Field-based molecular detection of Batrachochytrium dendrobatidis in critically endangered Atelopus toads and aquatic habitats in Ecuador

Batrachochytrium dendrobatidis (Bd) is a lethal fungal species that parasitizes vertebrates and is associated with the worldwide decline of amphibian populations. The development of sensitive, rapid detection methods, particularly DNA-based techniques, is critical for effective management strategies. This study evaluates the efficacy of DNA extraction and a portable PCR device in a mountable field laboratory setup for detecting Bd near the habitats of three critically endangered Atelopus toad species in Ecuador. We collected skin swabs from Atelopus balios, A. nanay, and A. bomolochos, and environmental DNA (eDNA) samples from streams in Andean and coastal regions of Ecuador. For eDNA, a comparison was made with duplicates of the samples that were processed in the field and in a standard university laboratory. Our findings revealed Bd detection in eDNA and swabs from 6 of 12 water samples and 10 of 12 amphibian swab samples. The eDNA results obtained in the field laboratory were concordant with those obtained under campus laboratory conditions. These findings highlight the potential of field DNA-based monitoring techniques for detecting Bd in amphibian populations and their aquatic habitats, particularly in remote areas. Furthermore, this research aligns with the National Action Plan for the Conservation of Ecuadorian Amphibians and contributes to the global effort to control this invasive and deadly fungus.

Ongoing declines for the world's amphibians in the face of emerging threats

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

Environmental DNA and visual encounter surveys for amphibian biomonitoring in aquatic environments of the Ecuadorian Amazon

Background

The development of anthropogenic activities has generated a decline in aquatic fauna populations, and amphibians have been the most affected. The decline of batrachofauna is concerning, as 41% of all species worldwide are endangered. For this reason, rapid, efficient, and non-invasive biodiversity monitoring techniques are needed, and environmental DNA (eDNA) is one such tool that has been sparsely applied in Ecuador. This technique has allowed scientists generates information on species diversity and amphibian community composition from a water sample. This study applied eDNA-based biomonitoring analyses and visual encounter surveys (VES) as inventory techniques to identify the diversity of aquatic amphibians in the Tena River micro-basin (TRMB).

Methods

The experimental design was divided into three components: (1) fieldwork: all amphibians were recorded by the VES technique and water samples were collected; (2) laboratory work: DNA isolation from amphibian tissue samples and eDNA-containing filters, amplification, electrophoresis, and sequencing were performed; (3) Data analysis: a local DNA reference database was constructed, and eDNA sequence data were processed for classification, taxonomic assignment, and ecological interpretation.

Results

Using both eDNA and VES, we detected 33 amphibian species (13 with eDNA only, five with VES only, and 15 with both methods). These species belonged to six amphibian families: Hylidae being the richest with 14 species (three eDNA, one VES, and 10 with both methods), followed by Strabomantidae with nine species (six eDNA, one VES, and two with both methods). All families were detected with both methods, except for the Aromobatidae, having one single record (Allobates aff. insperatus) by VES. Individually, eDNA detected 28 species and had a detection probability (DP) of 0.42 CI [0.40-0.45], while VES recorded 20 species with a DP of 0.17 CI [0.14-0.20]. Similarly, using VES, Cochranella resplendens was detected for the first time in TRMB, while with eDNA, four mountain frogs Pristimantis acerus, Pristimantis eriphus, Pristimantis mallii, and Pristimantis sp. (INABIO 15591) previously recorded at 1,518 m.a.s.l. at altitudes below 600 m.a.s.l. were detected.

Conclusions

Results obtained in this study showed that eDNA-based detection had a greater capacity to detect amphibians in aquatic environments compared to VES. The combination of VES and eDNA improves the sensitivity of species detection and provides more reliable, robust, and detailed information. The latter is essential for developing conservation strategies in the Ecuadorian Amazon.

Rediscovery of Laura's glassfrog Nymphargus laurae (Anura: Centrolenidae) with new data on its morphology, colouration, phylogenetic position and conservation in Ecuador

We report the rediscovery of Laura’s Glassfrog, Nymphargus laurae Cisneros-Heredia & McDiarmid, 2007, based on two specimens collected at the Colonso-Chalupas Biological Reserve, province of Napo, Ecuador. The species was described and known from a single male specimen collected in 1955 at Loreto, north-eastern Andean foothills of Ecuador. Limited information was available about the colouration, systematics, ecology, and biogeography of N. laurae. We provide new data on the external morphology, colouration, distribution and comment on its conservation status and extinction risk. We discuss the phylogenetic relationships of N. laurae, which forms a clade together with N. siren and N. humboldti. The importance of research in unexplored areas must be a national priority to document the biodiversity associated, especially in protected areas.

