New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding

DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.

Evolutionary trade-offs between testes size and parenting in Neotropical glassfrogs

In males, large testes size signifies high sperm production and is commonly linked to heightened sperm competition levels. It may also evolve as a response to an elevated risk of sperm depletion due to multiple mating or large clutch sizes. Conversely, weapons, mate or clutch guarding may allow individuals to monopolize mating events and preclude sperm competition, thereby reducing the selection of large testes. Herein, we examined how paternal care, sexual size dimorphism (SSD), weaponry and female fecundity are linked to testes size in glassfrogs. We found that paternal care was associated with a reduction in relative testes size, suggesting an evolutionary trade-off between testes size and parenting. Although females were slightly larger than males and species with paternal care tended to have larger clutches, there was no significant relationship between SSD, clutch size and relative testes size. These findings suggest that the evolution of testes size in glassfrogs is influenced by sperm competition risk, rather than sperm depletion risk. We infer that clutch guarding precludes the risk of fertilization by other males and consequently diminishes selective pressure for larger testes. Our study highlights the prominent role of paternal care in the evolution of testes size in species with external fertilization.

Two new species of terrestrial frogs of the Pristimantisgladiator complex (Anura, Strabomantidae) from the Ecuadorian Andes, with insights on their biogeography and skull morphology

The explosive diversity of rainfrogs (Pristimantis spp) reaches its highest levels in the mountains of the Tropical Andes, with remarkable cryptic species mainly in unexplored areas of Ecuador. Based on phylogenetics, morphometric traits, skull osteology and bioacoustics, we describe two new species of Pristimantis, previously confused with Pristimantisgladiator, that belong to the subgenus Trachyphrynus traditionally known as the Pristimantismyersi species group. The two new taxa are closely related, but have allopatric distributions. We discuss the importance of the Quijos and Pastaza River valleys in the diversification along Amazonian slopes of the Ecuadorian Andes.

Evolutionary genomics of oceanic island radiations

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.

Environment rather than character displacement explains call evolution in glassfrogs

The acoustic adaptation hypothesis (AAH) and ecological character displacement (ECD) are two potential mechanisms shaping call evolution that can predict opposite trends for the differentiation of signals. Under AAH, signals evolve to minimize environmental degradation and maximize detection against background noise, predicting call homogenization in similar habitats due to environmental constraints on signals. In contrast, ECD predicts greater differences in call traits of closely related taxa in sympatry because of selection against acoustic interference. We used comparative phylogenetic analyses to test the strength of these two selective mechanisms on the evolution of advertisement calls in glassfrogs, a highly diverse family of neotropical anurans. We found that, overall, acoustic adaptation to the environment may outweigh effects of species interactions. As expected under the AAH, temporal call parameters are correlated with vegetation density, but spectral call parameters had an unexpected inverse correlation with vegetation density, as well as an unexpected correlation with temperature. We detected call convergence among co-occurring species and also across multiple populations from the same species in different glassfrogs communities. Our results indicate that call convergence is common in glassfrogs, likely due to habitat filtering, while character displacement is relatively rare, suggesting that costs of signal similarity among related species may not drive divergent selection in all systems.

Human impacts outpace natural processes in the Amazon

Amazonian environments are being degraded by modern industrial and agricultural activities at a pace far above anything previously known, imperiling its vast biodiversity reserves and globally important ecosystem services. The most substantial threats come from regional deforestation, because of export market demands, and global climate change. The Amazon is currently perched to transition rapidly from a largely forested to a nonforested landscape. These changes are happening much too rapidly for Amazonian species, peoples, and ecosystems to respond adaptively. Policies to prevent the worst outcomes are known and must be enacted immediately. We now need political will and leadership to act on this information. To fail the Amazon is to fail the biosphere, and we fail to act at our peril.

A pilot study to estimate the population size of endangered Galápagos marine iguanas using drones

BACKGROUND

Large-scale species monitoring remains a significant conservation challenge. Given the ongoing biodiversity crisis, the need for reliable and efficient methods has never been greater. Drone-based techniques have much to offer in this regard: they allow access to otherwise unreachable areas and enable the rapid collection of non-invasive field data. Herein, we describe the development of a drone-based method for the estimation of population size in Galápagos marine iguanas, Amblyrhynchus cristatus. As a large-bodied lizard that occurs in open coastal terrain, this endemic species is an ideal candidate for drone surveys. Almost all Amblyrhynchus subspecies are Endangered or Critically Endangered according to the IUCN yet since several colonies are inaccessible by foot, ground- based methods are unable to address the critical need for better census data. In order to establish a drone-based approach to estimate population size of marine iguanas, we surveyed in January 2021 four colonies on three focal islands (San Cristobal, Santa Fe and Espanola) using three techniques: simple counts (the standard method currently used by conservation managers), capture mark-resight (CMR), and drone-based counts. The surveys were performed within a 4-day window under similar ambient conditions. We then compared the approaches in terms of feasibility, outcome and effort.

RESULTS

The highest population-size estimates were obtained using CMR, and drone-based counts were on average 14% closer to CMR estimates-and 17-35% higher-than those obtained by simple counts. In terms of field-time, drone-surveys can be faster than simple counts, but image analyses were highly time consuming.

