Développement d’un modèle centré sur l’individu des déplacements du caribou, du loup et de l’orignal, et de leurs interactions, en forêt boréale aménagée

Le caribou forestier est une espèce menacée au Canada, la principale hypothèse au déclin des populations étant l’intensification de la prédation provoquée par les perturbations anthropiques du paysage. Afin de faire face à cette situation, il est nécessaire d’étudier et comprendre l’impact de l’environnement sur les interactions prédateur-proies entre le caribou et le loup, ainsi qu’avec l’orignal, qui est sa principale proie alternative. Pour cela, cette thèse présente la conception d’un modèle centré sur l’individu des déplacements de ces trois espèces en fonction de leur environnement, dont résulteront les interactions prédateur-proies. Afin de permettre l’application de ce modèle sur de longues périodes, et donc pour un environnement changeant, une méthodologie a été développée, qui s’articule atour de deux aspects principaux. Tout d’abord, la notion de niveaux d’émergence est introduite, permettant d’ordonner les comportements observables du système selon leurs interdépendances, afin de choisir comme trait du modèle un com- portement correspondant au domaine d’applicabilité visé. Ordonner les comportements selon leurs niveaux d’émergence permet également d’identifier la redondance entre les patrons, qui peut être à l’origine d’un phénomène de sur-apprentissage lorsqu’ils sont utilisés lors de la calibration. Dans un second temps, un nouveau protocole pour la calibration et la validation du ou des traits choisis à l’aide des niveaux d’émergence, nommé réplication de système basé sur l’individu (Individual Based System Replication - IBSRtion) est également présenté. Ce protocole met l’emphase sur la modélisation directe, contrairement au principal protocole existant, la modélisation orientée patrons (Pattern Oriented Modelling - POM), et permet une approche empirique en générant artificiellement des données non disponibles ou ne pouvant être récoltées par des études de terrains. IBSRtion a également l’avantage de pouvoir être intégrée dans POM, afin de contribuer à la création d’une méthodologie universelle pour la conception de modèles centrés sur l’individu. Le processus de conception de ce modèle aura entre autre permis de faire une synthèse des connaissances et d’identifier certaines lacunes. Une étude visant à palier le manque de connaissances satisfaisantes sur les réponses comportementales à court-terme des proies face au risque de prédation a notamment permis d’observer que celles-ci sont une combinaison de comportements chroniques et éphémères, et que les mécanismes qui en sont à l’origine sont complexes et non-linéaires. Le résultat de ce travail est un modèle complexe utilisant de nombreux sous-modèles, et calibré de façon empirique, applicable à une grande variété d’environnements. Ce modèle a permis de tester l’impact de l’enfeuillement sur les relations prédateur-proies. Des simulations ont été effectuées pour différentes quantités d’enfeuillement, suivant deux configurations spatiales différentes. Les résultats de simulation suggèrent que des plans d’aménagement considérant également l’habitat de l’orignal pourraient être bénéfiques pour le caribou forestier, car ils permettraient d’améliorer la ségrégation spatiale entre les deux espèces, et donc entre le caribou et le loup. En le couplant avec un module de naissances et de morts naturelles ainsi qu’un modèle d’évolution du paysage, ce modèle permettra par la suite d’évaluer l’impact de plans d’aménagement forestier sur la viabilité des populations de caribou forestier.Forest-dwelling woodland caribou are considered threatened in Canada. The main hypothesis to the decrease of populations is the intensification of predation provoked by anthropogenic perturbations in the landscape. To deal with this situation, it is necessary to study and to understand the impact of the environment on the predator-prey interactions between the caribou and the wolf, and with the moose, its main alternative prey. In this perspective, this thesis presents the design of an individual-based model of displacements of these three species with respect to their environment, from which the predator-prey interactions will result. To allow for the application of this model for long periods of time, i.e. for changing environments, a methodology has been developed, which is based on two key points. First, the notion of levels of emergence is introduced, allowing to order the different observable comportments of the system according to their inter-dependencies, to help with choosing a trait of the model corresponding to the intended domain of applicability. Ordering the comportments according to their levels of emergence also permits to identify redundancy between patterns, which can lead to over-fitting when they are used for calibration. Second, a new methodology for calibration and validation of the trait(s) chosen by means of the levels of emergence framework is also presented, named Individual Based System Replication (IBSRtion). This protocol emphasizes forward modelling, contrary to the main existing methodology, Pattern Oriented Modelling (POM), and allows to use an empirical approach by artificially generating data that are unavailable or that cannot be obtained by means of field studies. IBSRtion can also be integrated into POM, to contribute to the establish- ment of a universal methodology for the design of individual based models. The design process of this model allowed for a synthesis of existing knowledge and to point out some gaps. More specifically, a study conducted to deal with the lack of sufficient information on the short-term response of prey to predation risk allowed to observe that their behavioural responses to prior presence of predators are a combination of chronic and ephemeral behaviours, and that the mechanisms that produce them are complex and non-linear. The outcome of this work is a complex model, using many sub-models, and calibrated in an empirical fashion, that can be applied to a wide variety of environments. This model allowed to test the impact of the encroachment of deciduous trees on predator-prey relations. Simulations have been run for different quantities of encroachment, according to two different spatial configurations. Simulation results suggest that management plans taking into account the moose’s habitat might benefit woodland caribou, because they could increase spatial segregation between the two species, and thus between caribou and wolf. Coupling this model with a module of birth and natural death, along with a model of landscape transformation, would allow the assessment of the impact of different forest management plans on the viability of woodland caribou populations

