Amphibian population genetics in agricultural landscapes: does viniculture drive the population structuring of the European common frog (Rana temporaria)?

Impacts of horticultural environments on Rhinella arenarum (Anura, Bufonidae) populations: exploring genocytotoxic damage and demographic life history traits

Horticulture poses a significant ecological risk, as agrochemicals are applied more frequently and in larger quantities per unit of production compared to extensive crop fields. The native amphibian Rhinella arenarum serves as a reliable bioindicator of environmental health. This study aimed to assess genocytotoxic damage and demographic life history traits of R. arenarum inhabiting horticultural environments. Sampling was conducted in suburban sites in central Argentina: H1 and H2 (sites associated with horticultural activity) and a reference site, RS. Environmental parameters were recorded, and the frequency of micronuclei (Mn), nuclear abnormalities (ENA), and indicators of cytotoxic damage were determined in tadpoles and adults. Demographic variables (age at maturity, longevity, potential reproductive lifespan, size at maturity, modal lifespan) were calculated. The highest nitrate and phosphate values, along with low dissolved oxygen values, were recorded at sites H1 and H2. Organisms inhabiting horticultural environments exhibited higher frequencies of Mn and ENA, surpassing those recorded in previous studies on tadpoles from sites with extensive crop production. Size at maturity and age at maturity of females, as well as size at maturity, longevity, mean age, and mean adult SVL of males, were lower in horticultural sites. The results support the hypothesis that anuran populations inhabiting horticultural environments demonstrate a diminished health status attributed to subpar environmental quality. Monitoring endpoints at different biological levels provides information on the ecotoxicological risk for amphibians and human populations inhabiting nearby areas.

Fine-scale spatial genetic structure and dispersal among Italian smooth newt populations in a rural landscape

Amphibians are particularly sensitive to habitat loss and fragmentation caused by the intensification and modernization of farming occurring in the second half of the twentieth century in the Mediterranean basin. However, artificial water bodies, associated with traditional husbandry, proved to be important surrogate for amphibian feeding and reproduction. Here, multilocus genotypes were used to investigate the spatial population structure of Lissotriton vulgaris meridionalis and the role of drinking troughs in supporting viable breeding populations within a rural landscape interested by traditional husbandry and agriculture. Our genetic analysis highlighted the conservation value and the potential stepping-stone function of artificial aquatic sites in the dispersal of the species and for the gene flow maintenance. Indeed, populations of drinking troughs show allelic richness and heterozygosity levels comparable to those from natural ponds and there is no great evidence of genetic bottlenecks. A complex system of artificial aquatic sites and few natural wetlands was identified sustaining a well-structured network of demes highly interconnected with themselves and natural aquatic sites. The conservation of the identified genetic clusters may be useful to prevent further population declines and future loss of genetic diversity within the study area characterized by scarce natural wetlands that frequently dried because of agricultural practices and strong seasonality. Site-specific protection measures are needed to contrast the progressive disappearance of drinking troughs observed in the last years in Italy because of the abandonment of traditional farming practices in favour of modern agriculture and intensive farming.

Phenology and plasticity can prevent adaptive clines in thermal tolerance across temperate mountains: The importance of the elevation-time axis

Critical thermal limits (CT_max and CT_min) decrease with elevation, with greater change in CT_min, and the risk to suffer heat and cold stress increasing at the gradient ends. A central prediction is that populations will adapt to the prevailing climatic conditions. Yet, reliable support for such expectation is scant because of the complexity of integrating phenotypic, molecular divergence and organism exposure. We examined intraspecific variation of CT_max and CT_min, neutral variation for 11 microsatellite loci, and micro- and macro-temperatures in larvae from 11 populations of the Galician common frog (Rana parvipalmata) across an elevational gradient, to assess (1) the existence of local adaptation through a P_ST-F_ST comparison, (2) the acclimation scope in both thermal limits, and (3) the vulnerability to suffer acute heat and cold thermal stress, measured at both macro- and microclimatic scales. Our study revealed significant microgeographic variation in CT_max and CT_min, and unexpected elevation gradients in pond temperatures. However, variation in CT_max and CT_min could not be attributed to selection because critical thermal limits were not correlated to elevation or temperatures. Differences in breeding phenology among populations resulted in exposure to higher and more variable temperatures at mid and high elevations. Accordingly, mid- and high-elevation populations had higher CT_max and CT_min plasticities than lowland populations, but not more extreme CT_max and CT_min. Thus, our results support the prediction that plasticity and phenological shifts may hinder local adaptation, promoting thermal niche conservatism. This may simply be a consequence of a coupled variation of reproductive timing with elevation (the "elevation-time axis" for temperature variation). Mid and high mountain populations of R. parvipalmata are more vulnerable to heat and cool impacts than lowland populations during the aquatic phase. All of this contradicts some of the existing predictions on adaptive thermal clines and vulnerability to climate change in elevational gradients.