CONCLUSION

Though CMR likely produces superior estimates, it cannot be performed in most cases due to lack of access and knowledge regarding colonies. Drone-based surveys outperformed ground-based simple counts in terms of outcome and this approach is therefore suitable for use across the range of the species. Moreover, the aerial approach is currently the only credible solution for accessing and surveying marine iguanas at highly remote colonies. The application of citizen science and other aids such as machine learning will alleviate the issue regarding time needed to analyze the images.

Unveiling the evolutionary relationships and the high cryptic diversity in Andean rainfrogs (Craugastoridae: Pristimantis myersi group)

Background

Pristimantis is the most diverse genus of terrestrial frogs. Historically, it has been divided into several phenetic groups in order to facilitate species identification. However, in light of phylogenetic analysis, many of these groups have been shown to be non-monophyletic, denoting a high degree of morphological convergence and limited number of diagnostic traits. In this study, we focus on the Pristimantis myersi group, an assemblage of small rainfrogs distributed throughout the Andes of Ecuador and Colombia, whose external morphology is highly conserved, and its species diversity and evolutionary relationships largely unknown.

Methods

We inferred a new phylogenetic hypothesis for the frog genus Pristimantis, including all available sequences of the mtDNA 16S rRNA, as well as new DNA sequences from 175 specimens. Our sampling included 19 of the 24 species currently recognized as part of the Pristimantis myersi group.

Results

Our new evolutionary hypothesis recovered the P. myersi group as non-monophyletic and composed of 16 species. Therefore, we exclude P. albujai, P. bicantus, P. sambalan, and P. nelsongalloi in order to preserve the monophyly of the group. We discovered at least eight candidate species, most of them hidden under the names of P. leoni, P. hectus, P. festae, P. gladiator, and P. ocreatus.

Discussion

Our results reveal the occurrence of a high level of cryptic diversity to the species level within the P. myersi group and highlight the need to redefine some of its species and reassess their conservation status. We suggest that the conservation status of six species within the group need to be re-evaluated because they exhibit smaller distributions than previously thought; these species are: P. festae, P. gladiator, P. hectus, P. leoni, P. ocreatus, and P. pyrrhomerus. Finally, given that the Pristimantis myersi group, as defined in this work, is monophyletic and morphologically diagnosable, and that Trachyphrynus is an available name for the clade containing P. myersi, we implement Trachyphrynus as a formal subgenus name for the Pristimantis myersi group.

Cryptic lineages and standing genetic variation across independent cane toad introductions

Widespread introduced species can be leveraged to investigate the genetic, ecological and adaptive processes underlying rapid evolution and range expansion, particularly the contributions of genetic diversity to adaptation. Rhinella marina, the cane toad, has been a focus of invasion biology for decades in Australia. However, their introduction history in North America is less clear. Here, we investigated the roles of introduction history and genetic diversity in establishment success of cane toads across their introduced range. We used reduced representation sequencing (ddRAD) to obtain 34,000 SNPs from 247 toads in native (French Guiana, Guyana, Ecuador, Panama, Texas) and introduced (Bermuda, southern Florida, northern Florida, Hawai'i, Puerto Rico) populations. Unlike all other cane toad introductions, we found that Florida populations were more closely related to native Central American lineages (R. horribilis), than to native Southern American lineages (R. marina). Furthermore, we found high levels of diversity and population structure in the native range, corroborating suggestions that R. marina is a species complex. We also found that introduced populations exhibit only slightly lower genetic diversity than native populations. Together with demographic analyses, this indicates founding populations of toads in Florida were larger than previously reported. Lastly, within R. marina, only one of 245 putatively adaptive SNPs showed fixed differences between native and introduced ranges, suggesting that putative selection in these introduced populations is based upon existing genetic variation. Our findings highlight the importance of genetic sequencing in understanding biological introductions and hint at the role of standing genetic variation in range expansion.

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.

Leaving no stone unturned: three additional new species of Atractus ground snakes (Serpentes, Colubridae) from Ecuador discovered using a biogeographical approach

The genus Atractus includes 146 species of cryptozoic snakes occurring from Panama to northeastern Argentina. Here, a molecular phylogeny of this genus is presented, which encompasses 29% (= 42; six are included here for the first time) of the species currently recognized. Morphological and phylogenetic support is found for three new species of ground snakes, which are described here based on their unique combination of molecular, meristic, and color pattern characteristics. The name A.arangoi Prado, 1939 is revalidated for a Colombian snake species previously subsumed under A.major Boulenger, 1894 based on new material collected in Ecuador. Reidentifications are provided for Atractus voucher specimens and sequences deposited in GenBank. With these changes, the number of Atractus reported in Ecuador increases from 27 to 31 species. Finally, attention is given to the importance of using a biogeographical framework that includes molecular data and a comprehensive geographic sampling when proposing species limits in complex taxonomic groups.

Two new glassfrogs (Centrolenidae: Hyalinobatrachium) from Ecuador, with comments on the endangered biodiversity of the Andes

Background

The Tropical Andes is the world's most biodiverse hotspot. This region contains >1,000 amphibian species, more than half of which are endemic. Herein we describe two new glassfrog species (Centrolenidae: Hyalinobatrachium) that we discovered within relatively unexplored and isolated localities of the Ecuadorian Andes.