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

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

Amphibian chytridiomycosis, a lethal pandemic disease caused by the killer fungus Batrachochytrium dendrobatidis: New approaches to host defense mechanisms and techniques for detection and monitoring

Chytridiomycosis is a catastrophic disease currently decimating worldwide amphibian populations, caused by the panzootic chytrid fungus Batrachochytrium dendrobatidis. Massive species decline to extinction catalyzes radical changes in ecosystems globally, including the largest continuous rainforest ecosystem on Earth, the Amazon rainforest. Innovative research that aims to propose feasible mechanisms of mitigation and the origins of the disease is vital, including studies addressing climatic effects on the expansion of chytridiomycosis. Thus, this publication aims to provide a comprehensive review of: i) the current technologies used for B. dendrobatidis detection and monitoring, and ii) the known Neotropical amphibian's skin microbiota with anti-fungal properties against B. dendrobatidis. Several immunologic and DNA-based methods are discussed to understand the emerging fungal pathogens and their effects on the biosphere, which can help to mitigate the devastating ecological impacts of mass amphibian morbidity. The establishment of rapid and highly accurate B. dendrobatidis detection techniques and methods for monitoring amphibian's cutaneous microbiome is crucial in the fight against chytridiomycosis.

Systematics of Ecnomiohyla tuberculosa with the description of a new species and comments on the taxonomy of Trachycephalus typhonius (Anura, Hylidae)

Ecnomiohylatuberculosa is an Amazonian hylid of uncertain phylogenetic position. Herein DNA sequences of mitochondrial and nuclear genes are used to determine its phylogenetic relationships. New sequences and external morphology of Trachycephalustyphonius are also analyzed to assess the status of Ecuadorian and Peruvian populations. The phylogeny shows unequivocally that Ecnomiohylatuberculosa is nested within the genus Tepuihyla, tribe Lophiohylini. This position was unexpected because the remaining species of Ecnomiohyla belong to the tribe Hylini. To solve the paraphyly of the genus Ecnomiohyla, Ecnomiohylatuberculosa is transferred to the genus Tepuihyla. Comparisons of DNA sequences, external morphology, and advertisement calls between populations of Ecnomiohylatuberculosa from Ecuador and Peru indicate that the Peruvian population represents an undescribed species. The new species is described and a species account is provided for Ecnomiohylatuberculosa. Trachycephalustyphonius is paraphyletic relative to Trachycephaluscunauaru, Trachycephalushadroceps, and Trachycephalusresinifictrix. The phylogenetic position of populations from western Ecuador indicates that they represent a species separate from Trachycephalustyphoniussensu stricto. We resurrect the name Hylaquadrangulum (Trachycephalusquadrangulumcomb. n.) for those populations. Amazonian populations of “Trachycephalustyphonius” from Ecuador and Peru are genetically and morphologically distinct from Trachycephalustyphoniussensu stricto and are conspecific with the holotype of Hylamacrotis. Therefore, we also resurrect Hylamacrotis, a decision that results in Trachycephalusmacrotiscomb. n.

A new species of small tree frog, genus Dendropsophus (Anura: Hylidae) from the eastern Amazon lowlands of Ecuador

We describe a new species of the hylid frog genus Dendropsophus from Amazonian Ecuador. The new species, Dendropsophus shiwiarum sp. nov., appears to be part of the D. microcephalus species group. Dendropsophus shiwiarum differs from its congeners by a combination of: (1) tympanic membrane non-differentiated and annulus evident only ventrally, (2) disc of Finger III and Toe IV with pointed tip, (3) dorsal surfaces of digital discs with a conical tubercle as result of projection of distal phalanx, and (4) small size (SVL < 19 mm). The new species is morphologically most similar to Dendropsophus riveroi. Examination of the type material of the latter suggests that some Ecuadorian populations reported as D. riveroi were misidentified and in fact belong to D. shiwiarum sp. nov.

Ecological and geographical analysis of the distribution of the mountain tapir (Tapirus pinchaque) in Ecuador: importance of protected areas in future scenarios of global warming

In Ecuador, Tapirus pinchaque is considered to be critically endangered. Although the species has been registered in several localities, its geographic distribution remains unclear, and the effects of climate change and current land uses on this species are largely unknown. We modeled the ecological niche of T. pinchaque using MaxEnt, in order to assess its potential adaptation to present and future climate change scenarios. We evaluated the effects of habitat loss due by current land use, the ecosystem availability and importance of Ecuadorian System of Protected Areas into the models. The model of environmental suitability estimated an extent of occurrence for species of 21,729 km2 in all of Ecuador, mainly occurring along the corridor of the eastern Ecuadorian Andes. A total of 10 Andean ecosystems encompassed ~98% of the area defined by the model, with herbaceous paramo, northeastern Andean montane evergreen forest and northeastern Andes upper montane evergreen forest being the most representative. When considering the effect of habitat loss, a significant reduction in model area (~17%) occurred, and the effect of climate change represented a net reduction up to 37.86%. However, the synergistic effect of both climate change and habitat loss, given current land use practices, could represent a greater risk in the short-term, leading to a net reduction of 19.90 to 44.65% in T. pinchaque's potential distribution. Even under such a scenarios, several Protected Areas harbor a portion (~36 to 48%) of the potential distribution defined by the models. However, the central and southern populations are highly threatened by habitat loss and climate change. Based on these results and due to the restricted home range of T. pinchaque, its preference for upland forests and paramos, and its small estimated population size in the Andes, we suggest to maintaining its current status as Critically Endangered in Ecuador.

