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Recognizing the influence of pathogen diversity on infection dynamics is crucial for mitigating emerging infectious diseases. Characterising such diversity is often complex, for instance when multiple pathogen variants exist that interact differently with the environment and host. Here, we explore genotypic and phenotypic variation of Batrachochytrium salamandrivorans (Bsal), an emerging fungal pathogen that is driving declines among an increasing number of European amphibian species. For thirteen isolates, spanning most of the known temporal and geographical Bsal range in Europe, we mapped phenotypic diversity through numerous measurements that describe varying reproductive rates in vitro across a range of temperatures. Bsal isolates are revealed to have different thermal optima and tolerances, with phenotypic variation correlating with genomic diversity. Using a mechanistic niche model of the fire salamander (Salamandra salamandra) as an example, we illustrate how host steady-state body temperature and Bsal thermal range variation may influence pathogen growth through space and time across Europe. Our combined findings show how the identity of emergent pathogen variants may strongly influence when and which host populations are most at risk.

Abstract Biodiversity loss is extreme in amphibians. Despite ongoing conservation action, it is difficult to determine where we stand in overcoming their extinction crisis. Among the most threatened amphibians are the 131 Neotropical harlequin toads. Many of them declined since the 1980s with several considered possibly extinct. Recently, more than 30 species have been rediscovered, raising hope for a reversing trend in the amphibian extinction crisis. We use past and present data available for harlequin toads (Atelopus), to examine whether the amphibian extinction crisis is still in an emergency state. Since 2004 no species has improved its population status, suggesting that recovery efforts have not been successful. Threats include habitat change, pathogen spread and climate change. More mitigation strategies need implementation, especially habitat protection and disease management, combined with captive conservation breeding. With harlequin toads serving as a model, it is clear that the amphibian extinction crisis is still underway.

Skin fungi are among the most dangerous drivers of global amphibian declines, and few mitigation strategies are known. For Batrachochytrium salamandrivorans (Chytridiomycota), available treatments rely on temperature, partially combined with antifungal drugs. We report the clearance of B. salamandrivorans in 2 urodelan species using a solely drug-based approach.

Abstract Background The morphology of anuran larvae is suggested to differ between species with tadpoles living in standing (lentic) and running (lotic) waters. To explore which character combinations within the general tadpole morphospace are associated with these habitats, we studied categorical and metric larval data of 123 (one third of which from lotic environments) Madagascan anurans. Results Using univariate and multivariate statistics, we found that certain combinations of fin height, body musculature and eye size prevail either in larvae from lentic or lotic environments. Conclusion Evidence for adaptation to lotic conditions in larvae of Madagascan anurans is presented. While lentic tadpoles typically show narrow to moderate oral discs, small to medium sized eyes, convex or moderately low fins and non-robust tail muscles, tadpoles from lotic environments typically show moderate to broad oral discs, medium to big sized eyes, low fins and a robust tail muscle.

Abstract Introduction In patients with common variable immunodeficiency (CVID), immunological response is compromised. Knowledge about COVID‐19 in CVID patients is sparse. We, here, synthesize current research addressing the level of threat COVID‐19 poses to CVID patients and the best‐known treatments. Method Review of 14 publications. Results The number of CVID patients with moderate to severe (~29%) and critical infection courses (~10%), and the number of fatal cases (~13%), are increased compared to the general picture of COVID‐19 infection. However, this might be an overestimate. Systematic cohort‐wide studies are lacking, and asymptomatic or mild cases among CVID patients occur that can easily remain unnoticed. Regular immunoglobulin replacement therapy was administered in almost all patients, potentially explaining why the numbers of critical and fatal cases were not higher. In addition, the application of convalescent plasma was demonstrated to have positive effects. Conclusions COVID‐19 poses an elevated threat to CVID patients. However, only systematic studies can provide robust information on the extent of this threat. Regular immunoglobulin replacement therapy is beneficial to combat COVID‐19 in CVID patients, and best treatment after infection includes the use of convalescent plasma in addition to common medication.