Effect of induced sublethal intoxication with neonicotinoid insecticides on Egyptian toads (Sclerophrys regularis)

The toxicity role of insecticides affecting nontarget vertebrate of wildlife population has become essential subject to focus on. In this vein, the current study aimed to illustrate some biochemical and histopathological alterations induced by two neonicotinoids in Egyptian toads. Forty-five toads were collected and divided equally into three groups (15 toads/group): control group, thiamethoxam group, and acetamiprid group. Both treatment groups received thiamethoxam and acetamiprid (30 and 40 mg/L, respectively) four times within 12 days for induction of sublethal toxicity. Blood and liver tissue samples were collected. Both insecticides cause the same changes, but acetamiprid group exhibited a pronounced significant (P ≥ 0.001) effect than thiamethoxam group on increasing serum lipid profile, ALT, and AST. Moreover, acetamiprid showed a significant (P ≥ 0.001) decrease in hepatic total protein, GSH, and SOD and increase in MDA levels in comparison with thiamethoxam and control groups, respectively. The histopathological hepatic examination showed markable alterations in hepatic architecture in treatment groups that was distinct in acetamiprid group. Finally, our findings illustrate the indirect effect of neonicotinoids on toads and may realize their life-threatening factors. Graphical Abstract.

Dermal Fungicide Exposure at Realistic Field Rates Induces Lethal and Sublethal Effects on Juvenile European Common Frogs (Rana temporaria)

Viticulture is one of the most pesticide-intensive agricultures in Europe, leading to a spatiotemporal overlap of amphibian migration and pesticide applications. Because postmetamorphic, terrestrial amphibian stages are mostly neglected in ecotoxicological studies, we investigated acute effects of viticultural fungicides on juvenile common frogs (Rana temporaria). Tadpoles from an uncontaminated pond were placed in enclosures in 8 ponds with an increasing degree of pesticide contamination in southwest Germany to represent different aquatic exposure backgrounds. After metamorphosis, juveniles were exposed to soil contaminated with 50% of the recommended field rates of the fungicides Folpan^® 80 water dispersible granule (WDG) and Folpan^® 500 suspension concentrate with the same amount of folpet as active ingredient and differing additives. After 48 h, effects on the survival, body mass, and behavior were investigated. No effect of the aquatic exposure background on terrestrial sensitivity could be detected. Acute terrestrial exposure led to mean mortality rates of 14% (13-17%, suspension concentrate) and 60% (17-100%, WDG) and resulted in adverse effects on locomotor activity as well as feeding behavior. Moreover, the results suggest that the toxicity of the 2 tested folpet formulations depends on their additives. Because the identified effects may result in severe impairments and thus in declines of amphibian populations, a more protective risk assessment of pesticides is needed for postmetamorphic amphibians to ensure proper conservation of amphibian populations. Environ Toxicol Chem 2021;40:1289-1297. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure, genetic diversity and landscape effects in an endangered amphibian

Revealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.

