The intensification of human activities is responsible for habitat loss which is the major cause of biodiversity regression. In this context, it becomes critical to consider with more attention ...highly transformed or artificial habitats that may have a significant value for biodiversity conservation. It is also equally important to evaluate the significance of management measures in remaining semi-natural habitat. Squamate reptiles (lizards and snakes) usually have limited dispersal capacities and are consequently particularly vulnerable to habitat changes. We studied the abundance of an endangered species, the smooth snake (
Coronella austriaca
), in 112 sites located in the southern part of Belgium. We wanted to compare population size and density in a semi-natural habitat (dry grassland) and two artificial ones (rocky habitats and railway). We also wanted to compare snake density in grasslands depending on management measures (either mowing, grazing, or no management). Our results suggest that smooth snake population sizes are low with fewer than 20 individuals on 85% of the sampled sites. Highest density and population sizes were reported along railways and in artificial rocky habitats when compared with grasslands. Population density was lower in nature reserves reflecting notably the negative effect of management (grazing). Our study suggests that transformed habitat can provide significant structural diversity and can be beneficial as long as human pressure remains low. In turn, management measures deployed in semi-natural habitats may dramatically affect microhabitat diversity and significantly impact squamate populations.
Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes and identified previously unknown secondary contact zones. Until now, little is known ...about gene flow across these contact zones. Using two mitochondrial markers and 13 microsatellite loci, we examined two contact zones. One, largely corresponding to the Rhine region, involves the western subspecies Natrix natrix helvetica and the eastern subspecies N. n. natrix, whereas in the other, more easterly, contact zone two lineages meet that are currently identified with N. n. natrix and N. n. persa. This second contact zone runs across Central Europe to the southern Balkans. Our analyses reveal that the western contact zone is narrow, with parapatrically distributed mitochondrial lineages and limited, largely unidirectional nuclear gene flow. In contrast, the eastern contact zone is very wide, with massive nuclear admixture and broadly overlapping mitochondrial lineages. In combination with additional lines of evidence (morphology, phylogeny, divergence times), we conclude that these differences reflect different stages in the speciation process and that Natrix helvetica should be regarded as a distinct species. We suggest a nomenclatural framework for presently recognized grass snake taxa and highlight the need for reconciling the conflicts between genetics and taxonomy.
Summary
The use of environmental DNA (eDNA) to detect species in aquatic environments such as ponds and streams is a powerful new technique with many benefits. However, species detection in ...eDNA‐based surveys is likely to be imperfect, which can lead to underestimation of the distribution of a species.
Site occupancy models account for imperfect detection and can be used to estimate the proportion of sites where a species occurs from presence/absence survey data, making them ideal for the analysis of eDNA‐based surveys. Imperfect detection can result from failure to detect the species during field work (e.g. by water samples) or during laboratory analysis (e.g. by PCR).
To demonstrate the utility of site occupancy models for eDNA surveys, we reanalysed a data set estimating the occurrence of the amphibian chytrid fungus Batrachochytrium dendrobatidis using eDNA. Our reanalysis showed that the previous estimation of species occurrence was low by 5–10%. Detection probability was best explained by an index of the number of hosts (frogs) in ponds.
Per‐visit availability probability in water samples was estimated at 0·45 (95% CRI 0·32, 0·58) and per‐PCR detection probability at 0·85 (95% CRI 0·74, 0·94), and six water samples from a pond were necessary for a cumulative detection probability >95%. A simulation study showed that when using site occupancy analysis, researchers need many fewer samples to reliably estimate presence and absence of species than without use of site occupancy modelling.
Our analyses demonstrate the benefits of site occupancy models as a simple and powerful tool to estimate detection and site occupancy (species prevalence) probabilities despite imperfect detection. As species detection from eDNA becomes more common, adoption of appropriate statistical methods, such as site occupancy models, will become crucial to ensure that reliable inferences are made from eDNA‐based surveys.
Even though reptiles are threatened worldwide, few studies address their conservation, especially snakes. The goal of our study was to measure the genetic structure of a widely distributed temperate ...reptile, the smooth snake
Coronella austriaca
using microsatellite markers in two different areas at the core (Alsace, north-eastern France) and at the edge (Wallonia, southern Belgium) of its range. We sampled 506 individuals in 38 localities (respectively 10 and 28). Analysis of genetic structure conducted with a clustering method detected three clusters in Alsace, one group gathering all populations but two. In Wallonia, differentiation was observed on both sides of the Meuse River and in the Southern Ardenne region (southernmost sampling sites). Spatial autocorrelation analysis showed that statisticaly more related individuals occur together up to a distance of 2.8 km in Alsace and up to 10 km in Wallonia. Isolation by distance was detected in Wallonia but the distance explained a very limited part of the differentiation (r = 0.033), whereas no isolation-by-distance pattern was detected in Alsace. Even though genetic differentiation between populations separated by large rivers, highways, or crop fields was detected, dispersal between populations seem currently sufficient to avoid any kind of genetic drift in both regions. These results are similar to a previous study conducted in Poland, but strongly contrast with another analysis held in England which detected a sharp genetic structuring among populations that are geographically close. We consequently suggest that discrepancies could be related to the ecology of island populations and smaller densities.
The fungus
Ophiodimyces ophiodiicola
is the etiologic agent of snake fungal disease. Recent findings date US occurrence at least as far back as 1945. We analyzed 22 free-ranging snakes with gross ...lesions consistent with snake fungal disease from museum collections from Europe. We found 5 positive samples, the oldest collected in 1959.
