abstract: A functioning food web is the basis of a functioning community and ecosystem. Thus, it is important to understand the dynamics that control species behaviors and interactions. Alterations to the fundamental dynamics can prove detrimental to the future success of our environment. Research and analysis focus on the global dynamics involved in intraguild predation (IGP), a three species subsystem involving both competition and predation. A mathematical model is derived using differential equations based on pre-existing models to accurately predict species behavior. Analyses provide sufficient conditions for species persistence and extinction that can be used to explain global dynamics. Dynamics are compared for two separate models, one involving a specialist predator and the second involving a generalist predator, where systems involving a specialist predator are prone to unstable dynamics. Analyses have implications in biological conservation tactics including various methods of prevention and preservation. Simulations are used to compare dynamics between models involving continuous time and those involving discrete time. Furthermore, we derive a semi-discrete model that utilizes both continuous and discrete time series dynamics. Simulations imply that Holling's Type III functional response controls the potential for three species persistence. Complicated dynamics govern the IGP subsystem involving the white-footed mouse, gypsy moth, and oak, and they ultimately cause the synchronized defoliation of forests across the Northeastern United States. Acorn mast seasons occur every 4-5 years, and they occur simultaneously across a vast geographic region due to universal cues. Research confirms that synchronization can be transferred across trophic levels to explain how this IGP system ultimately leads to gypsy moth outbreaks. Geographically referenced data is used to track and slow the spread of gypsy moths further into the United States. Geographic Information Systems (GIS) are used to create visual, readily accessible, displays of trap records, defoliation frequency, and susceptible forest stands. Mathematical models can be used to explain both changes in population densities and geographic movement. Analyses utilizing GIS softwares offer a different, but promising, way of approaching the vast topic of conservation biology. Simulations and maps are produced that can predict the effects of conservation efforts. / Dissertation/Thesis / M.S. Applied Biological Sciences 2012

L’étude du sujet et du lien social tels que Lacan les a conceptualisés semble d’emblée problématique lorsqu’il s’agit de les soumettre à l’épreuve de l’histoire. Cette problématique relance le débat de la difficile articulation de la structure et de l’histoire. Il apparaît important de réinvestir ce questionnement parce qu’il semble au fondement d’une controverse plus contemporaine émanant de l’étude des rapports qu’entretient le sujet avec le social et ses mutations. En explorant les déplacements se réalisant dans la structure du sujet, nous exploiterons l’histoire, en tant qu’étude du changement, afin d’entrevoir la manière dont elle se réalise au sein du sujet et du lien social. Nous tenterons d’éclairer comment le sujet est réactif à l’événement que nous différencions du fait social et dégagerons une temporalité permettant d’unir l’ordre synchronique et l’ordre diachronique s’incarnant simultanément dans la structure du sujet et du lien social. / The study of the subject and of the social link as conceptualized by Lacan seems problematic as soon as these are exposed to the test of history. This problematic revives the debate about the difficulty of articulating structure and history. It seems important to re-examine this question because it appears to underlie a more contemporary controversy which comes from the study of the relationships the subject maintains with its social context and its variants. By exploring the changes occurring in the subject’s structure, we will use history as a means to study this change. We will try to identify the way it happens both within the subject and within the social link. We will attempt to elucidate how the subject is responsive to the event, which we will distinguish from the social context. We will afterwards identify a temporality enabling us to bring together the synchronic and the diachronic orders at work simultaneously in both the structure of the subject and of the social link.

