La perte d’habitat et la fragmentation sont les principales causes de déclin des amphibiens en Europe de l’ouest. Malgré les réglementations mises en place concernant la construction de nouvelles infrastructures, le manque de connaissances fondamentales concernant les espèces et leurs habitats rendent difficiles l’évaluation des impacts ainsi que la mise en place de solutions efficaces pour conserver la biodiversité. En se basant sur l’exemple du triton marbré (Triturus marmoratus), espèce protégée présente dans l’ouest de la France, ce travail vise à évaluer la pertinence des méthodes de terrain et de modélisation disponibles pour la récolte des données nécessaires à la caractérisation de la dynamique des populations chez cette espèce. Pour ce faire, deux populations de tritons marbrés (Loire Atlantique et Vendée) ont été étudiées grâce à des techniques de comptages à la lampe, piégeage, utilisation d’épuisettes avec un suivi intensif par capture-marquage-recapture (CMR), complété par la méthode de l’ADN environnemental (ADNe). Dans une première partie ce travail a permis de montrer que dans le cadre de la caractérisation quantitative de la dynamique d’une population, les informations apportées par la CMR sont les plus fiables. Ceci est notamment dû au taux de détection faible et hétérogène dans l’espace et dans le temps du triton marbré, qui ne permet pas aux autres méthodes s’en affranchissant de produire des résultats reproductibles et transposables. L’ADNe est la méthode permettant d’estimer l’occurrence le plus efficacement mais la possibilité d’une utilisation pour estimer des abondances absolues voire des abondances relatives reste du domaine des perspectives prometteuses mais non abouties à ce jour. Dans un second chapitre, nous avons montré comment les récentes avancées méthodologiques dans les approches de modélisation permettent de déterminer le temps passé par une espèce sur un site grâce aux données de CMR. Ces méthodes ont été appliquées au triton marbré pour mettre en évidence une phénologie particulière avec des individus arrivant et repartant du site de reproduction de manière non simultanée et n’occupant chacun la mare qu’une partie de la période de reproduction. L’ensemble de ces résultats permettent de définir un cadre méthodologique adapté pour développer un suivi dans le temps des mesures de compensation envisagées dans le cadre du projet de construction, mais aussi pour le suivi des populations d’urodèles en général. / Habitat loss and fragmentation are the main causes of amphibian decline in Western Europe. In spite of regulations concerning the construction of new infrastructures, the lack of knowledge concerning species and their habitat make difficult to evaluate the impact as well as the implementation of effective solutions to preserve biodiversity. Using the example of marbled newt (Triturus marmoratus), a protected species presents in Western France, this works aims at estimating the relevance of the fieldwork and modeling methods available to obtain data necessary for characterizing the dynamic of population for this species. To do so, two populations of marbled newts (situated in Loire Atlantique and Vendée) were studied using torch counts, traps, dip nets, with an intensive capture recapture (CR) protocol, and environmental DNA (eDNA) method. In the first part, this work allowed us to show that within the framework of quantitative characterization of the dynamics of a population, the information gathered by CR is the most reliable. This is especially due to the low and heterogeneous detection rate in space and time for marbled newt, which does not allow traditional methods to get reproducible and transposable results. eDNA is the most accurate method when it comes to estimating occurence but the possibility to use it to estimate absolute or even relative abundances stays a promising perspective that did not succeed yet. In a second chapter, we showed how recent methodological advances in modeling approaches allow estimating time spent by a species in a site thanks to CR data. These methods were applied to marbled newts to highlight a particular phenology, with arriving and leaving individuals being not simultaneous but progressive and each individual occupying the pond only for a part of the breeding season. These results allows to define a methodological frame adapted to develop long term studies of compensation measures within the framework of the construction project, but also more generally for future studies of urodele species.

