Malgré des ressemblances frappantes dans les processus qui les contrôlent, la diversité génétique et la diversité spécifique ont été majoritairement étudiées de manière disjointe, d'une part par la génétique des populations, d'autre part par l'écologie des communautés. L'objectif de cette thèse est de quantifier les processus qui contrôlent la diversité génétique au sein des espèces et la diversité spécifique au sein des communautés. Mon étude porte sur la métacommunauté de mollusques d'eau douce présente sur l'île de Grande-Terre (800 km²) en Guadeloupe. Celle-ci se compose de 29 espèces qui vivent dans une mosaïque de milieux d'eau douce soumis à une forte instabilité temporelle (à-secs fréquents), supposée induire une dynamique en extinction-colonisation des espèces. Cependant, tout à-sec n'entraîne pas nécessairement une extinction, car certaines espèces ont la capacité de rester en vie ralentie dans le sol (estivation). Je me suis tout d'abord focalisé sur le gastéropode pulmoné Drepanotrema depressissimum en combinant trois approches complémentaires : (1) une étude de la distribution spatiale et temporelle de la diversité génétique, (2) un modèle de dynamique de l'occupation des sites qui prend en compte les formes de résistance (estivation) et (3) une expérience en laboratoire pour évaluer si cette espèce peut utiliser l'autofécondation lors de la recolonisation de sites vides. Ces approches révèlent que les extinctions ne sont pas aussi fréquentes que présumées au départ, et qu'elles ne sont pas liées aux à-secs. Au contraire, les sites instables sont les moins touchés. En effet, D. depressissimum surmonte très efficacement les périodes d'à-sec en estivant, et recourt très peu à l'autofécondation. Les extinctions sont en revanche plus importantes dans les sites stables qui correspondent aussi aux communautés les plus riches en espèces. Enfin, à l'échelle d'étude, la diversité génétique dépend des variations de taille et de connectivité des sites plutôt que de l'âge supposé de la population, suggérant un impact relativement mineur de la dynamique d'extinction-colonisation dans ce système. Dans la dernière partie de ma thèse, je mesure l'impact des processus neutres sur l'assemblage des communautés locales. Pour ce faire, j'analyse la corrélation entre la diversité moléculaire (microsatellites) des deux espèces les plus fréquentes, diversité considérée comme une référence reflétant uniquement les processus neutres d'échantillonnage, avec la diversité spécifique des communautés locales. Cette corrélation se révèle très significativement positive, et résulte de l'action parallèle d'une même variable (la connectivité des sites au réseau hydrographique lors de la saison des pluies) sur la migration et la colonisation à la fois des allèles et des espèces, révélant ainsi un rôle important de processus neutres dans la régulation de la diversité spécifique locale. / Striking similarities underlies those processes involved in the dynamics of genetic diversity and species diversity. However these diversities have been considered separately as part of the agenda of population genetics and community ecology respectively. My work aims at quantifying processes that govern genetic diversity within species and species diversity within communities. To address this question I focus on the freshwater snail metacommunity from Grande-Terre Island (800 km²) in Guadeloupe. Twenty-nine snail species inhabit a network of highly unstable freshwater habitats that frequently dry out. This instability probably triggers extinction-colonization cycles of local populations. However, drying-out periods do not necessarily lead to extinction as some species are able to aestivate. First, I focused on the pulmonate gastropod Drepanotrema depressissimum. I used three complementary approaches: (1) an analysis of the spatial and temporal distribution of genetic diversity, (2) a patch occupancy model that take into account the presence of resistance forms such as aestivating snails and (3) a laboratory experiment in order to infer whether this species can rely on selfing to recolonize empty sites. These analyses reveal that extinction is not as frequent as previously thought and is not positively related to instability. Indeed, unstable sites are less prone to extinction. D. depressissimum overcome efficiently drying-out events aestivating in the ground and do not rely on selfing. Besides, extinction is more frequent in stable environments that encompass more speciose communities. Finally, at the scale of investigation, genetic diversity depends much more on patch size and connectivity than on apparent population age, suggesting that extinction-colonization cycles play a minor role in the species dynamics. In the last chapter, I quantify the impact of neutral processes on community assemblage. To this aim, I analyze the correlation between genetic diversity (microsatellites) of the two most-commonly encountered species – this diversity reflects neutral sampling process, with species diversity of local communities. This correlation is highly positive and relies on the parallel effect of a single site characteristic (connection to the local hydrographic network during the rainy season) on migration and colonization of both alleles and species. This suggests that neutral processes play an important role on the regulation of both genetic diversity and local species occurrence.

