Generalities of vertebrate responses to landscape composition and configuration gradients in a highly heterogeneous Mediterranean region

Aim To examine the distributional patterns of vertebrates (including birds, bats, carnivores and lagomorphs) along landscape composition and configuration gradients to better understand the effects of landscape modification on occurrence patterns at both species and community level. Location The region of Alentejo, a forest-dominated area of southern Portugal. Methods The study area was framed using 1647 hexagonal plots, each of 259 ha in size. Composition and configuration gradients were obtained for each plot by integrating the proportions of the main land cover types and their configuration patterns using multivariate analyses. Species-specific vertebrate responses were investigated using data from 75 plots in which carnivores, bats and lagomorphs were sampled, and from 135 plots in the case of birds. Community- level responses were investigated through changes in species richness and beta-diversity in 57 plots where all vertebrate groups were simultaneously sampled. At the species-level, an information-theoretic approach was used to determine the effects of landscape gradients on species’ responses. At the community level, Mantel tests were used to determine between-plot differences in species composition using the Sørensen dissimilarity index. Results We found that the occurrence patterns of most vertebrate species were best predicted by composition-related gradients, although configuration gradients were also frequently included in species-specific occurrence models. We also found a weak correlation between species richness and most landscape gradients suggesting a turnover in the identity of species, something that was corroborated by the stronger correlation between environmental gradients and beta-diversity measures. The amount of forest cover and landscape complexity (estimated as the heterogeneity in the size and number of land cover types) were the main composition and configuration gradients determining vertebrate responses at both species and community level. Main conclusions Our work contributes to a more refined understanding of the mechanisms underlying species distributional patterns in real-world human-modified landscapes. By uncovering generalities of species with multiple ecological requirements and by describing the entire landscape mosaic through landscape gradients, we also suggest that our work greatly helps to fill the gap between existing conceptual landscape models aimed to understand species distributional patterns in human-modified landscapes.

New perspectives in statistical mechanics and high-dimensional inference

The main purpose of this thesis is to go beyond two usual assumptions that accompany theoretical analysis in spin-glasses and inference: the i.i.d. (independently and identically distributed) hypothesis on the noise elements and the finite rank regime. The first one appears since the early birth of spin-glasses. The second one instead concerns the inference viewpoint. Disordered systems and Bayesian inference have a well-established relation, evidenced by their continuous cross-fertilization. The thesis makes use of techniques coming both from the rigorous mathematical machinery of spin-glasses, such as the interpolation scheme, and from Statistical Physics, such as the replica method. The first chapter contains an introduction to the Sherrington-Kirkpatrick and spiked Wigner models. The first is a mean field spin-glass where the couplings are i.i.d. Gaussian random variables. The second instead amounts to establish the information theoretical limits in the reconstruction of a fixed low rank matrix, the “spike”, blurred by additive Gaussian noise. In chapters 2 and 3 the i.i.d. hypothesis on the noise is broken by assuming a noise with inhomogeneous variance profile. In spin-glasses this leads to multi-species models. The inferential counterpart is called spatial coupling. All the previous models are usually studied in the Bayes-optimal setting, where everything is known about the generating process of the data. In chapter 4 instead we study the spiked Wigner model where the prior on the signal to reconstruct is ignored. In chapter 5 we analyze the statistical limits of a spiked Wigner model where the noise is no longer Gaussian, but drawn from a random matrix ensemble, which makes its elements dependent. The thesis ends with chapter 6, where the challenging problem of high-rank probabilistic matrix factorization is tackled. Here we introduce a new procedure called "decimation" and we show that it is theoretically to perform matrix factorization through it.