Methods

We employed morphological, acoustic, and molecular methods to test the hypothesis that Hyalinobatrachium mashpi sp. nov and H. nouns sp. nov. are species new to science. Following standard methods, we generated mitochondrial sequences (16S) of 37 individuals in the genus Hyalinobatrachium. We inferred the phylogenetic relationships of the two new species in comparison to all other glassfrogs using Maximum Likelihood. In addition to describing the call of H. mashpi sp. nov., we performed a discriminant analysis of principal components (DAPC) with the advertisement call characteristics of several congeners.

Results

Based on an integrative taxonomy approach, we describe two new species. Morphological traits and the inferred phylogeny unambiguously place the new taxa in the genus Hyalinobatrachium. Both species are distinguished from other glassfrogs mainly by their dorsal coloration (i.e., dorsum lime green with small light yellow spots, head usually with interorbital bar) and transparent pericardium (i.e., the heart is visible through the ventral skin). The new species exhibit a high morphological similarity (i.e., cryptic) and occur within relatively close geographical proximity (closest aerial distance = 18.9 km); however, their uncorrected p distance for the mitochondrial gene 16S is 4.6-4.7%, a value that greatly exceeds the genetic distance between closely related species of centrolenid frogs. The DAPC revealed that the advertisement call of H. mashpi sp. nov. is acoustically distinct.

Discussion

Our findings are congruent with several previous studies that report a high degree of endemism in the Toisán mountain range, which appears to be isolated from the main Andean cordillera for some amphibian groups. We recommend that both H. mashpi sp. nov. and H. nouns sp. nov. be listed as Endangered, following IUCN criteria. These new species provide another example of cryptic diversity in the Andes-further evidence that the region fosters much more biodiversity than we have the resources to catalog. Threatened by mining and other exploitative industries, these glassfrogs and many other yet-to-be-discovered Andean species highlight the dire need for effective conservation measures-especially in northwestern Ecuador.

A new species of the genus Noblella (Amphibia: Strabomantidae) from Ecuador, with new information for Noblella worleyae

We describe a new species of terrestrial-breeding frog of the genus Noblella from the northwestern slopes of the Andes of Ecuador, in the province of Pichincha, Ecuador, and report a new locality for the recently described N. worleyae. We include a detailed description of the osteology of both species and discuss their phylogenetic relationships. The new species is differentiated from other species of Noblella by having discs of fingers rounded, without papillae; distal phalanges only slightly T-shaped; toes slightly expanded and rounded distally, without papillae; dorsum uniform brown with irregular suprainguinal dark brown marks; venter yellowish cream, ventral surfaces of legs and thighs reddish to brownish cream; and dark brown throat. The new locality for N. worleyae is located in Los Cedros Reserve, an area highly threatened by mining. We highlight the importance of protecting endemic species of small vertebrates in northwestern Ecuador.

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.

International fisheries threaten globally endangered sharks in the Eastern Tropical Pacific Ocean: the case of the Fu Yuan Yu Leng 999 reefer vessel seized within the Galápagos Marine Reserve

Shark fishing, driven by the fin trade, is the primary cause of global shark population declines. Here, we present a case study that exemplifies how industrial fisheries are likely depleting shark populations in the Eastern Tropical Pacific Ocean. In August 2017, the vessel Fu Yuan Yu Leng 999, of Chinese flag, was detained while crossing through the Galápagos Marine Reserve without authorization. This vessel contained 7639 sharks, representing one of the largest seizures recorded to date. Based on a sample of 929 individuals (12%), we found 12 shark species: 9 considered as Vulnerable or higher risk by the IUCN and 8 listed in CITES. Four species showed a higher proportion of immature than mature individuals, whereas size-distribution hints that at least some of the fishing ships associated with the operation may have been using purse-seine gear fishing equipment, which, for some species, goes against international conventions. Our data expose the magnitude of the threat that fishing industries and illegal trade represent to sharks in the Eastern Tropical Pacific Ocean.

Concentrations and stable isotopes of mercury in sharks of the Galapagos Marine Reserve: Human health concerns and feeding patterns

