Relicts in the mist: Two new frog families, genera and species highlight the role of Pantepui as a biodiversity museum throughout the Cenozoic.

The iconic mountains of the Pantepui biogeographical region host many early-diverging endemic animal and plant lineages, concurring with Conan Doyle's novel about an ancient "Lost World". While this is the case of several frog lineages, others appear to have more recent origins, adding to the controversy around the diversification processes in this region. Due to its remoteness, Pantepui is challenging for biological surveys, and only a glimpse of its biodiversity has been described, which hampers comprehensive evolutionary studies in many groups. During a recent expedition to the Neblina massif on the Brazil-Venezuela border, we sampled two new frog species that could not be assigned to any known genus. Here, we perform phylogenetic analyses of mitogenomic and nuclear loci to infer the evolutionary relationships of the new taxa and support their description. We find that both species represent single lineages deeply nested within Brachycephaloidea, a major Neotropical clade of direct-developing frogs. Both species diverged >45 Ma from their closest relatives: the first is sister to all other Brachycephaloidea except for Ceuthomantis, another Pantepui endemic, and the second is sister to Brachycephalidae, endemic to the Brazilian Atlantic Forest. In addition to these considerable phylogenetic and biogeographic divergences, external morphology and osteological features support the proposition of two new family and genus-level taxa to accommodate these new branches of the amphibian tree of life. These findings add to other recently described ancient vertebrate lineages from the Neblina massif, providing a bewildering reminder that our perception of the Pantepui's biodiversity remains vastly incomplete. It also provides insights into how these mountains acted as "museums" during the diversification of Brachycephaloidea and of Neotropical biotas more broadly, in line with the influential "Plateau theory". Finally, these discoveries point at the yet unknown branches of the tree of life that may go extinct, due to global climate change and zoonotic diseases, before we even learn about their existence, amphibians living at higher elevations being particularly at risk.

Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy.

Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.

Diversity, biogeography, and reproductive evolution in the genus Pipa (Amphibia: Anura: Pipidae).

The genus Pipa is a species-poor clade of Neotropical frogs and one of the most bizarre-looking due to many highly derived anatomical traits related to their fully aquatic lifestyle. With their African relatives, they form the Pipidae family, which has attracted much attention, especially regarding its anatomy, reproductive biology, paleontology and biogeography. However, the actual diversity and phylogenetic relationships within Pipa remain poorly understood, and thus so do their historical biogeography and the evolution of striking features, such as the absence of teeth and endotrophy in some species. Using short mtDNA sequences across the distribution of the genus, we identified 15 main lineages (Operational Taxonomic Units - OTUs). This more than doubles the number of the currently seven valid nominal species. Several closely related OTUs do not share nuDNA alleles, confirming species divergence. Time-calibrated phylogenies obtained from mitogenomes and from 10 nuclear loci provide highly similar topologies but strikingly distinct node ages for Pipa. High dN/dS ratios and the variation of substitution rates across the trees suggest a strong effect of saturation on fast evolving positions of mtDNA, producing a substantially shorter stem branch of Pipa. Focusing on the nuDNA topology, we inferred an early Neogene Amazonian origin of the diversification of Pipa, with an initial split between the Guiana-Brazilian Shields and Western Amazonia, a pattern observed in many other co-distributed groups. All the western species are edentate, suggesting a single loss in the genus. Each of these groups diversified further out of Amazonia, toward the Atlantic Forest and toward trans-Andean forests, respectively. These events are concomitant with paleogeographic changes and match patterns observed in other co-distributed taxonomic groups. The two Amazonian lineages have probably independently acquired endotrophic larval development.

Phylogeny, diversity and biogeography of Neotropical sipo snakes (Serpentes: Colubrinae: Chironius).

