Naturvärdesinventering (NVI) görs inför exploatering av naturmiljöer som en del i bevarande- och förstärkningsarbetet av den biologiska mångfalden. I Sverige har en standard för utförandet av NVI tagits fram. Studien gjordes på uppdrag av Trafikverket, beställare av NVI och Boreal Partner AB, potentiell ny utförare av NVI. Syftet var att jämföra olika grupper av utförarorganisationers NVI-rapporter för att utröna av vilka och på vilket sätt högts kravefterlevnad uppnås. Vidare skulle en redovisningsmall för att optimera kravefterlevnaden föreslås. Beskrivningarna av arbetssätt var för få och övergripande för att kunna användas för att utveckla ett arbetssätt för en ny utförare. Skillnaderna mellan gruppernas kravefterlevnad visade sig vara små till följd av variationer inom grupperna. Att vara väl insatt i standarden visade på högre och jämnare kravefterlevnad. Den föreslagna redovisningsmallen utgår från standardens krav och ska underlätta redovisning med hög kravefterlevnad och vara till nytta för så väl beställare som utförare.

Analysis of soil-derived DNA has been shown to minimize problems seen during traditional vegetation surveys, e.g. by matching the eDNA to a reference database for taxonomic identification rather than relying solely on taxonomic expertise. However, it has been debated to what extent and how accurately eDNA acts as a proxy for biodiversity. The reliability on eDNA and the awareness on influencing factors is also important for palaeoenvironmental reconstructions where above-ground vegetation cannot be used. This study aimed to investigate how well modern soil-derived eDNA reflects the contemporary vascular vegetation communities in a subarctic environment, and if the efficiency of the taxonomic identification differed between spatial scales. Near-surface soil samples at altitudinal gradients along numerous transects were collected in combination with vegetation surveys. The eDNA was amplified through metabarcoding using the P6 loop region of the chloroplast trnL intron, followed by a high-throughput sequencing. No difference in the number of identified taxa between eDNA and vegetation survey was seen at landscape scale. In contrast, the number of identified taxa was consistently higher in the vegetation survey at smaller spatial scales. The efficiency of identified taxa per scale remained stable for the vegetation survey, whereas for eDNA, a decreasing trend was seen. This study highlights the variations on taxa identification between both methods and which factors might cause it. Combining the methods allows for a more precise modern biodiversity estimation, as well as to minimize wrongful conclusions. This allows for a more accurate palaeoenvironmental reconstructions, which in turn can improve future species conservation decisions.