Atelopus is a species-rich group of Neotropical bufonids. Present knowledge on bioacoustics in this genus is relatively poor, as vocalisations have been described in only about one fifth of the ca. 100 species known. All studied members of the genus produce vocalisations although, with a few exceptions, most species lack a middle ear. Nonetheless, hearing has been demonstrated even in earless Atelopus making bioacoustics in these toads an inspiring research field. So far, three structural call types have been identified in the genus. As sympatry is uncommon in Atelopus, calls of the same type often vary little between species. Based on recordings from the 1980s, we describe vocalisations of three Venezuelan species (A. carbonerensis, A. mucubajiensis, A. tamaense) from the Cordillera de Mérida, commonly known as the Andes of Venezuela and the Tamá Massif, a Venezuelan spur of the Colombian Cordillera Oriental. Vocalisations correspond, in part, to the previously identified call types in Atelopus. Evaluation of the vocalisations of the three species presented in this study leads us to recognise a fourth structural call type for the genus. With this new addition, the Atelopus acoustic repertoire now includes (1) pulsed calls, (2) pure tone calls, (3) pulsed short calls and (4) pure tone short calls. The call descriptions provided here are valuable contributions to the bioacoustics of these Venezuelan Atelopus species, since all of them have experienced dramatic population declines that limit possibilities of further studies.

Abstract Background Many intriguing questions about predator-prey interactions can be addressed by using clay models of prey animals. These are placed in the field to test predators’ avoidances or preferences (testing e.g. color or shape) or to gain insights into predator identity. Modeling clay allows teeth, beak and jaw marks to remain on the model for identification. First used 30 years ago, clay models are now widely deployed. Ever since, the complexity of hypotheses, modeled species as well as the number of clay models used per study has increased. Although clay models are a valuable research tool, the method has limitations. Some questions cannot be addressed with these experiments, yet there is potential for improvement. Main body We focus on the following aspects that need attention for clay model studies (CMS) in the future: (1) Use of proper clay materials, (2) how to standardize attack identification, (3) limitations of clay model studies, (4) use of clay models beyond predation experiments and (5) the next generation of clay model studies. Conclusion We conclude that certain aspects of the clay model paradigm urgently need greater standardization. We advocate the use of harmless clay products and non-toxic inks, as well as having a neutral person to evaluate the marks left in the clay against pre-defined inclusion criteria. Further we suggest to use experimental data more cautiously in respect to evolutionary explanations, to use clay studies in detection experiments and to develop methods for attacker identification based on predator salivary DNA.

Abra de Zamora is an important biodiversity hotspot in southern Ecuador. Between 1938 and 2010, eleven species of frogs were described from here: Lynchius flavomaculatus, Gastrotheca psychrophila, Pristimantis balionotus, P. colodactylus, P. cryptomelas, P. percultus, P. versicolor, P. vidua, Telmatobius cirrhacelis, P. andinognomus, and Atelopus podocarpus. Unfortunately, many of these species were not re-encountered after their original description, and for the majority DNA samples were not available, making their phylogenetic position unknown. In this study, we assess the current state of the amphibians from Abra de Zamora, by: i. redescribing the species which were first reported from the area, by contributing genetic delimitation (for L. flavomaculatus, P. balionotus, P. colodactylus, P. percultus, and P. vidua), release call (L. flavomaculatus) and advertisement call descriptions (for P. balionotus, P. vidua and P. versicolor); ii. presenting an updated amphibian species list of Abra de Zamora, with the description of two additional Pristimantis species; iii. updating the distribution of these species, including data collected in similar montane habitats from surrounding areas; and iv. amending recommendations regarding their conservation status.

Lycian salamanders (genus Lyciasalamandra) constitute an exceptional case of micro-endemism of an amphibian species on the Asian Minor mainland. These viviparous salamanders are confined to karstic limestone formations along the southern Anatolian coast and some islands. We here study the genetic differentiation within and among 118 populations of all seven Lyciasalamandra species across the entire genus' distribution. Based on circa 900 base pairs of fragments of the mitochondrial 16SrDNA and ATPase genes, we analysed the spatial haplotype distribution as well as the genetic structure and demographic history of populations. We used 253 geo-referenced populations and CHELSA climate data to infer species distribution models which we projected on climatic conditions of the Last Glacial Maximum (LGM). Within all but one species, distinct phyloclades were identified, which only in parts matched current taxonomy. Most haplotypes (78%) were private to single populations. Sometimes population genetic parameters showed contradicting results, although in several cases they indicated recent population expansion of phyloclades. Climatic suitability of localities currently inhabited by salamanders was significantly lower during the LGM compared to recent climate. All data indicated a strong degree of isolation among Lyciasalamandra populations, even within phyloclades. Given the sometimes high degree of haplotype differentiation between adjacent populations, they must have survived periods of deteriorated climates during the Quaternary on the spot. However, the alternative explanation of male biased dispersal combined with a pronounced female philopatry can only be excluded if independent nuclear data confirm this result.

