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.

A global reptile assessment highlights shared conservation needs of tetrapods.

Comprehensive assessments of species' extinction risks have documented the extinction crisis1 and underpinned strategies for reducing those risks2. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction3. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods4-7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs6. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened-confirming a previous extrapolation8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods-agriculture, logging, urban development and invasive species-although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles-including most species of crocodiles and turtles-require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments.

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpression, and sequence evolution. Frogs provide an excellent, yet understudied, system for visual evolution research due to their diversity of ecologies (including biphasic aquatic-terrestrial life cycles) that we hypothesize imposed different selective pressures leading to adaptive evolution of the visual system, notably the opsins that encode the protein component of the visual pigments responsible for the first step in visual perception. Here, we analyze the diversity and evolution of visual opsin genes from 93 new eye transcriptomes plus published data for a combined dataset spanning 122 frog species and 34 families. We find that most species express the four visual opsins previously identified in frogs but show evidence for gene loss in two lineages. Further, we present evidence of positive selection in three opsins and shifts in selective pressures associated with differences in habitat and life history, but not activity pattern. We identify substantial novel variation in the visual opsins and, using microspectrophotometry, find highly variable spectral sensitivities, expanding known ranges for all frog visual pigments. Mutations at spectral-tuning sites only partially account for this variation, suggesting that frogs have used tuning pathways that are unique among vertebrates. These results support the hypothesis of adaptive evolution in photoreceptor physiology across the frog tree of life in response to varying environmental and ecological factors and further our growing understanding of vertebrate visual evolution.

The Andes as a semi-permeable geographical barrier: Genetic connectivity between structured populations in a widespread spider.

Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis, have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi-permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross-Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long-distance dispersal modes together with altitudinal depressions.

Las barreras geográficas como las cordilleras montañosas impiden el intercambio genético entre poblaciones, promoviendo la diversificación. La efectividad de estas barreras para limitar el flujo genético varía entre linajes debido a los modos y capacidades de dispersión de cada especie. Nuestra comprensión de cómo la orogenia de los Andes contribuye a la diversificación de especies proviene de vertebrados y algunos artrópodos y plantas bien estudiados, descuidando a los organismos incapaces de volar o caminar grandes distancias. Se ha hipotetizado que algunas arañas, como Gasteracantha cancriformis, se dispersan a grandes distancias mediante la técnica de "ballooning" (es decir, utilizando su seda para interactuar con el viento). Sin embargo, no sabemos cómo el entorno y la geografía han dado forma a su diversidad genética. Por lo tanto, probamos si los Andes contribuyeron a la diversificación de G. cancriformis actuando como una barrera absoluta o permeable para la conectividad genética entre poblaciones de esta araña en lados opuestos de la cordillera. Muestreamos miles de loci a través de la distribución de la especie e implementamos análisis de genética de poblaciones, filogenéticos y de genética del paisaje. Identificamos dos grupos genéticamente distintos estructurados por los Andes Centrales, y un tercer grupo menos estructurado en los Andes del Norte que comparte ascendencia con los dos anteriores. Esta estructura se explica en gran medida por la altitud a lo largo de los Andes, que disminuye en algunas regiones, posiblemente facilitando la dispersión y el flujo genético a través de los Andes. Nuestros hallazgos apoyan que la altitud en los Andes juega un papel importante en la estructuración de las poblaciones en América del Sur, pero la fuerza de esta barrera puede ser superada por organismos con modos de dispersión a larga distancia junto con depresiones altitudinales.

Patterns, biases and prospects in the distribution and diversity of Neotropical snakes.

Motivation: We generated a novel database of Neotropical snakes (one of the world's richest herpetofauna) combining the most comprehensive, manually compiled distribution dataset with publicly available data. We assess, for the first time, the diversity patterns for all Neotropical snakes as well as sampling density and sampling biases. Main types of variables contained: We compiled three databases of species occurrences: a dataset downloaded from the Global Biodiversity Information Facility (GBIF), a verified dataset built through taxonomic work and specialized literature, and a combined dataset comprising a cleaned version of the GBIF dataset merged with the verified dataset. Spatial location and grain: Neotropics, Behrmann projection equivalent to 1° × 1°. Time period: Specimens housed in museums during the last 150 years. Major taxa studied: Squamata: Serpentes. Software format: Geographical information system (GIS). Results: The combined dataset provides the most comprehensive distribution database for Neotropical snakes to date. It contains 147,515 records for 886 species across 12 families, representing 74% of all species of snakes, spanning 27 countries in the Americas. Species richness and phylogenetic diversity show overall similar patterns. Amazonia is the least sampled Neotropical region, whereas most well-sampled sites are located near large universities and scientific collections. We provide a list and updated maps of geographical distribution of all snake species surveyed. Main conclusions: The biodiversity metrics of Neotropical snakes reflect patterns previously documented for other vertebrates, suggesting that similar factors may determine the diversity of both ectothermic and endothermic animals. We suggest conservation strategies for high-diversity areas and sampling efforts be directed towards Amazonia and poorly known species.