A new synonym for Pristimantis luscombei (Duellman and Mendelson 1995) and the description of a new species of Pristimantis from the upper Amazon basin (Amphibia: Craugastoridae)

We consider Pristimantis achuar as junior synonym of P. luscombei, based on morphological and genetic evidence. Paratype specimens of P. luscombei are part of a new species, which lead to taxonomic confusion regarding the identity of P. luscombei. We describe and name this new species as Pristimantis miktos sp. nov. from Juyuintza, Pastaza province, eastern lowlands of Ecuador. Morphological diagnostic characters used to distinguish the new species from other brownish Amazonian Pristimantis are: (1) skin of dorsum shagreen with scattered tubercles or pustules; (2) tympanum prominent; (3) a thick X-shaped scapular dermal ridge in males; and (4) an orange iris in life. Pristimantis miktos is an inhabitant of the lowlands forests of the Pastaza and Napo drainages in eastern Ecuador and northern Loreto in Peru, reaching elevations of up to 350 m; P. luscombei is widely distributed in the upper Amazon Basin of Ecuador, northern Peru and extreme western Brazil, up to 1000 m. Phylogenetic analyses reveals that P. luscombei and the new species are not closest relatives, as also deduced from morphological evidence.

Novel data on the ecology of Cochranella mache (Anura: Centrolenidae) and the importance of protected areas for this critically endangered glassfrog in the neotropics

We studied a population of the endangered glassfrog, Cochranella mache, at Bilsa Biological Station, northwestern Ecuador, from 2008 and 2009. We present information on annual abundance patterns, behavioral ecology, habitat use and a species distribution model performed with MaxEnt. We evaluate the importance of the National System of Protected Areas (SNAP) in Colombia and Ecuador, under scenarios of climate change and habitat loss. We predicted a restricted environmental suitability area from 48,509 Km² to 65,147 Km² along western Ecuador and adjacent Colombia; ∼8% of the potential distribution occurs within SNAP. We examined four aspects of C. mache ecology: (1) ecological data suggests a strong correlation between relative abundance and rainfall, with a high probability to observe frogs through rainy months (February–May); (2) habitat use and the species distribution model suggest that this canopy dweller is restricted to small streams and rivulets in primary and old secondary forest in evergreen lowland and piedmont forest of western Ecuador, with predictions of suitability areas in adjacent southern Colombia; (3) the SNAP of Colombia and Ecuador harbor a minimum portion of the predicted model of distribution (<10%); and (4) synergetic effects of habitat loss and climate change reduces in about 95% the suitability areas for this endangered frog along its distributional range in Protected Areas. The resulting model allows the recognition of areas to undertake conservation efforts and plan future field surveys, as well as forecasting regions with high probability of C. mache occurrence in western Ecuador and southern Colombia. Further research is required to assess population tendencies, habitat fragmentation and target survey zones to accelerate the discovery of unknown populations in unexplored areas with high probability of suitability. We recommend that Cochranella mache must be re-categorized as “Critically Endangered” species in national and global status, according with criteria and sub-criteria A4, B1ab(i,ii,iii,iv),E.

Herpetofauna of the Bilsa Biological Station, province of Esmeraldas, Ecuador

The Bilsa Biological Station is located on the Mache-Chindul mountains and protects some of the last rainforest remnants in the province of Esmeraldas, northwestern Ecuador. Since 2004, we have been inventorying the amphibians and reptiles of Bilsa. We found 109 species of herpetofauna (37 amphibians and 72 reptiles), representing 8 % and 18 % of the known species from Ecuador, respectively. We report distribution extensions for Sachatamia albomaculata, Hyalinobatrachium valerioi, Pristimantis muricatus, and P. rosadoi, and report the presence of several putatively undescribed species. We propose the Mache–Chindul mountains as a Key Biodiversity Area within the West Ecuadorian Endemic Area.

Agalychnis spurrelli Boulenger (Anura, Hylidae): variación, distribución y sinonimia

Agalychnis spurrelli Boulenger, 1913 es el nombre válido más reciente para una especie hylida de rana Phyllomedusina que habita los bosques tropicales de tierras bajas y premontanos del Pacífico, desde el sur de Costa Rica hasta el centro-occidente de Ecuador. Presento datos que apoyan la ubicación de Agalychnis litodryas Duellman & Trueb, 1967 como un sinónimo junior de A. spurrelli. Agalychnis spurrelli es una rana medianamente grande con extensas membranas interdigitales que se distingue de otras especies del género Agalychnis por tener los flancos y extremidades uniformemente amarillo, anaranjado, rosado pálido o morado pálido, sin barras oscuras. Su dorso es verde, comúnmente con verrugas pustulares bordeadas de negro.

Amphibia, Centrolenidae, Cochranella pulverata, Hyalinobatrachium aureoguttatum: distribution extension, Ecuador

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Reptilia, Squamata, Gymnophthalmidae, Echinosaura horrida: distribution extension and new geographic distribution map for Ecuador

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