La biodiversité et le fonctionnement des écosystèmes sont des propriétés écologiques essentielles qui ont une incidence sur le bien-être humain. Des études sur la manière dont les deux biens sont affectés par les activités humaines et par le changement climatique fournissent les connaissances indispensables pour orienter la gestion des ressources naturelles. Les données de rétroobservation à long terme permettent de reconstituer l’histoire environnementale passée et offrent d’excellentes opportunités d’acquérir de telles connaissances. L'ADN sédimentaire est un outil émergent permettant de reconstituer la biodiversité passée détaillée au niveau du bassin versant, grâce à son excellente résolution taxonomique et à ses origines très localisées. Cependant, les études antérieures basées sur l'ADN sédimentaire utilisaient rarement le riche arsenal de méthodes d'analyse écologique numérique existantes, développées pour différents types de données écologiques. Dans la présente thèse, nous avons examiné les applications potentielles de telles méthodes sur des études basées sur l'ADN sédimentaire. Avec plusieurs exemples d’études, nous avons montré comment ces méthodes peuvent optimiser les connaissances acquises lors de l’analyse d’ensembles de données multiproxy comprenant des enregistrements sédimentaires d’ADN, de sédimentologie et climatiques. Malgré certaines limitations, l’analyse numérique basée sur l’ADN sédimentaire combinée aux enregistrements de proxies traditionnels est un outil puissant pour démêler les interactions complexes écosystémiques. Les futurs progrès méthodologiques dans l'analyse de l'ADN et les méthodes numériques sont prometteurs pour fournir une compréhension inestimable sur les facteurs de changement de la biodiversité et du fonctionnement des écosystèmes à grande échelle spatiale et temporelle. / Biodiversity and ecosystem functioning are crucial ecological properties that impact human welfare. Studies on how both properties are affected by human activities and by climate change provide indispensable knowledge to guide natural resource management. Long-term retro-observational data allow to reconstruct past environmental history and offer excellent opportunities to gain such knowledge. Sedimentary DNA is an emerging tool to reconstruct detailed past biodiversity in catchment level, thanks to its excellent taxonomic resolution and highly localized origins. However, previous studies based on sedimentary DNA rarely utilized the existing rich arsenal of numerical ecological analysis methods, which are developed for various types of ecological data. In the present thesis we reviewed the potential applications of such methods on sedimentary-DNA-based studies. With several example studies, we showed how these methods can maximize the knowledge gained from the analysis of multiproxy datasets that included sedimentary-DNA-, sedimentological- and climate records. Despite some limitations, numerical analysis based on sedimentary DNA combined with traditional proxy records is a powerful tool to unravel complex ecosystemic interactions. Future methodological advancements in both DNA analysis and numerical methods are promising to provide invaluable understanding over the drivers of changes in biodiversity and in ecosystem functioning across large spatial and temporal scales.

Recent years have seen an explosion of interest in the use of freely available DNA present in aquatic systems, otherwise known as environmental DNA (eDNA), as a tool for monitoring aquatic organisms. However, much remains unknown about the behavior of eDNA over a range of environmental conditions. This is particularly true in high gradient headwater streams, which have received less attention than other types of water bodies. In the summer of 2011, a headwater stream system with well established species distributions was sampled using eDNA techniques. Though species were detected where known to be present, detections also occurred where traditional techniques failed to detect species. This suggests that a cautious approach to positive eDNA detections is advisable. In 2012 a second study was conducted to better understand the dynamics of eDNA concentration in lotic systems. Caged brook trout (Salvelinus fontinalis) were introduced into two otherwise fishless headwater streams, and eDNA samples were collected at evenly spaced intervals downstream of the cage. This was repeated 19 times from mid-summer through autumn, over flows ranging from approximately 1 to 96 l/sec. Quantitative PCR was used to relate DNA copy number to distance from source for each of these 19 sampling events. In all cases, DNA was detectable at 239.5 m from the cage. Increasing flows generally decreased eDNA copy number near the cage but had relatively little effect at downstream sites. Additionally, the presence of leaf biomass during the fall period had the potential to completely erase otherwise high DNA levels.

