Theoretical and Experimental Studies of Dendritic Metacommunities

The present thesis deals with the understanding of the origins and the mechanisms of maintenance of biodiversity in natural landscapes, in particular by identifying key processes that define large-scale patterns of abundance and diversity. Biological communities often occur in spatially structured habitats where connectivity directly affects dispersal and metacommunity processes. Recent theoretical work suggests that dispersal constrained by the connectivity of specific habitat structures affects diversity patterns and species interactions. This is particularly relevant in dendritic networks epitomized by fluvial ecological corridors. This thesis addresses whether connectivity alone can explain observed features of biodiversity and selectively promote different components of community composition in river-like landscapes, such as local species richness or the among-community similarity. The relevance of this thesis lies in the major ecological challenges posed by the topic, and its fundamental importance to conservation biology. The studies pursued herein are also deemed relevant because of the influence of the spatial connectivity and dispersal on population dynamics and of the relevance of biodiversity to ecosystem functioning. Mechanisms of species coexistence were investigated with a blend of theoretical tools (broadly related to statistical mechanics and the theory of stochastic processes) and experimental work using laboratory microbial communities. The research tools ranged from aspects of modern coexistence theory in a local perspective to the recent concept of the metacommunity in spatial ecology, within a unified framework. The study of biodiversity in riverine ecosystems guided by observational data has been addressed by combining theoretical metacommunity models with laboratory experiments. The results are diverse. First, they show experimentally that connectivity per se shapes key components of biodiversity in metacommunities. Local dispersal in isotropic lattice landscapes homogenizes local species richness and leads to pronounced spatial persistence. By contrast, dispersal along dendritic landscapes leads to higher variability in local diversity and among-community composition. Although headwaters exhibit relatively lower species richness, they are crucial for the maintenance of regional biodiversity. By suitably arranging patch sizes within river-like networks the effect of local habitat capacity (i.e., the patch size) and dendritic connectivity on biodiversity can be experimentally disentangled in aquatic microcosm metacommunities. It is shown in this thesis that species coexistence and community assembly depend on intricate, non-trivial interactions of local community capacity and network positioning. Furthermore, an interaction of spatial arrangement of habitat capacity and dispersal along river-like networks also affects a key ecosystem descriptor, namely regional evenness. High regional evenness in community composition is found only in landscapes preserving geomorphological scaling properties of patch sizes. In riverine environments some of the rarer species sustained regionally more abundant populations and were better able to track their own niche requirements compared to landscapes with homogeneous patch size or landscapes with spatially uncorrelated patch size. All the experimental results were supported and extended by a theoretical analysis where the above mechanisms have been generalized. This thesis provides the first direct experimental evidence that spatially constrained dendritic connectivity is a key factor for community composition and population persistence in riverine landscapes. As such, this thesis assesses a longstanding issue in spatial community ecology. It offers unique insights into the ecological forces structuring natural communities in a key ecosytem, and demonstrates principles that can be further tested in theoretical metacommunity models possibly to be extended to real riverine ecosystems. Taken together, the analyses show how the structure of ecological networks interacts with the spatial environmental matrix in determining biodiversity patterns and the functioning of biological communities. The analyses also suggest that altering the natural linkage between dendritic connectivity and patch size strongly affects community properties at multiple scales. The first part of this thesis (chapters 2 and 3) addresses key aspects of biodiversity-ecosystem functioning research where the combination of theory-guided experiments and theoretical investigations shows how a stochastic implementation of population dynamics proves fundamental for key community properties such as species persistence and community stability. The diversity-productivity and diversity-stability relationships are explored. Both experimental findings and the results of a stochastic model fitted to the experimental interaction matrix, suggest the emergence of strong stabilizing forces when species from different functional groups interact in the same environment, increasing species coexistence and community biomass production. The last part (chapter 6) provides a synthesis of this thesis work, in that it aims at unifying aspects from niche-theory, usually adopted in spatially implicit models, with those characteristic of a spatially explicit context from a typical real-life mountainous regions. It is dedicated to the possible explanation for a macroecological pattern routinely observed from organisms in different domains of life, that is, the mid-elevational peak in local species richness. Guided by empirical observations on diversity of macroinvertebrates in Swiss river basins, a theoretical ansatz is provided which is deemed to capture the essential geomorphological drivers and controls relating species-fitness to altitude. A set of overarching conclusions and perspectives for future research are discussed in the concluding chapter

Phase-field modeling of brittle fracture in heterogeneous bars

We investigate phase-field modeling of brittle fracture in a one-dimensional bar featuring a continuous variation of elastic and/or fracture properties along its axis. Our main goal is to quantitatively assess how the heterogeneity in elastic and fracture material properties influences the observed behavior of the bar, as obtained from the phase-field modeling approach. The results clarify how the elastic limit stress, the peak stress and the fracture toughness of the heterogeneous bar relate to those of the reference homogeneous bar, and what are the parameters affecting these relationships. Overall, the effect of heterogeneity is shown to be strictly tied to the non-local nature of the phase-field regularization. Finally, we show that this non-locality may amend the ill-posedness of the sharp-crack problem in heterogeneous bars where multiple points compete as fracture locations

