High Genetic Differentiation Among French Populations of the Orsini's Viper (Vipera ursinii ursinii) Based on Mitochondrial and Microsatellite Data: Implications for Conservation Management

The Orsini's viper (Vipera ursinii) is one of the most threatened snakes in Europe due to its highly fragmented distribution and specific open environment (steppic habitat) requirement. French populations are isolated on top of mountain massifs of the southern Prealps/Alps. Mitochondrial sequences (cytochrome b) and 6 microsatellite loci have been used to estimate the levels of genetic diversity and isolation within and among 11 French fragmented populations (a total of 157 individuals). Eleven cytochrome b haplotypes with a limited divergence were observed (mean divergence between haplotypes: 0.31%). However, we detected considerable genetic differentiation among populations (global FST = 0.76 and 0.26 for mitochondrial and nuclear DNA, respectively). Results indicate that 3 populations possibly went through a bottleneck and 1 population showed low genetic diversity compared with the others. Although a significant isolation by distance was detected for both markers, strong differentiation was also observed between geographically close populations, probably due to the ragged landscape that constitutes a serious barrier to gene flow owing to the limited dispersal capability of the viper. Despite some discrepancies between the 2 markers, 8 Management Units have been identified and should be considered for future management project

Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision‐making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long‐term plausibility and comparability

Quantifying biodiversity using eDNA from water bodies : general principles and recommendations for sampling designs

Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision-making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long-term plausibility and comparability

Conservation of the French populations of the Orsini's meadow viper (multidisciplinary and integrative approach)

La région méditerranéenne est un des 25 points chauds de la biodiversité mondiale. Cette richesse est associée à des milieux semi-naturels façonnés par l'action de l'homme depuis des siècles, notamment par élevage extensif. Depuis la fin du 19ème siècle, la déprise rurale se traduit par l'abandon des pratiques pastorales qui conduit à la dégradation de ces milieux ouverts semi-naturels par embroussaillement et reforestation. Les conséquences de cette modification des habitats sont explorées sur une espèce endémique rare et difficile à détecter, la vipère d'Orsini (Vipera ursinii). Les travaux réalisés montrent que les populations sont fragmentées, isolées les unes des autres, et marquées par une forte structuration spatiale interne. Quatre unités évolutives distinctes sont détectées, représentant chacune une part originale et unique de la variabilité génétique de l'espèce en France dont la perte doit alors être considérée définitive. Nos résultats montrent que la distribution de l'espèce est très peu étendue par rapport aux habitats favorables disponibles. Cette différence ne résulte pas d'un biais lié à la non-détection de l'espèce ni à l'omission d'un paramètre important dans les modèles de distribution mais probablement d'une faible capacité de colonisation des sites devenus favorables après la dernière glaciation. Nous avons montré que les effets des brûlages dirigés menés par les gestionnaires pour entretenir les milieux méditerranéens sont fortement négatifs pour la survie de l'espèce. Enfin l'analyse de la gestion forestière abordée de manière théorique montre le fort potentiel des coupes forestières pour améliorer le statut des populations. Ainsi cette thèse s'est attachée à définir une démarche simple et efficace à adopter pour obtenir une évaluation rapide du statut des populations et des risques d'extinction d'une espèce rare et difficile à observer. Par ailleurs les résultats obtenus sur cette espèce sont de portée générale pour comprendre l'impact de la reforestation à la suite de l'abandon des pratiques pastorales séculaires, des changements climatiques à venir ainsi que celui des modes de gestion actuellement préconisés sur des espèces méditerranéennes à faible capacité de dispersionThe Mediterranean region is one of the 25 hotspots in the world. This biological richness is linked from centuries with human-made seminatural habitats, such as agropastoral grasslands. Since the end of the 19th century, the rural decolonization is followed by land abandonment and that conducts to alteration of seminatural grasslands by encroachment and afforestation. Consequences of this habitat alteration are investigated on a rare endemic species particularly difficult to detect, the Orsini's meadow viper (Vipera ursinii). This study shows that populations are fragmented and isolated, and have a high within spatial structure. Four distinct evolutionary units have been identified, each one representing an original and unit part of the genetic variability of the species in France, whose loss should be considered as definitive. Our results show that the species range is narrow extended compared to suitable habitats. This difference does not result from non detection bias neither missing of an important parameter in using models but rather by a low colonization ability of sites which became favourable after the last glaciation. We showed that prescribed fire effects used to maintain open grasslands are strongly unfavourable to the Orsini's meadow viper. In last, analysis of forest management with theoretical approach showed the strong potentiality of forest cuttings to population status improvement. Thus, this thesis aims to define a simple and effective method to obtain quickly an assessment of populations status and extinction risks of this rare species difficult to detect. In addition results obtained on this species are of broader inferences to understand impact of afforestation due to pastoral abandonment, near-future climatic change and management practice that are currently proposed for Mediterranean species with low dispersal rateMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Quel avenir pour la vipère d’Orsini en France ?

Cheylan Marc, Lyet Arnaud, Orsini Philippe, Penloup Aura. Quel avenir pour la vipère d’Orsini en France ?. In: Ecologia mediterranea, tome 30 n°2, 2004. pp. 241-242

eDNA sampled from stream networks correlates with camera trap detection rates of terrestrial mammals

Abstract Biodiversity monitoring delivers vital information to those making conservation decisions. Comprehensively measuring terrestrial biodiversity usually requires costly methods that can rarely be deployed at large spatial scales over multiple time periods, limiting conservation efficiency. Here we investigated the capacity of environmental DNA (eDNA) from stream water samples to survey terrestrial mammal diversity at multiple spatial scales within a large catchment. We compared biodiversity information recovered using an eDNA metabarcoding approach with data from a dense camera trap survey, as well as the sampling costs of both methods. Via the sampling of large volumes of water from the two largest streams that drained the study area, eDNA metabarcoding provided information on the presence and detection probabilities of 35 mammal taxa, 25% more than camera traps and for half the cost. While eDNA metabarcoding had limited capacity to detect felid species and provide individual-level demographic information, it is a cost-efficient method for large-scale monitoring of terrestrial mammals that can offer sufficient information to solve many conservation problems

Modelling of spatial dynamics and biodiversity conservation on Lure mountain (France)

International audienceOur study is part of a multi-disciplinary research project aimed at stimulating debate among researchers and local managers. The central question of this multi-disciplinary research project was to better understand and manage high biodiversity value open habitats threatened with shrub encroachment and landscape closure, a common problem throughout Europe. Here, we study shrub encroachment and its impact on biodiversity conservation in Mount Ventoux, a MAB Biosphere Reserve located at the southernmost tip of the French Alps. We show how using a multi-agent modelling approach provide a valuable framework to confront two potentially conflicting conservation efforts in this mountain Mediterranean landscape, that of the within-species diversity of a tree (Abies alba, the European silver fir) and that of an endangered species (Vipera ursinii ursinii, the Orsini viper). A companion modelling approach – approach which aims at transmitting and sharing knowledge, methods and tools that help understand and strengthen the collective decision making process of stakeholders sharing a common resource – was used in order to collectively represent the main activities underway on the mountain and to have a tool to address both open landscapes rehabilitation and restoration of forest environments. The co-construction of the model allowed us to build a shared representation of the territory under study and to develop and compare alternative management scenarios with local stakeholders, both to evaluate their impact on biodiversity and to provide information for forest and grazing management practic

From the Lab to the Classroom and Beyond: Extending a Game-Based Research Platform for Teaching AI to Diverse Audiences

Recent years have seen increasing interest in AI from outside the AI community. This is partly due to applications based on AI that have been used in real-world domains, for example, the successful deployment of game theory-based decision aids in security domains. This paper describes our teaching approach for introducing the AI concepts underlying security games to diverse audiences. We adapted a game-based research platform that served as a testbed for recent research advances in computational game theory into a set of interactive role-playing games. We guided learners in playing these games as part of our teaching strategy, which also included didactic instruction and interactive exercises on broader AI topics. We describe our experience in applying this teaching approach to diverse audiences, including students of an urban public high school, university undergraduates, and security domain experts who protect wildlife. We evaluate our approach based on results from the games and participant surveys

Let more big fish sink: Fisheries prevent blue carbon sequestration—half in unprofitable areas

Contrary to most terrestrial organisms, which release their carbon into the atmosphere after death, carcasses of large marine fish sink and sequester carbon in the deep ocean. Yet, fisheries have extracted a massive amount of this “blue carbon,” contributing to additional atmospheric CO2 emissions. Here, we used historical catches and fuel consumption to show that ocean fisheries have released a minimum of 0.73 billion metric tons of CO2 (GtCO2) in the atmosphere since 1950. Globally, 43.5% of the blue carbon extracted by fisheries in the high seas comes from areas that would be economically unprofitable without subsidies. Limiting blue carbon extraction by fisheries, particularly on unprofitable areas, would reduce CO2 emissions by burning less fuel and reactivating a natural carbon pump through the rebuilding of fish stocks and the increase of carcasses deadfall