Human activities have a major impact on habitat connectivity and landscape structure. In this context, it is critical to better understand animal movements and gene flow to develop appropriate ...conservation and land management measures. It is also important to better understand difference between sexes in space use and spatial scale of dispersal. We studied the common adder (
Vipera berus
), an elusive snake species with low mobility that is facing a substantial decline in Europe. A systematic sampling was carried out to clarify the dispersal pattern at a fine spatial scale (10 × 7 km
2
) in a rural landscape with both semi-natural (preserved heathlands, hedgerow networks) and degraded (crops, roads) habitats. Based on 280 captured adults and using 11 microsatellite markers, we detected no marked genetic differentiation, however, we detected relatively strong isolation-by-distance (IBD). Under IBD, we quantified a low neighborhood size (
N
s
≈ 50) associated with limited natal dispersal (σ ≤ 1 km). We detected sex-biased dispersal in favor of males, but the pattern was dependent on the spatial scale considered. Our results also suggest that there is higher genetic diversity in the preserved habitat, notably among males. Overall, our study underlines the importance of sex variation in dispersal, and the spatial scale of landscape effects. This contrast between sexes should be considered to improve functional connectivity at fine spatial scales for reptile conservation.
Most of Switzerland is inhabited by the nominotypical subspecies of the barred grass snake ( Natrix helvetica helvetica ), which is characterized by mitochondrial DNA lineage E. Only in the northeast ...of the country, the common grass snake ( N. natrix ) occurs and hybridizes with N. h. helvetica in a narrow contact zone. However, we discovered that in southern and western Switzerland barred grass snakes representing another mtDNA lineage (lineage C) are widely distributed. Lineage C is typical for Alpine populations of the southern subspecies N. h. sicula . Our microsatellite analyses of the Swiss samples revealed differences between the two subspecies and also a substructure with two clusters in each subspecies. Furthermore, we discovered a contact and hybrid zone of N. h. helvetica and N. h. sicula along the northern shore of Lake Geneva and also confirm that interbreeding with alien common grass snakes ( N. n. moreotica , mtDNA lineage 7) occurs there. This finding is of concern for nature conservation and measures should be taken to prevent further genetic pollution. Using morphometrics, we found no differences between the two subspecies of N. helvetica , while N. natrix was slightly distinct from N. helvetica .
Next-generation sequencing is increasingly used in conservation biology to resolve complex interactions between species, either diet or gut parasites studies. We applied a recent long metabarcoding ...method to elucidate the green whip snake’s (Hierophis viridiflavus) prey consumption based on DNA extracted from stomach contents. Illegally introduced in Canton of Vaud (Switzerland), three populations of the green whip snake have strongly developed in two regions, East (Chablais) and North. We suspect that this introduced species is threatening part of the local herpetofauna, especially the Asp viper and the Western green lizard in this region. Consequently, an extermination program has been implemented from 2016 to mitigate Hierophis viridiflavus expansion and its impact arising from its generalist diet. Stomach contents of 94 individuals removed from introduction sites were analysed by long metabarcoding. Our study revealed the consumption of 67 prey belonging to 9 species, primarily small mammals and reptiles. The recurrent presence of two parasitic nematodes was also discovered. Although cannibalistic behaviour could not be highlighted with this approach, a scavenging behaviour was suspected based on the presence of an insect used in forensic entomology (Calliphora vicina). These results confirm the opportunistic feeding behaviour of Hierophis viridiflavus and its ability to predate on threatened species. Although 86.6 % of preys were not listed on the Swiss Red List, the impact on the Asp viper population can be important (up to 20 % of consumed preys) and could partially explain its strong decline.
•The green whip snake’s prey consumption was elucidated by long metabarcoding of DNA extracted from stomach contents.•Stomachs of 94 individuals revealed the consumption of 67 prey belonging to 9 species, mainly small mammals and reptiles.•13.4 % of preys were listed on the Swiss Red List.•At one site, 20% of consumed preys belonged to the critically endangered Asp viper, maybe linked to its strong decline.
Knowledge of patterns of genetic diversity in populations of threatened species is vital for their effective conservation. However, destructive sampling should be avoided in threatened species so as ...not to additionally increase the risk of local population extinction. We exclusively used beetle remains and beetles collected after death to analyze local and regional patterns of genetic variation in the endangered flightless longhorn beetle Iberodorcadion fuliginator in the border region of Switzerland, France and Germany, in grassland remnants. We extracted DNA from the beetles’ remains and genotyped 243 individuals at 6 microsatellite loci. We found moderate genetic differentiation between populations, each belonging to one of two metapopulations situated on either side of the river Rhine, but distinct genetic differentiation between populations across metapopulation. The genetic distance between populations was correlated with the geographic distance between the sites sampled. Genetic structure analysis inferred the presence of two genetic clusters. The populations in the Alsace (France) represent one cluster, together with the Swiss populations near Basel, which is separated by the river Rhine from the cluster composed of the populations in southwestern Germany. Thus, the historical separation by the river Rhine surpasses more recent effects of human-induced habitat fragmentation on the genetic differentiation in I. fuliginator.
The fire-bellied toad Bombina bombina has recently been introduced in Moselle, north-eastern France, in an area where the yellow-bellied toad Bombina variegata occurs naturally. Both species ...hybridize in a wide area throughout Europe where their distribution overlaps. Therefore, there is a risk of introgression regarding the Bombina variegata population in north-eastern France. In order to assess the status of the introduced population of Bombina bombina and its origin, we investigated its genetic characteristics and structure using both mitochondrial (cytochrome b) and nuclear DNA (microsatellites markers). The results demonstrated a lack of introgression in the Bombina variegata population. Though experiencing a bottleneck effect, the introduced Bombina bombina population displays a high genetic diversity. If a propensity for expansion is found within the introduced population of Bombina bombina, it could be considered as a potential invasive species in France, and thus threaten the native species. Keywords. Invasive species, population genetics, conservation, cytochrome b, microsatellites.
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