Agricultural landscapes and the Loire River influence the genetic structure of the marbled newt in Western France

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.

Pool Age and Local Habitat Are Associated with Effective Number of Breeders in Spotted Salamander Populations Colonizing Created Vernal Pools

Population genetics can reveal whether colonization of created habitats has been successful and inform future strategies for habitat creation. We used genetic analysis to investigate spotted salamander (Ambystoma maculatum) colonization of created vernal pools and explored the impact of habitat characteristics on the genetic diversity and connectivity of the pools. Our first objective was to examine genetic structure, differentiation, diversity, and potential for a founder effect. Our second objective was to determine if habitat characteristics were associated with effective number of breeders, relatedness, or genetic diversity. We sampled spotted salamander larvae in 31 created vernal pools (1–5 years old) in Monongahela National Forest (WV) in May and June 2015 and 2016. The youngest pools exhibited genetic differentiation, a founder effect, and low effective number of breeders. Effective number of breeders was positively associated with pool age, vegetation cover, pool diameter, and sample size. Vegetation cover was also negatively associated with relatedness. Genetic diversity did not have strong environmental predictors. Our results indicated the effective number of breeders increased and genetic differentiation decreased within 4–5 years of pool creation, a sign of rapid colonization and potential population establishment. Our research also showed that higher vegetative cover within the pool and larger pool diameters could impact habitat quality and should be incorporated into future pool creation.

Population structure and genetic diversity of the threatened pygmy newt Triturus pygmaeus in a network of natural and artificial ponds

Pond physical characteristics (connectivity, hydroperiod) have shown to be highly relevant in explaining species presence, reproductive success, and survival in breeding-pond amphibians. However, few studies have addressed the influence that these factors may have on the genetic variability of pond populations. We examined genetic variation at 11 microsatellite loci in Iberian endemic, the pygmy newt (Triturus pygmaeus), from 58 breeding ponds in the Doñana National Park (Andalusia), including both temporary ponds and artificially deepened ponds that remain wet during the whole year. Temporary ponds are located in the North part of the region where the surrounding habitat-wet meadows-facilitates the connectivity among populations, whereas the deepest ponds (‘zacallones’) are located in the southern edge embedded in a matrix of unsuitable habitat (thickets and dry underbrush). We investigated genetic diversity and structure within and among ponds. Our results show that both regions (Doñana-North and Doñana-South) are well-differentiated and form two main clusters. We found higher genetic diversity within ponds from the North region, which also exhibited a higher degree of genetic admixture in comparison with populations from the southern edge. Although we found an isolation-by-distance pattern within each cluster, it arose due to the effect of a few isolated ponds located on the edge of each zone, suggesting the existence of substantial gene flow between ponds in the core area. According to our findings, landscape’s permeability to movement (pond connectivity) may constitute a more important factor than hydroperiod length in determining the genetic diversity and viability of pygmy newt populations in this area. Although Doñana populations show a good state, more peripheral and isolated populations present a more worrisome condition as a result of fragmentation and thus, require conservation efforts. Our study provides key insights that could help guide management practices of this threatened and poorly-studied salamander.

The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander (Plethodon mississippi)

In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual's dispersal distance, for low-mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal-limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite-based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum-likelihood population effects models that assessed the nature and strength of their relationship with each of five land-use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best-fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land-use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.

Urbanization reduces gene flow but not genetic diversity of stream salamander populations in the New York City metropolitan area

Natural landscape heterogeneity and barriers resulting from urbanization can reduce genetic connectivity between populations. The evolutionary, demographic, and ecological effects of reduced connectivity may lead to population isolation and ultimately extinction. Alteration to the terrestrial and aquatic environment caused by urban influence can affect gene flow, specifically for stream salamanders who depend on both landscapes for survival and reproduction. To examine how urbanization affects a relatively common stream salamander species, we compared genetic connectivity of Eurycea bislineata (northern two-lined salamander) populations within and between streams in an urban, suburban, and rural habitat around the New York City (NYC) metropolitan area. We report reduced genetic connectivity between streams within the urban landscape found to correspond with potential barriers to gene flow, that is, areas with more dense urbanization (roadways, industrial buildings, and residential housing). The suburban populations also exhibited areas of reduced connectivity correlated with areas of greater human land use and greater connectivity within a preserve protected from development. Connectivity was relatively high among neighboring rural streams, but a major roadway corresponded with genetic breaks even though the habitat contained more connected green space overall. Despite greater human disturbance across the landscape, urban and suburban salamander populations maintained comparable levels of genetic diversity to their rural counterparts. Yet small effective population size in the urban habitats yielded a high probability of loss of heterozygosity due to genetic drift in the future. In conclusion, urbanization impacted connectivity among stream salamander populations where its continual influence may eventually hinder population persistence for this native species in urban habitats.

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.