The CRISPR-Cas system is a bacterial adaptative immune system which protects against infection by phages: viruses that infect bacteria. To develop immunity, bacteria integrate spacers — fragments of the invading nucleic acids — into their CRISPR array to serve as the basis for sequence-targeted DNA cleavage. However, upon infection, phages quickly take over the metabolism of the bacteria, leaving no time for the bacteria to acquire new spacers, transcribe them and use them to cut the invading DNA. To develop CRISPR immunity, bacteria must be safely exposed to phage DNA. Phage infection releases eDNA which could be involved in the development of CRISPR immunity. Using S. thermophilus and phages 2972 and 858 as a model for CRISPR immunity, I show that eDNA is crucial to the development of optimal CRISPR immunity, as generation of phage-immune bacterial colonies decrease with eDNA digestion. Furthermore, it is phage eDNA specifically that impacts CRISPR immunity since its addition increases the generation of phage-immune colonies. I also show that the effect of eDNA is phage-specific, sequence specific and can even be traced to a region of the genome covering the early-expressed genes which differ between phages 2972 and 858. While the acquisition of CRISPR spacers is not random and while the supplementation of eDNA influences that bias, eDNA is not used as a source of genetic information for spacer acquisition. This suggests that the effect of eDNA involves a new mechanism of phage resistance. Moreover, the effect of eDNA is highly dependent on environmental conditions as variation in media suppliers are sufficient to interfere with this effect. These results link environmental conditions, specifically eDNA, to the CRISPR-Cas system, providing a better understanding of the context of the emergence of CRISPR immunity and could inform our understanding of the mechanisms through which bacteria detect the presence of phages before infection. / Thesis / Doctor of Philosophy (PhD) / Phages are viruses that can infect and kill bacteria with a 99.9999% success rate. To defend themselves, bacteria have evolved an adaptive immune system called the CRISPR-Cas system. This system uses a piece of DNA, called a spacer, that matches the phage to destroy it. However, in order to use their CRISPR-Cas system, they need to obtain this spacer. Given how dangerous phages are, how bacteria acquire this spacer is a mystery. My project investigates the possibility that bacteria use DNA floating in the environment to vaccinate themselves against phages before ever encountering them. In this thesis I show that DNA floating in the environment helps bacteria acquire these spacers. I also show that it is specific sections of phage DNA that helps bacteria. This shows that bacteria can use their environment to defend themselves against threats before they even happen.

Utilizing environmental DNA (eDNA) for the detection of species in the field is a potentially cost-effective and time-saving technology that may be useful in understanding the distribution and abundance of threatened or endangered species such as the Eastern Massasauga (Sistrurus catenatus). I describe the development of an eDNA assay for the species and evaluate its ability to detect eDNA in laboratory and field conditions. In the field samples, I also investigated the potential for abiotic conditions to influence eDNA detection. Species-specific primers and probe were designed to amplify a 152 bp segment of the massasauga COI gene. Target eDNA could be detected in samples containing as little as 100 copies of target DNA/μL. Water samples collected from laboratory housed snakes indicated that eDNA can be detected in water 56 days after massasauga removal. Field samples were taken from crayfish burrows, known overwintering habitat for the species, from four sites that vary in snake use as ascertained by traditional visual surveys. Of the 60 burrows sampled, seven had a positive detection for massasauga eDNA with no difference in detection rate between DNA extracted from burrow water and burrow sediment. Occupancy models fitted to burrow water indicated that larger amounts of total DNA in a sample may increase the probability of detection of a massasauga eDNA. Large confidence intervals in site occupancy (ѱ) and burrow detection (Θ) values suggest that a larger sample size is needed for more reliable occupancy models. Abiotic conditions within crayfish burrows varied among sites but correlation with eDNA detection was not supported. Estimates of qPCR detection within a burrow with eDNA (ρ) suggest that up to 10 qPCR replicates per burrow sample may be necessary. Further studies need to examine eDNA degradation in the field, improve upon the limit of detection, and sample a larger number of sites for eDNA sampling to be a stand-alone survey method for Eastern Massasaugas.