The amphibian skin disease chytridiomycosis, caused by the pathogenetic fungus Batrachochytrium dendrobatidis (Bd) has become one of the major contributors to global amphibian population declines and extinctions. This fungus has spread globally and has caused mortalities in nearly every continent. In South America, Suriname, Guyana and Paraguay are among the remaining three countries where Bd has not been detected to date. To complete the assessment of the possible presence of Bd in Suriname, 205 specimens from the Zoological Collection of Suriname, compromising 6 frog families and 15 genera were sampled for chytrid fungus. No specimens were found to be infected by this fungus and as such the outcome strengthens the previous result of field sampling that there is no support that Bd has spread to Suriname.

Common variable immunodeficiency (CVID), although the most common primary immunodeficiency in humans, is a rare disease. We explored the spatial global distribution and country-wise prevalence of CVID, based on published data and those available from databases. As a country’s medical progress is linked to its technological and socio-economic developmental status, we expected that observed CVID prevalence was linked to human wellbeing. To assess this, we examined the correlation of observed CVID prevalence and the UNDP Human Development Index (HDI), which is a key measure of human development. Seventy-four data sets from 47 countries were available (most of them no older than 10 years). Analyses revealed that observed CVID prevalence ranged from 0.001 to 3.374 per 100,000 (mean 0.676±0.83) and was highest in “high” HDI countries (Spearman’s rho=0.757). Observed prevalence was particularly high in countries where immunodeficiencies are systematically documented in registers. In “low” and “middle” HDI countries, CVID awareness is extremely poor. Assuming that true CVID prevalence does not differ among countries, this study, though preliminary, provides evidence that the discrepancy between observed and (unknown) true prevalence can be clearly linked to the countries’ developmental status. As a potential alternative explanation, we briefly discuss the possibility that variation in CVID prevalence is related to human genetic lineage.

We reconstructed nearly complete mitogenomes for three species of poison frogs, Dendrobates auratus, D. leucomelas, and D. tinctorius, from RNAseq data. We recovered the 13 protein-coding genes, 22 tRNA genes (except tRNA-Val for D. leucomelas), and two rRNA genes for all three species, plus partial sequences of the control region. The order of genes agrees with that known from a previously sequenced D. auratus, being the most commonly found for neobatrachian frogs. Based on full-sibling comparisons we estimate the probable error rate of Illumina-RNAseq reconstructed mitogenomes of up to 0.15%.

Emerging fungal diseases can drive amphibian species to local extinction. During 2010–2016, we examined 1,921 urodeles in 3 European countries. Presence of the chytrid fungus Batrachochytrium salamandrivorans at new locations and in urodeles of different species expands the known geographic and host range of the fungus and underpins its imminent threat to biodiversity.

Native biodiversity on the Galapagos Archipelago is severely threatened by invasive alien species. On Santa Cruz Island, the abundance of introduced plant species is low in the arid lowlands of the Galapagos National Park, but increases with elevation into unprotected humid highlands. Two common alien plant species, guava (Psidium guajava) and passion fruit (Passiflora edulis) occur at higher elevations yet their seeds are dispersed into the lowlands by migrating Galapagos tortoises (Chelonoidis spp.). Tortoises transport large quantities of seeds over long distances into environments in which they have little or no chance of germination and survival under current climate conditions. However, climate change is projected to modify environmental conditions on Galapagos with unknown consequences for the distribution of native and introduced biodiversity. We quantified seed dispersal of guava and passion fruit in tortoise dung piles and the distribution of adult plants along two elevation gradients on Santa Cruz to assess current levels of 'wasted' seed dispersal. We computed species distribution models for both taxa under current and predicted future climate conditions. Assuming that tortoise migratory behaviour continues, current levels of "wasted" seed dispersal in lowlands were projected to decline dramatically in the future for guava but not for passion fruit. Tortoises will facilitate rapid range expansion for guava into lowland areas within the Galapagos National Park where this species is currently absent. Coupled with putative reduction in arid habitat for native species caused by climate change, tortoise driven guava invasion will pose a serious threat to local plant communities.

