Les forêts dunaires d’Aquitaine de pin maritime (Pinus pinaster) représentent un intérêt économique et écologique important de par leur rôle multifonctionnel (production de bois,protection contre l’érosion, préservation de la biodiversité, tourisme). La régénération naturelle est pratiquée après coupe rase pour les renouveler. Mais, de nombreux échecs de régénération sont observés depuis 20 ans, entrainant des pertes économiques non négligeables.L’objectif de ce travail a été d’identifier les mécanismes écologiques impliqués dans ces échecs récurrents, afin de proposer des recommandations de gestion pour favoriser le renouvellement de ces pinèdes. Pour cela, nous avons étudié quatre étapes-clés du processus de régénération : dispersion des graines, germination, survie, et croissance. Un réseau de sites d’observation le long du cordon dunaire a été utilisé pour quantifier la régénération, en interactions avec des pratiques sylvicoles (coupe rase vs coupe progressive, semis de graines de pin maritime vs absence de semis). Deux sites semi-expérimentaux ont été installé afin d’étudier en détail certains facteurs explicatifs potentiellement importants dans notre contexte(climat, interactions plante-plante, herbivorie). Nos résultats confirment que la régénération naturelle est un processus complexe, influencé par de nombreux facteurs environnementaux et d’autres liés à la gestion, pouvant être eux mêmes en interaction. La quantité de graines atteignant le sol ne semble pas être limitante. La germination des graines est fortement liée à l’humidité du sol, et est influencée par l’hétérogénéité de la microtopographie. La sécheresse estivale, cause majeure de mortalité des plantules, peut-être modulée par le maintien d’arbres semenciers. Les interactions biotiques directes et indirectes avec la végétation de sous-bois impactent fortement la survie des plantules, mais varient grandement en direction et en intensité selon les saisons et les années.Bien que nos résultats permettent de mieux comprendre les mécanismes impliqués dans le cycle de régénération du pin maritime, il apparaît difficile de mettre en avant un seul facteur expliquant les échecs de régénération sur certains secteurs. Cependant, dans l’ensemble, le maintien d’arbres semenciers pendant quelques années permet d’obtenir une régénération réussie sur la globalité des forêts dunaires, grâce à l’apport pluriannuel de graines mais aussi à travers les modifications du microclimat sous leur canopée. Contrôler la végétation spontanée afin de réduire la compétition avec les plantules de pin, et augmenter les plans de chasse afin de réduire la pression des herbivores sur les plantules, doit aussi être envisagé dans les secteurs où les échecs de régénération sont fréquents. / In south-western France, the coastal fringe with maritime pine (Pinus pinaster) forest has a multifunctional role, with erosion protection, preservation of biodiversity, tourism, and wood production as main objectives. Natural regeneration is used to renew these stands after clear-cutting. However, in recent years, regeneration failures have increased in some areas,leading to significant economic losses.The objective of this work was to identify the ecological mechanisms involved in these recurrent failures, in order to propose adapted forestry management practices to ensure forest regeneration. To do this, we studied four stages of the regeneration process: seed dispersal, germination, survival, and growth. A monitoring network of five sites along the Aquitaine Coast was also used to quantify the regeneration and characterize local differences in terms of forest management practices (clear-cut vs seed-tree regeneration,and sowing vs no sowing). Two experimental sites were set up to study in detail some factors potentially important in our context (climate, plant-plant interactions, herbivory).Our results confirm that natural regeneration is a complex process, influenced by many –often interacting – environmental and management factors. The quantity of seeds reaching the forest soil does not seem to be limiting. Seed germination is strongly related to soil moisture, and is influenced by the heterogeneity of the micro topography. Summer drought, the main cause of seedling mortality, may be mitigated by remaining seed trees on the stand.Direct and indirect biotic interactions with understorey vegetation have a strong impact on seedling survival, but vary greatly both in direction and intensity, depending on the seasonand the year.Even though our results provide a better understanding of the mechanisms involved in there generation cycle of maritime pine, it is difficult to put forward a single factor explaining local regeneration failures. However, overall, maintaining seed trees for a few years allows obtaining a successful regeneration in the entire coastal forest, thanks to the multi-yearsupply of seeds but also through the modifications of the microclimate under their canopy. Controlling understorey vegetation to reduce competition with pine seedlings and increasing hunting plans to reduce herbivory pressure on seedlings should also be considered in areas where regeneration failures are common.