To exist and to count: A note on the minimalist view

Sometimes mereologists have problems with counting. We often don't want to count the parts of maximally connected objects as full-fledged objects themselves, and we don't want to count discontinuous objects as parts of further, full-fledged objects. But whatever one takes \u201cfull-fledged object\u201d to mean, the axioms and theorems of classical, extensional mereology commit us to the existence both of parts and of wholes \u2013 all on a par, included in the domain of quantification \u2013 and this makes mereology look counterintuitive to various philosophers. In recent years, a proposal has been advanced to solve the tension between mereology and familiar ways of counting objects, under the label of Minimalist View. The Minimalist View may be summarized in the slogan: \u201cCount x as an object iff it does not overlap with any y you have already counted as an object\u201d. The motto seems prima facie very promising but, we shall argue, when one looks at it more closely, it is not. On the contrary, the Minimalist View involves an ambiguity that can be solved in quite different directions. We argue that one resolution of the ambiguity makes it incompatible with mereology. This way, the Minimalist View can lend no support to mereology at all. We suggest that the Minimalist View can become compatible with mereology once its ambiguity is solved by interpreting it in what we call an epistemic or conceptual fashion: whereas mereology has full metaphysical import, the Minimalist View may account for our ways of selecting \u201cconceptually salient\u201d entities. But even once it is so disambiguated, it is doubtful that the Minimalist View can help to make mereology more palatable, for it cannot make it any more compatible with commonsensical ways of counting objects

Alpine Glaciology: An Historical Collaboration between Volunteers and Scientists and the Challenge Presented by an Integrated Approach

European Alpine glaciology has a long tradition of studies and activities, in which researchers have often relied on the field work of some specialized volunteer operators. Despite the remarkable results of this cooperation, some problems in field data harmonization and in covering the whole range of monitored glaciers are still present. Moreover, dynamics of reduction, fragmentation and decline, which in recent decades characterize Alpine glaciers, make more urgent the need to improve spatial and temporal monitoring, still maintaining adequate quality standards. Scientific field monitoring activities on Alpine glaciers run parallel to a number of initiatives by individuals and amateur associations, keepers of alternative, experiential and para-scientific knowledge of the glacial environment. Problems of harmonization, coordination, recruitment and updating can be addressed with the help of a collaborative approach—citizen science-like—in which the scientific coordination guarantees information quality and web 2.0 tools operate as mediators between expert glaciologists and non-expert contributors. This paper gives an overview of glaciological information currently produced in the European Alpine region, representing it in an organized structure, functional to the discussion. An empowering solution is then proposed, both methodological and technological, for the integration of multisource data. Its characteristics, potentials and problems are discussed

Natural search algorithms as a bridge between organisms, evolution, and ecology

The ability to navigate is a hallmark of living systems, from single cells to higher animals. Searching for targets, such as food or mates in particular, is one of the fundamental navigational tasks many organisms must execute to survive and reprod uce. Here, we argue that a recent surge of studies of the proximate mechanisms that underlie search behavior offers a new opportunity to integrate the biophysics and neuroscience of sensory systems with ecological and evolutionary processes, closing a feedback loop that promises exciting new avenues of scientific exploration at the frontier of systems biology. Keywords: sensing; navigation; evolutionary strategy; encounter rates; exploration–exploitationGordon and Betty Moore Foundation (Award GBMF3783

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor

Western Diet-Induced Metabolic Alterations Affect Circulating Markers of Liver Function before the Development of Steatosis

Since nutrition might have a significant impact on liver function, we analyzed the early effect of Western-type diet on hepatic tissue and lipid and drug metabolism in Wistar-Kyoto rats (n = 8); eight rats fed with a standard diet were used as controls. Histological analysis of liver tissue was performed, and plasma biochemical parameters were measured. Plasma concentration of six bile acids was determined by ultra-liquid chromatography-tandem mass spectrometry UHPLC-MS/MS. Hepatic gene expressions of enzymes involved in drug and lipid metabolism were assessed by means of real-time reverse transcription (qRT)-PCR. Liver of rats fed with a Western diet did not show macroscopic histological alterations, but number and diameter of lipid droplets increased, as well as DGAT1, GPAT4, SCD, FASN and SREBP2 expression. Furthermore, Western diet-fed animals showed an increase in the activation of hepatic stellate cells and macrophage number in liver tissue, as well as a significant increase in AST and bilirubin levels (p < 0.01), and in the LDL:HDL cholesterol ratio (p < 0.001). Plasma chenodeoxycholic acid concentration increased significantly, whereas cholic acid decreased (p < 0.05), and cytochrome P450 genes were generally downregulated. Significant changes in hepatic lipid and drug metabolism are early induced by the Western diet, prior to steatosis development. Such changes are associated with a peculiar alteration in circulating bile acids, which could represent an early marker of non-alcoholic fatty liver disease (NAFLD) development

The Genetic Origin of Daunians and the Pan-Mediterranean Southern Italian Iron Age Context.

The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula