Le réchauffement climatique entraîne des changements dans la dynamique et la distribution des populations. J'ai utilisé une étude de 19 ans, en Bretagne, sur un limicole longévif et migrateur partiel, l'Avocette élégante, pour quantifier et comparer les paramètres démographiques associés aux différentes stratégies de migration. Les taux de survie et les manifestations de la sénescence associées étaient similaires chez les résidents et les migrateurs, mais les migrateurs montraient un âge de recrutement plus tardif que les résidents. L'investissement reproductif était plus élevé et exempt de sénescence chez les individus recrutés à l'âge d'un an, alors que ceux commençant à se reproduire plus tard subissaient de la sénescence reproductive. La fitness des migrateurs était inférieure à celle des résidents, ce qui explique leur déclin pendant la période étudiée, alors que la population résidente est elle restée stable. La faible productivité, due à la prédation, entraîne le déclin de la population bretonne malgré un taux d'immigration important, ce qui doit absolument être pris en compte lors de la définition des politiques locales de conservation. / Global warming causes changes in the dynamics and distribution of populations. I used a 19-year study, in Brittany, on a long-lived and partial migrant, the Pied Avocet, to quantify and compare the demographic rates associated with different migration strategies. Survival rates and associated senescence patterns were similar in residents and in migrants, but migrants exhibited a delayed recruitment age. Reproductive investment was higher and senescence was absent in individuals recruited at the age of one year, whereas those who began to reproduce later showed reproductive senescence. The fitness of migrants was lower than the fitness of residents, which explained their decline over the study period, while the resident population remained stable. Low productivity, due to predation, caused the Brittany population to decline despite a high immigration rate, which questions local conservation policies.

The Tasmanian lacewing (Micromus tasmaniae Walker) is one of the most common aphid predators occurring in lucerne crops in New Zealand. A comparison of sampling techniques, and the output from a simulation model, suggest that the abundance of this lacewing may have been significantly underestimated in the past. Although the occurrence of aphid predators was erratic M. tasmaniae occurred more often and in far greater numbers (up to 100 m⁻²) than any other predator species. A simulation model for lacewing development in the field indicated that the large adult populations which occurred could be accounted for on the basis of reproductive recruitment. Independent evidence that immigration was not involved in the occurrence of these large populations was gathered using directional flight traps around the field perimeter. The major factors influencing lacewing population dynamics were the availability of aphid prey and, in the autumn, parasitism. Otherwise, survival of all life-histoty stages was high with no evidence of egg or larval cannibalism. Several instances of high lacewing mortality were identified by the model and the lack of any obvious cause for these highlights inadequacies in the understanding of lacewing bionomics. The model, which used a linear relationship (day-degrees) between development and temperature, was incapable of accurately predicting lacewing emergence under field temperatures which fluctuated outside the linear region of the development rate curve. Temperature thresholds and thermal requirements estimated under fluctuating temperatures similar to those in the field produced almost identical model output to those estimated under constant temperatures in the laboratory. Prey species was capable of influencing the rate of lacewing development. M. tasmaniae has the attributes necessary to produce large populations in the short time available between lucerne harvests. The asymptote of the functional response curve is low but the efficiency at converting aphids to eggs is high. Therefore, the lacewing is able to attain maximun reproductive output at low prey densities. A low temperature threshold for development (4-5° C), rapid development and short preoviposition period results in a short generation time (49 days at 15° C). Long adult life, high fecundity and the absence of any form of estivation or diapause, results in complete overlap of generations and multiple generations per year. M. tasmaniae's role as an aphid predator is restricted by its low appetite for prey and by the lucerne management regime currently practiced in New Zealand. Because it consumes relatively few aphids per day the lacewing's ability to destroy large aphid populations is limited. However, this may be offset by its ability to attack aphids early in the aphid population growth phase, and by the large numbers of lacewings which may occur. Under the present lucerne management schemes the large lacewing populations which do occur are forced out of the fields, or die, following harvest. A number of management options for increasing the lacewings impact as an aphid predator are briefly discussed.