[résumé trop long] / The important relationship between structure and function has always been a fundamental question in neuroscience research. In particular in the case of movement, brain controls large groups of muscles and combines it with sensory informations from the environment to execute purposeful motor behavior. Mapping dynamics encoded in a high dimensional neural space onto low-dimensional behavioral space has always been a difficult challenge as far as theory is concerned. Here, we develope a framework to study spike/burst dynamics having low dimensional phase description, which can readily be extended under certain biological constraints on the coupling to low dimensional functional descriptions. In general, phase models are amongst the simplest of neuron models reproducing spike-burst behavior, excitability and bifurcations towards periodic firing. However, the coupling among neurons has only been considered using generic arguments valid close to the bifurcation point, and the distinction between electric and synaptic coupling remains an open question. In this thesis we aim to address this question and derive a mathematical formulation for the various forms of biologically realistic coupling. We begin by constructing a mathematical model based on a planar simplification of the Morris-Lecar model. Using geometric arguments we then derive a phase description of a network of neurons with biologically realistic electric coupling and subsequently with chemical coupling under the fast synapse approximation. We then demonstrate that electric and synaptic coupling are expressed differently on the level of the network’s phase description, exhibiting qualitatively different dynamics. Our numerical investigations confirm these findings and show excellent correspondence between the dynamics of the full network and the network’s phase description. Following the success of the phase description of the spiking neural network, we extend this approach in order to propose a generating mechanism for parabolic bursting captured by only a single phase variable. This is the first model in the literature which captures bursting dynamics in one dimension. In order to study the emergent behavior we extend this to a network of bursters with global coupling and analytically reduce a high dimensional system to only two dimensions. Further, we investigate the bifurcation properties numerically as well as analytically. One of the key conclusion is that the stability states remain invariant to the increasing number of spikes per burst. Finally we investigate a spikeburst neuron network coupled via mean field type of fast synapses developed in this thesis and systematically carry out a detailed bifurcation analysis of the model, for a tractable special case. Numerical simulations investigate this mean field model beyond special case and clearly reveals qualitative correspondence with the full network model. Moreover, these network displays rich collective dynamics as a function of two parameters, mainly the synaptic coupling strength and the width of the distribution in applied stimulus. Besides incoherence, frequency locking, and oscillator death (a total cessation of firing caused by excessively strong coupling), there exist multistable solutions in the full and the phase network of neurons.

Field and laboratory experiments were conducted to elucidate various factors influencing the temperature-dependent larval eclosion of winter moth, Operophtera brumata L, in New England. We found no difference in duration of the embryonic stage of eggs reared from larvae collected in Massachusetts (MA) and on Vancouver Island, British Columbia (BC), where winter temperatures are rarely below freezing. The number of growing degree days (GDD) required for larval eclosion declined with the number of days chilled in the laboratory and number of days below freezing in the field, confirming the findings of previous studies. Thus, eggs hatched with fewer GDD, when the spring came later than usual. Date of oviposition had no effect on date of hatch. Eggs laid by naturally occurring (feral) females hatched sooner with lower GDD than eggs from laboratory-reared females from MA and BC held on the same trees over the winter. South-facing eggs on the stems of trees hatched on average 1.6 days sooner than north-facing eggs. Growing degree days calculated from bi-hourly measures of temperature were 15% greater than GDD estimates based on the average of daily maximum and minimum temperatures, as used by many GDD estimates made for online sources. Over two years, the mean GDD in ⁰C for hatch of feral eggs based on bihourly temperature measurements, a 1 Jan start date and a 3.9⁰C developmental threshold was 176.53 ± 6.35SE

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18674号 / 理博第4023号 / 新制||理||1580(附属図書館) / 31607 / 京都大学大学院理学研究科生物科学専攻 / (主査)准教授 中川 尚史, 教授 中務 真人, 教授 高橋 淑子 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