Incompressible limit and well-posedness of PDE models of tissue growth

Both compressible and incompressible porous medium models are used in the literature to describe the mechanical aspects of living tissues. Using a stiff pressure law, it is possible to build a link between these two different representations. In the incompressible limit, compressible models generate free boundary problems where saturation holds in the moving domain. Our work aims at investigating the stiff pressure limit of reaction-advection-porous medium equations motivated by tumor development. Our first study concerns the analysis and numerical simulation of a model including the effect of nutrients. A coupled system of equations describes the cell density and the nutrient concentration and the derivation of the pressure equation in the stiff limit was an open problem for which the strong compactness of the pressure gradient is needed. To establish it, we use two new ideas: an L3-version of the celebrated Aronson-Bénilan estimate, and a sharp uniform L4-bound on the pressure gradient. We further investigate the sharpness of this bound through a finite difference upwind scheme, which we prove to be stable and asymptotic preserving. Our second study is centered around porous medium equations including convective effects. We are able to extend the techniques developed for the nutrient case, hence finding the complementarity relation on the limit pressure. Moreover, we provide an estimate of the convergence rate at the incompressible limit. Finally, we study a multi-species system. In particular, we account for phenotypic heterogeneity, including a structured variable into the problem. In this case, a cross-(degenerate)-diffusion system describes the evolution of the phenotypic distributions. Adapting methods recently developed in the context of two-species systems, we prove existence of weak solutions and we pass to the incompressible limit. Furthermore, we prove new regularity results on the total pressure, which is related to the total density by a power law of state.

Study of charm hadronisation in pp collisions at $\sqrt{s}$ = 13 TeV with the ALICE experiment

In high-energy hadron collisions, the production at parton level of heavy-flavour quarks (charm and bottom) is described by perturbative Quantum Chromo-dynamics (pQCD) calculations, given the hard scale set by the quark masses. However, in hadron-hadron collisions, the predictions of the heavy-flavour hadrons eventually produced entail the knowledge of the parton distribution functions, as well as an accurate description of the hadronisation process. The latter is taken into account via the fragmentation functions measured at e$^+$e$^-$ colliders or in ep collisions, but several observations in LHC Run 1 and Run 2 data challenged this picture. In this dissertation, I studied the charm hadronisation in proton-proton collision at $\sqrt{s}$ = 13 TeV with the ALICE experiment at the LHC, making use of a large statistic data sample collected during LHC Run 2. The production of heavy-flavour in this collision system will be discussed, also describing various hadronisation models implemented in commonly used event generators, which try to reproduce experimental data, taking into account the unexpected results at LHC regarding the enhanced production of charmed baryons. The role of multiple parton interaction (MPI) will also be presented and how it affects the total charm production as a function of multiplicity. The ALICE apparatus will be described before moving to the experimental results, which are related to the measurement of relative production rates of the charm hadrons $\Sigma_c^{0,++}$ and $\Lambda_c^+$, which allow us to study the hadronisation mechanisms of charm quarks and to give constraints to different hadronisation models. Furthermore, the analysis of D mesons ($D^{0}$, $D^{+}$ and $D^{*+}$) as a function of charged-particle multiplicity and spherocity will be shown, investigating the role of multi-parton interactions. This research is relevant per se and for the mission of the ALICE experiment at the LHC, which is devoted to the study of Quark-Gluon Plasma.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KM-GAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KM-GAP is based on the PRA model framework (Pöschl-Rudich-Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modelled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmo- spheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270 K is close to unity. Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for eðcient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Kinetic multi-layer model of gas-particle interactions in aerosols and clouds (KM-GAP): linking condensation, evaporation and chemical reactions of organics, oxidants and water

We present a novel kinetic multi-layer model for gas-particle interactions in aerosols and clouds (KMGAP) that treats explicitly all steps of mass transport and chemical reaction of semi-volatile species partitioning between gas phase, particle surface and particle bulk. KMGAP is based on the PRA model framework (P¨oschl-Rudich- Ammann, 2007), and it includes gas phase diffusion, reversible adsorption, surface reactions, bulk diffusion and reaction, as well as condensation, evaporation and heat transfer. The size change of atmospheric particles and the temporal evolution and spatial profile of the concentration of individual chemical species can be modeled along with gas uptake and accommodation coefficients. Depending on the complexity of the investigated system and the computational constraints, unlimited numbers of semi-volatile species, chemical reactions, and physical processes can be treated, and the model shall help to bridge gaps in the understanding and quantification of multiphase chemistry and microphysics in atmospheric aerosols and clouds. In this study we demonstrate how KM-GAP can be used to analyze, interpret and design experimental investigations of changes in particle size and chemical composition in response to condensation, evaporation, and chemical reaction. For the condensational growth of water droplets, our kinetic model results provide a direct link between laboratory observations and molecular dynamic simulations, confirming that the accommodation coefficient of water at 270K is close to unity (Winkler et al., 2006). Literature data on the evaporation of dioctyl phthalate as a function of particle size and time can be reproduced, and the model results suggest that changes in the experimental conditions like aerosol particle concentration and chamber geometry may influence the evaporation kinetics and can be optimized for efficient probing of specific physical effects and parameters. With regard to oxidative aging of organic aerosol particles, we illustrate how the formation and evaporation of volatile reaction products like nonanal can cause a decrease in the size of oleic acid particles exposed to ozone.

