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.

Understanding the Potential Impact of Different Drug Properties on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission and Disease Burden: A Modelling Analysis

BACKGROUND

The public health impact of the coronavirus disease 2019 (COVID-19) pandemic has motivated a rapid search for potential therapeutics, with some key successes. However, the potential impact of different treatments, and consequently research and procurement priorities, have not been clear.

METHODS

Using a mathematical model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, COVID-19 disease and clinical care, we explore the public-health impact of different potential therapeutics, under a range of scenarios varying healthcare capacity, epidemic trajectories; and drug efficacy in the absence of supportive care.

RESULTS

The impact of drugs like dexamethasone (delivered to the most critically-ill in hospital and whose therapeutic benefit is expected to depend on the availability of supportive care such as oxygen and mechanical ventilation) is likely to be limited in settings where healthcare capacity is lowest or where uncontrolled epidemics result in hospitals being overwhelmed. As such, it may avert 22% of deaths in high-income countries but only 8% in low-income countries (assuming R = 1.35). Therapeutics for different patient populations (those not in hospital, early in the course of infection) and types of benefit (reducing disease severity or infectiousness, preventing hospitalization) could have much greater benefits, particularly in resource-poor settings facing large epidemics.

CONCLUSIONS

Advances in the treatment of COVID-19 to date have been focused on hospitalized-patients and predicated on an assumption of adequate access to supportive care. Therapeutics delivered earlier in the course of infection that reduce the need for healthcare or reduce infectiousness could have significant impact, and research into their efficacy and means of delivery should be a priority.

Signatures of the Venezuelan Humanitarian Crisis in the First Wave of COVID-19: Fuel Shortages and Border Migration

Testing and isolation have been crucial for controlling the COVID-19 pandemic. Venezuela has one of the weakest testing infrastructures in Latin America and the low number of reported cases in the country has been attributed to substantial underreporting. However, the Venezuelan epidemic seems to have lagged behind other countries in the region, with most cases occurring within the capital region and four border states. Here, we describe the spatial epidemiology of COVID-19 in Venezuela and its relation to the population mobility, migration patterns, non-pharmaceutical interventions and fuel availability that impact population movement. Using a metapopulation model of SARS-CoV-2 transmission dynamics, we explore how movement patterns could have driven the observed distribution of cases. Low within-country connectivity most likely delayed the onset of the epidemic in most states, except for those bordering Colombia and Brazil, where high immigration seeded outbreaks. NPIs slowed early epidemic growth and subsequent fuel shortages appeared to be responsible for limiting the spread of COVID-19 across the country.

Estimating large carnivore populations at global scale based on spatial predictions of density and distribution - Application to the jaguar (Panthera onca)

Broad scale population estimates of declining species are desired for conservation efforts. However, for many secretive species including large carnivores, such estimates are often difficult. Based on published density estimates obtained through camera trapping, presence/absence data, and globally available predictive variables derived from satellite imagery, we modelled density and occurrence of a large carnivore, the jaguar, across the species' entire range. We then combined these models in a hierarchical framework to estimate the total population. Our models indicate that potential jaguar density is best predicted by measures of primary productivity, with the highest densities in the most productive tropical habitats and a clear declining gradient with distance from the equator. Jaguar distribution, in contrast, is determined by the combined effects of human impacts and environmental factors: probability of jaguar occurrence increased with forest cover, mean temperature, and annual precipitation and declined with increases in human foot print index and human density. Probability of occurrence was also significantly higher for protected areas than outside of them. We estimated the world's jaguar population at 173,000 (95% CI: 138,000-208,000) individuals, mostly concentrated in the Amazon Basin; elsewhere, populations tend to be small and fragmented. The high number of jaguars results from the large total area still occupied (almost 9 million km2) and low human densities (< 1 person/km2) coinciding with high primary productivity in the core area of jaguar range. Our results show the importance of protected areas for jaguar persistence. We conclude that combining modelling of density and distribution can reveal ecological patterns and processes at global scales, can provide robust estimates for use in species assessments, and can guide broad-scale conservation actions.