Reproductive success can be influenced by interspecific and intraspecific competition, which consequently affect the distribution of species. The Spanish slug (Arion vulgaris) is an invasive terrestrial gastropod originating from southern Europe, and it causes substantial damage to horticulture and agriculture in Sweden.The leopard slug (Limax maximus) has been documented to have negative effects on the reproductive success of other slugs. Therefore, it has been suggested that the local distribution of the Spanish slug can be regulated by interspecific competition from leopard slugs. This competitive effect was tested in a laboratory experiment using mesocosms. The experiment had three different treatments: (1) two Spanish slugs, (2) four Spanish slugs and (3) two Spanish slugs and two leopard slugs. There was a significant effect of treatment on egg mass, where higher densities of slugs resulted in lower egg mass. Furthermore, there was a positive effect of body mass on the total number of eggs, mass, and size of the eggs. However, there was no clear effect of density of slugs on the size of the eggs produced and there was no difference between intra- and interspecific competition on the reproductive success of the Spanish slug. Because the level of intra- and interspecific competition on eggs laying was similar, my study does not support the hypothesis that leopard slugs can control Spanish slug populations, but it does show that intraspecific competition likely regulate egg production. / Reproduktiv framgång kan påverkas av inter- och intraspecifik konkurrens vilket i förlängningen kan påverka lokal utbredning. Spansk skogssnigel (Arion vulgaris) är en invasiv snigel som härstammar från sydeuropa och orsakar omfattande skador på trädgårdar och jordbruk i Sverige. Pantersnigeln (Limax maximus) har visat sig ha negativ påverkan på andra sniglars äggläggning. Min studie undersöker om interspecifik konkurrens från pantersnigeln har större effekt på spansk skogssnigels äggläggning än den från intraspecifik konkurrens från artfränder. Pantersnigeln kan då verka som en begränsande faktor för den spanska skogssnigelns lokala utbredning. För att undersöka detta utfördes ett experiment där individer av de båda arterna hölls i mesokosmer i olika tätheter och kombinationer i tre olika behandlingar: (1) två spanska skogssniglar, (2) fyra spanska skogssniglar och (3) två spanska skogssniglar och två pantersniglar. Experimentet visade tydligt att täthet av sniglar hade en effekt på de lagda äggens massa, och det fanns en positiv effekt av sniglars kroppsmassa på äggens storlek, antal och massa. Däremot fanns det ingen effekt av snigeltäthet på äggens storlek. Vidare hade intraspecifik konkurrens lika stor effekt på äggläggningen hos spansk skogssnigel som interspecifik konkurrens från pantersniglar. Min studie stödjer därför inte hypotesen att leopardsniglar kan kontrollera populationer av spansk skogssnigel, men den visar däremot att intraspecifik konkurrens påverkar äggläggningen.

Spartina anglica est une espèce exotique hybride qui peuple les zones humides littorales. Elle s’est installée dans le Bassin d’Arcachon au cours des années 1980, envahissant fortement les prés salés et les platiers vaseux préalablement occupés par, respectivement, Spartina maritima et Zostera noltei. Face aux inquiétudes suscitées par cette installation, cette thèse vise à comprendre, par une approche pluridisciplinaire, les mécanismes d’invasion et ses conséquences sur le milieu physique et sur les espèces végétales natives. L’objectif de ce travail est d’étudier l’occupation de niche par S. anglica et ses interactions avec deux espèces intertidales natives : S. maritima et Z. noltei.L’analyse d’images aériennes et satellitales a montré que, 30 ans après l’invasion, dans une zone densément peuplée par la Spartine native, la zone haute des prés salés a peu changé : la Spartine anglaise a occupé des niches vides et n’a pas remplacé la végétation native. Une expérience de transplantation réciproque et de mesures de biomasses confirment ce résultat, en montrant que l’espèce native offre une résistance à la colonisation de l’espèce exotique. L’expansion de la Spartine anglaise vers les replats de marée de l’intérieur du Bassin serait ainsi liée à sa capacité à tolérer les perturbations physiques, à sa forte plasticité de croissance en milieu oxygéné et riche en nutriments et à son comportement auto-facilitateur. Sa forte capacité d’ingénieur d’écosystèmes semble être liée à son système racinaire très développé, qui améliore l’aération des sols fortement anoxiques.Les effets de la colonisation par l’espèce exotique des zones intertidales basses à subtidales sur la Zostère naine sont importants sur le long-terme (dizaines d’années). En tant qu’ingénieur d’écosystèmes, la Spartine exotique favorise l’élévation du sol par sédimentation, entrainant une dessiccation du sédiment, peu favorable à la Zostère. Des mesures physiques au sein de patchs de l’espèce exotique suggèrent que l’élévation du sédiment est toutefois lente, surtout liée à une allocation de biomasse spécifique aux racines ainsi qu’à des rhizomes qui permettent de résister à l’érosion.En termes de gestion et de conservation des prés salés du Bassin d’Arcachon, ces résultats indiquent l’importance de limiter les perturbations physiques et les apports nutritifs qui pourraient rompre la résistance