Determinants of anuran assemblages in Amazonian White-sand Ecosystems.

Amazonian white-sand ecosystems have predominantly sandy soils and a high amount of endemism, and several species found within them are adapted to long periods of drought. However, little is known about the variation in the structure of anuran assemblages in these ecosystems. Considering that most species are not uniformly distributed in heterogeneous landscapes, we tested the hypothesis that anuran assemblage variation in white-sand ecosystems is related to changes in vegetation structure. Specifically, we focused on a heterogeneous patch of white-sand ecosystems of the central Amazon and evaluated whether vegetation structure and soil characteristics, including root depth, influence the richness, abundance, and composition of anuran assemblages. Our results showed that low amounts of clay in the soil play an important role in structuring vegetation in these ecosystems, and these are the main factors that organize anuran assemblages. The Campinaranas close to the water bodies have a high species richness, while Campina landscapes limit the occupation of most of species. Our findings indicate that anurans undergo environmental filtering in white-sand ecosystems and are organized into hierarchical subgroups, in which only species with specialized reproduction can successfully occupy the most water-restricted environments.

A new species of Pristimantis (Anura: Strabomantidae) from white-sand forests of central Amazonia, Brazil.

The white-sand ecosystems in the Solimões-Negro Interfluve are among the less studied in Amazonia. Recent herpetological surveys conducted west of Manaus, Brazil (central Amazonia) indicate that white-sand forests host a unique anuran fauna comprising habitat specialized and endemic species. In the present study we describe a new species of rain frog belonging to the Pristimantis unistrigatus species group from the white-sand forest locally called "campinarana" (thin-trunked forests with canopy height below 20 m). The new species is phylogenetically close to rain frogs from western Amazonian lowlands (P. delius, P. librarius, P. matidiktyo and P. ockendeni). It differs from its closest relatives mainly by its size (male SVL of 17.3-20.1 mm, n = 16; female SVL of 23.2-26.5 mm, n = 6), presence of tympanum, tarsal tubercles and dentigerous processes of vomers, its translucent groin without bright colored blotches or marks, and by its advertisement call (composed of 5-10 notes, call duration of 550-1,061 ms, dominant frequency of 3,295-3,919 Hz). Like other anuran species recently discovered in the white-sand forests west of Manaus, the new species seems to be restricted to this peculiar ecosystem.

Chytrid fungus in amphibians from the lowland Brazilian Amazon.

Infectious diseases are one of the main threats to biodiversity. The fungus Batrachochytrium dendrobatidis (Bd) is associated with several amphibian losses around the globe, and environmental conditions may dictate the success of pathogen spread. The Brazilian Amazon has been considered climatically unsuitable for chytrid fungus, but additional information on Bd dynamics in this ecoregion is still lacking. We sampled 462 amphibians (449 anurans, 4 caudatans and 9 caecilians), representing 57 species from the Brazilian Amazon, and quantified Bd infections using qPCR. We tested whether abiotic variables predicted the risk of Bd infections, and tested for relationships between biotic variables and Bd. Finally, we experimentally tested the effects of Bd strains CLFT 156 and CLFT 102 (from the southern and northern Atlantic Forest, respectively) on Atelopus manauensis. We detected higher Bd prevalence than those previously reported for the Brazilian Amazon, and positive individuals in all 3 orders of amphibians sampled. Both biotic and abiotic predictors were related to prevalence, and no variable explained infection load. Moreover, we detected higher Bd prevalence in forested than open areas, while the host's reproductive biology was not a factor. We detected higher mortality in the experimental group infected with CLFT 156, probably because this strain was isolated from a region characterized by discrepant climatic conditions (latitudinally more distant) when compared with the host's sampling site in Amazon. The lowland Brazilian Amazon is still underexplored and future studies targeting all amphibian orders are essential to better understand Bd infection dynamics in this region.

A new nurse frog of the Allobates tapajos species complex (Anura: Aromobatidae) from the upper Madeira River, Brazilian Amazonia.