Population dynamics of the critically endangered toad Atelopus cruciger and the fungal disease chytridiomycosis

Harlequin toads (Atelopus) are among the most severely impacted amphibians by the emergence of chytridiomycosis, a fungal disease caused by the pathogen Batrachochytrium dendrobatidis (Bd). Many species disappeared while others suffered drastic contractions of their geographic distribution to lower altitudes. A diminished virulence of Bd in warm habitats was proposed to explain the survival of lowland populations of harlequin toads (i.e. thermal refuge hypothesis). To understand the mechanisms that allow some populations to reach an endemic equilibrium with this pathogen, we estimated demographic and epidemiological parameters at one remnant population of Atelopus cruciger in Venezuela using mark-recapture data from 2007–2013. We demonstrated that Bd is highly virulent for A. cruciger, increasing the odds of dying of infected adults four times in relation to uninfected ones and reducing the life expectancy of reproductive toads to a few weeks. Despite an estimated annual loss of 18% of the reproductive population due to Bd-induced mortality, this population has persisted in an endemic equilibrium for the last decade through the large recruitment of healthy adults every year. Given the high vulnerability of harlequin toads to Bd in lowland populations, thermal refuges need to be redefined as habitats of reduced transmission rather than attenuated virulence.

The cane or marine toad, Rhinella marina (Anura, Bufonidae): two genetically and morphologically distinct species

Rhinella marina is a Neotropical toad that has been introduced widely worldwide. Its toxic effects to frog-eating predators threaten the native and domestic fauna of some regions where it has been introduced. Despite previous studies suggesting two genetically distinct cryptic species within R. marina, one east and one west of the Andes, its taxonomic status remained unresolved due to the absence of morphological complementary evidence. For the first time, data from two mitochondrial genes (ND3 and CR) and 23 morphometric landmarks are combined to evaluate the taxonomic status of this species. Our results support the hypothesis of two separate evolutionary lineages within R. marina and demonstrate that these lineages have significantly diverged in skull shape. We identified two distinct morphotypes, one eastern and one Andean western, with no overlapping morphospaces. The geographic pattern of genetic variation was consistent with a stable structured population with no evidence of recent demographic or geographic expansions. The concordance between the observed geographic patterns in morphometric and genic traits calls for the recognition of two species under R. marina name.

Global invasion of Lantana camara: has the climatic niche been conserved across continents?

Lantana camara, a native plant from tropical America, is considered one of the most harmful invasive species worldwide. Several studies have identified potentially invasible areas under scenarios of global change, on the assumption that niche is conserved during the invasion process. Recent studies, however, suggest that many invasive plants do not conserve their niches. Using Principal Components Analyses (PCA), we tested the hypothesis of niche conservatism for L. camara by comparing its native niche in South America with its expressed niche in Africa, Australia and India. Using MaxEnt, the estimated niche for the native region was projected onto each invaded region to generate potential distributions there. Our results demonstrate that while L. camara occupied subsets of its original native niche in Africa and Australia, in India its niche shifted significantly. There, 34% of the occurrences were detected in warmer habitats nonexistent in its native range. The estimated niche for India was also projected onto Africa and Australia to identify other vulnerable areas predicted from the observed niche shift detected in India. As a result, new potentially invasible areas were identified in central Africa and southern Australia. Our findings do not support the hypothesis of niche conservatism for the invasion of L. camara. The mechanisms that allow this species to expand its niche need to be investigated in order to improve our capacity to predict long-term geographic changes in the face of global climatic changes.

Assessing host extinction risk following exposure to Batrachochytrium dendrobatidis

Wildlife diseases are increasingly recognized as a major threat to biodiversity. Chytridiomycosis is an emerging infectious disease of amphibians caused by the fungus Batrachochytrium dendrobatidis (Bd). Using a mathematical model and simulations, we study its effects on a generic riparian host population with a tadpole and adult life stage. An analytical expression for the basic reproduction quotient, Qo, of the pathogen is derived. By sampling the entire relevant parameter space, we perform a statistical assessment of the importance of all considered parameters in determining the risk of host extinction, upon exposure to Bd. We find that Qo not only gives a condition for the initial invasion of the fungus, but is in fact the best predictor for host extinction. We also show that the role of tadpoles, which in some species tolerate infections, is ambivalent. While tolerant tadpoles may provide a reservoir for the fungus, thus facilitating its persistence or even amplifying its outbreaks, they can also act as a rescue buffer for a stressed host population. Our results have important implications for amphibian conservation efforts.