Pesticide exposure affects reproductive capacity of common toads (Bufo bufo) in a viticultural landscape

Amphibian populations are declining worldwide at alarming rates. Among the large variety of contributing stressors, chemical pollutants like pesticides have been identified as a major factor for this decline. Besides direct effects on aquatic and terrestrial amphibian stages, sublethal effects like impairments in reproduction can affect a population. Therefore, we investigated the reproductive capacity of common toads (Bufo bufo) in the pesticide-intensive viticultural landscape of Palatinate in Southwest Germany along a pesticide gradient. In a semi-field study, we captured reproductively active common toad pairs of five breeding ponds with different pesticide contamination level and kept them in a net cage until spawning. Toads from more contaminated ponds showed an increased fecundity (more eggs) but decreased fertilization rates (fewer hatching tadpoles) as well as lower survival rates and reduced size in Gosner stage 25, suggesting that the higher exposed populations suffer from long-term reproductive impairments. In combination with acute toxicity effects, the detected sublethal effects, which are mostly not addressed in the ecological risk assessment of pesticides, pose a serious threat on amphibian populations in agricultural landscapes.

Avoidance behavior of juvenile common toads (Bufo bufo) in response to surface contamination by different pesticides

Most agricultural soils are expected to be contaminated with agricultural chemicals. As the exposure to pesticides can have adverse effects on non-target organisms, avoiding contaminated areas would be advantageous on an individual level, but could lead to a chemical landscape fragmentation with disadvantages on the metapopulation level. We investigated the avoidance behavior of juvenile common toads (Bufo bufo) in response to seven pesticide formulations commonly used in German vineyards. We used test arenas filled with silica sand and oversprayed half of each with different pesticide formulations. We placed a toad in the middle of an arena, filmed its behavior over 24 hours, calculated the proportion of time a toad spent on the contaminated side and compared it to a random side choice. We found evidence for the avoidance of the folpet formulation Folpan® 500 SC, the metrafenone formulation Vivando® and the glyphosate formulation Taifun® forte at maximum recommended field rates for vine and a trend for avoidance of Wettable Sulphur Stulln (sulphur). No avoidance was observed when testing Folpan® 80 WDG (folpet), Funguran® progress (copper hydroxide), SpinTorTM (spinosad), or 10% of the maximum field rate of any formulation tested. In the choice-tests in which we observed an avoidance, toads also showed higher activity on the contaminated side of the arena. As video analysis with tracking software is not always feasible, we further tested the effect of reducing the sampling interval for manual data analyses. We showed that one data point every 15 or 60 minutes results in a risk of overlooking a weak avoidance behavior, but still allows to verify the absence/presence of an avoidance for six out of seven formulations. Our findings are important for an upcoming pesticide risk assessment for amphibians and could be a template for future standardized tests.

Small-scale population divergence is driven by local larval environment in a temperate amphibian

Genomic variation within and among populations is shaped by the interplay between natural selection and the effects of genetic drift and gene flow. Adaptive divergence can be found in small-scale natural systems even when population sizes are small, and the potential for gene flow is high, suggesting that local environments exert selection pressures strong enough to counteract the opposing effects of drift and gene flow. Here, we investigated genomic differentiation in nine moor frog (Rana arvalis) populations in a small-scale network of local wetlands using 16,707 ddRAD-seq SNPs, relating levels of differentiation with local environments, as well as with properties of the surrounding landscape. We characterized population structure and differentiation, and partitioned the effects of geographic distance, local larval environment, and landscape features on total genomic variation. We also conducted gene-environment association studies using univariate and multivariate approaches. We found small-scale population structure corresponding to 6-8 clusters. Local larval environment was the most influential component explaining 2.3% of the total genetic variation followed by landscape features (1.8%) and geographic distance (0.8%), indicative of isolation-by-environment, -by-landscape, and -by-distance, respectively. We identified 1000 potential candidate SNPs putatively under divergent selection mediated by the local larval environment. The candidate SNPs were involved in, among other biological functions, immune system function and development. Our results suggest that small-scale environmental differences can exert selection pressures strong enough to counteract homogenizing effects of gene flow and drift in this small-scale system, leading to observable population differentiation.