Les insectes sont encore aujourd’hui peu pris en compte dans les programmes de conservation de la biodiversité, malgré leur rôle majeur dans le fonctionnement des écosystèmes terrestres. Du fait de leur grande diversité, et d’une grande méconnaissance des patrons de structuration des communautés, la conservation de ces organismes se heurte à des problématiques liées à l’évaluation et à la hiérarchisation des enjeux ainsi qu’à l’estimation de la richesse spécifique des communautés. Parce qu’ils constituent deux groupes d’insectes particulièrement impactés par les changements environnementaux, les Rhopalocères et les Odonates constituent une part importante des insectes protégés en Europe. Dans ce contexte de faible prise en compte de la diversité entomologique en biologie de la conservation, cette thèse a eu pour objectifs (1) de mesurer les dynamiques récentes (déclin, stabilité ou essor) de ces deux taxa en France, et d’identifier les facteurs climatiques et écologiques susceptibles de les conditionner, (2) pour les Rhopalocères, d’utiliser une description fine des réseaux d’interaction entre les larves et leurs plantes-nourricières pour questionner les statuts de conservation selon une approche systémique (3) et enfin, dans un objectif résolument opérationnel, d’évaluer les liens entre les gains d’informations et les efforts/coûts d’échantillonnage mobilisés au cours des études d’impacts.L’étude comparative des dynamiques temporelles des populations de ces deux taxons a été réalisée à l’échelle de trois pays d’Europe de l’Ouest grâce à une analyse diachronique des patrons de répartition des espèces sur un pas de temps de 35 ans. Ce travail a mis en évidence une forte corrélation entre l’artificialisation des paysages (urbanisation, intensification agricole, régression des zones humides) et le déclin de nombreuses espèces, majoritairement caractérisées par des exigences écologiques strictes et actuellement non protégées. A cette même échelle, l’analyse de l’architecture du réseau d’interactions entre les larves de Rhopalocères et leurs plantes nourricières a quant à elle révélé une structure modulaire en relation avec la taxonomie des partenaires, ainsi qu’un lien entre le degré de spécialisation et la vulnérabilité des espèces (sans que la similarité du régime alimentaire des espèces ne semble conditionner leur statut de conservation). Une dernière partie a été ciblée sur l’évaluation du degré d’exhaustivité des inventaires entomologiques réalisés lors d’études d’impact réalisées en amont d’aménagements. Une procédure de repasse systématique et calibrée, sur des sites échantillonnés en garrigue méditerranéenne, a permis de mettre en évidence les limites des protocoles actuels, en termes d’estimation de la richesse spécifique et de détection d’espèces à enjeux. Sur cette base, des recommandations sont formulées pour optimiser les protocoles d’échantillonnage à mettre en œuvre pour la détection des espèces à enjeux.Cette thèse contribue à l’articulation entre problématiques fondamentale et besoins opérationnels, en permettant à la fois une meilleure compréhension des mécanismes de structuration des communautés d’insectes et la formulation de recommandations pour une meilleure application locale des politiques de conservation. / Insects are still poorly considered in biodiversity conservation programs, despite their major role in the functioning of terrestrial ecosystems. Because of their great diversity, and a great lack of knowledge of community structuring patterns, the conservation of these organisms faces major challenges related to the evaluation and prioritization of issues as well as the estimation of the species richness of communities. Because they constitute two groups of insects particularly impacted by environmental changes, butterflies and dragonflies are an important part of protected insects in Europe. In this context of low consideration of entomological diversity in conservation biology, this thesis aims to (1) measure the recent dynamics (decline, stability or expansion) of these two taxa in France, and to identify the climatic and ecological factors likely to condition them, (2) for butterflies, to use a fine description of the interactions network between the larvae and their hostplants to question the conservation status according to a systemic approach (3) and finally, with a clearly operational objective, to evaluate the links between the information gains and the efforts / sampling costs mobilized during environmental impact assessments.The comparative study of the temporal dynamics of the populations of these two taxa was carried out at the scale of three countries of Western Europe through a diachronic analysis of the species distribution patterns on a time step of 35 years. This work has highlighted a strong correlation between the artificialisation of landscapes (urbanization, agricultural intensification, regression of wetlands) and the decline of many species, mainly characterized by strict ecological requirements and currently unprotected. On this same scale, the analysis of the architecture of the interactions network between butterfly larvae and their food plants revealed a modular structure in relation to the taxonomy of the partners, as well as a link between the degree specialization and species vulnerability (although the similarity of the species' diet did not seem to condition their conservation status). A final part was focused on the evaluation of the completeness of entomological surveys carried out during environmental impact assessments. A systematic and calibrated return procedure, on sites sampled in Mediterranean scrublands, allowed highlighting the limits of the current protocols in the estimation of species richness and the detection of protected or vulnerable species.This thesis contributes to the articulation between fundamental issues and operational needs, by allowing both a better understanding of the structuring mechanisms of insect communities and the formulation of recommendations for a better local application of conservation policies.

<p>Urbanisation and infrastructure developments impact on the surrounding natural environment and threaten biodiversity. The fragmentation of natural habitats in particular is a major obstacle for the preservation of biodiversity in a long-term perspective. In the planning process, both the environmental impact assessment and strategic environmental assessment processes play a central role in the identification and prediction of impacts on biodiversity. At the same time, the devel-opment of GIS technologies and GIS-based ecological models offer new perspectives in the elaboration of predictions. In order to analyse current practices and identify the need for im-provements in the environmental impact process, a review of environmental impact assessment reports was carried out. Further, a review of existing GIS methods and GIS-based ecological models is presented. The results of the review of environmental impact assessment reports show a lack of predictions in current biodiversity assessments. These asssessments often concentrate on impacts at the local scale, failing to consider large-scale and widespread impacts at the ecosys-tem and landscape levels. The review of GIS methods and GIS-based ecological models demon-strate the possibility to generate quantitative predictions for a specific area as well as for it’s sur-rounding environment. At the same time, the flexibility and reproducibility of such methods would allow predictions to be made for different alternatives or scenarios, therefore providing decision makers with relevant information of potential impacts on biodiversity. This would, in turn, result in an improved integration of biodiversity issues in physical planning and contribute to a sustainable development.</p>