La diversité des protistes marins planctoniques, après avoir été historiquement étudiée sur des critères morphologiques, est depuis récemment sujette à une intense recherche à l’aide d’approches moléculaires. Notamment, les études basées sur l’amplification directe de marqueurs moléculaires à partir d’ADN environnemental ont révélées une exceptionnelle diversité. L’objectif central de ce travail est d’améliorer notre compréhension sur le lien existant entre la connaissance classique des eucaryotes unicellulaires et leur diversité estimée à partir des données moléculaires, en particulier pour une meilleure interprétation des processus évolutifs et écologiques. Pour cela, nous avons utilisé comme système modèle l’ordre des ciliés tintinnidés (Tintinnida) qui constituent un groupe riche en espèces, aisément identifiables au microscope grâce à leur coquille externe (lorica) et communément rencontrés dans l’ensemble des eaux marines et lacustres du monde. Un suivi approfondi sur deux ans des tintinnidés de la Baie de Villefranche-sur-Mer (Mer Méditerrannée, France), couplant des analyses moléculaires de la diversité à partir de cellules individuelles et à partir d’ADN environnemental, a permis de caractériser la composition de ces communautés et leur dynamique temporelle aux échelles macro- et micro-évolutives. La première partie de ce travail a été destinée à la réalisation d’une phylogénie moléculaire de référence pour les tintinnidés en incorporant les séquences de 62 individus de morphologies diverses pour lesquelles des données moléculaires n'étaient pas disponibles. Nous avons amplifié et séquencé les gènes codant pour les ARN ribosomiques (ARNr 18S, 5.8S et 28S) et les espaces intergéniques correspondants (ITS1 et ITS2). La classification taxonomique a été réévaluée d’après les données moléculaires. Dans un deuxième temps, nous avons testé l’efficacité des approches moléculaires conventionnelles (amplification, clonage et séquençage Sanger du gène de l'ARNr 18S) et plus récentes (amplification et pyroséquençage de régions de l'ARNr 18S et de l’ITS), pour décrire la composition des communautés des tintinnidés dans des échantillons environnementaux en les comparant avec des estimations de la diversité par observation morphologique sur les mêmes échantillons. Si il existe de légères incongruences entre les approches et/ou les différents marqueurs employés, les approches cultureindépendantes s’avèrent efficaces pour décrire la diversité morphologique. En revanche, afin de ne pas surévaluer artificiellement le nombre d’espèces estimées à partir des données de pyroséquençage, il faut que des méthodes de débruitage et de regroupement en unités taxonomiques opérationnelles (UTOs) contraignantes soient appliquées. La troisième partie de ce travail a été dédiée au suivi temporel des communautés de tintinnidés à différentes profondeurs dans la baie de Villefranche, basé sur le clonage et le séquençage du gène de l'ARNr 18S et des régions ITS. Il apparaît des différences de distribution au cours de l’année à une même profondeur, en particulier en termes d’abondance de séquences pour une UTO donnée. Malgré un cadre phylogénétique solide et assez enrichi, l’approche moléculaire révèle des séquences éloignées des espèces déjà séquencées. La découverte de ces clades environnementaux souligne potentiellement l’importance écologique d’espèces encore mal connues. Enfin, le séquençage direct du gène de l'ARNr 18S et de l'ITS2 à partir des cellules individuelles de l'espèce <Undella claparedei> a offert l’opportunité d’une étude populationnelle sur une période de deux ans. La diversité intra-spécifique mesurée met à jour des phénomènes d’hybridation entre variantes génétiques. Une structuration génétique temporelle a également été observée pour le gène de l'ARNr 18S. Les implications de ces différentes recherches sont discutées dans le cadre de l’étude de la diversité et de l’écologie des tintinnidés, et plus largement, des protistes marins. / The marine protistan diversity has been historically studied based on morphological characterization but has recently been the object of intense research using molecular approaches. Studies based on the amplification of molecular markers from environmental DNA revealed an outstanding diversity, partly new and uncharacterized. However, the actual extent of this diversity remains poorly known and highly debated. The main goal of this work was to improve our knowledge on protistan diversity to bridge the gap between molecular environmental surveys and classical protistology to better understand the ecology and evolution of unicellular eukaryotes. For this purpose, we used as a model the species-rich order of the tintinnid ciliates (Tintinnida, Ciliophora), which are easily distinguishable because of their secreted shell, the lorica, and commonly found in marine waters all around the globe. A two-year monitoring of the tintinnid populations in the Bay of Villefranche-sur- Mer (Mediterranean Sea, France), combining molecular analyses of the diversity based on single-cells and environmental DNA, gave us the opportunity to describe the tintinnid community composition and its temporal