Depuis plusieurs décennies, un déclin important de la biodiversité est observé à l'échelle mondiale. Les amphibiens constituent aujourd'hui le groupe le plus vulnérable sur la planète. Près d'un tiers des espèces recensées dans le monde est à ce jour menacé d'extinction. Dans le cadre de ce doctorat, nous nous sommes intéressés dans un premier temps à l'émergence d'une maladie infectieuse des amphibiens, la chytridiomycose, provoquée par le champignon pathogène Batrachochytrium dendrobatidis (Bd). Nous avons étudié la répartition actuelle de ce champignon en France, démontré son impact sur la batrachofaune locale et mis en évidence le rôle de la Grenouille taureau (Lithobates catesbeianus) comme vecteur de transmission du pathogène. Afin de limiter la dissémination de Bd, nous avons également élaboré deux protocoles d'hygiène à mettre en oeuvre lors d'interventions sur le terrain ou lors d'utilisations d'amphibiens en laboratoire. Dans une seconde partie, nous avons développé une nouvelle méthode d'inventaire de la biodiversité basée sur la détection de l'ADN environnemental (ADNe). Nous avons mis en évidence que la persistance de l'ADNe dans un écosystème d'eau douce était d'environ 15 jours et que cette méthode innovante permettait d'améliorer la détection d'espèces exotiques envahissantes, comme la Grenouille taureau. Nous avons ensuite développé cette approche pour le suivi d'autres groupes taxonomiques (poissons, macro-invertébrés, chiroptères, etc.), dans des milieux différents et en utilisant notamment les technologies de séquençage nouvelle génération. / Since several decades, a significant decline in biodiversity is observed worldwide. Amphibians are now the most vulnerable group on the planet. Nearly a third of known species in the world is today threatened of extinction. Among many causes, diseases appear as an emerging threat worldwide. As part of this PhD, we were interested at first to the emergence of an infectious disease of amphibians, chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). We studied the current distribution of this fungus mostly in France, showed the impact on local batrachofauna and highlighted the role of the Bullfrog (Lithobates catesbeianus) as a vector for transmission of the pathogen. To limit the spread of Bd, we also developed two hygiene protocols to implement during field trips or use of amphibians in the laboratory. In the second part of this thesis, we have developed a new method of biodiversity inventory based on the detection of environmental DNA (eDNA). We have shown that the persistence of vertebrates (fish and amphibian) eDNA in freshwater ecosystems was about 15 days and that this innovative method greatly improves the detection of invasive alien species, such as Bullfrog. We are then developed this approach for monitoring other taxonomic groups (fish, macro-invertebrates, bats, etc...), in various environments, taking advantage of bio-technological developments such as next generation DNA sequencing.

No description available.

Recent research has revealed human settlement on the Pacific coast of Canada extending back nearly 14,000 years, but much of the late Pleistocene record is unknown due to shifting sea levels, poor understanding of Cordilleran ice extent, and limited research on the biota of the coast during this time. This study, undertaken in Quatsino First Nation and ‘Namgis First Nation territories as part of the Northern Vancouver Island Archaeology and Palaeoecology Project, employs modern multi-proxy analysis of lake sediment cores from two sites on northern Vancouver Island to reconstruct palaeoenvironments during and immediately following the Fraser Glaciation in coastal British Columbia. Evidence from radiocarbon samples, pollen, ancient environmental DNA, plant macrofossils, and diatoms indicates that Topknot Lake on the outer coast of Vancouver Island has remained unglaciated through most of the local Last Glacial Maximum since ca. 18,000 cal BP. A non-arboreal herb-shrub tundra assemblage prevailed from ca. 17,500-16,000 cal BP with taxa including willows (Salix), grasses, sedges (Cyperaceae), heathers (Ericaceae), and sagewort (Artemisia). After ca. 16,000 and into the terminal Pleistocene, Topknot Lake was dominated by pine, alder (Alnus), ferns, and aquatic plant species. In the Nimpkish River Valley deep in the Vancouver Island Ranges, Little Woss Lake also demonstrates a record extending to the late Pleistocene (ca. 14,300 cal BP). The environment comprised dry and cool conifer woodland dominated first by fir (Abies) until ca. 14,000 cal BP, then by pine, alder, and ferns from ca. 14,000-12,000 cal BP. eDNA evidence from ca. 14,000 cal BP corroborates these plant taxa as well as indicating brown bear and Chinook salmon in and around the basin at that time. A mixed-conifer assemblage consisting of pine, western hemlock, and alder followed from ca. 12,000-11,100 cal BP into the early Holocene. Collectively, these indicators demonstrate an open environment on the outer coast of northern Vancouver Island since ca. 18,000-17,500 cal BP and well-established biotic communities across the region throughout the late Pleistocene. These results inform future archaeological research for early human habitation in coastal British Columbia and provide key evidence to support the viability of the coastal migration route for the first peopling of the Americas. / Graduate / 2020-12-11