En la presente tesis doctoral se aborda el estudio de las comunidades de peces presentes en las zonas someras litorales del Mar Menor. La comunidad objeto de estudio estuvo conformada principalmente por individuos en estado de postlarva e individuos juveniles, junto con los adultos de especies de talla pequeña.Los objetivos planteados fueron:A) Caracterización específica de la ictiofauna.B) Análisis de la biología poblacional y relaciones con el hábitat de especies de peces bentónicos.C) Análisis de las relaciones entre los tipos de hábitats litorales y la comunidad de peces.Los resultados obtenidos ponen de manifiesto la elevada importancia de las zonas someras litorales de la laguna como hábitats esenciales para la multitud de especies ícticas, tanto aquellas que poseen interés pesquero comercial (familias Atherinidae, Mugilidae y Sparidae) como aquellas que presentan interés conservacionista (familias Cyprinodontidae y Syngnathidae). / The present PhD thesis investigates the small-sized fish assemblages in the shallow littoral areas of the Mar Menor coastal lagoon. The study was focused on juveniles of migrant fish species that recruit into the lagoon and short-lived resident fish species that spend their entire lives in it.The objectives were:A) To characterize the fish assemblages.B) To examine population biology and habitat associations of benthic fish species.C) To analyse the relationship between littoral habitat types and fish assemblages.The results pointed out the importance of shallow littoral areas of the lagoon as essential habitats for many fish species, both juvenile fish species of commercial interest (Atherinidae, Mugilidae and Sparidae families) and threatened fish species (Cyprinodontidae and Syngnathidae families).

Crop rotation may be used to prevent the continuous selection of particular weed species adapted to one crop type. This might be useful for weed management, economy in herbicide applications and promoting biodiversity. Common simple crop sequences might be diversified by introducing perennial forage crops. Impacts of such perennial crops on weeds were studied with four approaches : 1) Large-scale weed surveys in 632 fields in western France showed that weed species composition differed most strongly between perennial alfalfa crops and annual crops. Comparisons of fields before, during and after perennial alfalfa suggested that community composition varies in a cyclic way during such crop rotations. Several weed species problematic in annual crops were suppressed during and after perennial crops, but the appearance of other species led to equal or even higher plant diversities. 2) A 3-year field experiment with contrasting crop management options allowed an investigation of the underlying mechanisms for this: The absence of soil tillage reduced weed emergence but increased the survival of established plants. The permanent vegetation cover and frequent hay cuttings reduced weed growth, plant survival and seed production. 3) Greenhouse experiments testing the regrowth ability of individual plants after cutting showed strong differences between species and functional groups. An two-factorial experiment suggested that the negative impacts of cutting and competition on weed growth were mainly additive. 4) Special measurements of weed seed predation in the field experiment showed positive correlations with vegetation cover, indicating that this ecosystem service may be particularly fostered by perennial crops. Consistent preferences of seed predators for certain weed species indicates that seed predation may be another cause of the observed weed community shifts.

The general aim of my dissertation was to investigate the role of plant interactions in driving population dynamics. Both theoretical and empirical approaches were employed. All my studies were conducted on the basis of metabolic scaling theory (MST), because the complex, spatially and temporally varying structures and dynamics of ecological systems are considered to be largely consequences of biological metabolism. However, MST did not consider the important role of plant interactions and was found to be invalid in some environmental conditions. Integrating the effects of plant interactions and environmental conditions into MST may be essential for reconciling MST with observed variations in nature. Such integration will improve the development of theory, and will help us to understand the relationship between individual level process and system level dynamics. As a first step, I derived a general ontogenetic growth model for plants which is based on energy conservation and physiological processes of individual plant. Taking the mechanistic growth model as basis, I developed three individual-based models (IBMs) to investigate different topics related to plant population dynamics: 1. I investigated the role of different modes of competition in altering the prediction of MST on plant self-thinning trajectories. A spatially-explicit individual-based zone-of-influence (ZOI) model was developed to investigate the hypothesis that MST may be compatible with the observed variation in plant self-thinning trajectories if different modes of competition and different resource availabilities are considered. The simulation results supported my hypothesis that (i) symmetric competition (e.g. belowground competition) will lead to significantly shallower self-thinning trajectories than asymmetric competition as predicted by MST; and (ii) individual-level metabolic processes can predict population-level patterns when surviving plants are barely affected by local competition, which is more likely to be in the case of asymmetric competition. 2. Recent studies implied that not only plant interactions but also the plastic biomass allocation to roots or shoots of plants may affect mass-density relationship. To investigate the relative roles of competition and plastic biomass allocation in altering the mass-density relationship of plant population, a two-layer ZOI model was used which considers allometric biomass allocation to shoots or roots and represents both above- and belowground competition simultaneously via independent ZOIs. In addition, I also performed greenhouse experiment to evaluate the model predictions. Both theoretical model and experiment demonstrated that: plants are able to adjust their biomass allocation in response to environmental factors, and such adaptive behaviours of individual plants, however, can alter the relative importance of above- or belowground competition, thereby affecting plant mass-density relationships at the population level. Invalid predictions of MST are likely to occur where competition occurs belowground (symmetric) rather than aboveground (asymmetric). 3. I introduced the new concept of modes of facilitation, i.e. symmetric versus asymmetric facilitation, and developed an individual-based model to explore how the interplay between different modes of competition and facilitation changes spatial pattern formation in plant populations. The study shows that facilitation by itself can play an important role in promoting plant aggregation independent of other ecological factors (e.g. seed dispersal, recruitment, and environmental heterogeneity). In the last part of my study, I went from population level to community level and explored the possibility of combining MST and unified neutral theory of biodiversity (UNT). The analysis of extensive data confirms that most plant populations examined are nearly neutral in the sense of demographic trade-offs, which can mostly be explained by a simple allometric scaling rule based on MST. This demographic equivalence regarding birth-death trade-offs between different species and functional groups is consistent with the assumptions of neutral theory but allows functional differences between species. My initial study reconciles the debate about whether niche or neutral mechanisms structure natural communities: the real question should be when and why one of these factors dominates. A synthesis of existing theories will strengthen future ecology in theory and application. All the studies presented in my dissertation showed that the approaches of individual-based and pattern-oriented modelling are promising to achieve the synthesis.