à l’invasion de la Spartine native. Ils supportent aussi l’idée que la Spartine anglaise pourrait être un allié robuste face à l’élévation du niveau de la mer. / Spartina anglica is a hybrid exotic cordgrass that inhabits coastal salt marshes. This species arrived in the Bay of Arcachon in the 1980s and since has importantly colonized the salt marshes and tidal flats formerly only occupied by the native Spartina maritima and Zostera noltei, respectively. This work aims at understanding, with an interdisciplinary perspective, the invasion mechanisms of this exotic cordgrass and the outcoming changes of its introduction in the Bay, both to the physical environment and to the native vegetation. Different approaches were considered in order to assess the niche occupancy by the exotic Spartina and its interactions with the native intertidal species, Spartina maritima and Zostera noltei.The analysis of aerial and satellite images has shown that, in about 30 years after the invasion, within a zone densely populated by the native Spartina, the global high marsh zone did not suffer significant changes with the arrival of the invasive species. Spartina anglica did not replace the existent marsh vegetation, it occupied empty niches along the intertidal area instead. Additionally, experimental works of cross transplantation and biomass measurements have corroborated that the native Spartina maritima offers resistance to the colonization by the exotic Spartina. It was also shown that the invasive occupies the same intertidal niche along the elevation and anoxic gradient than the native. The successful extension of Spartina anglica into the mudflat towards the inner Bay was related to its likely ability to tolerate physical disturbances, its strong growth plasticity in nutrient- and oxygen- rich patches and its self-facilitator behaviour. This latter trait is related to its strong ecosystem-engineering ability due to its prominent root system and consequent ability to ameliorate the oxygenation of highly anoxic soils.The main effect of the exotic Spartina species on the seagrass is related to its stronger ecosystem-engineering ability, favouring bed accretion up to levels that are not favourable to Z. noltei through enhancement of desiccation stress. However, hydrodynamic and altimetry measurements have shown that the process of bed accretion is slow and, due to the cordgrass’ specific preferential biomass allocation to roots, its efficiency is more linked to its resistance to erosion rather than sediment trapping.The results of this study provide relevant information for the definition of appropriate action and conservation strategies of marsh zones in the Bay of Arcachon, and in particular the importance of limiting physical disturbance and nutrient pollution that could disrupt the biotic resistance of the native cord grass. They also suggest a potentially important role of the exotic species in facing increasing Sea Level Rise.

Le desman des Pyrénées (Galemys pyrenaicus) est un petit mammifère semi-aquatique endémique du quart nord-ouest de la Péninsule Ibérique et des Pyrénées. Le déclin avéré de ses populations au sein de son aire de répartition déjà restreinte soumet actuellement l'espèce à un risque élevé d'extinction. Bien que les connaissances sur les exigences écologiques du desman des Pyrénées à différentes échelles spatiales aient été récemment améliorées, les causes de la contraction de sa distribution demeurent encore incomprises. Cette thèse a donc pour objectif d'identifier de nouveaux facteurs qui pourraient jouer un rôle dans la distribution du desman des Pyrénées à l'échelle locale du tronçon de rivière, afin de mieux comprendre les raisons de son déclin. Pour cela, cette étude s'est focalisée sur l'influence sur le desman des Pyrénées de facteurs (i) abiotiques tels que la chimie de l'eau et les perturbations anthropiques dans la rivière, et (ii) biotiques tels que les ressources trophiques, la compétition trophique et spatiale avec un compétiteur potentiel, la crossope aquatique Neomys fodiens, et l'impact de deux prédateurs potentiels, la loutre d'Europe Lutra lutra et le vison d'Amérique Neovison vison. Les résultats obtenus ont permis de proposer des mesures de gestion pour le desman des Pyrénées qui est une espèce vulnérable et protégée. / The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the northwest of the Iberian Peninsula and the Pyrenees mountains. The species is subject to an increased risk of extinction due to its observed substantial populations' decline across its whole and already limited range. Knowledge about the ecological requirements of the species was recently improved but the causes of its range contraction are still poorly understood. The aim of this PhD thesis was to identify new factors that could influence the species distribution at the reach scale, in order to better understand its decline. Thus, this study focused on the influence on the Pyrenean desman of (i) abiotic factors such as water chemistry and anthropogenic impacts on the riverbed and (ii) biotic factors such as trophic resources, the trophic and spatial competition with the Eurasian water shrew Neomys fodiens and the impact of two potential predators the European otter Lutra lutra and the American mink Neovison vison. The results enabled to suggest conservation measures for this vulnerable and protected species.