dynamics. In the first part of this work, we constructed a reference molecular phylogeny for the tintinnids including new sequences from 62 specimens of diverse morphologies, for which we amplified and sequenced the ribosomal coding genes (18S, 5.8S and 28S rRNA) and the corresponding intergenic spacers (ITS1 and ITS2). The taxonomic classification of the Tintinnida has been revised based on these molecular data. In the second part, in order to assess the accuracy of molecular-based approaches to describe the natural species assemblages of tintinnids, we compared the morphology-based diversity estimates with those derived from classical (amplification, cloning and Sanger sequencing of the 18S rRNA gene) and more recent (direct pyrosequencing of amplified 18S rRNA genes and ITS regions) molecular approaches. Even if there are still some disagreements between the different methods and/or molecular markers, the culture-independent approaches were efficient to describe the morphological diversity. However, a careful and rigorous analysis of pyrosequencing datasets, including sequence denoising and stringent sequence clustering in Operational Taxonomic Units (OTUs) with well-adjusted parameters, is necessary to avoid overestimating the species number. The third part of the thesis is dedicated to the study of the genetic diversity of tintinnids over a one-year survey in the Bay of Villefranche at five different depths by combining community fingerprinting analysis using denaturing gradient gel electrophoresis (DGGE) with direct PCR amplification and sequencing of 18S, 5.8S, and 28S rRNA genes and ITS regions. These analyses revealed marked seasonal changes, in particular in the sequence abundances of certain OTUs. In addition, despite an enriched phylogenetic reference sequence dataset for the tintinnids, we retrieved two abundant phylotypes without any closely related known species, highlighting the possible ecological relevance of unidentified species. Finally, we studied the intra-specific diversity of populations of the species <Undella claparedei> based on 18S rDNA and ITS direct sequencing of single-cells collected over a period of two years. We detected signals of hybridization and sexual recombination among different genetic variants. We also found genetic structuring of the 18S rRNA gene data differentiating populations collected at different times. The implications of all these results are discussed in the framework of the diversity and ecology of tintinnid ciliates and, more generally, of marine protists

Les requins forment un des groupes de prédateurs les plus diversifiés, jouant des rôles importants au sein des écosystèmes marins. Ils forment également l’un des groupes les plus menacés car vulnérables aux pressions anthropiques du fait de leurs traits de vie particuliers. Malgré l’importance des ressources déployées pour le suivi des populations de requins, 41% des 482 espèces recensées dans la Liste Rouge de l’UICN n’ont pas de statut de conservation par manque de données. Il devient donc primordial d’améliorer les connaissances sur ces espèces afin de les protéger et enrayer leur déclin. Il s’agit notamment de mieux caractériser la présence, la structure et la connectivité des populations de requins pour mieux définir leur statut UICN, les zones prioritaires de gestion et optimiser les efforts de conservation mis en place. Cette thèse s’appuie sur l’émergence de nouvelles technologies pour combler les lacunes de connaissances sur les requins des récifs coralliens tropicaux et proposer des actions de gestion. D’une part, une méthode d’analyse des communautés de requins par collecte et séquençage d’ADN présent dans l’environnement (métabarcoding d’ADN environnemental ; ADNe) a été développée au cours de cette thèse, puis mise en parallèle avec des suivis exhaustifs par des méthodes traditionnelles d’étude des populations de requins. Cette approche rapide et non-invasive a permis d’identifier 21 espèces de requins dans les eaux de deux domaines biogéographiques distincts (Caraïbes et Nouvelle-Calédonie). De plus, les patrons de diversité et d’abondance des fragments d’ADNe détectés coïncident avec les gradients de pression anthropique et les niveaux de protection des zones échantillonnées. L’analyse de 22 échantillons d’ADNe dans l’archipel de la Nouvelle-Calédonie a permis de déceler la présence de plus d’espèces que par 2 758 plongées scientifiques réparties sur presque 30 ans et 385 caméras appâtées déployées pendant deux ans, et ce, à la fois proche de l’homme et dans les récifs éloignés. D’autre part, la structure et connectivité des populations d’une espèce plus commune, Carcharhinus amblyrhynchos, ont été caractérisées par une approche de génomique du paysage. Cette thèse s’appuie sur un échantillonnage génétique conséquent en Nouvelle-Calédonie et dans plusieurs autres sites de l’Indo-Pacifique (515 requins). Une approche d’isolement par la résistance via la théorie des circuits a été développée afin de caractériser les paramètres influençant la dispersion de cette espèce. Ainsi, il a été montré que les zones de forte bathymétrie constituent une forte barrière à la dispersion tandis que