Le déclin de la biodiversité lié à l'augmentation des pressions sur les ressources naturelles, fait l'objet d'un large consensus. Cette situation souligne un besoin urgent de développer des outils de diagnostic et de suivi de l'état de la biodiversité qui soient spatialisés, rapides à mettre en œuvre, peu coûteux et qui permettent de réaliser des expertises à l'échelle des territoires. Une des hypothèses centrales en écologie est qu'il existe des relations positives entre l'hétérogénéité spatiale mesurée dans la mosaïque paysagère et la richesse en espèces qui peut y cohabiter à différentes échelles. Dans ce travail, nous nous appuyons sur cette hypothèse pour développer un Indice de Biodiversité Spécifique Potentielle afin de réaliser un diagnostic de l'état de la biodiversité dans la mosaïque paysagère intra-forestière à différentes échelles, en prenant l'exemple du massif du Vercors. Cet indice s'appuie sur des indicateurs et des critères capables de refléter le niveau de biodiversité potentiellement présente dans une zone géographique donnée, et permet d'approfondir les connaissances sur les relations entre la structure des peuplements, les caractéristiques de la mosaïque forestière et la richesse ou la répartition géographique des espèces. Les étapes clés de la méthodologie et de son évaluation sont valorisées sous forme d'articles. La représentation spatiale de la biodiversité potentielle à différentes échelles permet d'envisager de nombreuses applications dans les domaines de la conservation et de la gestion forestière multifonctionnelle. / There is a general consensus that as pressures on natural resources increase, biodiversity is being lost, and the rate of loss is not sustainable. Within the present situation is become a critical need to develop methods and tools for biodiversity monitoring and conservation. In particular, we need spatially-explicit tools and rapid assessment methods that are relatively easy to implement at different scales and at a relatively low cost. One of the basic assumptions in ecology is that there are positive relationships at different spatial scales between landscape heterogeneity and species richness in a given landscape mosaic. In this thesis, we focus on this assumption in order to build a Potential Species Biodiversity Index. Our aim was to assess potential biodiversity within a forest landscape mosaic, considering the Vercors' mountain range as a case study. The index encompasses indirect biodiversity indicators and criteria as a surrogate to biodiversity potential present for a given area. This approach allows a better understanding of the relationships between forests stand structure, forest landscape characteristics and species richness or geographical distribution. The main steps of the method and its evaluation are presented in scientific papers. The analysis of geographical distribution of the index at different spatial scales provides practical applications for conservation planning and multifunctional forest management related fields.

A key challenge in biodiversity is: How many species are there on earth? This issue is especially acute in poorly surveyed regions with high diversity, particularly Southeast Asia that also experiences many limitations such as lack of funds, documents and experts. To help meet this challenge, I have developed a five-tiered approach for diversity measurement of freshwater fish for use in Thailand. This is: (1) the creation of a newly updated species inventory that uses existing data; (2) exploration of the patterns of species richness, endemism, and uniqueness; (3) estimation of the total species richness; (4) investigation of patterns of rarity; and (5) integration of this knowledge into conservation practice. The system should be applicable to other regions and other taxa where a similar challenge exists. My work shows that eight hundred and seventy-two species in 17 orders, 55 families and 255 genera of freshwater fishes, accounting for roughly 10% of the world's freshwater fish diversity, have been reported for Thailand to date. This number was derived from information in the museum collections, literature and all other available sources, including reports written in Thai as well as in English. During this work I uncovered many gaps in biodiversity information, in terms of taxonomic and spatial records, though some families and basins are better represented than others. Taxonomic uncertainty also continues to be a challenge for taxonomists and users. The high diversity of freshwater fishes in Thailand is the result of both high alpha (α) diversity (diversity within a particular locality) and beta (β) diversity (diversity differences between localities). I concluded that the substantial beta diversity I detected is associated with the geographical separation of the six river basins in Thailand. For example, the species composition of freshwater fishes in the Salween Basin dramatically differs from all other basins of Thailand. In contrast, the Chao Phraya Basin and the Mekong Basin contain the greatest number of shared species. Approximately 55% of species have a wide distribution range (being reported from more than two basins), whereas 45% are highly restricted within a single basin. Analyses using species richness estimators suggest that the figure of 872 species is an underestimate and that there may be between 1000 and 1300 fish species in Thailand, in other words an increase of between 14.7% and 49.1% over the list I compiled (which is itself an increase of 52.2% over the last report in 1997). Freshwater fish have become increasingly vulnerable to anthropogenic activities. Of the 872 Thai fish species, 6.8% and 15.1% are globally and nationally threatened, respectively. Nonetheless, a striking feature of the database is that the conservation status of the vast majority of species has not so far been assessed, either globally or nationally. Scientists and policy makers will find these results useful in appreciating the magnitude of the tasks involved in surveying, describing and conserving the country's freshwater fish biota. My work highlights localities and taxa where conservation is a priority and is thus an important resource for policy makers and conservation planners concerned with the management of freshwater fish in Thailand.