In dense mating aggregations, such as insect and anuran choruses, signals produced at the same time can overlap and interfere with one another, reducing the ability of receivers to discriminate between individual signals. Thus, evolution by sexual selection is expected to result in mating signal timing strategies that avoid overlap. Patterns of signal alternation between competing males are commonly observed in leks and choruses across taxa. In some species, however, signalers instead deliberately overlap, or ‘synchronize’, their mating signals with neighboring conspecifics. Given the assumed high cost of reduced mate attraction when signals overlap, mating signal synchronization has remained an evolutionary puzzle. Synchronization may be beneficial, however, if overlapping signals reduce the attraction of nontarget receivers (predator avoidance hypothesis). Synchronized signals could also constructively interfere, increasing female attraction to the mating aggregation (the beacon effect hypothesis). I investigate these functions of synchronized signaling in two species of tree frogs that synchronize their mating calls: the pug-nosed tree frog (<i>Smilisca sila</i>) and the Ryukyu Kajika frog (<i>Buergeria japonica</i>). To examine the trade-offs imposed by call synchronization in each species, I conduct a series of field and laboratory playback experiments on target (female frogs) and nontarget (eavesdropping predators) receivers of frog calls. Results from these experiments support both hypotheses, suggesting that synchronized frog calls can reduce the attraction of predators and attract mates to the chorus. In addition, I found reduced preferences for fine-scale call timings in female <i>S. sila</i> and <i>B. japonica</i>, deviating from the expected preferences observed in many other anuran and non-anuran species. Thus, while males may enjoy multiple benefits from synchronized mating signals, relaxed sexual selection for non-synchronous signals may be key to the evolution and maintenance of mating signal synchrony.

Recent multielectrode array recordings in ganglionated plexi of canine atria have opened the way to the study of population dynamics of intrinsic cardiac neurons. These data provide critical insights into the role of local processing that these ganglia play in the regulation of cardiac function. Low firing rates, marked non-stationarity, interplay with the cardiovascular and pulmonary systems and artifacts generated by myocardial activity create new constraints not present in brain recordings for which almost all neuronal analysis techniques have been developed. We adapted and extended the jitter-based synchrony index (SI) to (1) provide a robust and computationally efficient tool for assessing the level and statistical significance of SI between cardiac neurons, (2) estimate the bias on SI resulting from neuronal activity possibly hidden in myocardial artifacts, (3) quantify the synchrony or anti-synchrony between neuronal activity and the phase in the cardiac and respiratory cycles. The method was validated on firing time series from a total of 98 individual neurons identified in 8 dog experiments. SI ranged from -0.14 to 0.66, with 23 pairs of neurons with SI > 0.1. The estimated bias due to artifacts was typically <1%. Strongly cardiovascular- and pulmonary-related neurons (SI > 0.5) were found. Results support the use of jitter-based SI in the context of intrinsic cardiac neurons.

This manuscript provides a critical review of the literature on parent–child physiological synchrony—the matching of biological states between parents and children. All eligible studies found some evidence of physiological synchrony, though the magnitude and direction of synchrony varied according to methodological factors, including the physiological system examined (i.e., parasympathetic or sympathetic nervous system activity, adrenocortical functioning) and the statistical approach used (e.g., multilevel modeling, correlation). The review underscores the need to consider the context in which physiological synchrony occurs (e.g., family risk) to best understand its significance. Furthermore, the review delineates vital avenues for future research, including the need to assess synchrony across multiple physiological systems and the importance of documenting continuity/change in physiological synchrony across developmental periods. Such research is crucial for understanding how the parent–child relationship unfolds at a physiological level and, in turn, how this relationship can facilitate or hinder parent, child, and family adjustment.

