Perturbation strength and the global structure of qap fitness landscapes

We study the effect of increasing the perturbation strength on the global structure of QAP fitness landscapes induced by Iterated Local Search (ILS). The global structure is captured with Local Optima Networks. Our analysis concentrates on the number, characteristics and distribution of funnels in the landscape, and how they change with increasing perturbation strengths. Well-known QAP instance types are considered. Our results confirm the multi-funnel structure of QAP fitness landscapes and clearly explain, visually and quantitatively, why ILS with large perturbation strengths produces better results. Moreover, we found striking differences between randomly generated and real-world instances, which warns about using synthetic benchmarks for (manual or automatic) algorithm design and tuning

How Perturbation Strength Shapes the Global Structure of TSP Fitness Landscapes

Local optima networks are a valuable tool used to analyse and visualise the global structure of combinatorial search spaces; in particular, the existence and distribution of multiple funnels in the landscape. We extract and analyse the networks induced by Chained-LK, a powerful iterated local search for the TSP, on a large set of randomly generated (Uniform and Clustered) instances. Results indicate that increasing the perturbation strength employed by Chained-LK modifies the landscape's global structure, with the effect being markedly different for the two classes of instances. Our quantitative analysis shows that several funnel metrics have stronger correlations with Chained-LK success rate than the number of local optima, indicating that global structure clearly impacts search performance

Interactions among species and ecosystems determine their responses to scale-specific fluctuations

Ecosystems are highly connected systems with many interacting components. Understanding the mechanisms creating ecosystem patterns requires an explicit consideration of the scales at which interactions among species and their environments occur. This dissertation focuses on the scale of temporal variability and how temporal variability is incorporated into communities’ dynamics. I first derive an abstract theory that describes the general patterns of variability propagation within communities. Next, I explore the role of species’ interaction strengths on community dynamics across time scales. Finally, I study the impact of human-induced hydrological changes of the Guadalquivir River on the European anchovy fishery in the Gulf of Cadiz.Chapter 1 uses linear response theory to extend the top down and bottom up views of ecology across time scales. Specifically, I study a tri-trophic food chain and how fluctuations in productivity filter up the food chain. I find that variability follows the pattern predicted by top-down equilibrium-based theories at slow time scales. However, at an intermediate time scale, consumers can both decrease and increase the sensitivity of lower trophic levels to variability. For example, perturbations at intermediate frequencies can excite the endogenous cycles of a community leading to resonance. Only at the fastest time scales do top down effects begin to break down as variability becomes dampened at higher trophic levels. This theory provides a robust new framework to interpret food web patterns resulting from resource pulses and other bottom up perturbations. Chapter 2 combines the metabolic theory of ecology and empirical information of consumer-resource interactions to ground the general theory developed in Chapter 1. Body size is not only a significant determinant of vital rates and but also species interaction strengths. This approach allows me to focus on biologically relevant parameter space. I predict that predators can control herbivores and producers\u27 variability at a time scale of days to years. This theory predicts that indirect effects actively shape communities\u27 responses across a wide range of ecologically relevant time scales. Finally, in Chapter 3, I explore the relationship between ecology and society by studying how agricultural water use is connected to the marine anchovy fishery in Spain’s Gulf of Cadiz. Using time series analysis, I explore the correlations between hydrology, the estuarine community, and anchovy recruitment to the Gulf of Cadiz. The Guadalquivir river’s mean annual discharge and seasonality have decreased over the last 90 years due to increasing river regulation and extraction. European anchovies use the river estuary as a nursery. These hydrological changes have reduced anchovy recruitment to the Gulf of Cadiz, connecting terrestrial water use with the marine fishery. I then produce a water allocation theory for terrestrial agriculture and a marine fishery. I predict that even practices that improve water efficiency will not necessarily prevent terrestrial ecosystems from total water consumption. I find that the protection of downriver ecosystem services is only protected when the benefits to marine ecosystems are considered nonsubstitutable with terrestrial ecosystems. The issue of scale – ecological and spatiotemporal – is at the heart of my thesis. My first chapter shows that the percolation of variability is not invariant across time scales. In my second chapter, I predict how body size drives differences in community responses to variability. These theories can provide new insights into how variability impacts communities. Finally, in my last chapter, I explore rivers and migration can create trade-offs between seemingly isolated ecosystems