The human ingestion of mercury (Hg) from sea food is of big concern worldwide due to adverse health effects, and more specifically if shark consumption constitutes a regular part of the human diet. In this study, the total mercury (THg) concentration in muscle tissue were determined in six sympatric shark species found in a fishing vessel seized in the Galapagos Marine Reserve in 2017. The THg concentrations in shark muscle samples (n = 73) varied from 0.73 mg kg^-1 in bigeye thresher sharks (Alopias superciliosus) to 8.29 mg kg^-1 in silky sharks (Carcharhinus falciformis). A typical pattern of Hg bioaccumulation was observed for all shark species, with significant correlation between THg concentration and shark size for bigeye thresher sharks, pelagic thresher sharks (Alopias pelagicus) and silky sharks. Regarding human health concerns, the THg mean concentration exceeded the maximum weekly intake fish serving in all the studied species. Mass-Dependent Fractionation (MDF, δ²⁰²Hg values) and Mass-Independent Fractionation (MIF, Δ¹⁹⁹Hg values) of Hg in whitetip sharks (Carcharhinus longimanus) and silky sharks, ranged from 0.70‰ to 1.08‰, and from 1.97‰ to 2.89‰, respectively. These high values suggest that both species are feeding in the epipelagic zone (i.e. upper 200 m of the water column). While, blue sharks (Prionace glauca), scalloped hammerhead sharks (Shyrna lewini) and thresher sharks were characterized by lower Δ¹⁹⁹Hg and δ²⁰²Hg values, indicating that these species may focus their foraging behavior on prey of mesopelagic zone (i.e. between 200 and 1000 m depth). In conclusion, the determination of THg concentration provides straight-forward evidence of the human health risks associated with shark consumption, while mercury isotopic compositions constitute a powerful tool to trace the foraging strategies of these marine predators. CAPSULE: A double approach combining Hg concentrations with stable isotopes ratios allowed to assess ontogeny in common shark species in the area of the Galapagos Marine Reserve and the human health risks concern associated to their consumption.

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.

Finding a shadow in the dark: rediscovery of Fugler’s Shadow Snake (Emmochliophis fugleri Fritts & Smith, 1969) after 54 years, with comments on its conservation status, distribution, and the tribe Diaphorolepidini

Herein we report the second known record of Emmochliophis fugleri Fritts & Smith, 1969, present the first color images of the species, extend its known distribution and elevational range, provide the snout–vent and tail lengths of the holotype, and demonstrate that the condition of fused prefrontals is an unreliable diagnostic character for the genus Diaphorolepis. Considering the rarity of this snake as well as the imminent threat that mining poses to the Río Manduriacu Reserve, we recommend a conservation status of Critically Endangered for E. fugleri. 

Temperature dependence of metabolic rate in tropical and temperate aquatic insects: Support for the Climate Variability Hypothesis in mayflies but not stoneflies

A fundamental gap in climate change vulnerability research is an understanding of the relative thermal sensitivity of ectotherms. Aquatic insects are vital to stream ecosystem function and biodiversity but insufficiently studied with respect to their thermal physiology. With global temperatures rising at an unprecedented rate, it is imperative that we know how aquatic insects respond to increasing temperature and whether these responses vary among taxa, latitudes, and elevations. We evaluated the thermal sensitivity of standard metabolic rate in stream-dwelling baetid mayflies and perlid stoneflies across a ~2,000 m elevation gradient in the temperate Rocky Mountains in Colorado, USA, and the tropical Andes in Napo, Ecuador. We used temperature-controlled water baths and microrespirometry to estimate changes in oxygen consumption. Tropical mayflies generally exhibited greater thermal sensitivity in metabolism compared to temperate mayflies; tropical mayfly metabolic rates increased more rapidly with temperature and the insects more frequently exhibited behavioral signs of thermal stress. By contrast, temperate and tropical stoneflies did not clearly differ. Varied responses to temperature among baetid mayflies and perlid stoneflies may reflect differences in evolutionary history or ecological roles as herbivores and predators, respectively. Our results show that there is physiological variation across elevations and species and that low-elevation tropical mayflies may be especially imperiled by climate warming. Given such variation among species, broad generalizations about the vulnerability of tropical ectotherms should be made more cautiously.

Zoological nomenclature: Suggestions to increase stability and facilitate the naming of Clades

Taxon names are at the core of communication related to biodiversity. Thus, systems that regulate such names should prevent unnecessary changes. Unfortunately, the current regulatory codes have some articles that produce confusion or, even, generate name instability. To promote nomenclatural stability, while maintaining a system that effectively conveys information about biological diversity and its evolution, we argue in favor of emendations to the current International Code of Zoological Nomenclature (ICZN). We propose that taxon names should be created within an evolutionary framework; ideally, this would mean including a phylogenetic tree or, at the very least, formulating a hypothesis in words based on explicit arguments (homologous traits) for the evolutionary relatedness of taxa, avoiding subjective perceptions. Additionally, we consider that some relatively minor changes of the ICZN would greatly increase name stability; the most relevant modifications that would facilitate long-term stability are: (i) immutability of the species epithet of species names, (ii) intercalation of unranked taxa between formal Linnaean ranks, (iii) elimination of homonyms in taxon names at the genus-group level, and (iv) inclusion of flexible phylogenetic definitions when supraspecific taxa are named.

Vastly underestimated species richness of Amazonian salamanders (Plethodontidae: Bolitoglossa) and implications about plethodontid diversification