Neotropical sipo snakes (Chironius) are large diurnal snakes with a long tail and big eyes that differ from other Neotropical snakes in having 10 or 12 dorsal scale rows at midbody. The 22 currently recognized species occur from Central America south to Uruguay and northeastern Argentina. Based on the largest geographical sampling to date including ∼90% of all species, we analyzed one nuclear and three mitochondrial genes using phylogenetic methods to (1) test the monophyly of Chironius and some of its widely distributed species; (2) identify lineages that could represent undescribed species; and (3) reconstruct ancestral distributions. Our best hypothesis placed C. grandisquamis (Chocoan Rainforest) + C. challenger (Pantepui) as sister to all other species. Based on phylogeny and geographic distribution, we identified 14 subclades as putative species within Chironius fuscus, C. multiventris (including C. foveatus and C. laurenti), C. monticola, and C. exoletus. Under current taxonomy, these species show nearly twice as much genetic diversity as other species of Chironius for ND4. Biogeographical analyses using BioGeoBEARS suggest that current distribution patterns of Chironius species across South America resulted from multiple range expansions. The MRCA of the clade C. challenger + C. grandisquamis was most likely distributed over the Pantepui region, the Andes, and the Chocoan Rainforest, whereas the remaining lineages probably evolved from an Amazonian ancestor.

Cryptic diversity in Amazonian frogs: Integrative taxonomy of the genus Anomaloglossus (Amphibia: Anura: Aromobatidae) reveals a unique case of diversification within the Guiana Shield.

Lack of resolution on species boundaries and distribution can hamper inferences in many fields of biology, notably biogeography and conservation biology. This is particularly true in megadiverse and under-surveyed regions such as Amazonia, where species richness remains vastly underestimated. Integrative approaches using a combination of phenotypic and molecular evidence have proved extremely successful in reducing knowledge gaps in species boundaries, especially in animal groups displaying high levels of cryptic diversity like amphibians. Here we combine molecular data (mitochondrial 16S rRNA and nuclear TYR, POMC, and RAG1) from 522 specimens of Anomaloglossus, a frog genus endemic to the Guiana Shield, including 16 of the 26 nominal species, with morphometrics, bioacoustics, tadpole development mode, and habitat use to evaluate species delineation in two lowlands species groups. Molecular data reveal the existence of 18 major mtDNA lineages among which only six correspond to described species. Combined with other lines of evidence, we confirm the existence of at least 12 Anomaloglossus species in the Guiana Shield lowlands. Anomaloglossus appears to be the only amphibian genus to have largely diversified within the eastern part of the Guiana Shield. Our results also reveal strikingly different phenotypic evolution among lineages. Within the A. degranvillei group, one subclade displays acoustic and morphological conservatism, while the second subclade displays less molecular divergence but clear phenotypic divergence. In the A. stepheni species group, a complex evolutionary diversification in tadpole development is observed, notably with two closely related lineages each displaying exotrophic and endotrophic tadpoles.

Origin and functional diversification of an amphibian defense peptide arsenal.

The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones. Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones.

Side-by-side secretion of Late Palaeozoic diverged courtship pheromones in an aquatic salamander.

Males of the advanced salamanders (Salamandroidea) attain internal fertilization without a copulatory organ by depositing a spermatophore on the substrate in the environment, which females subsequently take up with their cloaca. The aquatically reproducing modern Eurasian newts (Salamandridae) have taken this to extremes, because most species do not display close physical contact during courtship, but instead largely rely on females following the male track at spermatophore deposition. Although pheromones have been widely assumed to represent an important aspect of male courtship, molecules able to induce the female following behaviour that is the prelude for successful insemination have not yet been identified. Here, we show that uncleaved sodefrin precursor-like factor (SPF) protein pheromones are sufficient to elicit such behaviour in female palmate newts (Lissotriton helveticus). Combined transcriptomic and proteomic evidence shows that males simultaneously tail-fan multiple ca 20 kDa glycosylated SPF proteins during courtship. Notably, molecular dating estimates show that the diversification of these proteins already started in the late Palaeozoic, about 300 million years ago. Our study thus not only extends the use of uncleaved SPF proteins outside terrestrially reproducing plethodontid salamanders, but also reveals one of the oldest vertebrate pheromone systems.

Caecilita Wake & Donnelly, 2010 (Amphibia: Gymnophiona) is not lungless: implications for taxonomy and for understanding the evolution of lunglessness .