L'intégration de composants dans un système peut s'avérer difficile lorsque ces composants ont été conçus selon différents paradigmes ou s'ils se basent sur différents cadres de temps devant être synchronisés. Cette synchronisation peut être dirigée par les évènements (un évènement est provoqué par un autre), ou dirigée par le temps (un évènement se produit parce qu'il en est l'heure). En considérant que chaque composant admet son propre cadre de temps et qu'ils peuvent ne pas être reliés, il est possible qu'une unique ligne de temps globale n'existe pas.Nous nous intéressons à la spécification de schémas de synchronisation pour de tels systèmes polychrones et polytemporisés. Notre étude nous a mené à la conception de modèles sémantiques pour un langage temporisé à évènements discrets, appelé TESL et développé par Boulanger et al. Ce langage a été utilisé pour coordonner la simulation de modèles composites et pour tester l'intégration de systèmes.Dans cette thèse, nous présentons une sémantique dénotationnelle fournissant une compréhension précise et logiquement cohérente du langage. Puis nous proposons une sémantique opérationnelle afin de dériver des traces d'exé-cutions satisfaisant une spécification TESL. Celui-ci a été utilisé pour les problématiques de test des systèmes, à travers l'implantation d'un solveur nommé Heron. Pour résoudre la question de cohérence et de correction de ces règles sémantiques, nous avons également développé une sémantique intermédiaire coinductive reliant les deux sémantiques dénotationnelles et opérationnelles. Nous établissons des propriétés sur la relation entre les deux sémantiques: correction, complétude, progrès ainsi que terminaison locale. Enfin, notre formalisation ainsi que les preuves associées ont été entièrement mécanisées dans l'assistant de preuve Isabelle/HOL. / Integrating components into systems turns out to be difficult when these components were designed according to different paradigms or when they rely on different time frames which must be synchronized. This synchronization may be event-driven (an event occurs because another event occurs) or time-driven (an event occurs because it is time for it to occur). Considering that each component admits its own time frame, and that they may not be related, a unique global time line may not exist.We are interested in specifying synchronization patterns for such polychronous and polytimed systems. Our study had led us to design semantic models for a timed discrete-event language, called the TESL language developed by Boulanger et al. This language has been used for coordinating the simulation of composite models and testing system integration.In this thesis, we present a denotational semantics providing an accurate and logic-consistent understanding of the language. Then we propose an operational semantics to derive satisfying runs from TESL specifications. It has been used for testing purposes, through the implementation of a solver, named Heron. To tackle the issue of the consistency and correctness of these semantic rules, we developed a co-inductive intermediate semantics that relates both the denotational and the operational semantics. Then we establish properties over the relation of our semantic models: soundness, completeness and progress, as well as local termination. Finally, our formalization and these proofs have been fully mechanized in the Isabelle/HOL proof assistant.

Au vu des changements globaux actuels engendrés en grande partie par l'être humain, il devient nécessaire de comprendre les moteurs de la stabilité des communautés d'êtres vivants. La synchronie des séries temporelles d'abondances fait partie des mécanismes les plus importants. Cette thèse propose trois angles différents permettant de répondre à différentes questions en lien avec la synchronie interspécifique ou spatiale. Les travaux présentés trouvent des applications en dehors du cadre écologique. Un premier chapitre est consacré à l'estimation du rang effectif de matrices à valeurs dans ℝ ou ℂ. Nous apportons ainsi des outils permettant de mesurer le taux de synchronisation d'une matrice d'observations. Dans le deuxième chapitre, nous nous basons sur les travaux existants sur le problème de détection de ruptures sur les chaînes afin de proposer plusieurs algorithmes permettant d'adapter ce problème au cas des arbres. Les méthodes présentées peuvent être utilisées sur la plupart des données nécessitant d'être représentées sous la forme d'un arbre. Afin d'étudier les liens entre la synchronie interspécifique et les tendances à long termes ou les traits d'espèces de papillons, nous proposons dans le dernier chapitre d'adapter des méthodes de clustering et d'apprentissage supervisé comme les Random Forest ou les Réseaux de Neurones artificiels à des données écologiques. / In the view of actual global changes widely caused by human activities, it becomes urgent to understand the drivers of communities' stability. Synchrony between time series of abundances is one of the most important mechanisms. This thesis offers three different angles in order to answer different questions linked to interspecific and spatial synchrony. The works presented find applications beyond the ecological frame. A first chapter is dedicated to the estimation of effective rank of matrices in ℝ or ℂ. We offer tools allowing to measure the synchronisation rate of observations matrices. In the second chapter, we base on the existing work on change-points detection problem on chains in order to offer algorithms which detects change-points on trees. The methods can be used with most data that have to be represented as a tree. In order to study the link between interspecific synchrony and long term tendencies or traits of butterflies species, we offer in the last chapter adaptation of clustering and supervised machine learning methods, such as Random Forest or Artificial Neural Networks to ecological data.