Synergistic interactions in mixed-species biofilms of pathogenic bacteria from the respiratory tract

IntroductionMixed-species biofilms are involved in a wide variety of infections. We studied the synergistic interactions during dual-species biofilm formation among isolates of Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia.MethodsIsolates were cultured as single-species and all possible combinations of dual-species biofilms.ResultsThe 61 A. baumannii biofilms increased by 26-fold when cultured with S. maltophilia isolates; 62 A. baumannii biofilms increased by 20-fold when cultured with S. maltophilia isolates; and 31 P. aeruginosa biofilms increased by 102-fold when cultured with S. maltophilia 106.ConclusionsSynergy was observed between two isolates, including those that inherently lacked biofilm formation ability.

Soil mineral N dynamics beneath mixtures of leaves from legume and fruit trees in Central Amazonian multi-strata agroforests

Long term applications of leguminous green mulch could increase mineralizable nitrogen (N) beneath cupuaçu trees produced on the infertile acidic Ultisols and Oxisols of the Amazon Basin. However, low quality standing cupuaçu litter could interfere with green mulch N release and soil N mineralization. This study compared mineral N, total N, and microbial biomass N beneath cupuaçu trees grown in two different agroforestry systems, north of Manaus, Brazil, following seven years of different green mulch application rates. To test for net interactions between green mulch and cupuaçu litter, dried gliricidia and inga leaves were mixed with senescent cupuaçu leaves, surface applied to an Oxisol soil, and incubated in a greenhouse for 162 days. Leaf decomposition, N release and soil N mineralization were periodically measured in the mixed species litter treatments and compared to single species applications. The effect of legume biomass and cupuaçu litter on soil mineral N was additive implying that recommendations for green mulch applications to cupuaçu trees can be based on N dynamics of individual green mulch species. Results demonstrated that residue quality, not quantity, was the dominant factor affecting the rate of N release from leaves and soil N mineralization in a controlled environment. In the field, complex N cycling and other factors, including soil fauna, roots, and microclimatic effects, had a stronger influence on available soil N than residue quality.

Competitive interactions between species of freshwater snails: I. Laboratory: Ia. General methodology

For the development of laboratory experiments on the competitive interacitons between freshwater snail populations, special snail rooms were set up in the main building of the Research Center "Aggeu Magalhães". In the current paper, the first of a series on this subject, the general methodology of the laboratory work is described in detail. Using indoor cement channels in which a uniform seminatural environment was created, interactions of freshwater snail populations can be studied with minimal interference of the usual variables. Controlled indoor environmental techniques, as described in the current paper, may also be utilized in different types of experiments in malacology, and represent a substantial technical advance in malacological work.

Competitive interactions between species of freshwater snails. I. Laboratory studies: Ib. Comparative studies of the dispersal and the vagility capabilities of Biomphalaria glabrata and Biomphalaria straminea

Experiments reported in the current paper, carried out under semi-field conditions created in the laboratory, have shown that b. straminea has competitive superiority when compared with B. glabrata. The former species has shown higher capabilities of both dispersal and vagility. In addition, B. straminea was able to compete sucessfully with B. glabrata.