Coevolution and the architecture of mutualistic networks

Although coevolution is widely recognized as an important evolutionary process for pairs of reciprocally specialized species, its importance within species-rich communities of generalized species has been questioned. Here we develop and analyze mathematical models of mutualistic communities, such as those between plants and pollinators or plants and seed-dispersers to evaluate the importance of coevolutionary selection within complex communities. Our analyses reveal that coevolutionary selection can drive significant changes in trait distributions with important consequences for the network structure of mutualistic communities. One such consequence is greater connectance caused by an almost invariable increase in the rate of mutualistic interaction within the community. Another important consequence is altered patterns of nestedness. Specifically, interactions mediated by a mechanism of phenotype matching tend to be antinested when coevolutionary selection is weak and even more strongly antinested as increasing coevolutionary selection favors the emergence of reciprocal specialization. In contrast, interactions mediated by a mechanism of phenotype differences tend to be nested when coevolutionary selection is weak, but less nested as increasing coevolutionary selection favors greater levels of generalization in both plants and animals. Taken together, our results show that coevolutionary selection can be an important force within mutualistic communities, driving changes in trait distributions, interaction rates, and even network structure. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.Peer Reviewe

Community stability and turnover in changing environments

Les communautés d'êtres vivants peuvent elles êtres considérées comme des organismes complexes, ou au contraire comme de simples groupes d'espèces, individuelles ? Cette question est à l'origine de nombreux débats en écologie, ces deux visions impliquant notamment des prédictions très différentes dans les patrons spatiaux et temporels de communautés. Lorsque l'environnement change graduellement dans l'espace ou dans le temps, la vision individualiste implique des changements graduels dans la composition des communautés, tandis que la vision du "super-organisme" prédit des changements davantage abrupts. L'objectif principal de cette thèse est de comprendre et déterminer sous quelles conditions ces différents types de réponse des communautés aux changements de l'environnement peuvent advenir. Dans une première partie, nous étudions le rôle que la compétition inter-spécifique peut jouer dans l'émergence de différents patrons spatiaux de communautés. Nous étudions notamment les conditions théoriques sous lesquelles la compétition peut faire apparaître des patrons graduels ou discontinus dans la composition des espèces. Dans une deuxième partie, nous étudions l'influence des interactions entre les espèces et leur environnement sur les patrons spatiaux de communautés. Nous montrons notamment comment des phénomènes de construction de niche peuvent mener à l'émergence de changements brutaux dans la composition des communautés, mais également dans les conditions de l'environnement. Enfin, dans une dernière partie, nous illustrons le rôle que peut jouer la biodiversité dans la protection des écosystèmes face à des effondrements écologique, et notamment le rôle que peut jouer la biomasse dans cette protection.The question whether communities should be viewed as superorganisms or loose collections of individual species has been the subject of a long-standing debate in ecology. Each view implies different spatial and temporal community patterns. When environment gradually changes in space or in time, the organismic view predicts that species turnover is discontinuous, while the individualistic view predicts gradual changes in species composition. The main objective of this thesis is to understand the theoretical conditions under which these various types of community response can occur. First, I study the role of interspecific competition can play in the emergence of various spatial community patterns. I investigate the theoretical conditions in competition under which smooth or discrete spatial patterns can emerge. Then, I study how interactions between species and their environment can lead to various community patterns in space. I notably show how ecological niche construction can lead to the emergence of abrupt changes in species composition and in the environment, and the role biodiversity plays therein. Finally, I focus on the role biodiversity can play against ecosystem collapse. In this section, I illustrate how diversity loss, through its effects on total biomass, can lead to ecosystem collapse

Optimal cellular mobility for synchronization arising from the gradual recovery of intercellular interactions