A new species of spider of the genus Sadala Simon, 1880 (Araneae, Sparassidae) from the Yasuni Biosphere Reserve, Amazonian lowlands of Ecuador.

We describe a new species of giant crab spider of the genus Sadala Simon, 1880 collected in Lowland Evergreen rainforests at the Tiputini Biodiversity Station, Yasuni Biosphere Reserve, Amazonian Ecuador. This new species corresponds to the first record of the genus from Ecuador. Females of the new species of Sadala are similar to S. punicea and S. nanay, by having the epigyne with a median septum diamond-shaped posteriorly. The new species is easily distinguished from S. punicea and S. nanay by having relatively straight anterior lateral margins of the median septum. This study increases to 10 the number of described species of Sadala.

Describimos una nueva especie de araña cangrejo gigante del género Sadala Simon, 1880 colectada en Bosque Lluvioso Siempreverde de Tierras Bajas en la Estación de Biodiversidad Tiputini, Reserva de la Biósfera Yasuní, Amazonía del Ecuador. Esta nueva especie corresponde al primer registro del género en Ecuador. Las hembras de la nueva especie de Sadala se diferencian de todos sus congéneres, excepto S. punicea y S. nanay, por un septo medio del epiginio con forma de diamante posteriormente. La nueva especie se diferencia fácilmente de S. punicea y S. nanay por tener los bordes anterolaterales del septo medio relativamente más rectos. Este estudio incrementa a diez el número de especies descritas de Sadala.

A new stream treefrog of the genus Hyloscirtus (Amphibia, Hylidae) from the Río Negro-Sopladora National Park, Ecuador.

Recent surveys in the Río Negro-Sopladora National Park revealed a striking new species of Hyloscirtus. The new species is easily diagnosed from all other congeners by its large body size (64.9 mm SVL in adult female); broad dermal fringes in fingers and toes; prepollex not projected into a prepollical spine and hidden under thenar tubercle; dorsum greyish-green, with paler-hued reticulum, yellow spots and black speckles; throat, venter, flanks and hidden surfaces of limbs golden-yellow with large black blotches and spots; fingers, toes and webbing yellow with black bars and spots; iris pale pink with black periphery. It is currently known only from its type locality, in the high montane forest on the southern slopes of the Cordillera Oriental of the Andes, southeastern Ecuador. The new species might be related to the H.larinopygion species group based on its morphology.

Two new syntopic species of glassfrogs (Amphibia, Centrolenidae, Centrolene) from the southwestern Andes of Ecuador.

We describe two new species of glassfrogs of the genus Centrolene living in syntopy at La Enramada, province of Azuay, southwestern Ecuador. They were found in a small creek in montane evergreen forests at 2,900 m elevation. The first new species is distinguished from all other members of the genus Centrolene by having the following combination of characters: dentigerous process of vomer absent; sloping snout in lateral view; thick, white labial stripe and a faint white line between the lip and anterior » of body; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); ulnar and tarsal ornamentation; dorsal skin shagreen with dispersed warts; uniform green dorsum with light yellowish green warts; and green bones. The new species is remarkable by being sister to a species from the opposite Andean versant, C. condor. The second new species is distinguished from all other Centrolene by having the following combination of characters: dentigerous process of vomer absent; round snout in lateral view; thin, yellowish labial stripe with a row of white tubercles between the lip and arm insertion, and a yellowish line between arm insertion and groin; uniform green dorsum; humeral spine in adult males; parietal peritoneum covered by iridophores, visceral peritonea translucent (except pericardium); dorsal skin shagreen with dispersed spicules; ulnar and tarsal ornamentation; and green bones. The second new species is sister to C. sabini and an undescribed species of Centrolene from southeastern Ecuador. Based on nuclear and mitochondrial DNA sequences, we present a new phylogeny for Centrolene and comment on the phylogenetic relationships inside the genus.

First genetic insights of Gonatodescaudiscutatus (Reptilia, Gekkota) in the Galapagos Islands and mainland Ecuador.