Competitive interactions between species of fresh-water snails: I. Laboratory. IC. Comparative survival of Biomphalaria glabrata and B. Straminea kept out of water

Biomphalaria glabrata and B. straminea were submitted to an out-door laboratory experiment for testing their comparative ability to resist desiccation. Results have shown that B. straminea is significantly higher resistant than B. glabrata. After five months under such distressing condition the survival ratios were: B. glabrata 8.1 per cent and B. straminea 18.4 per cent.

Amoebae as a tool to isolate new bacterial species, to discover new virulence factors and to study the host-pathogen interactions.

Amoebae are unicellular protozoan present worldwide in several environments mainly feeding on bacteria. Some of them, the amoebae-resistant bacteria (ARBs), have evolved mechanisms to survive and replicate inside amoebal species. These mainly include legionella, mycobacteria and Chlamydia-related bacteria. Amoebae can provide a replicative niche, can act as reservoir for bacteria whereas the cystic form can protect the internalized bacteria. Moreover, the amoebae represent a Trojan horse for ARBs to infect animals. The long interaction between amoebae and bacteria has likely selected for bacterial virulence traits leading to the adaptation towards an intracellular lifestyle, and some ARBs have acquired the ability to infect mammals. This review intends to highlight the important uses of amoebae in several fields in microbiology by describing the main tools developed using amoebal cells. First, amoebae such as Acanthamoeba are used to isolate and discover new intracellular bacterial species by two main techniques: the amoebal co-culture and the amoebal enrichment. In the second part, taking Waddlia chondrophila as example, we summarize some important recent applications of amoebae to discover new bacterial virulence factors, in particular thanks to the amoebal plaque assay. Finally, the genetically tractable Dictyostelium discoideum is used as a model organism to study host-pathogen interactions, in particular with the development of several approaches to manipulate its genome that allowed the creation of a wide range of mutated strains largely shared within the Dictyostelium community.

Species distributions and interactions in a changing world : from understanding to forecasting