Fast incremental learning of stochastic context-free grammars in radar electronic support

Radar Electronic Support (ES) involves the passive search for, interception, location, analysis and identification of radiated electromagnetic energy for military purposes. Although Stochastic Context-Free Grammars (SCFGs) appear promising for recognition of radar emitters, and for estimation of their respective level of threat in radar ES systems, the computations associated with well-known techniques for learning their production rule probabilities are very computationally demanding. The most popular methods for this task are the Inside-Outside (IO) algorithm, which maximizes the likelihood of a data set,and the Viterbi Score (VS) algorithm, which maximizes the likelihood of its best parse trees. For each iteration, their time complexity is cubic with the length of sequences in the training set and with the number of non-terminal symbols in the grammar. Since applications of radar ES require timely protection against threats, fast techniques for learning SCFGs probabilities are needed. Moreover, in radar ES applications, new information from a battlefield or other sources often becomes available at different points in time. In order to rapidly refiect changes in operational environments, fast incremental learning of SCFG probabilities is therefore an undisputed asset. Several techniques have been developed to accelerate the computation of production rules probabilities of SCFGs. In the first part of this thesis, three fast alternatives, called graphical EM (gEM), Tree Scanning (TS) and HOLA, are compared from several perspectives - perplexity, state estimation, ability to detect MFRs, time and memory complexity, and convergence time. Estimation of the average-case and worst-case execution time and storage requirements allows for the assessment of complexity, while computer simulations, performed using radar pulse data, facilitates the assessment of the other performance measures. An experimental protocol has been defined such that the impact on performance of factors like training set size and level of ambiguity of grammars may be observed. In addition, since VS is known to have a lower overall computational cost in practice, VS versions of the original 10-based gEM and TS have also been proposed and compared. Results indicate that both gEM(IO) and TS(IO) provide the same level of accuracy, yet the resource requirements mostly vary as a function of the ambiguity of the grammars. Furthermore, for a similar quality in results, the gEM(VS) and TS(VS) techniques provide significantly lower convergence times and time complexities per iteration in practice than do gEM(IO) and TS(IO). All of these algorithms may provide a greater level of accuracy than HOLA, yet their computational complexity may be orders of magnitude higher. Finally, HOLA is an on-line technique that naturally allows for incremental learning of production rule probabilities. In the second part of this thesis, two new incremental versions of gEM, called Incremental gEM (igEM) and On-Line Incremental gEM (oigEM), are proposed and compared to HOLA. They allow for a SCFG to efficiently learn new training sequences incrementally, without retraining from the start an all training data. An experimental protocol has been defined such that the impact on performance of factors like the size of new data blocks for incremental learning, and the level of ambiguity of MFR grammars, may be observed. Results indicate that, unlike HOLA, incremental learning of training data blocks with igEM and oigEM provides the same level of accuracy as learning from all cumulative data from scratch, even for relatively small data blocks. As expected, incremental leaming significantly reduces the overall time and memory complexities associated with updating SCFG probabilities. Finally, it appears that while the computational complexity and memory requirements of igEM and oigEM may be greater than that of HOLA, they both provide the higher level of accuracy