We present data showing that the number of salamander species in Amazonia is vastly underestimated. We used DNA sequences of up to five genes (3 mitochondrial and 2 nuclear) of 366 specimens, 189 corresponding to 89 non-Amazonian nominal species and 177 Amazonian specimens, including types or topotypes, of eight of the nine recognized species in the region. By including representatives of all known species of Amazonian Bolitoglossa, except for one, and 73% of the currently 132 recognized species of the genus, our dataset represents the broadest sample of Bolitoglossa species, specimens, and geographic localities studied to date. We performed phylogenetic analyses using parsimony with tree-alignment and maximum likelihood (ML) with similarity alignment, with indels as binary characters. Our optimal topologies were used to delimit lineages that we assigned to nominal species and candidate new species following criteria that maximize the consilience of the current species taxonomy, monophyly, gaps in branch lengths, genetic distances, and geographic distribution. We contrasted the results of our species-delimitation protocol with those of Automated Barcode Gap Discovery (ABGD) and multi-rate Poisson Tree Processes (mPTP). Finally, we inferred the historical biogeography of South American salamanders by dating the trees and using dispersal-vicariance analysis (DIVA). Our results revealed a clade including almost all Amazonian salamanders, with a topology incompatible with just the currently recognized nine species. Following our species-delimitation criteria, we identified 44 putative species in Amazonia. Both ABGD and mPTP inferred more species than currently recognized, but their numbers (23-49) and limits vary. Our biogeographic analysis suggested a stepping-stone colonization of the Amazonian lowlands from Central America through the Chocó and the Andes, with several late dispersals from Amazonia back into the Andes. These biogeographic events are temporally concordant with an early land bridge between Central and South America (~10-15 MYA) and major landscape changes in Amazonia during the late Miocene and Pliocene, such as the drainage of the Pebas system, the establishment of the Amazon River, and the major orogeny of the northern Andes.

Response to Comment on "Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity"

Lambert et al question our retrospective and holistic epidemiological assessment of the role of chytridiomycosis in amphibian declines. Their alternative assessment is narrow and provides an incomplete evaluation of evidence. Adopting this approach limits understanding of infectious disease impacts and hampers conservation efforts. We reaffirm that our study provides unambiguous evidence that chytridiomycosis has affected at least 501 amphibian species.

Validating anthropogenic threat maps as a tool for assessing river ecological integrity in Andean-Amazon basins

Anthropogenic threat maps are commonly used as a surrogate for the ecological integrity of rivers in freshwater conservation, but a clearer understanding of their relationships is required to develop proper management plans at large scales. Here, we developed and validated empirical models that link the ecological integrity of rivers to threat maps in a large, heterogeneous and biodiverse Andean–Amazon watershed. Through fieldwork, we recorded data on aquatic invertebrate community composition, habitat quality, and physical-chemical parameters to calculate the ecological integrity of 140 streams/rivers across the basin. Simultaneously, we generated maps that describe the location, extent, and magnitude of impact of nine anthropogenic threats to freshwater systems in the basin. Through seven-fold cross-validation procedure, we found that regression models based on anthropogenic threats alone have limited power for predicting the ecological integrity of rivers. However, the prediction accuracy improved when environmental predictors (slope and elevation) were included, and more so when the predictions were carried out at a coarser scale, such as microbasins. Moreover, anthropogenic threats that amplify the incidence of other pressures (roads, human settlements and oil activities) are the most relevant predictors of ecological integrity. We concluded that threat maps can offer an overall picture of the ecological integrity pattern of the basin, becoming a useful tool for broad-scale conservation planning for freshwater ecosystems. While it is always advisable to have finer scale in situ measurements of ecological integrity, our study shows that threat maps provide fast and cost-effective results, which so often are needed for pressing management and conservation actions.

Integrating alpha, beta, and phylogenetic diversity to understand anuran fauna along environmental gradients of tropical forests in western Ecuador

The study of current distribution patterns of amphibian species in South America is of particular interest in areas such as evolutionary ecology and conservation biology. These patterns could be playing an important role in biological interactions, population size, and connectivity, and potential extinction risk in amphibians. Here, we tested the effects of spatial and environmental factors on the variation, turnover, and phylogenetic diversity of anuran amphibian species in tropical forests of western Ecuador. Data for presence/absence of 101 species of 34 genera and 10 families registered in 12 sites (nested in four biogeographic units) were obtained through fieldwork, museum collections, and literature records. We examined the influence of geographical, altitudinal, temperature, and precipitation distances on differences in anuran composition between sites. We found significant positive correlations among all of these variables with anuran distribution. The greatest alpha diversity (species richness) was found in the Equatorial Chocó biogeographic unit. Equatorial Pacific biogeographic unit could act as a transition zone between the Equatorial Chocó and Equatorial Tumbes. The western Andes (Western Cordillera biogeographic unit) was the most dissimilar and exhibited a higher species turnover rate than the other biogeographic units. Our results suggest that precipitation and elevation play a key role in maintaining the diversity of amphibian species in western Ecuador.

Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity

Anthropogenic trade and development have broken down dispersal barriers, facilitating the spread of diseases that threaten Earth's biodiversity. We present a global, quantitative assessment of the amphibian chytridiomycosis panzootic, one of the most impactful examples of disease spread, and demonstrate its role in the decline of at least 501 amphibian species over the past half-century, including 90 presumed extinctions. The effects of chytridiomycosis have been greatest in large-bodied, range-restricted anurans in wet climates in the Americas and Australia. Declines peaked in the 1980s, and only 12% of declined species show signs of recovery, whereas 39% are experiencing ongoing decline. There is risk of further chytridiomycosis outbreaks in new areas. The chytridiomycosis panzootic represents the greatest recorded loss of biodiversity attributable to a disease.