Cryptic diversity is extremely common in widespread Amazonian anurans, but especially in nurse frogs of the genus Allobates. There is an urgent need to formally describe the many distinct but unnamed species, both to enable studies of their basic biology but especially to facilitate conservation of threatened environments in which many are found. Here, we describe through integrative taxonomy a new species of the Allobates tapajos species complex from the upper Madeira River, southwestern Amazonia. Species delimitation analyses based on molecular data are congruent and delimit five candidate species in addition to A. tapajos sensu stricto. The new species is recovered as sister to A. tapajos clade F, a candidate species from Teles-Pires River, southeastern Amazonia. The new species differs from nominal congeners in adult and larval morphology and in male advertisement call. Egg deposition sites differ between east and west banks of the upper Madeira River, but there is no evidence of corresponding morphologic or bioacoustic differentiation. The new species appears to be restricted to riparian forests; its known geographic range falls entirely within the influence zone of reservoirs of two large dams, which underscores the urgent need of a conservation assessment through long-term monitoring. This region harbors the richest assemblage of Allobates reported for Brazilian Amazonia, with six nominal species and four additional candidate species awaiting formal description.

Long-term standardized ecological research in an Amazonian savanna: a laboratory under threat.

A few decades ago, researchers from the National Institute for Amazonian Research (INPA) started a pilot study to integrate the ecological studies of several organisms using monitoring plots, which then became the embryo for the creation of the RAPELD (Rapid Assessments and Long-term Ecological Research) system used by the Program for Biodiversity Research (PPBio) and the Long-term ecological research site POPA (PELD Western Pará). They installed and maintained permanent plots in an Amazonian-savanna patch near to the village of Alter do Chão. Amazonian savannas constitute a threatened ecosystem comprising only 6% of the Amazon biome. Most of the studies focused on three main long-term ecological research questions, but the site was also of importance for other inquiries and for the training of young researchers, contributing 71 articles so far and 32 masters and doctorate theses. Here, we present the experimental design and results of standardized studies in the savannas and forest fragments near Alter do Chão that have been carried out over the years. We discuss the future prospects and local threats to the area (e.g. soy crops and land speculation), and highlight the need to incorporate Alter do Chão villagers in land-use planning in the region.

A new nurse frog (Anura: Allobates) from Brazilian Amazonia with a remarkably fast multi-noted advertisement call.

Nurse frogs (Aromobatidae: Allobates) are probably the most extensively studied genus by taxonomists in Brazilian Amazonia. The southwestern portion of Amazonia is the most species-rich: as many as seven species may occur in sympatry at a single locality. In this study, we describe a new species of nurse frog from this region. The description integrates data from larval and adult morphology, advertisement calls and DNA sequences. Allobates velocicantus sp. nov. is distinguished from other Allobates mainly by the absence of hourglass-shaped dark marks on the dorsum and dark transverse bars on the thigh; a throat that is white centrally and yellow marginally; basal webbing on toes II and III; finger I longer than finger II; and an advertisement call composed of 66-138 pulsed notes with a note duration of 5-13 ms, inter-note intervals of 10-18 ms and a dominant frequency of 5,512-6,158 Hz. Tadpoles of the new species have 3-4 short, rounded papillae on the anterior labium, 16-23 papillae on the posterior labium, and a labial keratodont row formula 2(2)/3(1). This is the fifth species of Allobates described from the state of Acre, southwestern Brazilian Amazonia.

The Influence of Environmental Variation on the Genetic Structure of a Poison Frog Distributed Across Continuous Amazonian Rainforest.

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism (SNP) loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure are associated with environmental variables also known to predict the density of A. femoralis.

The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus.

While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs). Four color categories were described (brown, blue, yellow, orange) and our models of frog and bird visual systems indicated that each color was distinguishable for these taxa. Using outlier and correlative analyses we found no compelling genetic evidence for color being under divergent selection. A time-calibrated mtDNA tree suggests that the present distribution of dorsal coloration resulted from processes occurring during the Pleistocene. Separate phylogenies based on SNPs and mtDNA resolved the same well supported clades, each containing different colored populations. Ancestral character state analysis provided some evidence for evolutionary transitions in color type. Genetic structure was more strongly associated with geographic features, than color category, suggesting that the distribution of color is explained by localized processes. Evidence for geographic isolation together with estimates of low effective population size implicates drift as playing a key role in color diversification. Our results highlight the relevance of considering the neutral processes involved with the evolution of traits with important fitness consequences.

Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog.

Osteocephalus vilarsi (Melin, 1941) is an Amazonian treefrog species known for over 75 years from its holotype only. Due to a lack of published data on its morphological diagnostic characters and their variations, as well as the absence of molecular, acoustic and ecological data supporting its identity, a highly dynamic taxonomic history has led this species to be confused and even synonymised with other Osteocephalus species from distinct species groups. The molecular phylogenetic relationships of O. vilarsi were investigated based on recently collected specimens from eight Northwestern Brazilian localities in the state of Amazonas, leading to its removal from the Osteocephalus taurinus species group and placement in the Osteocephalus planiceps species group. Furthermore, detailed data on morphology and colour variation are provided, as well as advertisement call and tadpole descriptions. Finally, the currently known geographic range of O. vilarsi is considerably extended, first data on the natural history of the species are provided, and the possible ecological preference of O. vilarsi for Amazonian white-sand forests is discussed.

Author Correction: Sole coloration as an unusual aposematic signal in a Neotropical toad.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A name for the nurse-frog (Allobates, Aromobatidae) of Floresta Nacional de Carajás, Eastern Brazilian Amazonia.

We describe a new species of nurse-frog (Aromobatidae, Allobates) from Floresta Nacional de Carajás, southeastern Brazilian Amazonia. Allobates carajas sp. nov. is distinguished from similar congeneric species by the combination of the following characters: body-size range (snout-to-vent length 16.5-19.1 mm), dorsal color pattern with a dark brown hourglass-shaped mark, by the absence of a pale dorsolateral stripe and presence of a pale ventrolateral stripe, absence of a pale paracloacal mark, by overall bright yellow ventral colors of live male and female specimens, and by the posterior labium of tadpoles, with a single row of pyramidal papillae medially. The advertisement call of the new species is highly variable, with four possible temporal arrangements of notes (continuous emission of notes separated by regular silent intervals, continuous emission of notes separated by irregular silent intervals, emission of discrete note trills, and sporadic emission of single notes). Duration of notes range between 0.020-0.060 s, and the dominant frequency of notes range from 4.75 to 5.38 kHz. The new species is currently known only from forested habitats within Floresta Nacional de Carajás.

Sole coloration as an unusual aposematic signal in a Neotropical toad.

Many animals have evolved remarkable strategies to avoid predation. In diurnal, toxic harlequin toads (Atelopus) from the Amazon basin, we find a unique colour signal. Some Atelopus populations have striking red soles of the hands and feet, visible only when walking. When stationary, the toads are hard to detect despite their yellow-black dorsal coloration. Consequently, they switch between high and low conspicuousness. Interestingly, some populations lack the extra colour display of the soles. We found comprehensive support that the red coloration can act as an aposematic signal directed towards potential predators: red soles are significantly more conspicuous than soles lacking red coloration to avian predators and the presence of the red signal significantly increases detection. Further, toads with red soles show bolder behaviour by using higher sites in the vegetation than those lacking this signal. Field experiments hint at a lower attack risk for clay models with red soles than for those lacking the signal, in a population where the red soles naturally occur. We suggest that the absence of the signal may be explained by a higher overall attack risk or potential differences of predator community structure between populations.

Different environmental gradients affect different measures of snake ß-diversity in the Amazon rainforests.

Mechanisms generating and maintaining biodiversity at regional scales may be evaluated by quantifying ß-diversity along environmental gradients. Differences in assemblages result in biotic complementarities and redundancies among sites, which may be quantified through multi-dimensional approaches incorporating taxonomic ß-diversity (TBD), functional ß-diversity (FBD) and phylogenetic ß-diversity (PBD). Here we test the hypothesis that snake TBD, FBD and PBD are influenced by environmental gradients, independently of geographic distance. The gradients tested are expected to affect snake assemblages indirectly, such as clay content in the soil determining primary production and height above the nearest drainage determining prey availability, or directly, such as percentage of tree cover determining availability of resting and nesting sites, and climate (temperature and precipitation) causing physiological filtering. We sampled snakes in 21 sampling plots, each covering five km2, distributed over 880 km in the central-southern Amazon Basin. We used dissimilarities between sampling sites to quantify TBD, FBD and PBD, which were response variables in multiple-linear-regression and redundancy analysis models. We show that patterns of snake community composition based on TBD, FBD and PBD are associated with environmental heterogeneity in the Amazon. Despite positive correlations between all ß-diversity measures, TBD responded to different environmental gradients compared to FBD and PBD. Our findings suggest that multi-dimensional approaches are more informative for ecological studies and conservation actions compared to a single diversity measure.