According to current understanding, five lineages of amphibians, but no other tetrapods, are secondarily lungless and are believed to rely exclusively on cutaneous gas exchange. One explanation of the evolutionary loss of lungs interprets lunglessness as an adaptation to reduce buoyancy in fast-flowing aquatic environments, reasoning that excessive buoyancy in such an environment would cause organisms being swept away. While not uncontroversial, this hypothesis provides a plausible potential explanation of the evolution of lunglessness in four of the five lungless amphibian lineages. The exception is the most recently reported lungless lineage, the newly described Guyanan caecilian genus and species Caecilita iwokramae Wake & Donnelly, 2010, which is inconsistent with the reduced disadvantageous buoyancy hypothesis by virtue of it seemingly being terrestrial and having a terrestrial ancestry. Re-examination of the previously only known specimen of C. iwokramae and of recently collected additional material reveal that this species possesses a reasonably well-developed right lung and is a species of the pre-existing caecilian genus Microcaecilia Taylor, 1968. We therefore place Caecilita in the synonymy of Microcaecilia, and re-evaluate the plausibility of the reduced disadvantageous buoyancy hypothesis as a general explanation of the evolution of lunglessness.

On the taxonomic validity of Pristimantis tepuiensis (Schlüter & Rödder, 2007) and P. stegolepis (Schlüter & Rödder, 2007), with remarks on the type series of P. guaiquinimensis (Schlüter & Rödder, 2007).

The type series of Pristimantis guaiquinimensis (Schlüter & Rödder, 2007), P. tepuiensis (Schlüter & Rödder, 2007) and P. stegolepis (Schlüter & Rödder, 2007) have been thoroughly examined. We highlight a number of discrepancies in the original descriptions that do not support the recognition of P. stegolepis and P. tepuiensis as valid species. We demonstrate that P. stegolepis should be considered ajunior synonym of P. vilarsi (Melin, 1941), and that P. tepuiensis should be considered a junior synonym of P. guaiquinimensis. We also point out that the sex of the holotype and paratype of P. guaiquinimensis have been wrongly determined.

A new species of the genus Pristimantis (Amphibia, Craugastoridae) associated with the moderately elevated massifs of French Guiana.

We describe a new Pristimantis from French Guiana, northern South America, which is mainly distinguished from known phenotypically related congeners (i.e. species from the polyphyletic unistrigatus species group) occurring at low and middle elevations in the Guiana Shield by the combination of a distinct tympanum, a lower ratio of tibia vs. hand length, a reddish groin region, and a distinct advertisement call consisting of clusters of generally four short notes. The new species inhabits pristine primary forests on the slopes of isolated massifs reaching more than 400 m elevation, and seems not to occur below ca. 200 m above sea level. Such a sharp altitudinal limit suggests a strong influence of thermal variation on the distribution of the species, and therefore a potential sensitivity to climate change. With only nine isolated populations documented so far, the new species should be prioritized for conservation. Historical climate fluctuations during the Quaternary are likely responsible for the distribution pattern of the new species. 

Bones and all: a new critically endangered Pantepui species of Stefania (Anura: Hemiphractidae) and a new osteological synapomorphy for the genus.

The hemiphractid frog genus Stefania is one of the many ancient (near-) endemic lineages of vertebrates inhabiting the biodiverse Pantepui biogeographical region in the Guiana Shield Highlands of northern South America-the famous "Lost World" of Arthur Conan Doyle. Previous molecular analyses of the genus Stefania have indicated that species boundaries and phylogenetic relationships are often incongruent with morphological traits in that clade. A substantial number of "taxonomically cryptic" species, often microendemic, remain to be described. This is notably the case for an isolated population from the summit of Wei-Assipu-tepui, a small table-top mountain at the border between Guyana and Brazil. That population was previously known as Stefania sp. 6 and belongs to the S. riveroi clade. The new species is phylogenetically distinct, but phenotypically extremely similar to S. riveroi, a taxon found only on the summit of Yuruaní-tepui in Venezuela and recovered as sister to all the other known species in the S. riveroi clade. The new taxon is described based on morphology and osteology. Data about genetic divergences within the S. riveroi clade are provided. A new synapomorphy for the genus Stefania is proposed: the presence of a distal process on the third metacarpal. Amended definitions are offered for the three other species in the S. riveroi clade (S. ayangannae, S. coxi, S. riveroi). The new species should be listed as Critically Endangered according to IUCN criteria.

Unveiling underestimated species diversity within the Central American Coralsnake, a medically important complex of venomous taxa.

Coralsnakes of the genus Micrurus are a diverse group of venomous snakes ranging from the southern United States to southern South America. Much uncertainty remains over the genus diversity, and understanding Micrurus systematics is of medical importance. In particular, the widespread Micrurus nigrocinctus spans from Mexico throughout Central America and into Colombia, with a number of described subspecies. This study provides new insights into the phylogenetic relationships within M. nigrocinctus by examining sequence data from a broad sampling of specimens from Mexico, Guatemala, Honduras, Nicaragua, Costa Rica, and Panama. The recovered phylogenetic relationships suggest that M. nigrocinctus is a species complex originating in the Pliocene and composed of at least three distinct species-level lineages. In addition, recovery of highly divergent clades supports the elevation of some currently recognized subspecies to the full species rank while others may require synonymization.