A new species of terrestrial frog of the genus Noblella Barbour, 1930 (Amphibia: Strabomantidae) from the Llanganates-Sangay Ecological Corridor, Tungurahua, Ecuador

We describe a new species of terrestrial frog of the genus Noblella from the eastern versants of the Ecuadorian Andes in the upper Pastaza watershed. Noblella naturetrekii sp. n. differs from its Ecuadorian congeners by the presence of a differentiated tympanic membrane and a weakly defined tympanic annulus, and eyelids with rounded tubercles. In addition, the new species is characterized by its blackish–dark brown ventral coloration scattered with little white dots and the absence of papillae at the tip of the fingers and toes. We provide a detailed description of the call and osteology of the new species. Finally, we present the most complete phylogeny of the genus, which confirms that Noblella is a non-monophyletic group.

Male principal investigators (almost) don't publish with women in ecology and zoology

Representation of women in science drops substantially at each career stage, from early student to senior investigator. Disparities in opportunities for women to contribute to research metrics, such as distinguished speaker events and authorship, have been reported in many fields in the U.S.A. and Europe. However, whether female representation in scientific contributions differs in other regions, such as Latin America, is not well understood. In this study, in order to determine whether female authorship is influenced by gender or institutional location of the last (senior) author or by subfield within ecology, we gathered author information from 6849 articles in ten ecological and zoological journals that publish research articles either in or out of Latin America. We found that female authorship has risen marginally since 2002 (27 to 31%), and varies among Latin American countries, but not between Latin America and other regions. Last author gender predicted female co-authorship across all journals and regions, as research groups led by women published with over 60% female co-authors whereas those led by men published with less than 20% female co-authors. Our findings suggest that implicit biases and stereotype threats that women face in male-led laboratories could be sources of female withdrawal and leaky pipelines in ecology and zoology. Accordingly, we encourage every PI to self-evaluate their lifetime percentage of female co-authors. Female role models and cultural shifts–especially by male senior authors–are crucial for female retention and unbiased participation in science.

Phylogenetic systematics, ecology, and conservation of marsupial frogs (Anura: Hemiphractidae) from the Andes of southern Ecuador, with descriptions of four new biphasic species

We review the systematics of the species of Gastrotheca (Anura: Hemiphractidae) in the highlands of the southern Ecuadorian Andes. We analyzed phylogenetic, morphological, ecological, and acoustic data from populations in the region. We provide an updated phylogenetic hypothesis inferred from a database that contains 42 species of Gastrotheca, and sequences from mitochondrial (12S, 16S, and ND1) and nuclear (POMC and RAG-1) genes. We describe four new endemic biphasic species for Ecuador (Gastrotheca cuencana, G. elicioi, G. turnerorum, and G. yacuri). In addition, we redefine G. lojana, recently resurrected from the synonymy of G. monticola, and redescribe G. litonedis. Furthermore, we describe the tadpoles and ontogenetic color changes in six species (G. cuencana, G. elicioi, G. litonedis, G. lojana, G. pseustes, and G. turnerorum). Also, we describe the calls of seven species (G. cuencana, G. elicioi, G. litonedis, G. lojana, G. pseustes, G. testudinea, and G. yacuri). The phylogenetic relationships estimated here are congruent with previous phylogenetic hypotheses for the group, except for the placement of G. galeata, G. plumbea, G. orophylax, G. nicefori, and G. griswoldi. Because most sister species in Gastrotheca are allopatric, the evolutionarly scenarios that likely have intervened in shaping the diversity are the uplift of the Andes and the formation of cross-Andean river valleys, which probably promoted conditions that acted as dispersal barriers that led to speciation. Many species of Gastrotheca (44%) are highly threatened. Most monophasic species have not been seen since the late 1980s, whereas the highland biphasic species have survived the catastrophic events that led to the disappearance of many other sympatric anurans. Research and conservation actions are urgently needed for all surviving species treated herein, five of which are either Critically Endangered or Endangered because of their restricted distributions (10-1600 km2), habitat destruction and fragmentation, climate change, and pathogens. Two of the new species, G. cuencana, and G. elicioi, mostly are known from the cities of Cuenca and Loja, respectively, where urbanization threatens their survival. In order to call attention to conservation issues, we name one new species to refer to the Yacuri National Park, and the other three in honor of the people from Cuenca, the Turner family, and Elicio E. Tapia, whose actions are helping to halt amphibian extinctions.

A new glassfrog (Centrolenidae) from the Chocó-Andean Río Manduriacu Reserve, Ecuador, endangered by mining

We describe a new glassfrog from Río Manduriacu Reserve, Imbabura Province, on the Pacific slopes of the Ecuadorian Andes. The new species can be distinguished from most other glassfrogs by having numerous yellow spots on the dorsum and lacking membranes among fingers. Both morphological and molecular data support the placement of the species in the genus Nymphargus. We present a new mitochondrial phylogeny of Nymphargus and discuss the speciation patterns of this genus; most importantly, recent speciation events seem to result from the effect of the linearity of the Andes. Finally, although the new species occurs within a private reserve, it is seriously endangered by mining activities; thus, following IUCN criteria, we consider the new species as Critically Endangered.