Susceptibility of the endangered frog Dendropsophus meridensis to the pathogenic fungus Batrachochytrium dendrobatidis

Chytridiomycosis is an emerging disease that has driven some amphibian species to extinction while leaving others apparently unharmed. Its causative agent, Batrachochytrium dendrobatidis (Bd), now persists endemically in many amphibian communities. Understanding host species response to Bd infection is critical for managing chytridiomycosis because the epidemiology of this disease is host-specific. Dendropsophus meridensis is an endangered hylid frog endemic to the Venezuelan Andes. This species is sympatric with the American bullfrog Lithobates catesbeianus, an introduced species known to act as a reservoir for Bd. High prevalence of infection and high zoospore burdens in wild populations of D. meridensis in the Venezuelan Andes suggested some tolerance for Bd. However, experimental exposure of post-metamorphic frogs resulted in 53% mortality, a value that represents a 14-fold increase in the odds of dying compared to control frogs. Repeated diagnostics using real-time polymerase chain reaction assays demonstrated that individuals that died accumulated a higher number of zoospores than those that survived, although this value was lower than the mean zoospore burdens observed in natural populations. Given the susceptibility of D. meridensis to a strain of Bd isolated from a nearby population of bullfrogs, we emphasize the need to limit the dispersion of this invasive species.

Immmunological clearance of Batrachochytrium dendrobatidis infection at a pathogen-optimal temperature in the hylid frog Hypsiboas crepitans

Amphibian declines worldwide have been linked to the fungal disease chytridiomycosis. Its causative agent (Batrachochytrium dendrobatidis, hereafter Bd), however, also infects many nondeclining species. Experimental infections have shown species-specific and temperature-dependent frog responses to Bd infection. Although Bd infection may be eliminated by housing amphibians at temperatures above those tolerated by the fungus, the question of whether frogs can eliminate infection under more favorable conditions remains unanswered. Repeated diagnostics using real-time polymerase chain reaction (rt-PCR) assays of postmetamorphic individuals at 28, 38, 45, 53, and 62 days after exposure demonstrated that Hypsiboas crepitans is able to clear infection within a few weeks at 23°C. Thus, we demonstrate a temperature-independent and likely immunological mechanism for the clearance of Bd in a resistant amphibian species. Future studies are needed to determine the generality of this mechanism among amphibians and to describe the immune factors affecting different outcomes of Bd exposure including resistance to infection, tolerance of infection, and clearance of infection.

Reproductive biology and mating system estimates of two Andean melocacti, Melocactus schatzlii and M. andinus (Cactaceae)

BACKGROUND AND AIMS

The genus Melocactus comprises 36 species of globose cacti with the most derived traits in the Cereeae tribe. It is the proper study system to examine what are the most derived reproductive strategies within that tribe. This study aims to characterize the reproductive biology and to estimate the mating system parameters of two Andean melocacti, Melocactus schatzlii and M. andinus.

METHODS

The reproductive attributes of the two species were described, including floral morphology, anthesis patterns, floral rewards, floral visitors and visitation patterns. Levels of self-compatibility and autonomous self-pollination were estimated by hand-pollination experiments. Mating system estimates were obtained by conducting progeny array analyses using isozymes.

KEY RESULTS

The flowers of the two species present the typical hummingbird-pollination syndrome. Despite their morphological resemblance, the two species differ in flower size, pollen and ovule production and anthesis pattern. Their main pollinator agents are hummingbirds, four species in M. schatzlii and one species in M. andinus. Both cacti are self-compatible and capable of self-pollination without the aid of pollen vectors. Population-level outcrossing rate was higher for M. schatzlii (t(m)=0.9) than for M. andinus (t(m)=0.4). At the family level, outcrossing rates for most mothers of M. schatzlii were higher (t(m)>0.8) than for M. andinus (t(m)<0.5).

CONCLUSIONS

Although the two cacti are capable of selfing, M. schatzlii is a predominantly outcrossing species, while M. andinus behaves as a mixed-mating cactus. Hummingbirds are the only pollinators responsible for outcrossing and gene flow events in these species. In their absence, both melocacti set seeds by selfing. Based on its low population size, restricted distribution in Venezuela, low rates of floral visits, and high levels of inbreeding, M. andinus is considered to be an endangered species deserving further study to define its conservation status.

Genetic relationships among some species groups within the genus Lutzomyia (Diptera: Psychodidae)

Molecular data on Lutzomyia are very scarce, despite the fact that this genus includes all the species involved in the transmission of leishmaniasis in America. We examine the genetic relationships among eight morphologic groups within the Lutzomyia genus and two Brumptomyia species, using nine enzyme loci and the last 285 basepairs of the mitochondrial cytochrome b gene. The structure of the genetic variation among the species analyzed indicated a closer genetic relationship among members of a morphologic group than between members of different groups. The lower levels of variation recorded among these groups compared with that between Brumptomyia and Lutzomyia suggest a subgeneric status for all of these groups, including Psychodopygus. A maximum likelihood tree for the allozyme data and a neighbor-joining consensus tree for the mitochondrial DNA sequences showed a general agreement with morphologic groups, with only minor differences. Nyssomyia, Verrucarum and Micropygomyia formed separate monophyletic groups. Lutzomyia could not be separated from Psathyromyia, and both Migonei species, L. dubitans and L. migonei, grouped in different clades according to the host species they are found on.

Ability of cellulose acetate and polyacrylamide enzyme electrophoresis to separate 13 species of phlebotomine sand flies (Diptera: Psychodidae) from Venezuela

The detection of cryptic species by biochemical methods indicates that within the phlebotomine fauna morphological data are not always adequate for species diagnosis. Cellulose acetate and polyacrylamide enzyme electrophoresis methods were compared for their effectiveness in identifying 13 species of Venezuelan phlebotomine sand flies and resolving alleles. Eight diagnostic loci unambiguously separated these 13 species of sand flies. Although acrylamide was as effective as cellulose acetate in species separation, differences were detected in the resolution of some alleles. Cellulose acetate identified more alleles at Ak and Fum, and resolved better at Pgm, whereas acrylamide identified more alleles at Gpi, Mdh, and Me. Therefore, erroneous species diagnoses may occur, if diagnostic loci detected by one technique are used by a second technique without adequate reference standards.

Phlebotomine sandflies in Venezuela. V. Review of the genus Brumptomyia (Diptera: Psychodidae), with description of the female of Brumptomyia devenanzii, re-description of the male and isozymatic profile

Recently collected data on the Venezuelan species of the genus Brumptomyia are used to produce an updated review of these sandflies. At present, four species are recognized in Venezuela: B. devenanzii, B. beaupertuyi, B. avellari and B. pintoi. A key for the males is given and the geographical distribution of each of these species is outlined. The previously unknown female of B. devenanzii is described, the male is re-described, and the genetic variability (based on 11 enzymatic loci) of this species and of B. beaupertuyi (a sympatric species in Rancho Grande, the type locality of B. devenanzii) are reported. Fixed allelic differences in one diagnostic locus (adenylate kinase; Ak), between sympatric and allopatric populations, allowed for the unequivocal separation of both sexes of B. beaupertuyi from those of B. devenanzii. Significant inter-specific differences were also detected in the allele frequencies of malate dehydrogenase (Mdh-2) and decarboxylating malate dehydrogenase (Me). For B. devenanzii, mean heterozygosity and mean number of alleles per locus ranged from 2.0%-3.1% and 1.1-1.5, respectively. The corresponding values for B. beaupertuyi were 3.8% and 1.2.

Gene flow between natural and domestic populations of Lutzomyia longipalpis (Diptera: Psychodidae) in a restricted focus of American visceral leishmaniasis in Venezuela

The epidemiology of the visceral leishmaniasis in the Americas is associated with both a natural and a domestic cycle. The existence of reproductively isolated populations of Lutzomyia longipalpis (Lutz & Neiva), and the scarcity of records of this species from natural habitats in areas where it has been associated with domestic habitats indicated that natural populations could be genetically distinct from domestic ones. Therefore, we compared the genetic structure and estimated the gene flow between L. longipalpis from domestic and peridomestic habitat and from an adjacent undisturbed natural environment along a 1.2-km transect. The analyses were performed on electrophoretic data from eight isozyme loci. The absence of fixed differences in the diagnostic loci Ak and Hk indicated that all specimens belonged to one of the two cryptic species identified in Venezuela. The average number of alleles per locus ranged from 2.0 to 2.9 and the average heterozygosity ranged from 7.8 to 13.4%. No differences were detected in the genetic structure of this species from domestic or peridomestic habitats and those trapped as far as 1.2 km from human dwellings. Nm, estimated from Wright's Fst, indicated that at least 208 individuals per generation migrated between the peridomestic habitat and a 1.2-km distant point to maintain the observed similarities in allelic frequencies. This high rate of gene flow indicated that this species has high migration rates between domestic and natural environments, and has the potential to transport for Leishmania from natural to domestic environments.

A possible role of bats as a blood source for the Leishmania vector Lutzomyia longipalpis (Diptera: Psychodidae)

Some evidence suggests that bats may provide an alternative blood source for Lutzomyia longipalpis, the main vector of American visceral leishmaniasis. Feeding trials were conducted to determine whether L. longipalpis feeds on captive bats. The high feeding success indicated that L. longipalpis is capable of feeding on at least four species of bats. Implications for the epidemiology of leishmaniases are discussed.

Occurrence of sibling species of Lutzomyia longipalpis (Diptera: Psychodidae) in Venezuela: first evidence from reproductively isolated sympatric populations

The delimitation of cryptic species within the main vector of the American visceral leishmaniasis, Lutzomyia longipalpis, remains a topic of controversy. An analysis of genetic variability based on 8 enzymatic loci revealed fixed differences in 2 diagnostic loci, adenylate kinase (Ak) and hexokinase (Hk), between sympatric and allopatric populations at 4 localities in Venezuela. The absence of heterozygotes for these 2 loci within 1 locality indicates, for the first time, the presence of 2 sympatric reproductively isolated populations or cryptic species within L. longipalpis. Significant differences were also detected between these cryptic species in the allele frequencies of glucose-6-phosphate isomerase (Gpi) and malate dehydrogenase, decarboxylating (Me). One species showed mean heterozygosities that ranged between 6.6% and 6.7%, with 1.6-1.9 alleles detected per locus, while the other had mean heterozygosities that ranged from 4.3% to 6.3%, with 1.3-1.6 alleles per locus. Comparisons of isozyme profiles with published data suggests that 1 species is similar to the L. longipalpis described in Colombian and Brazilian populations, whereas the other has not been previously reported.

Population genetic structure of a three-host tick, Amblyomma dissimile, in eastern Venezuela

Patterns of genetic variation for the tick Amblyomma dissimile were analyzed from a total of 200 ticks collected on 12 toads (Bufo marinus), 14 snakes (Boa constrictor), and 8 lizards (Iguana iguana) at 11 localities. The analyses were performed on electrophoretic data from 8 isozyme loci. Mean heterozygosity per locus was 6% (+/-3.1) per population. Differences in allelic frequencies among ticks from different individual hosts were the major source of genetic variability in this study. Host species was a smaller source of genetic variation. Genetic distances between localities varied according to which host species was present in each locality, and these appeared to be related to the extent of habitat overlap between host species. The smallest genetic distances between samples from different host species were recorded for I. iguana and B. constrictor. In contrast, the genetic distances between tick samples from B. marinus and either of the reptile species were significantly larger than between tick samples from this amphibian species. Ecological variables or the geographic distance did not explain the local patterns of differentiation observed in A. dissimile. Major genetic differences between island and mainland sites (0.03702) suggested an association between genetic distances and geographic isolation. The consistency between patterns of genetic variation and those of host home range overlap suggests that host dispersion is the main force structuring the genetic variation within this tick species.

Genetic markers for the identification of two tick species, Amblyomma dissimile and Amblyomma rotundatum

Genetic markers are described for 2 species of reptile and amphibian ticks, Amblyomma dissimile and Amblyomma rotundatum, by allozyme electrophoresis. Fixed allelic differences in 4 out of the 8 examined loci allowed the unequivocal separation of both of these species. A strong correlation was found between these genetic markers and the relative size of the spurs in coxae IV but not with the punctuation pattern of the scutum. Moreover, no overlap was found in the distribution of relative spur sizes between samples of both species. The percent polymorphic loci and the mean percent heterozygosity per locus for A. rotundatum was considerably lower than that for A. dissimile. Differences in the amount of genetic variability may be related to their modes of reproduction.

Density estimates of cane toads from native populations based on mark-recapture data

The cane toad (Bufo marinus) has received considerable attention because of its rapid spread in Australia and the potential threat it may represent to native species. Although the introduction of pathogens from native populations is now being considered to control this species, population estimates based on comparable methods that demonstrate that native populations are in fact less dense than the introduced ones are not available. Accurate population estimates are necessary to evaluate potential techniques for the control of the cane toad. We estimated population densities of cane toads over a wide range of habitat types and climate conditions by means of mark-recapture data. The capture history and location of toads each night were analysed to explore the validity of some of the assumptions of mark-recapture models. Because migrations, deaths and recruitment over three nights appear to be unimportant, populations may be legitimately regarded as closed for that period. However, cane toads seem highly sensitive to disturbance effects due to trapping andlor handling. Consequently, density estimates based on removal methods seem the most reliable because they are not sensitive to handling and trapping effects. Similarly, analyses of residuals of regressions between 1-night counts and density estimates suggested that toad nightly activity is affected by the air temperature during sampling. However, only 60% of the variation in estimated densities can be predicted by 1-night counts and air temperature. Estimates of population density over a wide range of habitats in South America were one order of magnitude lower than estimates in Australia. We speculate on the possible factors that may account for the lower densities in populations in the native range of the species.