From Amazonia to the Atlantic forest: molecular phylogeny of Phyzelaphryninae frogs reveals unexpected diversity and a striking biogeographic pattern emphasizing conservation challenges.

Documenting the Neotropical amphibian diversity has become a major challenge facing the threat of global climate change and the pace of environmental alteration. Recent molecular phylogenetic studies have revealed that the actual number of species in South American tropical forests is largely underestimated, but also that many lineages are millions of years old. The genera Phyzelaphryne (1 sp.) and Adelophryne (6 spp.), which compose the subfamily Phyzelaphryninae, include poorly documented, secretive, and minute frogs with an unusual distribution pattern that encompasses the biotic disjunction between Amazonia and the Atlantic forest. We generated >5.8 kb sequence data from six markers for all seven nominal species of the subfamily as well as for newly discovered populations in order to (1) test the monophyly of Phyzelaphryninae, Adelophryne and Phyzelaphryne, (2) estimate species diversity within the subfamily, and (3) investigate their historical biogeography and diversification. Phylogenetic reconstruction confirmed the monophyly of each group and revealed deep subdivisions within Adelophryne and Phyzelaphryne, with three major clades in Adelophryne located in northern Amazonia, northern Atlantic forest and southern Atlantic forest. Our results suggest that the actual number of species in Phyzelaphryninae is, at least, twice the currently recognized species diversity, with almost every geographically isolated population representing an anciently divergent candidate species. Such results highlight the challenges for conservation, especially in the northern Atlantic forest where it is still degraded at a fast pace. Molecular dating revealed that Phyzelaphryninae originated in Amazonia and dispersed during early Miocene to the Atlantic forest. The two Atlantic forest clades of Adelophryne started to diversify some 7 Ma minimum, while the northern Amazonian Adelophryne diversified much earlier, some 13 Ma minimum. This striking biogeographic pattern coincides with major events that have shaped the face of the South American continent, as we know it today.

Thriving in a hostile world: Insights from the dietary strategy of two allopatric, closely related tepui summit endemic amphibians.

To date, there has been no published investigation on the trophic diversity in any tepui summit vertebrate. In this paper, we analyzed the dietary composition of a tepui summit endemic toad, Oreophrynella quelchii from Roraima-tepui, and compared it with that of O. nigra from Kukenán-tepui, to examine to what extent diet differs between these two sister species across isolated, although neighboring, tepui tops. The digestive tracts of a total of 197 toads were dissected: 111 from O. quelchii and 86 from O. nigra. The diet composition of O. quelchii was relatively diverse, with 13 major prey categories; mites (Acari, 36.5%) and beetles (Coleoptera, 21.0%) numerically dominated its diet. Despite occurring on two different tepui summits, O. quelchii and O. nigra exhibited a similar diet composition, although in O. nigra mites (Acari, 42.4%) and hymenopterans (especially ants, 16.9%) numerically dominated the diet. The present data suggest that tepui summit Oreophrynella species are flexible in their diet and are active foragers that also feed on aquatic arthropods, successful strategies in tepui competitive environments.

Two new species of Anomaloglossus (Anura: Aromobatidae) of the stepheni group from Suriname.

Anomaloglossus is a species-rich genus of frogs endemic to the Guiana Shield that still harbours several unnamed species. According to a recent integrative taxonomic survey, the A. stepheni species group includes five valid nominal species and at least four putatively unnamed species, two in Brazil and two in Suriname. In this paper, we describe the two species from Suriname based on adult and tadpole morphology as well as their calls and natural history. Both have exotrophic tadpoles transported by the male to small water bodies. These two new species differ from each other and from other congeners in body size, colouration pattern, call characteristics and breeding sites. Both have narrow distributions and should be considered Endangered according to IUCN criteria.

Predation by non-bioluminescent firefly larvae on a tepui-summit endemic toad.