Emerging infectious diseases cause extirpation of wildlife populations. We use an epidemiological model to explore the effects of a recently emerged disease caused by the salamander-killing chytrid fungus Batrachochytrium salamandrivorans (Bsal) on host populations, and to evaluate which mitigation measures are most likely to succeed. As individuals do not recover from Bsal, we used a model with the states susceptible, latent and infectious, and parametrized the model using data on host and pathogen taken from the literature and expert opinion. The model suggested that disease outbreaks can occur at very low host densities (one female per hectare). This density is far lower than host densities in the wild. Therefore, all naturally occurring populations are at risk. Bsal can lead to the local extirpation of the host population within a few months. Disease outbreaks are likely to fade out quickly. A spatial variant of the model showed that the pathogen could potentially spread rapidly. As disease mitigation during outbreaks is unlikely to be successful, control efforts should focus on preventing disease emergence and transmission between populations. Thus, this emerging wildlife disease is best controlled through prevention rather than subsequent actions.

Species are being lost at increasing rates due to anthropogenic effects, leading to the recognition that we are witnessing the onset of a sixth mass extinction. Emerging infectious disease has been shown to increase species loss and any attempts to reduce extinction rates need to squarely confront this challenge. Here, we develop a procedure for identifying amphibian species that are most at risk from the effects of chytridiomycosis by combining spatial analyses of key host life-history variables with the pathogen's predicted distribution. We apply our rule set to the known global diversity of amphibians in order to prioritize pecies that are most at risk of loss from disease emergence. This risk assessment shows where limited conservation funds are best deployed in order to prevent further loss of species by enabling ex situ amphibian salvage operations and focusing any potential disease mitigation projects.

The chytrid fungus Batrachochytrium salamandrivorans (Bsal) is a dangerous pathogen to salamanders and newts. Apparently native to Asia, it has recently been detected in Western Europe where it is expected to spread and to have dramatic effects on naïve hosts. Since 2010, Bsal has led to some catastrophic population declines of urodeles in the Netherlands and Belgium. More recently, it has been discovered in additional, more distant sites including sites in Germany. With the purpose to contribute to a better understanding of Bsal, we modelled its potential distribution in its invasive European range to gain insights about the factors driving this distribution. We computed Bsal Maxent models for two predictor sets, which represent different temporal resolutions, using three different background extents to account for different invasion stage scenarios. Beside 'classical' bioclimate, we employed weather data, which allowed us to emphasize predictors in accordance with the known pathogen's biology. The most important predictors as well as spatial predictions varied between invasion scenarios and predictor sets. The most reasonable model was based on weather data and the scenario of a recent pathogen introduction. It identified temperature predictors, which represent optimal growing conditions and heat limiting conditions, as the most explaining drivers of the current distribution. This model also predicted large areas in the study region as suitable for Bsal. The other models predicted considerably less, but shared some areas which we interpreted as most likely high risk zones. Our results indicate that growth relevant temperatures measured under laboratory conditions might also be relevant on a macroecological scale, if predictors with a high temporal resolution and relevance are used. Additionally, the conditions in our study area support the possibility of a further Bsal spread, especially when considering that our models might tend to underestimate the potential distribution of Bsal.

The evolution of chemical communication and the discrimination between evolved functions (signals) and unintentional releases (cues) are among the most challenging issues in chemical ecology. The accurate classification of inter- or intraspecific chemical communication is often puzzling. Here we report on two different communication systems triggering the same parental care behavior in the poison frog Ranitomeya variabilis. This species deposits its tadpoles and egg clutches in phytotelmata and chemically recognizes and avoids sites with both predatory conspecific and non-predatory heterospecific tadpoles (of the species Hyloxalus azureiventris). Combining chemical analyses with in-situ bioassays, we identified the molecular formulas of the chemical compounds triggering this behavior. We found that both species produce distinct chemical compound combinations, suggesting two separate communication systems. Bringing these results into an ecological context, we classify the conspecific R. variabilis compounds as chemical cues, advantageous only to the receivers (the adult frogs), not the emitters (the tadpoles). The heterospecific compounds, however, are suggested to be chemical signals (or cues evolving into signals), being advantageous to the emitters (the heterospecific tadpoles) and likely also to the receivers (the adult frogs). Due to these assumed receiver benefits, the heterospecific compounds are possibly synomones which are advantageous to both emitter and receiver ‒ a very rare communication system between animal species, especially vertebrates.