la proximité à l’habitat récifal en est un facilitateur. La modélisation de la différenciation génétique à haute résolution et à l’échelle de l’aire de répartition de cette espèce (Indo-Pacifique) a permis de définir des unités de conservation hiérarchiques et un nombre important de sites isolés. Enfin, une approche intégrant le déclin des abondances dans les zones anthropisées a montré une fragmentation des populations de C. amblyrhynchos et a permis d’identifier certains récifs éloignés de l’homme comme refuges mais aussi sources pour un repeuplement éventuel des récifs où les populations sont menacées. Cette thèse démontre ainsi le potentiel de l’analyse de l’ADNe pour dévoiler la présence d’espèces rares et furtives telles que les requins, donnant espoir pour combler les lacunes dans leurs statuts de conservation UICN. Elle révèle également la persistance des populations résiduelles en milieu anthropisé, qui pourraient éventuellement montrer des altérations comportementales comme l’utilisation d’habitats plus profonds ou une nocturnalité plus importante. Elle décrit enfin non seulement la structure fine à grande échelle des populations d’une espèce quasi-menacée, mais identifie également des unités de conservation et des zones prioritaires à protéger pour une spatialisation des mesures de gestion à différentes échelles. / Sharks represent one of the most diverse groups of predators, playing important functional roles in coastal and oceanic ecosystems. They are also one of the most threatened groups because of their vulnerability to anthropogenic pressures due to their particular life history traits. Shark populations are therefore collapsing with drastic decrease in abundance in all marine ecosystems. Even relatively common species are near- threatened. Despite the deployment of important resources for shark population assessments, 41% of the 482 shark species on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species lack a conservation status due to data deficiency. Improving our knowledge on such species is thus crucial for efficient protection to slow down their decline. More particularly, there is a necessity for a better characterization of presence, structure and connectivity of shark populations to define their conservation status, prioritize spatial management and optimize conservation efforts. This thesis relies on the emergence of new technologies to fill knowledge gaps on tropical coral reef sharks and to suggest conservation measures for better management. First, a method to survey shark communities has been developed during this thesis, based on the collection and sequencing of DNA present in the environment (environmental DNA metabarcoding; eDNA). Then, this method has been compared to exhaustive surveys of reef shark communities with traditional methods. This quick and non-invasive approach detected at least 21 shark species in waters of two distinct biogeographical areas (Caribbean and New Caledonia). Moreover, diversity and abundance patterns of DNA reads match with anthropogenic impact gradients and protected status of the sampled areas. The analysis of 22 eDNA samples detected more species in both remote reefs and impacted areas of the New Caledonian archipelago than 2758 scientific dives conducted during nearly 30 years and 385 baited remote underwater videos deployed over two years. Then, population structure and connectivity of a more common reef shark species, Carcharhinus amblyrhynchos, have been characterized using a seascape genomics approach. This thesis is based on a substantial genetic sampling in the archipelago of New Caledonia but also in several other sites in the Indo-Pacific (515 sharks in total). An isolation-by-resistance approach using circuit theory has been developed to explore what parameters are driving the genetic differentiation of C. amblyrhynchos. Here I show that deep oceanic areas act as strong barriers and proximity to habitat is a facilitator for dispersal. High-resolution modelling of genetic differentiation at the entire distribution range of the species (Indo-Pacific) led to the definition of hierarchical conservation units and a high number of isolated sites. Then, an approach taking into account the decline of abundance in impacted reefs showed an important fragmentation of shark populations and allowed the identification of remote reefs as refuges but also sources through dispersal towards impacted areas, insuring population persistence at a regional scale. This thesis demonstrates the potential of eDNA analysis for unveiling the presence of rare and elusive species such as sharks and for filling knowledge gaps in the conservation status of sharks. It also reveals the persistence of residual populations in impacted areas, that could show behavioral alterations like shifts in habitat use towards deeper waters or increased nocturnality. Finally, this thesis not only describes the population structure of a near-threatened species at high resolution and global scale, but also identifies conservation units and areas of high conservation priority that could help in the near future for the spatialization of marine management at multiple scales.