Comprendre comment les variations du climat pourraient influencer le recrutement des arbres en forêt est un défi car la germination, la croissance et la survie des semis sont particulièrement sensibles aux facteurs biotiques et abiotiques. Plusieurs modèles conceptuels généraux, (la « stress gradient hypothesis » SGH et « latitudinal herbivory theory » LHT,) suggèrent que la nature et l'intensité des interactions biotiques varient le long de gradients environnementaux. Ces modèles constituent une base théorique utile pour déterminer le rôle des interactions biotiques dans la réponse des communautés végétales aux variations du climat. Cependant, les études portant sur la SGH se sont limitées aux interactions directes entre plantes et ont négligé les interactions complexes. Les théories développées pour des niveaux trophiques supérieurs (comme la LHT) sont quant-à elles sujettes à débat et ne considèrent qu'un nombre limité d'interactions. Les interactions avec les micro-organismes du sol ont par exemple été négligées. Dans cette thèse, j'ai analysé comment les interactions directes et indirectes entre les semis, les arbres adultes, la végétation herbacée, les insectes herbivores et les pathogènes du sol varient en nature et en intensité le long de gradients climatiques. Pour explorer les interactions entre plantes, j'ai effectué une expérimentation s'appuyant sur la variabilité spatio-temporelle des conditions climatiques dans les Alpes. Les résultats montrent que les effets directs de compétition de la canopée et de la végétation herbacée augmentent avec la température. Cependant, pour les sites les plus chauds, la facilitation indirecte pourrait limiter la compétition directe des herbacées. Pour les interactions avec insectes herbivores,nous avons montré que le long de gradients d'altitude et de latitude, l'herbivorie est minimale là où les stress thermiques et hydriques est fort. Enfin, pour les interactions avec les micro-organismes du sol, nous avons mesuré en chambre de culture la survie de plantules de hêtre dans des sols, stérilisés ou non, collectés le long d'un gradient d'altitude. Les résultats montrent que les effets négatifs des micro-organismes sont plus faibles quand les communautés microbiennes proviennent de sols d'altitudes. Cette thèse suggère que les effets directs négatifs des plantes, des insectes herbivores et des pathogènes du sol sur les semis dominent dans les environnements chauds et productifs et s'atténuent dans des conditions plus froides. Les interactions indirectes semblent varier inversement et pourraient ainsi tamponner l'effet des interactions directes. / Understand how climate change could influence forest tree recruitment is a challenge because germination, seedling growth and seedling survival are especially sensitive to biotic and abiotic factors. Several conceptual models (as the “Stress Gradient Hypothesis”, SGH, and the “Latitudinal Herbivory Theory”, LHT) propose that the nature and intensity of biotic interactions vary along environmental gradients. These models constitute a useful theoretical basis to determine the role played by biotic interactions in the response of vegetation communities to climate variations. However, SGH studies have nevertheless been limited until now to direct interactions between plants and have neglected complex interactions. Theories including higher trophic levels, as the LGH, are still debated and have focused on a limited number of interactions. For example, interactions with soil biota have been neglected. In this thesis, we have analysed how direct and indirect interactions between seedlings, adult trees, ground vegetation, herbivorous insects, and soil pathogens vary in nature and intensity along climate gradients. To study interactions between plants, we established an experimentation using the spatio-temporal climatic variability in the French Alps. The results show that the direct effects of competition from adult tree canopy and ground vegetation diminish at higher altitudes. However, for warmer sites, indirect facilitation by canopy could limit direct competition by ground vegetation. To study the interactions between seedlings and herbivorous insects, we have analysed the altitudinal and latitudinal variation of herbivory on young trees across Europe. Results show that herbivory is the lowest where temperature and water stresses are strong. Finally, to study interactions with soil microorganisms, we have measured in a greenhouse the survival of European beech seedlings on soils either sterilized or not, collected along an altitudinal gradient. The results show that the negative effect of microorganisms is lower when microbe communities come from higher altitudes. The results suggest that the negative direct effects of plants, herbivorous insects and soil pathogens on seedlings are dominant in warm and productive environments and diminish in cold environments. Indirect interactions seem to vary inversely and could buffer the effects of direct interactions.