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.

The distribution of modern symbiont-bearing larger foraminifera is confined to tropical and subtropical shallow water marine habitats and a narrow range of environmental variables (e.g. temperature). Most of today's taxa are restricted to tropical and subtropical regions (between 30°N and 30°S) and their minimum temperature limits are governed by the 14 to 20°C isotherms. However, during times of extensive global warming (e.g., the Eocene and Miocene), larger foraminifera have been found as far north as 50°N (North America and Central Europe) as well as towards 47°S in New Zealand. During the last century, sea surface temperatures have been rising significantly. This trend is expected to continue and climate change scenarios for 2050 suggest a further increase by 1 to 3°C. We applied Species Distribution Models to assess potential distribution range changes of three taxa of larger foraminifera under current and future climate. The studied foraminifera include Archaias angulatus, Calcarina spp., and Amphistegina spp., and represent taxa with regional, superregional and global distribution patterns. Under present environmental conditions, Amphistegina spp. shows the largest potential distribution, apparently due to its temperature tolerance. Both Archaias angulatus and Calcarina spp. display potential distributions that cover currently uninhabited regions. Under climate conditions expected for the year 2050, all taxa should display latitudinal range expansions between 1 to 2.5 degrees both north- and southward. The modeled range projections suggest that some larger foraminifera may colonize biogeographic regions that so far seemed unsuitable. Archaias angulatus and Calcarina spp. also show an increase in habitat suitability within their native occurrence ranges, suggesting that their tolerance for maximum temperatures has yet not been fully exploited and that they benefit from ocean warming. Our findings suggest an increased role of larger foraminifera as carbonate producers and reef framework builders in future oceans.

Species-range expansions are a predicted and realized consequence of global climate change. Climate warming and the poleward widening of the tropical belt have induced range shifts in a variety of marine and terrestrial species. Range expansions may have broad implications on native biota and ecosystem functioning as shifting species may perturb recipient communities. Larger symbiont-bearing foraminifera constitute ubiquitous and prominent components of shallow water ecosystems, and range shifts of these important protists are likely to trigger changes in ecosystem functioning. We have used historical and newly acquired occurrence records to compute current range shifts of Amphistegina spp., a larger symbiont-bearing foraminifera, along the eastern coastline of Africa and compare them to analogous range shifts currently observed in the Mediterranean Sea. The study provides new evidence that amphisteginid foraminifera are rapidly progressing southwestward, closely approaching Port Edward (South Africa) at 31°S. To project future species distributions, we applied a species distribution model (SDM) based on ecological niche constraints of current distribution ranges. Our model indicates that further warming is likely to cause a continued range extension, and predicts dispersal along nearly the entire southeastern coast of Africa. The average rates of amphisteginid range shift were computed between 8 and 2.7 km year(-1), and are projected to lead to a total southward range expansion of 267 km, or 2.4° latitude, in the year 2100. Our results corroborate findings from the fossil record that some larger symbiont-bearing foraminifera cope well with rising water temperatures and are beneficiaries of global climate change.

BACKGROUND: Species Distribution Models (SDMs) aim on the characterization of a species' ecological niche and project it into geographic space. The result is a map of the species' potential distribution, which is, for instance, helpful to predict the capability of alien invasive species. With regard to alien invasive species, recently several authors observed a mismatch between potential distributions of native and invasive ranges derived from SDMs and, as an explanation, ecological niche shift during biological invasion has been suggested. We studied the physiologically well known Slider turtle from North America which today is widely distributed over the globe and address the issue of ecological niche shift versus choice of ecological predictors used for model building, i.e., by deriving SDMs using multiple sets of climatic predictor. PRINCIPAL FINDINGS: In one SDM, predictors were used aiming to mirror the physiological limits of the Slider turtle. It was compared to numerous other models based on various sets of ecological predictors or predictors aiming at comprehensiveness. The SDM focusing on the study species' physiological limits depicts the target species' worldwide potential distribution better than any of the other approaches. CONCLUSION: These results suggest that a natural history-driven understanding is crucial in developing statistical models of ecological niches (as SDMs) while "comprehensive" or "standard" sets of ecological predictors may be of limited use.