Similar compositional turnover but distinct insular environmental and geographical drivers of native and exotic ants in two oceans

Aim This study aims to quantify the patterns in compositional turnover of native and exotic ants on small islands in two oceans, and to explore whether such patterns are driven by similar environmental, geographical and potentially biotic variables. Location Pacific and Atlantic islands. Time period Present. Major taxa studied Ants. Methods We applied Multi‐Site Generalised Dissimilarity Modelling (MS‐GDM), which relates zeta diversity, the number of species shared by a given number of islands, to differences in environmental, geographical and biotic drivers. The use of zeta diversity enabled us to differentiate the contribution of rare species (shared by few islands) from those of widespread ones (shared by multiple islands) to compositional turnover. For completion, we also related species richness of insular ants per island with the same set of explanatory variables using Generalised Additive Models (GAM). Results Pacific and Atlantic islands have similar patterns of ant species turnover and richness, albeit partly driven by different drivers. Native and exotic species turnover are mostly explained by the same set of variables in the Pacific (annual precipitation and distance to the nearest island), but not in the Atlantic (annual precipitation is a good predictor of native species turnover, but none of the variables considered in our study explained exotic species turnover). No signal of biotic interactions was detected at the insular community level. Main conclusions Successful invasion strategies may depend on a combination of factors specific to the region in question. In the Pacific, milder environments and the absence of natives on certain islands enable exotic ants to select the same types of environment as native ants. In the harsher Atlantic Ocean, however, native ant species are likely to be well adapted to local environmental conditions, making it harder for exotics to become established. Exotic ant species, therefore, potentially rely on other attributes to establish, such as a combination of tolerance to a wide range of environmental conditions and human‐mediated colonization

The effect of cross-boundary management on the trajectory to commonness in biological invasions

The number of alien species introduced and undergoing range expansion in novel environments is steadily increasing, with important consequences for native ecosystems. The efficacy of management planning and decision making to limit such invasions can be improved by understanding how interventions will impact the population dynamics of recently introduced species. To do so, here we expand on a typological framework that enables the classification of populations over time into 10 categories of commonness, and apply it to a spatially discrete metapopulation with heterogeneous abundance across spatial units (patches). We use this framework to assess the effect of cross-boundary management on the capacity of a metapopulation with different demographic and dispersal characteristics, including time lags in population growth, to become common. We demonstrate this framework by simulating a simple theoretical metapopulation model capable of exploring a range of environments, species characteristics, and management actions. Management can vary in the efficacy of propagule interception between patches, and in the synchronisation of the implementation of these measures across patches (i.e. if management is implemented simultaneously across patches). Simulations show that poor interception efficacy that only modestly reduces the number of propagules entering a given spatial unit cannot be compensated for by strong management synchronisation between spatial units. Management synchronisation will nonetheless result in a reduction in rates of spread once a critical threshold of interception efficacy has been met. Finally, time lags in population growth that may result in delayed spread are an important aspect to be considered in management as they can amplify the efficacy of management. Our results demonstrate how a typological framework of categories of commonness can be used to provide practical insights for the management of biological invasions

A vision for global monitoring of biological invasions

Managing biological invasions relies on good global coverage of species distributions. Accurate information on alien species distributions, obtained from international policy and cross-border co-operation, is required to evaluate trans-boundary and trading partnership risks. However, a standardized approach for systematically monitoring alien species and tracking biological invasions is still lacking. This Perspective presents a vision for global observation and monitoring of biological invasions. We show how the architecture for tracking biological invasions is provided by a minimum information set of Essential Variables, global collaboration on data sharing and infrastructure, and strategic contributions by countries. We show how this novel, synthetic approach to an observation system for alien species provides a tangible and attainable solution to delivering the information needed to slow the rate of new incursions and reduce the impacts of invaders. We identify three Essential Variables for Invasion Monitoring; alien species occurrence, species alien status and alien species impact. We outline how delivery of this minimum information set by joint, complementary contributions from countries and global community initiatives is possible. Country contributions are made feasible using a modular approach where all countries are able to participate and strategically build their contributions to a global information set over time. The vision we outline will deliver wide-ranging benefits to countries and international efforts to slow the rate of biological invasions and minimize their environmental impacts. These benefits will accrue over time as global coverage and information on alien species increases