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2016-06-08T19:09:02Z No. of bitstreams: 2 Tese - Denis Silva Nogueira - 2015.pdf: 6759912 bytes, checksum: d94527b0911d75bd269ddbf67184a1ce (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-06-09T11:45:09Z (GMT) No. of bitstreams: 2 Tese - Denis Silva Nogueira - 2015.pdf: 6759912 bytes, checksum: d94527b0911d75bd269ddbf67184a1ce (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-06-09T11:45:09Z (GMT). No. of bitstreams: 2 Tese - Denis Silva Nogueira - 2015.pdf: 6759912 bytes, checksum: d94527b0911d75bd269ddbf67184a1ce (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2015-03-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Lotic ecosystems are highly complex interacting with acting factors in different spatial and temporal scales. Small forested streams receive direct influence of the surrounding vegetation through the input of organic matter which is the base of the food chain in these ecosystems. I studied the effect of the reduced-impact selective logging on communities of aquatic insects streams to test the hypothesis that communities are affected by their impacts. Despite the metrics used appropriately capture the impact, there were no negative effects on insect communities. However, the results of this study may not be generalizable to other systems because we studied only a fraction of the diversity of Amazonian streams, specifically the insect orders Trichoptera, Plecoptera and Coleoptera. In addition, the absence of the low impact management effects is dependent on the operating system adopted in each enterprise. Another predominant feature in any lotic ecosystem is its directional flow, which consequently affects the distribution of substrates, habitats, and food resources within the streams. I studied the effects of water flow taking it as the main predictor of the selective effect of habitat on the attributes of insect taxa. My hypothesis was confirmed by showing that most rapid flowing streams in Amazon has faunas with morphological and ecological attributes of greater resistance to flow. Environmental factors such as the preference for habitats, dispersive limitation and biotic interactions are among the main mechanisms responsible for structuring communities, and has been widely emphasized in the context of metacommunity theory. A metacommunity is defined as the set of communities in a region which are interconnected by the flow of individuals, which emphasizes the spatial dynamics in structuring the diversity and composition of species in each local community. I tested the effects of environmental factors, spatial filters and biotic interactions in aquatic insects of forested streams of the Amazon, specifically the intraguild segregation and interguild predation effect. My results support the existence of predation effects on the organization of the metacommunity, as evidenced by the exclusive fraction of the predators matrix on prey assemblages of different guilds, and still withstand environmental effects and dispersive limitation in different trophic guilds. The study developed in this thesis help us understand more clearly the effects of the selective logging impacts on aquatic insect communities, assist in understanding about what are the characteristics of the stream habitats filter ecological and morphological attributes of aquatic insects in the Amazon, and advance our understanding of the effects that biotic interactions may have on the structuring streams metacommunities. / Ecossistemas aquáticos lóticos são altamente complexos interagindo com fatores atuando em diferentes escalas espaciais e temporais. Especialmente pequenos riachos florestados recebem a influência direta da vegetação circundante por meio da entrada de matéria orgânica a qual representa a base da cadeia alimentar nestes ecossistemas. Estudei os efeitos do corte manejado de madeira sobre as comunidades de insetos aquáticos de riachos, testando a hipótese de que as comunidades seriam afetadas por estes impactos. Apesar das métricas utilizadas capturarem apropriadamente os impactos, não houveram efeitos negativos sobre nenhum aspecto das comunidades estudadas. Entretanto, os resultados deste estudo não podem ser generalizados considerando que estudamos apenas uma parcela da diversidade dos riachos, especificamente as ordens Trichoptera, Plecoptera e Coleoptera. Além disso, a ausência de efeitos do manejo de baixo impacto é dependente do regime de exploração adotado em cada empreendimento. Outra característica predominante em qualquer ecossistema lótico é seu fluxo direcional da correnteza, que por conseguinte, afeta a distribuição dos substratos, habitats, e de recursos alimentares dentro dos riachos. Estudei os efeitos da velocidade do fluxo tomando-o como o principal preditor do efeito seletivo dos hábitats sobre os atributos das espécies. Minha hipótese foi corroborada, mostrando que riachos de águas mais correntes apresentam faunas com atributos morfológicos e ecológicos de maior resistência a correnteza. Fatores ambientais, como a preferência por habitats, limitação dispersiva e interações bióticas estão entre os principais mecanismos responsáveis pela estruturação de comunidades, e tem sido amplamente enfatizados no contexto da teoria de metacomunidades. Uma metacomunidade é definida como o conjunto de comunidades numa região que são interligadas pelo fluxo de indivíduos, o que enfatiza a importância das dinâmicas espacias estruturando a diversidade e composição de espécies em cada comunidade local e para a diversidade regional. Testei os efeitos de fatores ambientais, filtros espaciais e interações bióticas em insetos aquáticos de riachos florestados da Amazônia, especificamente padrões de segregação intraguildas, como um sinal de competição, e da predação entre guildas, assumindo explicitamente que a abundância e distribuição de predadores devem seguir a disponibilidade das presas consumidas. Meus resultados suportam a existência de efeitos de predação sobre a organização da metacomunidade, como evidenciado pela fração exclusiva da matriz de predadores sobre a comunidade de presas de diferentes guildas, além de suportar efeitos ambientais e limitação dispersiva em diferentes guildas tróficas. Os estudo desenvolvidos na presente tese ajudam a compreender mais claramente como os efeitos dos impactos do corte seletivo de madeira podem afetar comunidades de insetos aquáticos, auxiliam na compreensão de quais são as características dos hábitats selecionando atributos ecológicos e morfológicos de insetos aquáticos na Amazônia, e avançam nossa compreensão dos efeitos que as interações bióticas podem causar sobre a estruturação das metacomunidades de riachos.