Tepuis are Precambrian sandstone tabletop mountains in South America that can reach up to ∼3,000 m in elevation. Their highest summits are both physiographically and ecologically isolated from the surrounding upland savannah and lush tropical rainforest, and they face particularly hostile, challenging environmental conditions [1,2] (Figure 1A). Taxa thriving on high tepui summits must adapt to resource-limited and highly competitive ecosystems. The toad genus Oreophrynella is exclusively found on tepui slopes and summits [3] and is particularly well-adapted to the tepui top environment. We here report on an unanticipated and possibly large-scale predation on this endemic toad by non-bioluminescent firefly larvae.

A new species of Anomaloglossus (Anura: Aromobatidae) of the stepheni group with the redescription of A. baeobatrachus (Boistel and de Massary, 1999), and an amended definition of A. leopardus Ouboter and Jairam, 2012.

Anomaloglossus is a species-rich genus of frogs endemic to the Guiana Shield that still harbors several unnamed species. Within the A. stepheni species group (which includes four valid nominal species), A. baeobatrachus has an uncertain taxonomic status, notably because the holotype was an unvouchered specimen depicted in a popular journal. Another member of this group, A. leopardus, was only superficially described, lacking information on the sex of specimens in the type series and on advertisement call. Therefore, these two taxa need clarifications in order to allow the description of the extant undescribed species. In this paper, we redescribe A. baeobatrachus based on newly collected material from the species type locality and provide information about its reproductive ecology. We also provide an amended definition of A. leopardus using newly collected material from its type locality. These two species form a clade along with a third species from the Eastern Guiana Shield, which is also described herein. The reproductive biology of A. baeobatrachus and A. stepheni is very similar. Both species have endotrophic and nidicolous tadpoles, despite being distantly related, suggesting independent evolution of this breeding mode. The new species and A. leopardus, on the other hand, have exotrophic tadpoles.

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

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

On the brink of extinction: two new species of Anomaloglossus from French Guiana and amended definitions of Anomaloglossus degranvillei and A. surinamensis (Anura: Aromobatidae).

A large portion of the amphibian species occurring in Amazonia remains undescribed. A recent study on species delineation in Anomaloglossus, a genus endemic to the Guiana Shield, demonstrated the existence of two undescribed species previously identified as A. degranvillei, which we describe herein. In addition to divergence at the molecular level, these two new taxa are also distinguished by subtle morphological characters and substantial differences in the advertisement calls (note length, dominant frequency, note structure). One species occurs in the hilly lowlands of north-eastern French Guiana and is mainly distinguished from its closest relatives by a small body size (15.9-18.8 mm in males) and by vocalisations characterized by the emission of short notes of 0.09 s on average. The other species is only known from the Itoupé Massif in southern French Guiana and is mainly distinguished from its closest relatives by a moderate body size (19.4-20.4 mm in males) and by vocalisations characterized by the emission of long notes of 0.23 s on average. We also provide amended definitions for two previously described species in the A. degranvillei species group: A. degranvillei, which is endemic to a few massifs in central French Guiana, and A. surinamensis, which is distributed throughout Suriname and French Guiana. The new species described here and A. degranvillei have very narrow ranges within French Guiana and seem to have rapidly declined during the last decade. Therefore, we suggest A. degranvillei and A. dewynteri to be considered as "Critically Endangered" and A. blanci as "Vulnerable" according to the IUCN standards.

Yolk removal generates hatching asynchrony in snake eggs.

Hatching synchrony is wide-spread amongst egg-laying species and is thought to enhance offspring survival, notably by diluting predation risks. Turtle and snake eggs were shown to achieve synchronous hatching by altering development rates (where less advanced eggs may accelerate development) or by hatching prematurely (where underdeveloped embryos hatch concurrently with full-term embryos). In Natricine snakes, smaller eggs tend to slow down metabolism throughout incubation in order to hatch synchronously with larger eggs. To explore the underlying mechanism of this phenomenon we experimentally manipulated six clutches, where half of the eggs were reduced in mass by removing 7.2% of yolk, and half were used as the control. The former experienced higher heart rates throughout the incubation period, hatched earlier and produced smaller hatchlings than the latter. This study supports the idea that developmental rates are related to egg mass in snake eggs and demonstrates that the relationship can be influenced by removing yolk after egg-laying. The shift in heart rates however occurred in the opposite direction to expected, with higher heart rates in yolk-removed eggs resulting in earlier hatching rather than lower heart rates resulting in synchronous hatching, warranting further research on the topic.