[Truncated abstract] Managed Aquifer Recharge (MAR) is a technique that can be used to capture and store water in aquifers for later reuse. This method recycles water that would normally be lost or discarded to the environment. MAR has been observed to have the potential for improving the quality of recharged water through a combination of physical, chemical and biological processes. The aim of this study was to investigate the changes in groundwater microbial population structure during MAR and the major influences that drive these population changes. Biogeochemical MAR studies have the potential to assist in the improved prediction of the removal of contaminants such as nutrients, pathogens and trace organics from the recharged water. Biological clogging during recharge also has the potential to overwhelm an aquifers ability to process wastewater thus reducing the hydraulic conductivity of the aquifer. Therefore further research into the spatial and temporal biogeochemical processes that occur during MAR is required. The geochemical and microbial population dynamics of two contrasting MAR techniques were investigated at two different geographical locations (Perth, Western Australia and Adelaide, South Australia). These MAR sites contained aquifers of dissimilar properties that were recharged with wastewater that contrasted in water quality. The Perth MAR site received secondary treated effluent which continuously infiltrated the unsaturated zone into an unconfined aquifer aided by infiltration galleries. Reclaimed water was extracted from a well at distance from the infiltration gallery. ... Notably the background and recovered water was most dissimilar in microbial and chemical population structure to that described for the infiltration gallery and injection well. Microbial and chemical evidence suggested that the background and extraction well groundwater were unaffected by plume migration. These results suggested that extraction well groundwater was similar in quality to that of ambient groundwater. Significant geochemical and microbial changes of secondary treated effluent during infiltration and lateral movement through aquifer were implicated in addition to the forced hydraulic gradient created from extracting fives time the volume of infiltrating wastewater. This study demonstrated that microbial populations and the geochemical processes associated with MAR can be studied and compared. Multivariate statistical methodology greatly simplified a vast array of dynamic biogeochemical information that could be dissected for meaningful interpretation over distance and time. The study evaluated the major biogeochemical influences which resulted in microbial and geochemical changes where it was noted that microbial populations were more dynamic than geochemical variation over time. Additionally biogeochemical comparative analysis indicated that microbial populations could change in population structure before a shift in aquifer geochemistry was detected. It is anticipated that the results from this study will benefit further research into the biogeochemical processes involved in water quality changes (e.g. nutrient removal, pathogen decay and biodegradation of trace organics) as well as controlling biological clogging of MAR schemes.

Le but de ce travail est l'étude d'un problème de transmission en dynamique de population entre deux habitats juxtaposés. Dans chacun des habitats, on considère une équation aux dérivées partielles, modélisant la dispersion généralisée, formée par une combinaison linéaire du laplacien et du bilaplacien. On commence d'abord par étudier et résoudre la même équation avec diverses conditions aux limites posée dans un seul habitat. Cette étude est effectuée grâce à une formulation opérationnelle du problème: on réécrit cette EDP sous forme d'équation différentielle, posée dans un espace de Banach construit sur les espaces Lp avec 1 < p < +∞, où les coefficients sont des opérateurs linéaires non bornés. Grâce au calcul fonctionnel, à la théorie des semi-groupes analytiques et à la théorie de l'interpolation, on obtient des résultats optimaux d'existence, d'unicité et de régularité maximale de la solution classique si et seulement si les données sont dans certains espaces d'interpolation. / The aim of this work is the study of a transmission problem in population dynamics between two juxtaposed habitats. In each habitat, we consider a partial differential equation, modeling the generalized dispersion, made up of a linear combination of Laplacian and Bilaplacian operators. We begin by studying and solving the same equation with various boundary conditions in a single habitat. This study is carried out using an operational formulation of the problem: we rewrite this PDE as a differential equation, set in a Banach space built on the spaces Lp with 1 < p < +∞, where the coefficients are unbounded linear operators. Thanks to functional calculus, analytic semigroup theory and interpolation theory, we obtain optimal results of existence, uniqueness and maximum regularity of the classical solution if and only if the data are in some interpolation spaces.