Cell movement and intercellular signaling occur simultaneously during the development of tissues, but little is known about how movement affects signaling. Previous theoretical studies have shown that faster moving cells favor synchronization across a population of locally coupled genetic oscillators. An important assumption in these studies is that cells can immediately interact with their new neighbors after arriving at a new location. However, intercellular interactions in cellular systems may need some time to become fully established. How movement affects synchronization in this situation has not been examined. Here we develop a coupled phase oscillator model in which we consider cell movement and the gradual recovery of intercellular coupling experienced by a cell after movement, characterized by a moving rate and a coupling recovery rate respectively. We find (1) an optimal moving rate for synchronization, and (2) a critical moving rate above which achieving synchronization is not possible. These results indicate that the extent to which movement enhances synchrony is limited by a gradual recovery of coupling. These findings suggest that the ratio of time scales of movement and signaling recovery is critical for information transfer between moving cells.Comment: 18 single column pages + 1 table + 5 figures + Supporting Informatio

Exploring the determinants of community structure and functioning : evidence from plankton communities

Les travaux récents sur la relation entre la biodiversité et le fonctionnement des écosystèmes ont souligné certains des aspects les plus dynamiques du fonctionnement des écosystèmes, tout en reconnaissant que la diversité répond à la fois aux variations le long de gradients environnementaux et à la dispersion des espèces entre les communautés locales. Les définitions de la diversité ont été de plus en plus caractérisés en intégrant la notion de traits fonctionnels et ont reconnu la nature flexible de la distribution des traits dans une communauté. Les chapitres de cette thèse se concentrent sur des questions liées à la façon dont la distribution des traits de la communauté est définis, comment ils peuvent informer les écologistes sur les processus associés à l'assemblage de la communauté, comment la composition des communautés pourrait changer sous différentes ampleurs de dispersion, et comment la fonctionnalité pourrait interagir avec la disponibilité des éléments nutritifs pour influencer le fonctionnement global de la communauté. Chaque chapitre va présenter l'un de ces thèmes dans les communautés zoo-et phytoplanctonique, qui emploient des analyses des données déjà recueillies, études de terrain et des expériences contrôlées en mésocosme. Les objectifs de cette thèse spécifiques sont: (1) de comparer les différentes mesures de la diversité (taxonomique et fonctionnelle) dans leur capacité de rendre compte de la biomasse dans les communautés de diatomées benthiques et planctoniques, (2) d'identifier un seuil de dispersion, au-delà duquel différentes communautés de zooplancton pourrait commencer à homogénéiser la composition, (3) de mieux comprendre les communautés de zooplancton naturelles en focusant sur les modèles de distribution dans les traits fonctionnels pour examiner les signes de filtrage ou de de compétition dans l'habitat en tant que facteurs influençant la structure de la communauté, et (4) de vérifier si la diversité fonctionnelle et la disponibilité des nutriments interagissent dans la production phytoplanctonique. En général, les mesures fonctionnelles de la diversité n'ont pas été surutilisées pour les mesures taxonomiques afin de modéliser le fonctionnement des écosystèmes, ils ont souvent permis de mieux comprendre les mécanismes qui sous-tendent les relations de l'importance. En outre, les processus de dispersion et les interactions locales ont tous deux été jugés influents dans la structure des communautés de zooplancton. La dispersion expérimentale de plus de\ud 1% a été jugée suffisante pour ouvrir une homogénéisation de la composition, et, sur le terrain, les filtres reliés à l'habitat ont été jugés plus influents que la compétition dans la définition de la diversité fonctionnelle du zooplancton. Finalement, aucune preuve n'implique la diversité fonctionnelle alguale comme étant un moteur important de la production primaire, ce qui suggère une redondance fonctionnelle qui pourrait définir les communautés phytoplanctoniques à des niveaux modestes de la richesse des espèces. ______________________________________________________________________________ MOTS-CLÉS DE L’AUTEUR : Diversité fonctionnelle, Fonctionnement des écosystèmes, Zooplancton, Phytoplancton, Dispersion

The Effect of Ecological Gradients on the Fish Assemblages of the Green and Tradewater River Basins of Kentucky

