L. eos. Phylogenetically, the specimens clustered according to the sequences of type locality of L. eos. Notably, our discovery increases the number of Leptobrachella species known to occur in Thailand to nine.

A new slippery frog (Amphibia, Conrauidae, Conraua Nieden, 1908) from the Fouta Djallon Highlands, west-central Guinea

We describe a new species of the genus Conraua from the Fouta Djallon Highlands in Guinea. The species is recognised as distinct from nominotypical C. alleni, based on morphological evidence and is supported by a recent species delimitation analysis, based on DNA sequence data. The new species is distinguished from its congeners by the unique combination of the following characters: medium body size, robust limbs, only one instead of two palmar tubercles, the first finger webbed to below the first subarticular tubercle, presence of a lateral line system, indistinct tympanum, two subarticular tubercles on fingers III and IV, venter in adults white with dark brown spots or dark brown with grey or whitish spots. The new species differs from all congeners by more than 6% in the DNA sequence of mitochondrial ribosomal 16S. We discuss isolation in Pliocene and Pleistocene forest refugia as a potential driver of speciation in the C. alleni complex. We also emphasise the importance of conserving the remaining forest fragments in the Fouta Djallon Region for the preservation of both its unique biodiversity and its valuable water sources for local people.

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.