La plupart des écosystèmes sont aujourd'hui soumis à une pression anthropique croissante. Les études portant sur l'effet des activités humaines sur la biodiversité se multiplient mais elles se focalisent, principalement pour des raisons méthodologiques, sur un nombre restreint de groupes taxonomiques. L'originalité de ces travaux repose sur l'application d'une approche basée sur l'ADN environnemental permettant d'accéder à l'ensemble de la diversité biologique. Elle a ici été utilisée pour étudier l'impact des activités anthropiques sur les communautés biologiques et la résilience de ces dernières, à travers différentes échelles spatiales et temporelles. Dans une première partie, les communautés édaphiques, sous l'influence de diverses perturbations anthropiques, ont été caractérisées grâce à l'ADN contenu dans les sols. Ces études, réalisées dans différents milieux, mettent en évidence l'impact direct des activités humaines et leur influence sur les paramètres biotiques et abiotiques déterminant la distribution spatiale de la biodiversité des sols. La seconde partie se propose d'examiner l'impact à long terme des activités anthropiques au travers d'un exemple particulier en milieu de montagne. L'ADN contenu dans les archives sédimentaires lacustres a permis de retracer l'histoire des activités pastorales au cours de l'Holocène mais également les changements environnementaux que ceux-ci ont engendrés dans le bassin versant. L'approche mise en œuvre se révèle pertinente pour étudier à la fois les changements induits par les perturbations humaines sur les communautés et les facteurs influençant leurs dynamiques. Les résultats obtenus mettent notamment en lumière l'impact à long terme qu'exercent les activités anthropiques sur les communautés biologiques via les modifications profondes qu'elles génèrent sur les caractéristiques abiotiques du milieu. / Most ecosystems undergo an increasing anthropogenic pressure. Studies about the effects of human activities on biodiversity are proliferating but they focus on few taxonomical groups, mainly for methodological reasons. The originality of this work is based on the application of an approach based on environmental DNA that allows access to the biodiversity as a whole. It was used here to study the impact of anthropogenic activities on biological communities and the resilience of these latter, across different spatial and temporal scales. In the first part, edaphic communities under the influence of several human disturbances were characterized from soil DNA. These studies, performed in various environments, bring out the direct impact of human activities and their influence on biotic and abiotic parameters driving spatial distribution of soil biodiversity. In the second part, long-term impact of human activities was investigated through the analysis of lake sediments in the Alps. DNA from lacustrine sediments allowed to reconstruct livestock farming history over the Holocene and environmental changes that they induced in the catchment. We showed that this approach was relevant to study both changes generated by human disturbances on communities and factors driving their dynamics. Our results highlight the long-term impact of anthropogenic activities on biological communities, in relation to the alteration of environmental characteristics.