En regardant de près les outils juridiques et autres leviers, pour la conservation de la biodiversité, il semblerait que les invertébrés, et notamment les insectes, soient minoritaires ou absents. Ce constat est d’autant plus paradoxal lorsque l’on sait que 2/3 de la diversité biologique est composée par des insectes. Comment cette diversité essentielle pour le fonctionnement des écosystèmes se retrouve-t-elle dans l’angle mort de la conservation ?La première réponse avancée est le manque d’outils techniques pour étudier ces organismes petits et relativement insaisissables. La rencontre avec les nouvelles méthodes techniques pour la détection et l’étude des insectes est plus que jamais nécessaire. En effet, ces leviers permettront de faciliter l’étude de ces organismes, d’augmenter les connaissances et ainsi de développer une conservation plus adéquate. Nous évoquerons deux approches en particulier : la détection avec des outils moléculaires et l’utilisation de modèles statistiques pour l’exploration de la distribution potentielle des espèces.Mais les connaissances sont également fondées sur la demande sociétale. Et les connaissances alimentent elles-mêmes les outils de protection et de conservation de la biodiversité. À l’échelle des invertébrés, des disparités existent, privilégiant les « grands papillons bleus » aux « petits diptères marrons ». De fait, l’enjeu le plus important pour déverrouiller la conservation des insectes réside dans l’humain et la perception qu’il a de cette biodiversité. À travers une approche de psychologie de la conservation, nous sonderons la perception du grand public sur les insectes. De même, avec une approche de recherche-action-participative, nous tenterons d’engager divers acteurs vers la conservation d’un groupe d’insectes ordinaires : les coléoptères coprophages. Notre volonté est de proposer des moyens pour sensibiliser, éduquer et engager la société dans cet enjeu majeur qu’est la conservation de l’entomofaune. / Looking closely at the legal tools and other levers for preserving biodiversity, it would seem that invertebrates, in particular insects, are in a minority, or absent. This observation is all the more paradoxical when we know that 2/3 of the biological diversity consists of insects. How does this diversity, essential for the functioning of the ecosystems, find itself in the dead angle of conservation?The first answer that is usually put forward is lack of technical tools to study these small and relatively elusive animals. Getting to know and use new technical methods for the detection and the study of insects is more than ever necessary. Indeed, these levers will facilitate the study of these animals, and will thus increase knowledge, which will lead to developing more adequate conservation strategies. We shall evoke two approaches in particular: detection with molecular tools and use of statistical models to explore the potential distribution of the species.But knowledge is also based on what society asks for. Public interest orients the tools of protection and preservation of biodiversity. Among invertebrates, disparities exist, favoring the “big blue butterflies” over the “small brown dipterans”. A simple coincidence? No. Actually, the decisive factor to unlock the preservation of insects rests in human beings and how they perceive this biodiversity. Using a conservation psychology approach, we will explore how the general public perceives insects. We will also draw on participatory action research to see how various conservation actors can be committed towards preserving a group of ordinary insects: coprophagous beetles. Our aim is to propose ways to raise awareness, educate and engage society to this major issue: preserving entomofauna.

No description available.