Une alternative prometteuse à la lutte chimique pour la régulation des ravageurs de culture consiste à favoriser les populations de leurs prédateurs en jouant sur la structure du paysage agricole. L'identification de structures spatio-temporelles favorables aux ennemis naturels peut se faire par l'exploration de scénarios paysagers via une modélisation couplée de paysages et de dynamiques de population. Dans cette approche, les dynamiques de populations sont simulées sur des paysages virtuels aux propriétés structurales contrôlées, et l'observation des motifs de populations associés permet l'identification de structures favorables. La modélisation des dynamiques de populations repose cependant sur une connaissance fine des processus écologiques et de leur variabilité entre les différentes unités du paysage. L'état actuel des connaissances sur les mécanismes écologiques régissant les dynamiques des ennemis naturels de la famille des carabidés demeure l'obstacle majeur à la recherche in silico de scénarios paysagers favorables. La littérature sur les liens entre motifs de population de carabes et variables paysagères permet de formuler un ensemble d'hypothèses en compétition sur ces mécanismes. Réduire le nombre de ces hypothèses en analysant les convergences entre les motifs de population qui leur sont associés, et étudier la stabilité de ces convergences le long d'un gradient paysager apparaît comme une première étape nécessaire vers l'amélioration de la connaissance sur les processus écologiques. Dans une première partie, nous proposons une heuristique méthodologique basée sur la simulation de modèles de réaction-diffusion porteurs de ces hypothèses en compétition. L'étude des motifs de population a permis d'effectuer une typologie des modèles en fonction de leur réponse à une variable paysagère, via un algorithme de classification, réduisant ainsi le nombre d’hypothèses en compétition. La sélection de l'hypothèse la plus plausible parmi cet ensemble irréductible doit s'effectuer sur la base d'une observation des motifs de population sur le terrain. Cela implique que ces derniers soient caractérisés à des résolutions spatiales et temporelles suffisantes pour sélectionner une unique hypothèse parmi celles en compétition. Dans la deuxième partie, nous proposons une heuristique méthodologique permettant de déterminer a priori des stratégies d'échantillonnage maximisant la robustesse de la sélection d'hypothèses écologiques. Dans un premier temps, la simulation de modèles de réaction-diffusion représentatifs des hypothèses écologiques en compétition permet de générer des données biologiques virtuelles en tout point de l'espace et du temps. Ces données biologiques sont ensuite échantillonnées suivant des protocoles différant dans l'effort total d'échantillonnage, le nombre de dates, le nombre de points par unité d'espace et le nombre de réplicats de paysages. Les motifs des populations sont caractérisés à partir de ces échantillons. Le potentiel des stratégies d'échantillonnage est évalué via un algorithme de classification qui classe les modèles biologiques selon les motifs de population associés. L'analyse des performances de classification, i.e. la capacité de l'algorithme à discriminer les processus écologiques, permet de sélectionner un protocole d'échantillonnage optimal. Nous montrons également que la manière de distribuer l'effort d'échantillonnage entre ses composantes spatiales et temporelles est un levier majeur sur l'inférence des processus écologiques. La réduction du nombre d'hypothèses en compétition et l'aide à l'échantillonnage pour la sélection de modèles répondent à un besoin fort dans le processus d'acquisition de connaissances écologiques pour l'exploration in silico de scénarios paysagers favorisant des services écosystémiques. Nous discutons dans une dernière partie des implications de nos travaux et de leurs perspectives d'amélioration. / A promising alternative to the chemical control of pests consists in favoring their natural enemies populations by managing the agricultural landscape structure. Identifying favorable spatio-temporal structures can be performed through the exploration of landscape scenarios using coupled models of landscapes and population dynamics. In this approach, population dynamics are simulated on virtual landscapes with controlled properties, and the observation of population patterns allows for the identification of favorable structures. Population modeling however relies on a good knowledge about the ecological processes and their variability within the landscape elements. Current state of knowledge about the ecological mechanisms underlying natural enemies’ of the carabid family population dynamics remains a major obstacle to in silico investigation of favorable landscape scenarios. Literature about the relationship between carabid population and landscape properties allows the formulation of competing hypotheses about these processes. Reducing the number of these hypotheses by analyzing the convergence between their associated population patterns and investigating the stability of their convergence along a landscape gradient appears to be a necessary tep towards a better knowledge about ecological processes. In a first step, we propose a heuristic method based on the simulation of reaction-diffusion models carrying these competing hypotheses. Comparing the population patterns allowed to set a model typology according to their response to the landscape variable, through a classification algorithm, thus reducing the initial number of competing hypotheses. The selection of the most likely hypothesis from this irreducible set must rely on the observation of population patterns on the field. This implies that population patterns are described with spatial and temporal resolutions that are fine enough to select a unique hypothesis among the ones in competition. In the second part, we propose a heuristic method that allows determining a priori sampling strategies that maximize the robustness of ecological hypotheses selection. The simulation of reaction-diffusion models carrying the ecological hypotheses allows to generate virtual population data in space and time. These data are then sampled using strategies differing in the total effort, number of sampling locations, dates and landscape replicates. Population patterns are described from these samples. The sampling strategies are assessed through a classification algorithm that classifies the models according to the associated patterns. The analysis of classification performances, i.e. the ability of the algorithm to discriminate the ecological processes, allows the selection of optimal sampling designs. We also show that the way the sampling effort is distributed between its spatial and temporal components is strongly impacting the ecological processes inference. Reducing the number of competing ecological hypotheses, along with the selection of sampling strategies for optimal model inference both meet a strong need in the process of knowledge improvement about the ecological processes for the exploration of landscape scenarios favoring ecosystem services. In the last chapter, we discuss the implications and future prospects of our work.