Parmi les problèmes les plus fréquemment soulevés en biogéographie, figure celui de l’intégration des interactions écologiques dans les modèles de distribution d’espèces. Bien que la littérature scientifique apporte un ensemble de preuves soulignant le rôle prépondérant des interactions dans la structuration des communautés locales, on trouve relativement peu d’études révélant les empreintes laissées par les interactions dans les données de distribution d’espèces. Proposer une explication simple et claire à ce problème demeure un défi important que la biogéographie doit mener. Le problème majeur que pose l’absence de réponse claire sur le rôle des interactions aux larges échelles spatiales est que la plupart des scénarios de changements de biodiversité partent de l’hypothèse que les interactions sont négligeables. Si cette hypothèse est régulièrement rejetée, alors il faut réviser ces scénarios et soutenir le développement de méthodologies incluant les relations entre les espèces. Je commence cette thèse par un travail théorique sur le sujet car les théories classiques en biogéographie relèguent souvent au second plan les interactions écologiques. Au premier chapitre, je traite de l'intégration des interactions écologiques dans un modèle théorique de distribution d'espèces issue d'une des théories les plus importantes en biogéographie: la théorie de la biogéographie des îles. Ce travail montre comment les effets conjoints des facteurs biotiques et abiotiques changent les attendus de la théorie classique. En m'appuyant sur ce premier chapitre, je montre au second chapitre comment les interactions peuvent se répercuter dans les données de co-occurrence d’espèces. Ces données indiquent la présence ou l’absence de plusieurs espèces sur un même ensemble de sites dispersés sur de larges étendues spatiales. À l’aide d’un modèle probabiliste, j'obtiens des résultats théoriques liant les données de co-occurrence et l’information contenue dans les réseaux écologiques.Je démontre clairement que les interactions affectent les données de co-occurrence. Je montre également que plus le nombre d’interactions séparant deux espèces est grand, moins leur interactions indirect est détectable. De même si une espèce entretient de nombreuses interactions, il sera difficile de trouver une quelconque trace des interactions dans les données de co-occurrence pour cette espèce. Au troisième chapitre, je présente l’analyse de cinq jeux de données de co-occurrence pour lesquels la description des interactions était disponible. Avec ces donnés, j'ai été capable de confirmer les hypothèses du second chapitre en montrant que les espèces qui interagissent co-occurrent différemment de celles n’interagissant pas. Mes résultats indiquent aussi que l’abondance d'interactions est un frein à leur détection dans les données de co-occurrence. Cependant, en intégrant la similarité des facteurs abiotiques pour les différents sites, je montre que les signaux de co-occurrence s’affaiblissent pour parfois disparaitre. Mes résultats suggèrent donc qu’en utilisant des facteurs abiotiques pour inférer les probabilités de co-occurrence,une partie du lien entre les espèces est capturée, mais cette part est entachée d’une grande incertitude. Ceci vient questionner la qualité des prédictions données par les modèles classiques de distribution d'espèces actuellement utilisés. Les résultats de ma recherche apportent des éléments théoriques nouveaux sur le rôle des interactions écologiques dans le tracé des aires de répartition des espèces en plus de proposer une méthode originale pour étudier les données de co-occurrence d’espèces : les regarder à la lumière des réseaux écologiques. Avant de conclure ma thèse, je propose au chapitre 4 une démarche prometteuse pour aller encore améliorer l’intégration des interactions en biogéographie : les introduire par le biais des contraintes énergétiques, ce qui offre une base solide pour une théorie métabolique de la biogéographie. / One of the most pressing challenges currently in the field of biogeography is the successful integration of ecological interactions in species distribution models. Although the scientific literature points out the evidence of the controlling role interactions play on local community structure, relatively few studies have demonstrated its importance over large geographical gradients. Developing a concise, clear explanation for this issue remains a significant challenge that biogeographers need to answer. The main issue associated to the lack of a clear answer concerning the role of interactions at broad spatial scales is that most of scenarios of biodiversity changes assume that interactions can be ignored. When tested, if this hypothesis is proven false, then a re-consideration of species distribution models and their development must be undertaken to include relationships among species. I begin this thesis with a theoretical investigation on this topic, where classical theories have typically ignored ecological interactions. In the first chapter of the thesis I present the integration of interaction networks into a theoretical model of species distribution coming from one of the most important theory in biogeography: the theory of island biogeography. This work shows how together the biotic and abiotic factors can affect the expectations derived from the classical theory. Building upon the findings in the first chapter, in the second chapter, I show how interactions can affect co-occurrence (between species) data. Such data contains the presence or absence of several species for a similar set of sites dispersed along large latitudinal gradients. Using a probabilistic model, I obtain theoretical results linking co-occurrence data and the information included in ecological networks. I clearly demonstrate that interactions shape co-occurrence data. Furthermore, I show that the higher the number of links between two species, the more difficult it is to detect their indirect interaction. Similarly, if a species experiences many interactions, it is then challenging to detect any sign of interactions in co-occurrence data for this species.In the third chapter of the thesis, I assess five sets of co-occurrence data, which had descriptions of their interactions available. Using this data, I was able to confirm my hypotheses put forth in my second chapter, by showing that species co-occur differently from non-interacting one. These results also point out that the abundance of interaction must preclude their detection in co-occurrence data. However, when accounting for abiotic similarities among sites, signals of interactions are weakened. Therefore, my results suggest that using abiotic factors to infer co-occurrence probabilities capture a part of the link between species and further pinpoint the uncertainty associated to this part. As a result of these findings, the predictive power of classical species distribution models used to date is brought into question. My research findings bring new theoretical elements to the forefront when considering the influence of ecological interactions and how they shape species geographical distributions, while also introducing an original methodology for studying species co-occurrence: examining them in the light of ecological networks. Before concluding, my fourth and final chapter, I propose a promising new avenue to further investigate integrating species interactions in biogeography. Here, I introduce interactions in terms of energetic constraints, which will provide a sound basis for a metabolic theory of biogeography.