Potential pesticide exposure during the post-breeding migration of the common toad (Bufo bufo) in a vineyard dominated landscape

Two important drivers of the global amphibian decline are habitat destruction due to an intensification of farming and a related increase of pesticide applications. Recent studies have shown that there might be an underestimated risk of pesticides on terrestrial amphibians. However, there are too few data on the terrestrial habitat use of amphibians in agricultural landscapes to estimate the exposure risk. To fill this knowledge gap, we used telemetry to investigate the post-breeding migration of 51 common toads (Bufo bufo) from a breeding pond in a vineyard-dominated landscape in Southern Palatinate (Germany). We expected most toads to migrate to the nearby Palatinate Forest as a terrestrial habitat. However, only four individuals reached the forest, suggesting that a part of the population is inhabiting the agricultural landscape over large parts of the year. Individuals were also found directly in the vineyards (15% of all relocations), but 23% less often than expected from a random choice and therefore tend to avoid vineyards as terrestrial habitat. To estimate a possible spatial-temporal overlap of toad migration and pesticide application, we combined telemetry data with information about pesticide applications from local wine growers. Seven individuals had a high probability (>75%) of being directly exposed to a pesticide application. Taking spray drift and the half-life values of applied pesticides into account, the number of toads potentially exposed raised to 15 individuals. We estimated that, on a single day up to 24% of the whole breeding population came in contact with pesticides, resulting in a high overall exposure risk. Pesticides can have negative effects on amphibians, and toads try to avoid vineyards as habitats. Therefore, we conclude that a heterogeneous cultural landscape, with buffer strips around ponds, uncultivated patches and migration corridors, might be the best management measure for sustaining amphibians in the agricultural landscape.

A genome-wide search for local adaptation in a terrestrial-breeding frog reveals vulnerability to climate change

Terrestrial-breeding amphibians are likely to be vulnerable to warming and drying climates, as their embryos require consistent moisture for successful development. Adaptation to environmental change will depend on sufficient genetic variation existing within or between connected populations. Here, we use Single Nucleotide Polymorphism (SNP) data to investigate genome-wide patterns in genetic diversity, gene flow and local adaptation in a terrestrial-breeding frog (Pseudophryne guentheri) subject to a rapidly drying climate and recent habitat fragmentation. The species was sampled across 12 central and range-edge populations (192 samples), and strong genetic structure was apparent, as were high inbreeding coefficients. Populations showed differences in genetic diversity, and one population lost significant genetic diversity in a decade. More than 500 SNP loci were putatively under directional selection, and 413 of these loci were correlated with environmental variables such as temperature, rainfall, evaporation and soil moisture. One locus showed homology to a gene involved in the activation of maturation in Xenopus oocytes, which may facilitate rapid development of embryos in drier climates. The low genetic diversity, strong population structuring and presence of local adaptation revealed in this study shows why management strategies such as targeted gene flow may be necessary to assist isolated populations to adapt to future climates.

Influence of substrate types and morphological traits on movement behavior in a toad and newt species

Background

Inter-patch movements may lead to genetic mixing, decreasing both inbreeding and population extinction risks, and is hence a crucial aspect of amphibian meta-population dynamics. Traveling through heterogeneous landscapes might be particularly risky for amphibians. Understanding how these species perceive their environment and how they move in heterogeneous habitats is an essential step in explaining metapopulation dynamics and can be important for predicting species’ responses to climate change and for conservation policy and management.

Methods

Using an experimental approach, the present study focused on the movement behavior (crossing speed and number of stops) on different substrates mimicking landscape components (human-made and natural substrates) in two amphibian species contrasting in locomotion mode: the common toad (Bufo bufo), a hopping and burrowing anuran and the marbled newt (Triturus marmoratus), a walking salamander. We tested the hypothesis that species reaction to substrate is dependent on specific ecological requirements or locomotion modes because of morphological and behavioral differences.

Results

In both species, substrate type influenced individual crossing speed, with individuals moving faster on soil than on concrete substrate. We also demonstrated that long-legged individuals moved faster than individuals with short legs. In both species, the number of stops was higher in females than in males. In common toads, the number of stops did not vary between substrates tested, whereas in marbled newts the number of stops was higher on concrete than on soil substrate.

Discussion

We highlighted that concrete substrate (mimicking roads) negatively affect the crossing speed of both studied species, with an effect potentially higher in marbled newts. Our findings corroborate negative effects of such heterogeneous landscapes on movement behavior of two amphibian species, which may have implications for the dynamics of metapopulations.