L'anthropisation croissante des territoires a conduit à la transformation profonde des écosystèmes et à une perte massive, rapide et irréversible de la biodiversité. La réglementation nationale française impose aujourd'hui aux aménageurs du territoire d'évaluer, a priori et a posteriori, les impacts environnementaux de leurs projets de construction (ex : infrastructures routières) et notamment les impacts sur la biodiversité. Cette réglementation impose également de proposer des mesures d'évitement, de réduction, et de compensation, lorsqu'il existe des impacts résiduels, par la création ou la restauration de la biodiversité dégradée. En l'absence d'outils performants à disposition des gestionnaires, les échecs de la prédiction des impacts et de l'évaluation de l'efficacité des mesures conservatoires sont nombreux. L'objectif général de cette thèse est de proposer une nouvelle approche méthodologique pour (i) caractériser les processus et les paramètres abiotiques impactant la diversité végétale des communautés, (ii) analyser l'efficacité d'un projet de création et (iii) proposer, à la lecture de ces résultats, des nouvelles mesures de valorisation de la biodiversité végétale du site d'étude. Le site étudié est un aménagement paysager autoroutier, au sein duquel des semis et des plantations ont été réalisées par le constructeur, deux ans avant le début de notre étude. Nous avons restreint l'étude mécaniste du compartiment abiotique à celle du fonctionnement hydrologique (modélisé à l'aide d'HYDRUS-1D). [...] Suite et fin du résumé dans la thèse. / Human activities are responsible for high modifications in ecosystems functioning. It is recognized that these impacts cause definitive and high losses rate of biodiversity in every components of wildlife. Due to regulation, construction companies are bound to evaluate environmental impacts of the infrastructure construction projects (eg: roads), and more particularly, impacts on biodiversity. Companies are also bound to propose measures to avoid, reduce or mitigate residuals impacts by the creation or restoration planning of biodiversity. Unfortunately, there are not existing tools and methods clearly defined by regulation for such plans. Most of the time, predictions and environmental evaluations fail in measuring the impacts on biodiversity and efficiency of conservation planning. The research program that we conducted aimed at (i) proposing a new methodological approach in order to characterise processes and abiotic parameters which impact biodiversity of plant communities, (ii) analysing conservatory plans efficiency and (iii) proposing measures for biodiversity valuation in our study case. Our study was realised in a landscaping project zone along the A19 highway, Loiret, France. Seedling and planting were done two years before our study began. Only hydrological processes were studied based on mechanistic modelling using Hydrus-1D software. Last and final summary in the thesis.

Urbanisation and infrastructure developments impact on the surrounding natural environment and threaten biodiversity. The fragmentation of natural habitats in particular is a major obstacle for the preservation of biodiversity in a long-term perspective. In the planning process, both the environmental impact assessment and strategic environmental assessment processes play a central role in the identification and prediction of impacts on biodiversity. At the same time, the devel-opment of GIS technologies and GIS-based ecological models offer new perspectives in the elaboration of predictions. In order to analyse current practices and identify the need for im-provements in the environmental impact process, a review of environmental impact assessment reports was carried out. Further, a review of existing GIS methods and GIS-based ecological models is presented. The results of the review of environmental impact assessment reports show a lack of predictions in current biodiversity assessments. These asssessments often concentrate on impacts at the local scale, failing to consider large-scale and widespread impacts at the ecosys-tem and landscape levels. The review of GIS methods and GIS-based ecological models demon-strate the possibility to generate quantitative predictions for a specific area as well as for it’s sur-rounding environment. At the same time, the flexibility and reproducibility of such methods would allow predictions to be made for different alternatives or scenarios, therefore providing decision makers with relevant information of potential impacts on biodiversity. This would, in turn, result in an improved integration of biodiversity issues in physical planning and contribute to a sustainable development. / QC 20101129

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