Soil and forest structure predicts large-scale patterns of occurrence and local abundance of a widespread Amazonian frog.

The distribution of biodiversity within the Amazon basin is often structured by sharp environmental boundaries, such as large rivers. The Amazon region is also characterized by subtle environmental clines, but how they might affect the distributions and abundance of organisms has so far received less attention. Here, we test whether soil and forest characteristics are associated with the occurrence and relative abundance of the forest-floor dwelling Aromobatid frog, Allobates femoralis. We applied a structured sampling regime along an 880 km long transect through forest of different density. High detection probabilities were estimated for A. femoralis in each of the sampling modules. Using generalized linear mixed-effects models and simple linear regressions that take detectability into account, we show that A. femoralis is more abundant in open forests than in dense forests. The presence and relative abundance of A. femoralis is also positively associated with clay-rich soils, which are poorly drained and therefore likely support the standing water bodies required for reproduction. Taken together, we demonstrate that relatively easy-to-measure environmental features can explain the distribution and abundance of a widespread species at different spatial scales. Such proxies are of clear value to ecologists and conservation managers working in large inaccessible areas such as the Amazon basin.

A new species of Amazonian snouted treefrog (Hylidae: Scinax) with description of a novel species-habitat association for an aquatic breeding frog.

The genus Scinax is one of the most specious genera of treefrogs of the family Hylidae. Despite the high number of potential new species of Scinax revealed in recent studies, the rate of species descriptions for Amazonia has been low in the last decade. A potential cause of this low rate may be the existence of morphologically cryptic species. Describing new species may not only impact the taxonomy and systematics of a group of organisms but also benefit other fields of biology. Ecological studies conducted in megadiverse regions, such as Amazonia, often meet challenging questions concerning insufficient knowledge of organismal alpha taxonomy. Due to that, detecting species-habitat associations is dependent on our ability to properly identify species. In this study, we first provide a description of a new species (including its tadpoles) of the genus Scinax distributed along heterogeneous landscapes in southern Amazonia; and secondly assess the influence of environmental heterogeneity on the new species' abundance and distribution. Scinax ruberoculatus sp. nov. differs from all nominal congeners by its small size (SVL 22.6-25.9 mm in males and 25.4-27.5 mm in females), by having a dark brown spot on the head and scapular region shaped mainly like the moth Copiopteryx semiramis (or a human molar in lateral view, or a triangle), bicolored reddish and grey iris, snout truncate in dorsal view, bilobate vocal sac in males, by its advertisement call consisting of a single pulsed note with duration of 0.134-0.331 s, 10-23 pulses per note, and dominant frequency 1,809-1,895 Hz. Both occurrence and abundance of the new species are significantly influenced by silt content in the soil. This finding brings the first evidence that edaphic factors influence species-habitat association in Amazonian aquatic breeding frogs.

Contrasting Patterns of Gene Flow for Amazonian Snakes That Actively Forage and Those That Wait in Ambush.

Knowledge of genetic structure, geographic distance and environmental heterogeneity can be used to identify environmental features and natural history traits that influence dispersal and gene flow. Foraging mode is a trait that might predict dispersal capacity in snakes, because actively foragers typically have greater movement rates than ambush predators. Here, we test the hypothesis that 2 actively foraging snakes have higher levels of gene flow than 2 ambush predators. We evaluated these 4 co-distributed species of snakes in the Brazilian Amazon. Snakes were sampled along an 880 km transect from the central to the southwest of the Amazon basin, which covered a mosaic of vegetation types and seasonal differences in climate. We analyzed thousands of single nucleotide polymorphisms to compare patterns of neutral gene flow based on isolation by geographic distance (IBD) and environmental resistance (IBR). We show that IBD and IBR were only evident in ambush predators, implying lower levels of dispersal than the active foragers. Therefore, gene flow was high enough in the active foragers analyzed here to prevent any build-up of spatial genotypic structure with respect to geographic distance and environmental heterogeneity.