Evaluating the utility of camera traps in field studies of predation

Artificial prey techniques—wherein synthetic replicas of real organisms are placed in natural habitats—are widely used to study predation in the field. We investigated the extent to which videography could provide additional information to such studies. As a part of studies on aposematism and mimicry of coral snakes (Micrurus) and their mimics, observational data from 109 artificial snake prey were collected from video-recording camera traps in three locations in the Americas (terra firme forest, Tiputini Biodiversity Station, Ecuador; premontane wet forest, Nahá Reserve, Mexico; longleaf pine forest, Southeastern Coastal Plain, North Carolina, USA). During 1,536 camera days, a total of 268 observations of 20 putative snake predator species were recorded in the vicinity of artificial prey. Predators were observed to detect artificial prey 52 times, but only 21 attacks were recorded. Mammals were the most commonly recorded group of predators near replicas (243) and were responsible for most detections (48) and attacks (20). There was no difference between avian or mammalian predators in their probability of detecting replicas nor in their probability of attacking replicas after detecting them. Bite and beak marks left on clay replicas registered a higher ratio of avian:mammalian attacks than videos registered. Approximately 61.5% of artificial prey monitored with cameras remained undetected by predators throughout the duration of the experiments. Observational data collected from videos could provide more robust inferences on the relative fitness of different prey phenotypes, predator behavior, and the relative contribution of different predator species to selection on prey. However, we estimate that the level of predator activity necessary for the benefit of additional information that videos provide to be worth their financial costs is achieved in fewer than 20% of published artificial prey studies. Although we suggest future predation studies employing artificial prey to consider using videography as a tool to inspire new, more focused inquiry, the investment in camera traps is unlikely to be worth the expense for most artificial prey studies until the cost:benefit ratio decreases.

A new (singleton) rainfrog of the Pristimantis myersi Group (Amphibia: Craugastoridae) from the northern Andes of Ecuador

Reserva Las Gralarias is one of the best-studied localities of the Ecuadorian Andes in terms of its batrachofauna. However, as expected in any community, some species are rare and, therefore, their discovery and description are problematic. Herein, based on a single specimen, we describe Pristimantis gralarias sp nov. Even though we are aware of the problems associated to singleton species (i.e., unknown intraspecific variation, limited ecological information), our efforts to finding additional specimens have been unsuccessful. Thus, given the importance of species descriptions in threatened areas (e.g. Andes), and that the new taxon is supported by both morphological and genetic data, we consider that the description is justified. Pristimantis gralarias sp nov is easily distinguished from all other members of the P. myersi group by its long and slender fingers and toes, with discs that are not expanded laterally (or are only slightly expanded). Furthermore, the new species is characterized by having a black venter with minute white spots and a red groin. A molecular phylogeny corroborates the placement of the new species in the P. myersi group and its distinctiveness in relation to other species. Finally, we discuss on the limitations and advantages associated to species descriptions based on one or few specimens.

Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)

The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.

Systematics of South American snail-eating snakes (Serpentes, Dipsadini), with the description of five new species from Ecuador and Peru

A molecular phylogeny of the Neotropical snail-eating snakes (tribe Dipsadini) is presented including 43 (24 for the first time) of the 77 species, sampled for both nuclear and mitochondrial genes. Morphological and phylogenetic support was found for four new species of Dipsas and one of Sibon, which are described here based on their unique combination of molecular, meristic, and color pattern characteristics. Sibynomorphus is designated as a junior subjective synonym of Dipsas. Dipsas latifrontalis and D. palmeri are resurrected from the synonymy of D. peruana. Dipsas latifasciata is transferred from the synonymy of D. peruana to the synonymy of D. palmeri. A new name, D. jamespetersi, is erected for the taxon currently known as Sibynomorphus petersi. Re-descriptions of D. latifrontalis and D. peruana are presented, as well as the first photographic voucher of an adult specimen of D. latifrontalis, along with photographs of all known Ecuadorian Dipsadini species. The first country record of D. variegata in Ecuador is provided and D. oligozonata removed from the list of Peruvian herpetofauna. With these changes, the number of Dipsadini reported in Ecuador increases to 22, 18 species of Dipsas and four of Sibon.

Molecular phylogeny of Atractus (Serpentes, Dipsadidae), with emphasis on Ecuadorian species and the description of three new taxa

We present a molecular phylogeny of snake genus Atractus, with an improved taxon sampling that includes 30 of the 140 species currently recognized. The phylogenetic tree supports the existence of at least three new species in the Pacific lowlands and adjacent Andean slopes of the Ecuadorian Andes, which we describe here. A unique combination of molecular, meristic and color pattern characters support the validity of the new species. With the newly acquired data, we propose and define the Atractus iridescens species group, as well as redefine the Atractus roulei species group. The species Atractus iridescens is reported for the first time in Ecuador, whereas Atractus bocourti and Atractus medusa are removed from the herpetofauna of this country. We provide the first photographic vouchers of live specimens for Atractus multicinctus, Atractus paucidens and Atractus touzeti, along with photographs of 19 other Ecuadorian Atractus species. The current status of Atractus occidentalis and Atractus paucidens is maintained based on the discovery of new material referable to these species. With these changes, the species number reported in Ecuador increases to 27, a number that is likely to increase as material not examined in this work becomes available and included in systematic studies.