A multi-site method to capture turnover in rare to common interactions in bipartite species networks

1. Ecological network structure is maintained by a generalist core of common species. However, rare species contribute substantially to both the species and functional diversity of networks. Capturing changes in species composition and interactions, measured as turnover, is central to understanding the contribution of rare and common species and their interactions. Due to a large contribution of rare interactions, the pairwise metrics used to quantify interaction turnover are, however, sensitive to compositional change in the interactions of, often rare, peripheral specialists rather than common generalists in the network. 2. Here we expand on pairwise interaction turnover using a multi-site metric that enables quantifying turnover in rare to common interactions (in terms of occurrence of interactions). The metric further separates this turnover into interaction turnover due to species turnover and interaction rewiring. 3. We demonstrate the application and value of this method using a host–parasitoid system sampled along gradients of environmental modification. 4. In the study system, both the type and amount of habitat needed to maintain interaction composition depended on the properties of the interactions considered, that is, from rare to common. The analyses further revealed the potential of host switching to prevent or delay species loss, and thereby buffer the system from perturbation. 5. Multi-site interaction turnover provides a comprehensive measure of network change that can, for example, detect ecological thresholds to habitat loss for rare to common interactions. Accurate description of turnover in common, in addition to rare, species and their interactions is particularly relevant for understanding how network structure and function can be maintained

The Convention on Biological Diversity (CBD)’s Post-2020 target on invasive alien species – what should it include and how should it be monitored?

The year 2020 and the next few years are critical for the development of the global biodiversity policy agenda until the mid-21st century, with countries agreeing to a Post-2020 Global Biodiversity Framework under the Convention on Biological Diversity (CBD). Reducing the substantial and still rising impacts of invasive alien species (IAS) on biodiversity will be essential if we are to meet the 2050 Vision where biodiversity is valued, conserved, and restored. A tentative target has been developed by the IUCN Invasive Species Specialist Group (ISSG), and formally submitted to the CBD for consideration in the discussion on the Post-2020 targets. Here, we present properties of this proposal that we regard as essential for an effective Post-2020 Framework. The target should explicitly consider the three main components of biological invasions, i.e. (i) pathways, (ii) species, and (iii) sites; the target should also be (iv) quantitative, (v) supplemented by a set of indicators that can be applied to track progress, and (vi) evaluated at medium- (2030) and long-term (2050) time horizons. We also present a proposed set of indicators to track progress. These properties and indicators are based on the increasing scientific understanding of biological invasions and effectiveness of responses. Achieving an ambitious action-oriented target so that the 2050 Vision can be achieved will require substantial effort and resources, and the cooperation of a wide range of stakeholders

What is valued in conservation? A framework to compare ethical perspectives

Perspectives in conservation are based on a variety of value systems. Such differences in how people value nature and its components lead to different evaluations of the morality of conservation goals and approaches, and often underlie disagreements in the formulation and implementation of environmental management policies. Specifically, whether a conservation action (e.g. killing feral cats to reduce predation on bird species threatened with extinction) is viewed as appropriate or not can vary among people with different value systems. Here, we present a conceptual, mathematical framework intended as a tool to systematically explore and clarify core value statements in conservation approaches. Its purpose is to highlight how fundamental differences between these value systems can lead to different prioritizations of available management options and offer a common ground for discourse. The proposed equations decompose the question underlying many controversies around management decisions in conservation: what or who is valued, how, and to what extent? We compare how management decisions would likely be viewed under three idealised value systems: ecocentric conservation, which aims to preserve biodiversity; new conservation, which considers that biodiversity can only be preserved if it benefits humans; and sentientist conservation, which aims at minimising suffering for sentient beings. We illustrate the utility of the framework by applying it to case studies involving invasive alien species, rewilding, and trophy hunting. By making value systems and their consequences in practice explicit, the framework facilitates debates on contested conservation issues, and complements philosophical discursive approaches about moral reasoning. We believe dissecting the core value statements on which conservation decisions are based will provide an additional tool to understand and address conservation conflicts