A modified SEIR compartmental model is constructed for COVID-19 in a metapopulational setting with fine-scaled population data. The model is stochastically simulated with GLEAMviz that provides realistic short and long distance mobility based on real-world data. A retrospective evaluation in both the temporal and spatial dimensions is conducted with over one year of collected data from the COVID-19 pandemic in Sweden. We find that to reproduce the multimodal behavior a seasonal scaling factor of 0.4 is necessary, which is introduced to the model by scaling R0 with corresponding sinusoidal. For the spatial dimension we divide Sweden into a southern, middle and northern region and the model is able to capture the dynamics in all regions. Additionally, we introduce compartmental models in a constructive manner and motivate metapopulational models, including how commuting is integrated by a force of infection. The next generation method for calculating the basic reproductive number for arbitrary compartmental models is also presented.

Brucellosis is a bacterial infection that primarily affects livestock and can also be transmitted to humans. In the Greater Yellowstone Ecosystem (GYE), elk (Cervus canadensis) and bison (Bison bison) are habitual carriers of Brucella abortus, which arrived to the region with cattle over a century ago. The disease was eliminated from cattle in the United States through widespread control efforts, but is now periodically transmitted back to cattle on open rangelands where they can come into contact with fetal tissues and fluids from disease-induced abortions that occur among elk during the late winter and spring. In Wyoming, south of Yellowstone National Park, there are 23 supplemental feedgrounds that operate annually and feed the majority of the region’s elk during a portion of the winter. The feedgrounds are controversial because of their association with brucellosis and may be shuttered in the future in part due to the arrival of chronic wasting disease. Using data collected at these feedgrounds, this study investigates the role of winter feedgrounds in the ecology of this host-pathogen relationship: it evaluates the full reproductive costs of the disease to affected elk, how herd demography influences pathogen transmission, and assesses management strategies aimed at reducing pathogen spread among elk. Using blood tests for pregnancy status and brucellosis exposure in female elk, I demonstrated a previously undocumented fertility cost associated with the pathogen which is not due to abortions, but which nearly doubles the estimated fertility cost to affected individuals. I also built mechanistic transmission models using time-series disease and count data from feedgrounds. Within that framework, I assessed various management actions including test-and-slaughter of test-positive elk, which I found to be counterproductive due to rapid recovery times and the protective effects of herd immunity. The overall picture that emerges of winter feedgrounds is one of imperfect practicality driven by social and political consideration, not pathogen control. These results illustrate the underappreciated importance that recruitment and population turnover have on the transmission dynamics of brucellosis in elk, a pathogen which itself flourishes in the reproductive tracts of individual animals and thus impacts vital rates at the population level. Together, this study contributes to the field of disease ecology using a unique long term disease data set of free-ranging wild ungulates.

The decline of Acropora cervicornis and Acropora palmata populations and consequent listing as endangered species has prompted the need for restoration. Since financial resources are limited, optimal sites for restoration should not only be environmentally suitable for outplant survival, but also have a greater capacity to replenish surrounding reefs with larvae. However, in Florida coral larval dispersal patterns and reef connectivity remain poorly studied. Here, we measured long term larval survival and competency of A. cervicornis to calibrate a high resolution (100m) biophysical larval dispersal model of Acropora in the Florida Reef Tract (FRT). This model revealed that there is potential connectivity between reefs along the FRT, with most source reefs being located in the southern portion of the reef track, and most sinks in the northern part. The connectivity matrix was used then to develop a metapopulation model accounting for larval dispersal patterns, current and historic habitat for the species, growth, fecundity, and density-dependent post-settlement mortality for A. cervicornis and A. palmata, which allows comparing the capacity of suitable restoration sites to recolonize other reefs through sexual recruitment. Furthermore, it can determine optimal mesoscale spatial scaling and temporal planning of restoration project. We found that there was regional variation in the optimal spatial scaling, due to differences in intra-reginal connectivity and exiting coral cover. We also found that temporally staggering outplanting effort is important in poor environmental conditions. Considering ecological processes in restoration will enhance genetic diversity, hasten coral recovery, and boost resilience across the entire reef system.