A marvelous new glassfrog (Centrolenidae, Hyalinobatrachium) from Amazonian Ecuador

Hyalinobatrachium is a behaviorally and morphologically conserved genus of Neotropical anurans, with several pending taxonomic problems. Using morphology, vocalizations, and DNA, a new species from the Amazonian lowlands of Ecuador is described and illustrated. The new species, Hyalinobatrachium yakusp. n., is differentiated from all other congenerics by having small, middorsal, dark green spots on the head and dorsum, a transparent pericardium, and a tonal call that lasts 0.27-0.4 s, with a dominant frequency of 5219.3-5329.6 Hz. Also, a mitochondrial phylogeny for the genus is presented that contains the new species, which is inferred as sister to H. pellucidum. Conservation threats to H. yakusp. n. include habitat destruction and/or pollution mainly because of oil and mining activities.

Reproductive traits associated with species turnover of amphibians in Amazonia and its Andean slopes

Assembly of ecological communities is important for the conservation of ecosystems, predicting perturbation impacts, and understanding the origin and loss of biodiversity. We tested how amphibian communities are assembled by neutral and niche-based mechanisms, such as habitat filtering. Species richness, β-diversities, and reproductive traits of amphibians were evaluated at local scale in seven habitats at different elevation and disturbance levels in Wisui Biological Station, Morona-Santiago, Ecuador, on the foothills of the Cordillera del Kutukú; and at regional scale using 109 localities across evergreen forests of Amazonia and its Andean slopes (0-3,900 m a.s.l.). At local scale, species composition showed strong differences among habitats, explained mainly by turnover. Reproductive modes occurred differently across habitats (e.g., prevalence of direct developers at high elevation, where breeding in ground level water disappears). At regional scale, elevation was the most important factor explaining the changes in species richness, reproductive trait occurrences, and biotic dissimilarities. Species number in all groups decreased with elevation except for those with lotic tadpoles and terrestrial reproduction stages. Seasonality, annual precipitation, and relative humidity partially explained the occurrence of some reproductive traits. Biotic dissimilarities were also mostly caused by turnover rather than nestedness and were particularly high in montane and foothill sites. Within lowlands, geographic distance explained more variability than elevation. Habitat filtering was supported by the different occurrence of reproductive traits according to elevation, water availability, and breeding microhabitats at both scales, as well as other assembly mechanisms based in biotic interactions at local scale. Human-generated land use changes in Amazonia and its Andean slopes reduce local amphibian biodiversity by alteration of primary forests and loss of their microhabitats and the interaction network that maintains their unique amphibian assemblages with different reproductive strategies.

Diversification of the rainfrog Pristimantis ornatissimus in the lowlands and Andean foothills of Ecuador

Geographic barriers and elevational gradients have long been recognized as important in species diversification. Here, we illustrate an example where both mechanisms have shaped the genetic structure of the Neotropical rainfrog, Pristimantis ornatissimus, which has also resulted in speciation. This species was thought to be a single evolutionary lineage distributed throughout the Ecuadorian Chocó and the adjacent foothills of the Andes. Based on recent sampling of P. ornatissimus sensu lato, we provide molecular and morphological evidence that support the validity of a new species, which we name Pristimantis ecuadorensis sp. nov. The sister species are elevational replacements of each other; the distribution of Pristimantis ornatissimus sensu stricto is limited to the Ecuadorian Chocó ecoregion (< 1100 m), whereas the new species has only been found at Andean localities between 1450–1480 m. Given the results of the Multiple Matrix Regression with Randomization analysis, the genetic difference between P. ecuadorensis and P. ornatissimus is not explained by geographic distance nor environment, although environmental variables at a finer scale need to be tested. Therefore this speciation event might be the byproduct of stochastic historic extinction of connected populations or biogeographic events caused by barriers to dispersal such as rivers. Within P. ornatissimus sensu stricto, morphological patterns and genetic structure seem to be related to geographic isolation (e.g., rivers). Finally, we provide an updated phylogeny for the genus, including the new species, as well as other Ecuadorian Pristimantis.

The complex evolutionary history of the tympanic middle ear in frogs and toads (Anura)

Most anurans possess a tympanic middle ear (TME) that transmits sound waves to the inner ear; however, numerous species lack some or all TME components. To understand the evolution of these structures, we undertook a comprehensive assessment of their occurrence across anurans and performed ancestral character state reconstructions. Our analysis indicates that the TME was completely lost at least 38 independent times in Anura. The inferred evolutionary history of the TME is exceptionally complex in true toads (Bufonidae), where it was lost in the most recent common ancestor, preceding a radiation of >150 earless species. Following that initial loss, independent regains of some or all TME structures were inferred within two minor clades and in a radiation of >400 species. The reappearance of the TME in the latter clade was followed by at least 10 losses of the entire TME. The many losses and gains of the TME in anurans is unparalleled among tetrapods. Our results show that anurans, and especially bufonid toads, are an excellent model to study the behavioural correlates of earlessness, extratympanic sound pathways, and the genetic and developmental mechanisms that underlie the morphogenesis of TME structures.