Gut microbiota is considered an important factor in the development of various diseases including inflammatory bowel disease (IBD, n = 127), Ulcerative colitis, Crohn's disease, and colorectal cancer (CRC, n = 64). A part of this thtesis is to prepare clinical material of different sorts (stool, biopsy) for sequencing on Illumina Miseq platform. This is achieved trough DNA isolation, amplification of 16S and internal transcribed spacer (ITS), normalization and ligation of sequencing adaptors. The aim of this project is to describe the differences between microbiota in healthy and diseased subjects in case of IBD or unimpaired and tumorous tissue for CRC patients. This research is also being based on cultivation, where a fresh stool samples (n = 3) are cultivated in a broad range of conditions, which enables us to obtain ecophysiological and species diversity of these samples by traditional and molecular methods. The cultivable fungi are also assigned reliable taxonomy by amplification of relevant genes (ITS1, β tubulin, second largest subunit of RNA polymerase II, RPB2) followed by both-sided Sanger sequencing. Selected species of fungi are processed into lysates, which are used for stimulation of mice macrofage cell line (RAW). Therefore the impact on immunity response is studied in vitro and...

Conservation of elasmobranch populations is often inhibited by a lack of data, particularly in understudied regions like the Red Sea. Survey efforts in this region have been infrequent and often highly localized. Establishing a broad baseline for elasmobranch diversity and abundance along the Saudi Arabian Red Sea coast could inform both conservation efforts and a nascent ecotourism industry. In this thesis, I describe a pilot study comparing biodiversity data from baited remote underwater video stations (BRUVS), unoccupied aerial vehicle surveys (UAVs), and eDNA sequencing at five islands in the Farasan Banks region of the Saudi Arabian Red Sea. Estimates of relative abundance were also compared between the BRUVS and UAVs. Each method identified species missed by the other two, but all three techniques exhibited clear habitat- and taxa-specific biases. I was able to identify key concerns for each approach that need to be addressed before large-scale implementation. If carefully planned and executed well, a full assessment of the Saudi Arabian coastline could establish a true baseline for shallow water elasmobranchs in the eastern Red Sea. Informing best conservation practices and identifying potential ecological attractions in accordance the environmental and economic goals of Saudi Arabia’s Vision 2030.

<p>  </p> <p>Semi-aquatic mammals, such as American beavers (<em>Castor canadensis</em>), muskrats (<em>Ondatra zibethicus</em>), North American river otters (<em>Lontra canadensis</em>), and American mink (<em>Neogale</em> <em>vison</em>), often play important roles in their ecosystem. Beavers and muskrats can manipulate plant community structure through the use of woody debris and forbs. As mesocarnivores, North American river otters and American mink can also drive community structure through the predation. Traditionally, these species are monitored using sign surveys (i.e., walking transects and visually identifying scat, tracks, and latrines). Camera trapping has also been used to survey semi-aquatic species occupancy to a lesser extent. However, due to their almost exclusive use of edge habitat, they may be ideal species to camera trap. Another more recently employed survey method is environmental DNA (eDNA), which involves the extraction of DNA from environmental samples (such as soil, water, air, and snow) to determine species occupancy. In this study, I evaluate environmental DNA and camera trapping as survey methods for detecting semi-aquatic mammals around northeastern Indiana. In the first chapter, I used eDNA sampling and camera trapping to monitor seven sites for three weeks during March – May 2021 in order to determine the presence of American mink. I found that the naïve occupancy for each site was 0.86. Although the detection probability of eDNA was lower than that of camera trapping (0.25 and 0.36, respectively), the occupancy models created suggest that there was no difference in detection probability between the two methods. I also compared the cost and time spent per sample and found that both were 20% lower for eDNA than camera trapping. The results of my study suggest eDNA may be a cost- and time-effective method for surveying for American mink occupancy. The objective of my second chapter was to determine the number of camera traps required to obtain reliable data for detecting semi-aquatic mammals. A minimum requirement for number of camera traps would be useful knowledge for wildlife managers in terms of budgeting and resource management and could also help to refine current camera trapping methodologies. I camera trapped four ponds for four weeks during June – July 2021, varying the number of camera traps (1 – 5) used at each pond each week. I collected a total of 66,543 photos and detected one semi-aquatic mammal throughout the study period (<em>Neogale vison</em>). Due to the lack of semi-aquatic mammals detected, I could not perform any analyses.</p>