Studies on genetic variability amongst native and introduced species contribute to a better understanding of the genetic diversity of species along their autochthonous distribution and identify possible routes of introduction. Gonatodescaudiscutatus is a gecko native to western Ecuador and introduced to the Galapagos Islands. Despite being a successful species in human-modified habitats along its native and non-native ranges, neither the colonisation process nor the genetic diversity of this gecko is known. In this study, we analysed 55 individuals from 14 localities in western Ecuador and six localities in San Cristobal Island, Galapagos - the only island with a large, self-sustaining population. We amplified and analysed the genetic variability of two nuclear genes (Cmos and Rag2) and one mitochondrial gene (16S). Cmos and Rag2 sequences presented little to none genetic variability, while 16S allowed us to build a haplotype network. We identified nine haplotypes across mainland Ecuador, two of which are also present in Galapagos. Low genetic diversity between insular and continental populations suggests that the introduction of G.caudiscutatus on the Islands is relatively recent. Due to the widespread geographical distribution of mainland haplotypes, it was not possible to determine the source population of the introduction. This study represents the first exploration of the genetic diversity of Gonatodescaudiscutatus, utilising genetic tools to gain insights into its invasion history in the Galapagos.

The Shortcomings of COVID-19 Testing in Ecuador: Time to Incentivize Research and Innovation.

The COVID-19 pandemic hit Ecuador severely. The country caught the attention of international media due to its high death toll and overwhelmed healthcare system. The clinical diagnostics system was rapidly overloaded, and the import of PCR tests was delayed. The case of Ecuador illustrates how middle-income countries rely heavily on the importation of biotechnological products for their healthcare systems. The Ecuadorian experience during the COVID-19 pandemic serves as a call for the formation of policies for the development of the biotechnological industry.

A spectacular new species of Hyloscirtus (Anura: Hylidae) from the Cordillera de Los Llanganates in the eastern Andes of Ecuador.

We have discovered a spectacular new species of frog in the genus Hyloscirtus, belonging to the H. larinopygion species group. The adult female is characterized by a mostly black body with large bright red spots on the dorsal and ventral surface, extremities, and toe pads. The adult male is unknown. Small juveniles are characterized by a yellow body with variable black markings on the flanks; while one larger juvenile displayed irregular orange or yellow marks on a black background color, with light orange or yellow toe pads. Additional distinctive external morphological features such as cloacal ornamentation are described, and some osteological details are imaged and analyzed. The performed phylogeny places the new species as the sister to a clade consisting of ten taxa, all of which are part of the H. larinopygion group. We use genetic distances to fit the new species into a published time-calibrated phylogeny of this group; our analysis based on the published chronology suggests that the divergence of the new species from its known congeners pre-dates the Quaternary period. The new species is currently only known only from Cerro Mayordomo, in Fundación EcoMinga´s Machay Reserve, at 2,900 m in the eastern Andes of Tungurahua province, Ecuador, near the southern edge of Los Llanganates National Park, but its real distribution may be larger.

Death by massive air sac fluke (Trematoda: Bothriogaster variolaris) infection in a free-ranging snail kite (Rostrhamus sociabilis).

Helminths are not usually considered important pathogens for birds of prey. There is a single published report of mortality in raptors due to an air sac trematode infection. We report a well-documented death case from massive infection by an air sac trematode of the family Cyclocoelidae in a wild-caught, juvenile male Snail Kite (Rostrhamus sociabilis) in Ecuador. The necropsy of a Snail Kite revealed more than 200 trematodes among air sacs, lungs, heart, gizzard, proventriculus, and liver. Within air sacs and lungs, mature flukes were associated with sacculitis, bronchitis, pneumonia, and atelectasis. Using an integrative taxonomic approach with morphological and molecular data, we identified the parasites as Bothrigaster variolaris (Trematoda: Cyclocoelidae: Ophthalmophaginae). This case provides the first evidence for the pathologic presence of air sac trematodes associated with morbidity in birds of prey in South America. Our results suggest that cyclocoelids may cause debilitation and significant clinical lesions in birds of prey, with potentially fatal consequences.

Description of a new minute frog of the genus Pristimantis (Anura: Strabomantidae) from Cordillera del Condor, Ecuador.

We describe a new species of Pristimantis from southern Ecuador, province of Zamora Chinchipe. The new species is closely related to an undescribed species of Pristimantis from Reserva Tapichalaca, Ecuador and with species of a clade historically assigned to the P. unistrigatus species group, such as P. parvillus, P. luteolateralis, P. walkeri, among others. The new species of Pristimantis is a miniaturized new frog (females 17.11.1 mm; males 13.20.9 mm), characterized by the presence of -shaped scapular folds, with two subconical tubercles on the medial and posterior regions of folds; tympanic membrane and tympanic annulus present but not externally visible; a prominent rostral papilla present; upper eyelid with one elongated conical tubercle; a conical tubercle on heels; groin with orange or yellow spots. The new species of Pristimantis is distributed in a restricted area in the Cordillera del Condor, a highly-diverse mountain range threatened by multiple anthropogenic activities. We recommend assigning the new species to the Endangered IUCN threatened category because it is only known from three nearby localities within mining concessions.