The peculiar breeding biology of the Amazonian frog Allobates subfolionidificans (Aromobatidae).

Allobates subfolionidificans is a vulnerable and endemic leaf-litter frog from the state of Acre, Brazilian Amazonia. We monitored a population of A. subfolionidificans through regular censuses and mark-recapture of 181 individuals during an entire breeding season to characterize its reproductive behavior. The space use of A. subfolionidificans individuals differed between sexes, with males using smaller and more segregated spaces. Males defended territories and were aggressive against same-sex individuals, which was not the case in females. The daily cycle of calling activity showed peaks in the morning and in the afternoon, and the occurrence of reproductive events was positively correlated with monthly rainfall. The breeding behavior comprised vocal and tactile interactions, although the species lacked reproductive amplexus. Egg and larvae attendance, as well as tadpole transport to water environments was performed mostly by males but occasionally by females, probably in cases of desertion by the father. This species is characterized by performing courtship, mating, oviposition, as well as egg and larvae attendance exclusively on the under surface of leaves, a unique behavior among members of the superfamily Dendrobatoidea.

The peculiar breeding biology of the Amazonian frog Allobates subfolionidificans (Aromobatidae)

ABSTRACT Allobates subfolionidificans is a vulnerable and endemic leaf-litter frog from the state of Acre, Brazilian Amazonia. We monitored a population of A. subfolionidificans through regular censuses and mark-recapture of 181 individuals during an entire breeding season to characterize its reproductive behavior. The space use of A. subfolionidificans individuals differed between sexes, with males using smaller and more segregated spaces. Males defended territories and were aggressive against same-sex individuals, which was not the case in females. The daily cycle of calling activity showed peaks in the morning and in the afternoon, and the occurrence of reproductive events was positively correlated with monthly rainfall. The breeding behavior comprised vocal and tactile interactions, although the species lacked reproductive amplexus. Egg and larvae attendance, as well as tadpole transport to water environments was performed mostly by males but occasionally by females, probably in cases of desertion by the father. This species is characterized by performing courtship, mating, oviposition, as well as egg and larvae attendance exclusively on the under surface of leaves, a unique behavior among members of the superfamily Dendrobatoidea.

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

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

Decoupled Evolution between Senders and Receivers in the Neotropical Allobates femoralis Frog Complex.

During acoustic communication, an audible message is transmitted from a sender to a receiver, often producing changes in behavior. In a system where evolutionary changes of the sender do not result in a concomitant adjustment in the receiver, communication and species recognition could fail. However, the possibility of an evolutionary decoupling between sender and receiver has rarely been studied. Frog populations in the Allobates femoralis cryptic species complex are known for their extensive morphological, genetic and acoustic variation. We hypothesized that geographic variation in acoustic signals of A. femoralis was correlated with geographic changes in communication through changes in male-male recognition. To test this hypothesis, we quantified male call recognition using phonotactic responses to playback experiments of advertisement calls with two, three and four notes in eight localities of the Amazonian basin. Then, we reconstructed the ancestral states of call note number in a phylogenetic framework and evaluated whether the character state of the most recent common ancestor predicted current relative responses to two, three and four notes. The probability of a phonotactic response to advertisement calls of A. femoralis males was strongly influenced by the call mid-frequency and the number of notes in most populations. Positive phonotaxis was complete for calls from each individual's population, and in some populations, it was also partial for allotopic calls; however, in two populations, individuals equally recognized calls with two, three or four notes. This evidence, in conjunction with our results from phylogenetic comparative methods, supports the hypothesis of decoupled evolution between sender and receiver in the male-male communication system of the A. femoralis complex. Thus, signal recognition appears to evolve more slowly than the calls.