L’objectif de ce travail était de mieux comprendre les mécanismes moléculaires de l’adaptation microbienne à l’environnement fromager par des approches de génomique fonctionnelle via le modèle de Brevibacterium, un genre bactérien largement utilisé en technologie fromagère, mais dont l’implantation est parfois difficile à maîtriser.L’analyse génomique comparative de 23 souches de Brevibacterium, dont 12 issues de fromages, a révélé des différences en déterminants génétiques impliqués dans la capacité à croître à la surface du fromage. Parmi ces différences, plusieurs sont corrélées à la phylogénie des souches, et d’autres résultent de transferts horizontaux, notamment dans le cas des gènes liés à l’acquisition du fer et à la biosynthèse de bactériocines. Nous avons identifié des îlots génomiques correspondant à des transferts de gènes d’acquisition du fer entre des souches fromagères de Brevibacterium et des bactéries d’affinage appartenant à d’autres genres. Nous avons également mis en évidence un transposon conjugatif codant pour la synthèse de bactériocines présent chez des souches de Brevibacterium d'origine fromagère mais aussi chez une souche fromagère du genre Corynebacterium.L’étude fonctionnelle des interactions biotiques entre Brevibacterium et Hafnia alvei, une autre bactérie d’affinage du fromage, a été menée dans un modèle fromager développé au cours de ce travail. En couplant des analyses microbiologiques, biochimiques et transcriptomiques (RNA-seq), nous avons mis en évidence l’existence de différents mécanismes d’interaction entre ces bactéries. Ceux-ci concernent notamment l’acquisition du fer, la protéolyse, la lipolyse, le métabolisme soufré et le catabolisme du D-galactonate. Nos résultats suggèrent que dans la relation mutualiste observée entre certaines souches de Brevibacterium et H. alvei, cette dernière sécrète des sidérophores qui sont utilisés par Brevibacterium pour capter le fer plus efficacement, stimulant ainsi sa croissance. En contrepartie, Brevibacterium sécrète des lipases et des protéases qui dégradent les caséines et triglycérides du fromage en constituants énergétiques favorisant la croissance de H. alvei. Ce type d’interaction est intéressant à considérer pour la formulation des ferments d'affinage car il en résulte une meilleure capacité de tous les partenaires à coloniser le fromage, et ainsi à générer les propriétés technologiques recherchées. / The objective of this study was to better understand the molecular mechanisms of microbial adaptation to the cheese habitat by functional genomic approaches using Brevibacterium as a model microorganism. This bacterium is widely used for the manufacturing of cheese but its growth on the cheese surface is sometimes difficult to control.Comparative genomic analysis of 23 Brevibacterium strains, including 12 strains isolated from cheeses, revealed differences in genetic determinants involved in the growth on the cheese surface. Some of them are correlated to strain phylogeny and others are the result of gene transfers, especially those involved in iron acquisition and bacteriocin biosynthesis. We identified genomic islands corresponding to transfers of genes involved in iron acquisition between cheese-associated Brevibacterium strains and cheese-associated strains belonging to other genera. We also detected a conjugative transposon encoding bacteriocin production, which is present in cheese-associated Brevibacterium strains as well as in a cheese-associated Corynebacterium strain.Functional study of biotic interactions between Brevibacterium and Hafnia alvei, another cheese-ripening bacterium, was performed in a model cheese developed in this study. By coupling microbial, biochemical and transcriptomic (RNA-seq) analyses, we revealed several interaction mechanisms between these bacteria. These concern, in particular, iron acquisition, proteolysis, lipolysis, sulfur metabolism and D-galactonate catabolism. Our findings suggest that in the mutualistic relationship between some Brevibacterium strains and H. alvei, the latter stimulates Brevibacterium growth by the secretion of siderophores, which can be used by Brevibacterium to capture iron more efficiently. In return, Brevibacterium secretes lipases and proteases, which degrade cheese caseins and triglycerides into energetic substrates that stimulate H. alvei growth. This type of interaction is interesting to consider in the formulation of ripening cultures because it results in a better ability of all partners to colonize the cheese, and thus to generate the desired technological properties.