Aquatic invasive species are a major threat to native freshwater biodiversity. The North American signal crayfish Pacifastacus leniusculus was introduced to Great Britain during the 1970s and is now widely distributed throughout England, Wales and Scotland. First recorded in Scotland in 1995, P. leniusculus is now established at more than twenty sites. The only other introduced crayfish species present in Scotland is the white-clawed crayfish Austropotamobius pallipes. A. pallipes is restricted to only two locations in Scotland, Loch Croispol and Whitemoss Reservoir. P. leniusculus negatively impacts macrophytes, invertebrates and fish though ecological and physical processes. Additionally, P. leniusculus has displaced A. pallipes throughout much of its native range within Great Britain due to competition and disease. Consequently, the two A. pallipes populations in Scotland have a high conservation value. This PhD study aimed to improve understanding of P. leniusculus invasion success by examining trophic dynamics and to develop methodologies that could improve the detection and control of P. leniusculus populations in Scotland. Stable isotope analysis was used to determine the diet composition, trophic position and whether an ontogenetic dietary shift occurs in the Loch Ken population of P. leniusculus. Bayesian mixing models indicated that P. leniusculus in Loch Ken do exhibit an ontogenetic dietary shift. Additionally, individuals of all sizes occupied the trophic position of a predator in Loch Ken suggesting that invertebrates and fish constitute an important component of P. leniusculus diet. Stable isotope analysis was used once again to compare the isotopic niche width and diet composition of P. leniusculus populations from Loch Ken and A. pallipes populations from Loch Croispol and Whitemoss Reservoir. At the species level, A. pallipes exhibited a larger niche width than that of P. leniusculus. At the population level, the isotopic signatures of the A. pallipes populations were considerably different from each other suggesting an overestimation of A. pallipes’ niche width at species level. Results showed no dietary overlap between species and Bayesian mixing models suggested P. leniusculus and A. pallipes were consuming different resources, indicating there would be no direct competition for food resources if they were to co-occur. A plus-maze study was used to determine if P. leniusculus exhibited a preference for one of four food attractants (Oncorhynchus mykiss, P. leniusculus, beef or vegetation), which could be used to improve trapping efficiency. In the maze system, P. leniusculus exhibited no preference for any food attractant presented. This would suggest that either the maze was not a good model or food attractants would not improve trapping efficiency of P. leniusculus. Additionally, a comparative investigation into the use of gill nets as a method to control P. leniusculus was conducted. Results showed that the net type and the presence of fish entangled in the net influenced the number of P. leniusculus caught. Finally, environmental DNA (eDNA) was used and evaluated for detection of P. leniusculus. A robust quantitative Polymerase Chain Reaction (qPCR) assay and DNA extraction protocol were developed. Using the developed qPCR assay, P. leniusculus eDNA was detected in controlled aquaria conditions but not in environmental water samples collected from the field. Furthermore, the quantities of P. leniusculus eDNA declined in aquaria conditions while individuals were still present suggesting the mechanisms for eDNA release by P. leniusculus are complex. Stable isotope analysis indicates that P. leniusculus exhibit an ontogenetic dietary shift, and in each life stage, P. leniusculus function as an omnivore but occupy the trophic position of a predator. Niche width analysis revealed that the diet of P. leniusculus was less general than that observed in A. pallipes and thus diet of P. leniusculus may not be responsible for invasive success. Food attractants will not enhance trapping efficiency but nets may present a potential new method to control P. leniusculus. Similarly, eDNA presents a promising new method for rapid detection of P. leniusculus. It will not be possible to eradicate P. leniusculus in Scotland but the findings of this PhD may help prevent establishment of new populations. These results should be incorporated into future management strategies for P. leniusculus populations in Scotland and may have broader applications in Great Britain and Europe.

No description available.

Abstract The Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus, Mitchell) is an anadromous species that spawns in tidal freshwater rivers from Canada to Florida. Overfishing, river sedimentation and alteration of the river bottom have decreased Atlantic Sturgeon populations, and NOAA lists the species as endangered. Ecologists sometimes find it difficult to locate individuals of a species that is rare, endangered or invasive. The need for methods less invasive that can create more resolution of cryptic species presence is necessary. Environmental DNA (eDNA) is a non-invasive means of detecting rare, endangered, or invasive species by isolating nuclear or mitochondrial DNA (mtDNA) from the water column. We evaluated the potential of eDNA to document the presence of Atlantic Sturgeon in the James River, Virginia. Genetic primers targeted the mitochondrial Cytochrome Oxydase I gene, and a restriction enzyme assay (DraIII) was developed. Positive control mesocosm and James River samples revealed a nonspecific sequence—mostly bacteria commonly seen in environmental waters. Methods more stringent to a single species was necessary. Novel qPCR primers were derived from a second region of Cytochrome Oxydase II, and subject to quantitative PCR. This technique correctly identified Atlantic Sturgeon DNA and differentiated among other fish taxa commonly occurring in the lower James River, Virginia. Quantitative PCR had a biomass detection limit of 32.3 ug/L and subsequent analysis of catchment of Atlantic Sturgeon from the Lower James River, Virginia from the fall of 2013 provided estimates of 264.2 ug/L Atlantic Sturgeon biomass. Quantitative PCR sensitivity analysis and incorporation of studies of the hydrology of the James River should be done to further define habitat utilization by local Atlantic Sturgeon populations. IACUC: AD20127