The composition of lotic assemblages is influenced by many landscape factors. Foremost among these are basin geomorphology, fluvial and substrate characteristics, stream size, and land use. The primary purpose of this investigation was to determine if fish assemblages within Kentucky\u27s Green River and Tradewater River Basins were associated with local scale environmental gradients and, if so, which gradients were the most important in shaping fish assemblages and which fish species were most closely associated with these gradients. A secondary purpose was to determine which regionalization or characterization strategy best segregated streams within the study area according to fish assemblages. Eighty-eight sites within the Green River and Tradewater River Basins were sampled with seine and backpack electroshocker between August 2001 and March 2002. Sampling resulted in the capture of 83 species. A suite of environmental characteristics was estimated or measured at each site. Fish and environmental data were tested for significant relationships with canonical correlation analysis (CCA). Further analyses for the effect of environmental gradients on individual species were done with Pearson correlations. Species data were exposed to detrended correspondence analysis (DCA) to analyze the effect of geographic and local scale classification strategies. CCA analysis indicated there were significant relationships between species and environmental data for both CCA Axis 1 and 2. Further analysis revealed that stream size and substrate composition had the strongest effect in structuring fish assemblages within the study area. Pearson correlations suggested species with special habitat needs were those mainly influenced by local environmental gradients, and thus, were most influential in the structuring offish assemblages. Habitat quality was higher in the eastern portion of the study area where high gradient streams were most common. This may be a reflection of expected upstream to downstream processes or of differing land use due to topography. Larger streams were found to generally support a greater diversity of fish species than smaller streams. DCA analysis of classification strategies indicated fish assemblages best grouped by combinations of hydrologic units (sub-drainages) within the study area. These groupings followed a general east to west trend. Further investigation is needed to separate the effects of natural riverine processes from that of anthropogenic land use

Host microbiota and infection outcomes in thermally extreme environments

Hosts, their collection of commensal and pathogenic microbes, and the environment are all interlinked in a disease pyramid. Their interactions contribute to host fitness, particularly relevant in the context of a changing world. Climate change is leading to higher average temperatures as well as shifting the global distribution of infectious diseases, posing great risk to wildlife, ecosystem biodiversity, and human health. Host microbiomes are increasingly regarded as conferring extended phenotypes, potentially buffering host organisms against abiotic and biotic stressors. In this thesis, I combine meta-analytical and experimental approaches to explore the impact of warming temperatures and infection on ecological dynamics (i.e., microbiomes, infection disease outcomes) and evolutionary dynamics (i.e., host gene-based resistance). Firstly, I used a meta-analytic approach to investigate whether and how experimental temperatures altered host microbiome structures, across a wide range of host species. I found that experimental warming and cooling drove microbiome diversity loss, with the magnitude affected more by host habitat and experimental protocols, rather than host biological traits. I then extended this work to empirically include a biotic factor – pathogen infection – to investigate changes in Caenorhabditis elegans microbiome composition. I revealed that warming and infection could destabilize microbiome communities within hosts, but their effects were not additive. Focusing more on the impact of warming to host-pathogen interactions, I subsequently used a meta-analytic approach to tackle the relationship between warming and disease outcomes across ectothermic animals. I found that experimental warming drove higher mortality of infected hosts, with larger temperature increases associated with more host deaths. The magnitude of these effects varied by pathogen taxonomy and their evolutionary history within the host. Lastly, I zoomed out to empirically capture the possible host evolutionary paths for resistance to pathogens due to warming. I competed two C. elegans genotypes (susceptible wild-type vs. resistant mutant) across 10 host generations, varying in pathogen presence and the timing of warming during their development. I detected a loss of genetic-based resistance under periodic warming despite infection. I revealed that such host evolutionary trajectories could be driven by the combination of fitness constraints on genetic-based resistance, temperature-mediated host protection, infection severity, as well as the dilution of pathogen cells by resistant hosts. Work in this thesis is a timely contribution to our understanding of the diversity of consequences of warming to host-microbe interactions across the mutualist-parasite continuum. Biologists seeking to refine predictions of biodiversity amidst climate change should strongly consider the relationships of animals with their resident and attacking microbes