As ecosystem engineers, invasive earthworms are one of the main drivers of plant community changes in North American forests previously devoid of earthworms. One explanation for these community changes is the effects of earthworms on the reproduction, recruitment, and development of plant species. However, few studies have investigated functional trait responses of native plants to earthworm invasion to explain the mechanisms underlying community changes. In a mesocosm (Ecotron) experiment, we set up a plant community composed of two herb and two grass species commonly found in northern North American forests under two earthworm treatments (presence vs. absence). We measured earthworm effects on above- and belowground plant biomass and functional traits after 3 months of experiment. Our results showed that earthworm presence did not significantly affect plant community biomass and cover. Furthermore, only four out of the fifteen above- and belowground traits measured were affected by earthworm presence. While some traits, such as the production of ramets, the carbon and nitrogen content of leaves, responded similarly between and within functional groups in the presence or absence of earthworms, we observed opposite responses for other traits, such as height, specific leaf area, and root length within some functional groups in the presence of earthworms. Plant trait responses were thus species-specific, although the two grass species showed a more pronounced response to earthworm presence with changes in their leaf traits than herb species. Overall, earthworms affected some functional traits related to resource uptake abilities of plants and thus could change plant competition outcomes over time, which could be an explanation of plant community changes observed in invaded ecosystems.

<p dir="ltr">The lichen-feeding tiger moth tribe Lithosiini (Erebidae: Arctiinae) represent the largest radiation of invertebrate lichenivory. Caterpillars feed on lichen and as they feed, also sequester lichen polyphenolics, a behavior unique to these insects. The role of these compounds is believed to defend lithosiines against predators as larvae have been found to be protected against predators such as ants and moths to predators such as birds and bats. Experimental testing with controlled diets is necessary to fully make this connection, however little is known about host specifics for lithosiines. Furthermore, although lithosiines are monophyletic, the lack of a fully resolved phylogeny hampers investigation into many of the shallower level relationships, e.g. those among genera and species, within the group.</p><p dir="ltr">I addressed these knowledge gaps using the subtribe Cisthenina. Members of this group have been used to investigate predator-prey interactions and been included in morphological and molecular studies. Thus, while the group still needs attention, there is an ample amount of legacy loci data available for its members. I used these data to investigate the evolutionary relationships at the genus level, but to increase resolution in my analyses I additionally sampled taxa throughout the group with a recently developed anchored hybrid enrichment (AHE) probe set. I combined it with the legacy loci to both increase taxon sampling and resolution. I confirmed that trees made strictly from the legacy loci were unsuccessful and resulted in poorly supported relationships that made little sense. The addition of the AHE data greatly helped resolve relationships, however, there remained areas that were poorly supported and they appear to be genera with only a few loci. Thus, there is still room for improvement, but this offers a way for moving forward in lithosiine research, particularly to involve others who may have limited funding, equipment, and/or personnel and may only be able to afford legacy loci in diverse collaborations.</p><p dir="ltr">As the AHE probe set worked well with genus-level relationships I further attempted to use it in species delimitation of the notorious <i>Hypoprepia fucosa</i>-<i>miniata </i>species complex. Members of this group are varying shades of yellows, oranges and reds and have a convoluted taxonomic history. I gathered and organized over 4,000 specimens and using the AHE probe set found support for five distinct species. Interestingly, I used other morphological characters such as genitalia, but found no differences between species and a large amount of intraspecific variation. This suggests other courtship behaviors may be present and external morphology, i.e., color patterns, remain the best way to identify species. As part of this I am describing a new species and raising one from subspecies and as species are now readily distinguishable, they can be used for further investigations into lithosiines.</p><p dir="ltr">I used a member of this complex, <i>H</i>. <i>fucosa</i> to then evaluate the use of species distribution models (SDMs) to better understand their niche and how it relates to plausible lichen hosts. I evaluated 17 lichen species from two lichen genera, <i>Physcia </i>(13 species) and <i>Myelochro</i><i>a </i>(4 species)<i>. </i>These genera were selected based on previous feeding assays and the metabolites found in them have also been found in <i>H</i>. <i>fucosa </i>further suggesting caterpillars may feed on them. SDMs typically only use environmental factors to define and predict species niches. I compared the niches described by traditional SDMs to assess how similar they were, but I also investigated the use of lichens as biotic factors in the models. I assessed the influence each lichen had on the moth’s distribution found the niche of every lichen to be significantly different than that of the moth and their inclusion in SDMs of <i>H</i>. <i>fucosa </i>to improve model performance. This suggests <i>H</i>. <i>fucosa </i>caterpillars to be polyphagous, but to have some connection with these lichens. Further investigation with live specimens is needed, but these results support this as an effective way to describe lithosiine niches to better understand lichen feeding.</p>