La distribution de l'abondance des espèces en un site, et la similarité de la composition taxonomique d'un site à l'autre, sont deux mesures de la biodiversité ayant servi de longue date de base empirique aux écologues pour tenter d'établir les règles générales gouvernant l'assemblage des communautés d'organismes. Pour ce type de mesures intégratives, le séquençage haut-débit d'ADN prélevé dans l'environnement (" ADN environnemental ") représente une alternative récente et prometteuse aux observations naturalistes traditionnelles. Cette approche présente l'avantage d'être rapide et standardisée, et donne accès à un large éventail de taxons microbiens jusqu'alors indétectables. Toutefois, ces jeux de données de grande taille à la structure complexe sont difficiles à analyser, et le caractère indirect des observations complique leur interprétation. Le premier objectif de cette thèse est d'identifier les modèles statistiques permettant d'exploiter ce nouveau type de données afin de mieux comprendre l'assemblage des communautés. Le deuxième objectif est de tester les approches retenues sur des données de biodiversité du sol en forêt amazonienne, collectées en Guyane française. Deux grands types de processus sont invoqués pour expliquer l'assemblage des communautés d'organismes : les processus "neutres", indépendants de l'espèce considérée, que sont la naissance, la mort et la dispersion des organismes, et les processus liés à la niche écologique occupée par les organismes, c'est-à-dire les interactions avec l'environnement et entre organismes. Démêler l'importance relative de ces deux types de processus dans l'assemblage des communautés est une question fondamentale en écologie ayant de nombreuses implications, notamment pour l'estimation de la biodiversité et la conservation. Le premier chapitre aborde cette question à travers la comparaison d'échantillons d'ADN environnemental prélevés dans le sol de diverses parcelles forestières en Guyane française, via les outils classiques d'analyse statistique en écologie des communautés. Le deuxième chapitre se concentre sur les processus neutres d'assemblages des communautés.[...] / Integrative patterns of biodiversity, such as the distribution of taxa abundances and the spatial turnover of taxonomic composition, have been under scrutiny from ecologists for a long time, as they offer insight into the general rules governing the assembly of organisms into ecological communities. Thank to recent progress in high-throughput DNA sequencing, these patterns can now be measured in a fast and standardized fashion through the sequencing of DNA sampled from the environment (e.g. soil or water), instead of relying on tedious fieldwork and rare naturalist expertise. They can also be measured for the whole tree of life, including the vast and previously unexplored diversity of microorganisms. Taking full advantage of this new type of data is challenging however: DNA-based surveys are indirect, and suffer as such from many potential biases; they also produce large and complex datasets compared to classical censuses. The first goal of this thesis is to investigate how statistical tools and models classically used in ecology or coming from other fields can be adapted to DNA-based data so as to better understand the assembly of ecological communities. The second goal is to apply these approaches to soil DNA data from the Amazonian forest, the Earth's most diverse land ecosystem. Two broad types of mechanisms are classically invoked to explain the assembly of ecological communities: 'neutral' processes, i.e. the random birth, death and dispersal of organisms, and 'niche' processes, i.e. the interaction of the organisms with their environment and with each other according to their phenotype. Disentangling the relative importance of these two types of mechanisms in shaping taxonomic composition is a key ecological question, with many implications from estimating global diversity to conservation issues. In the first chapter, this question is addressed across the tree of life by applying the classical analytic tools of community ecology to soil DNA samples collected from various forest plots in French Guiana. The second chapter focuses on the neutral aspect of community assembly.[...]