The Raso lark is a Critically Endangered bird endemic to the islet of Raso, Cape Verde. This thesis investigates two phenomena that particularly put the species at risk: its extreme fluctuations in population size, and its potentially very low genetic diversity arising from small population size and severe past population contraction. More specifically, two chapters estimate year-to-year survival and explore the factors - environmental and individual - that influence it, while two other chapters examine the lark’s genetic characteristics compared to its two continental closest relatives, including phylogenetic relationships and levels of genetic diversity. The conclusion of the thesis then uses these results to make recommendations for the conservation of the Raso lark. Each of the data chapters is summarized below: Chapter 3 estimates adult survival in the Raso lark and tests whether it could be linked to two population phenomena observed in the field: a highly variable population size and a male-biased sex ratio in certain years. Using a dataset spanning 10 years, I estimated survival for both sexes to fluctuate between 0.76 and 0.94 over this period. This is much higher than the survival rate of its closest relative, the skylark. I also found strong evidence for survival fluctuating over time and differing between males and females (with males having higher survival until 2011, at which point the trend inverted), which could play a role in the aforementioned population size fluctuations and male-biased sex ratio, respectively. Chapter 4 aims at understanding which factors shape survival in the Raso lark. Two types of variables were considered: year-dependent (rainfall, population size, population mean clutch size) and individual-dependent (age, body size characters, size ratio with mate, Ase18 genotype). Amongst the year-dependent variables, only sameyear rainfall impacted survival, with a 13% decrease in survival in the wettest year compared to the driest year, making it the most likely explanation for the inter-annual fluctuations in survival found in Chapter 3. Results also hint at some of the individual factors - morphological measurements and Ase18 genotype - influencing survival. The picture that emerges is that of a species whose life history strategy is to invest heavily in maintenance and survival, but less into fecundity, which stands in sharp contrast with the mainland-dwelling skylark. This is consistent with the theory that island birds generally have slower life history strategies than their continental counterparts. Chapter 5 determines the precise relationship between members of the Alauda clade, resolving a node on the phylogenetic tree of all larks that the study by Alström et al. (2013) was unable to resolve. My RADseq results indicate that the Raso lark and the skylark are sister species, and that the Oriental lark is likely to be a subpopulation, or maybe a subspecies, of the skylark. Chapter 6 compares the population genetics of the Raso lark with those of the skylark. In particular, it estimates the genetic diversity of the Raso lark and investigates the drivers behind it. I found unexpectedly high nucleotide diversity in the Raso lark, and explain this by showing that the population contraction that the species underwent was recent enough for most of the diversity to still be present. Moreover, 16% of the Raso lark genome has levels of heterozygosity on average 6.6 times higher than elsewhere on the genome, likely due to suppressed recombination and the existence of a neo-sex chromosome in larks. Despite this, I found high levels of relatedness and of linkage disequilibrium in the Raso lark, two clear genetic signs that it underwent a severe population contraction several centuries ago.

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