Amphibians of the equatorial seasonally dry forests of Ecuador and Peru.

Seasonally dry forests (SDFs) are one of the most challenging ecosystems for amphibians, fueling the diversity of this group of vertebrates. An updated inventory of native amphibians present in the Equatorial SDF is provided, which extends along the Pacific coast of Ecuador and northwestern Peru. The study is based on an extensive field sampling (two thirds of the total records) carried out throughout the Equatorial SDF, along with a compilation of the available information on distribution of amphibians in the region from published scientific papers, museum collections and on-line databases. The final dataset included 2,032 occurrence records for 30 amphibian species, belonging to eight anuran families. Additionally, data regarding conservation status, habitat use, spawn deposition site, reproductive mode, and body size, along with an identification key for all encountered species are provided. The results indicate a strong sampling bias with a deficit in the Peruvian part of the study area, and a need for urgent inventories targeted at under-sampled areas, using modern taxonomic methods. The study emphasizes the conservation priorities in the Equatorial SDF, based on the distribution, conservation status and life-history data. This information should be useful for the local authorities and institutions involved in the management and conservation of biodiversity in SDF.

Automatic ladybird beetle detection using deep-learning models.

Fast and accurate taxonomic identification of invasive trans-located ladybird beetle species is essential to prevent significant impacts on biological communities, ecosystem functions, and agricultural business economics. Therefore, in this work we propose a two-step automatic detector for ladybird beetles in random environment images as the first stage towards an automated classification system. First, an image processing module composed of a saliency map representation, simple linear iterative clustering superpixels segmentation, and active contour methods allowed us to generate bounding boxes with possible ladybird beetles locations within an image. Subsequently, a deep convolutional neural network-based classifier selects only the bounding boxes with ladybird beetles as the final output. This method was validated on a 2, 300 ladybird beetle image data set from Ecuador and Colombia obtained from the iNaturalist project. The proposed approach achieved an accuracy score of 92% and an area under the receiver operating characteristic curve of 0.977 for the bounding box generation and classification tasks. These successful results enable the proposed detector as a valuable tool for helping specialists in the ladybird beetle detection problem.

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.

Contributions to ophiology in Zootaxa 20012020: patterns and trends.

There are currently 3,900 recognized, extant snake species belonging to 529 genera globally (Uetz et al. 2021; this study), making snakes one of the most diverse major groups of squamates. Of the 665 currently recognized species that were described between 2001 and 2020 (a ~17% increase in total species), ~34% of these (226 species) were described in Zootaxa. This number does not include species resurrected from synonymy. The other ~66% (439) species were described in 105 other journals, bulletins or books (Fig.1a). Overall, the number of new snake species described every year is gradually increasing, and 40% of the new species described since 2011 were published in Zootaxa. Following Zootaxa, the second ranked journal, with 37 described species since 2001, is Herpetologica (Fig. 2). Anecdotally, the choice of Zootaxa as a publication outlet for new species descriptions by most authors is based on speed of publication post-acceptance, publication free of charge, relatively unconstrained number of papers published per year, relatively unconstrained manuscript length, expert section editors and reviewers, and consolidated scientometric parameters.

A new Andean treefrog (Amphibia: Hyloscirtus bogotensis group) from Ecuador: an example of community involvement for conservation.

We provide several lines of evidence to delimit a new species of Hyloscirtus and define its phylogenetic position inside the Hyloscirtus bogotensis group. The new species is the sister taxon to Hyloscirtus mashpi and is related to a clade formed by H. alytolylax and a putative new species from the province of El Oro in, southwestern Ecuador. Hyloscirtus conscientia sp. nov. is described from the montane forests of the Mira River basin in the extreme northwestern Ecuador. The new species is characterized as follows: tympanic annulus conspicuous, tip of snout in dorsal view subacuminate, middorsal stripe formed by melanophores larger and less dense, dorsal skin with individual iridophores forming dots, scarcely distributed across dorsum. Our study also highlights the importance of the Mira River Valley as a biogeographic barrier; suggesting research efforts north and south of the valley are likely to reveal additional endemic cryptic diversity. Finally, our partnership with Reserva: The Youth Land Trust, Rainforest Trust and EcoMinga Foundation has produced a novel and meaningful way to connect young people with biodiversity discovery and habitat conservation.

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.