with non-native invasive species is considered a major threat to many rare native species. As such, invasives removals are a common management strategy. Rare native species that interact uniquely with other organisms in their community (e.g., hemiparasitic plants) may be adversely affected by removing invasives. A management plan for a regionally rare hemiparasitic plant in Massachusetts, Pedicularis lanceolata Michx., identified invasives as a threat, but more quantitative evidence is needed to determine how P. lanceolata‟s persistence is influenced by its co-occurrence with native or invasive hosts. This research asks how P. lanceolata is affected by growth with native versus invasive hosts. Chapter I describes the species associated with P. lanceolata throughout its range, comparing areas where it is considered common and rare. Relative abundances of natives, non-native invasives, non-native non-invasives, and species with both native and non-native genotypes growing with P. lanceolata did not differ significantly at sites where the species is considered common in the Midwest compared to sites where the species is considered rare in the east. Chapter II outlines greenhouse and field removal experiments in which the types of host plants growing with P. lanceolata were manipulated. In the greenhouse, P. lanceolata growth, survival, and flowering were lower when it was growing with invasive compared to native graminoids. However, differences in P. lanceolata growth and survival when natives versus non-native were removed in the field varied from year to year due to succession of native shrubs at the site during the study. Chapter III asks how the population growth of P. lanceolata differs in uninvaded and invaded patches using an Integral Projection Model to perform population projections, sensitivity and elasticity analyses, and a life table response experiment. The population growth rate of P. lanceolata in uninvaded patches was lower than in invaded patches due to the succession of native shrubs in uninvaded patches. Chapter IV describes a metapopulation model for the invaded population of P. lanceolata in Massachusetts. The quasi-extinction probability was significantly affected by probabilities of dispersal, positive correlations in vital rates between sites, and catastrophes. These data will be used to update the management plan for P. lanceolata.

I Sverige finns många rödlistade arter vilka hotas av utrotning i olika utsträckning. Det finns även flera exempel där skydds- och bevarandeåtgärder utförts och som framgångsrikt bidragit till en stabilisering av arten. Vitryggig hackspett är en art i akut behov av kraftiga insatser för att Sverige ska kunna få en livskraftig stam. Två åtgärdsprogram har hittills tagits fram med just detta mål, ett för perioden 2005–2008 och ett som gäller från 2017–2021. Ett flertal åtgärder föreslås i programmen, främst med fokus på återupprättande av lämpliga habitat för vitryggen. 2020 blev ett lyckat år för arten men dess hotstatus kvarstår. Frågan är varför de åtgärder som utförs inte har gett det önskade resultatet? Det största problemet är just bristen på lämpliga habitat. De områden som finns är inte av tillräckligt hög kvalitet och kan därför inte hysa populationer stora nog för att hackspetten inte ska dö ut. Nationellt hade troligtvis en population på runt 200 – 300 par utgjort en tillräckligt stor grupp för att undvika ett utdöende. Som det ser ut nu är den svenska stammen uppdelad i ett antal delpopulationer. Om dessa grupper vore sammanlänkade genom att individer hade möjlighet att röra sig mellan områden i en så kallad metapopulation hade överlevnadschanserna ökat ytterligare. Både den norska, finska och ryska stammen är stabilare än den svenska och en förhoppning finns om att alla dessa populationer i framtiden ska kunna utgöra en mer storskalig metapopulation. För att detta ska ske krävs i första hand bättre habitatbiotoper som dessutom innehåller de vedlevande insekter som främst utgör hackspettens föda. Det är osäkert om de arter vitryggen livnär sig på finns i tillräckligt stor utsträckning i de svenska skogarna. Det krävs storskaliga restaureringsåtgärder av lövskog för att främja både de vedlevande insekterna och hackspetten. Trädslag som asp, björk och al behöver gynnas genom skötselåtgärder och produktionen av död ved, främst stående, måste stimuleras för att snabbare få fram tillräckliga volymer. Om inte dessa åtgärder vidtas har den vitryggiga hackspetten knappast en framtid i de svenska skogarna.

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