Les écosystèmes fournissent de nombreuses ressources et services écologiques qui sont utiles à la population humaine. La biodiversité est une composante essentielle des écosystèmes et maintient de nombreux services. Afin d'assurer la permanence des services écosystémiques, des mesures doivent être prises pour conserver la biodiversité. Dans ce but, l'acquisition d'informations détaillées sur la distribution de la biodiversité dans l'espace est essentielle. Les modèles de distribution d'espèces (SDMs) sont des modèles empiriques qui mettent en lien des observations de terrain (présences ou absences d'une espèce) avec des descripteurs de l'environnement, selon des courbes de réponses statistiques qui décrive la niche réalisée des espèces. Ces modèles fournissent des projections spatiales indiquant les lieux les plus favorables pour les espèces considérées. Le principal objectif de cette thèse est de fournir des projections plus réalistes de la distribution des espèces et des communautés en montagne pour le climat présent et futur en considérant non-seulement des variables abiotiques mais aussi biotiques. Les régions de montagne et l'écosystème alpin sont très sensibles aux changements globaux et en même temps assurent de nombreux services écosystémiques. Cette thèse est séparée en trois parties : (i) fournir une meilleure compréhension du rôle des interactions biotiques dans la distribution des espèces et l'assemblage des communautés en montagne (ouest des Alpes Suisses), (ii) permettre le développement d'une nouvelle approche pour modéliser la distribution spatiale de la biodiversité, (iii) fournir des projections plus réalistes de la distribution future des espèces ainsi que de la composition des communautés. En me focalisant sur les papillons, bourdons et plantes vasculaires, j'ai détecté des interactions biotiques importantes qui lient les espèces entre elles. J'ai également identifié la signature du filtre de l'environnement sur les communautés en haute altitude confirmant l'utilité des SDMs pour reproduire ce type de processus. A partir de ces études, j'ai contribué à l'amélioration méthodologique des SDMs dans le but de prédire les communautés en incluant les interactions biotiques et également les processus non-déterministes par une approche probabiliste. Cette approche permet de prédire non-seulement la distribution d'espèces individuelles, mais également celle de communautés dans leur entier en empilant les projections (S-SDMs). Finalement, j'ai utilisé cet outil pour prédire la distribution d'espèces et de communautés dans le passé et le futur. En particulier, j'ai modélisé la migration post-glaciaire de Trollius europaeus qui est à l'origine de la structure génétique intra-spécifique chez cette espèce et évalué les risques de perte face au changement climatique. Finalement, j'ai simulé la distribution des communautés de bourdons pour le 21e siècle afin d'évaluer les changements probables dans ce groupe important de pollinisateurs. La diversité fonctionnelle des bourdons va être altérée par la perte d'espèces spécialistes de haute altitude et ceci va influencer la pollinisation des plantes en haute altitude. - Ecosystems provide a multitude of resources and ecological services, which are useful to human. Biodiversity is an essential component of those ecosystems and guarantee many services. To assure the permanence of ecosystem services for future generation, measure should be applied to conserve biodiversity. For this purpose, the acquisition of detailed information on how biodiversity implicated in ecosystem function is distributed in space is essential. Species distribution models (SDMs) are empirical models relating field observations to environmental predictors based on statistically-derived response surfaces that fit the realized niche. These models result in spatial predictions indicating locations of the most suitable environment for the species and may potentially be applied to predict composition of communities and their functional properties. The main objective of this thesis was to provide more accurate projections of species and communities distribution under current and future climate in mountains by considering not solely abiotic but also biotic drivers of species distribution. Mountain areas and alpine ecosystems are considered as particularly sensitive to global changes and are also sources of essential ecosystem services. This thesis had three main goals: (i) a better ecological understanding of biotic interactions and how they shape the distribution of species and communities, (ii) the development of a novel approach to the spatial modeling of biodiversity, that can account for biotic interactions, and (iii) ecologically more realistic projections of future species distributions, of future composition and structure of communities. Focusing on butterfly and bumblebees in interaction with the vegetation, I detected important biotic interactions for species distribution and community composition of both plant and insects along environmental gradients. I identified the signature of environmental filtering processes at high elevation confirming the suitability of SDMs for reproducing patterns of filtering. Using those case-studies, I improved SDMs by incorporating biotic interaction and accounting for non-deterministic processes and uncertainty using a probabilistic based approach. I used improved modeling to forecast the distribution of species through the past and future climate changes. SDMs hindcasting allowed a better understanding of the spatial range dynamic of Trollius europaeus in Europe at the origin of the species intra-specific genetic diversity and identified the risk of loss of this genetic diversity caused by climate change. By simulating the future distribution of all bumblebee species in the western Swiss Alps under nine climate change scenarios for the 21st century, I found that the functional diversity of this pollinator guild will be largely affected by climate change through the loss of high elevation specialists. In turn, this will have important consequences on alpine plant pollination.

Cleaning wrasse species vary with respect to dependency on the mutualism and behavioural adaptations in interactions

Interspecific mutualisms are an essential feature of life on earth, yet we know little about their evolution and stability. In many mutualisms several species are available as partners, raising questions about the similarity in function and behavioural repertoire depending on the partner species. Furthermore, variation between species in the quantity and quality of interactions resulting in variation in payoffs may allow us to infer the potential evolutionary origin of a multispecies mutualism complex. We addressed these issues in the marine cleaning mutualism, in which so-called 'cleaners' remove ectoparasites from so-called 'client' reef fish. We measured several parameters concerning the quantity and quality of cleaning interactions in six sympatric cleaner wrasse species. We found significant variation between cleaner species with respect to client diversity, the number of interactions with predatory clients, the duration of interactions, the frequency of client jolts as a correlate of 'cheating' by cleaners, and behaviours used for manipulation of client decisions. Exploratory correlations between cleaner species' dependency and our variables of interest suggest that cleaning originated as a conflict-free by-product mutualism and evolved towards more sophisticated behaviours, including strategic behaviours for interactions with predators, cheating and manipulation specifically adapted to the client type.

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling.

Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km(2) to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally, these data should be sampled to reflect variation in the underlying environment across large spatial extents, and at fine spatial resolution. Simplified ecosystems where there are relatively few interacting species and sometimes a wealth of existing ecosystem monitoring data (e.g. arctic, alpine or island habitats) offer settings where the development of modelling tools that account for biotic interactions may be less difficult than elsewhere.