Space Competition and Time Delays in Human Range Expansions. Application to the Neolithic Transition

Space competition effects are well-known in many microbiological and ecological systems. Here we analyze such an effectin human populations. The Neolithic transition (change from foraging to farming) was mainly the outcome of a demographic process that spread gradually throughout Europe from the Near East. In Northern Europe, archaeological data show a slowdown on the Neolithic rate of spread that can be related to a high indigenous (Mesolithic) population density hindering the advance as a result of the space competition between the two populations. We measure this slowdown from a database of 902 Early Neolithic sites and develop a time-delayed reaction-diffusion model with space competition between Neolithic and Mesolithic populations, to predict the observed speeds. The comparison of the predicted speed with the observations and with a previous non-delayed model show that both effects, the time delay effect due to the generation lag and the space competition between populations, are crucial in order to understand the observations

The lower Triassic anachronistic carbonate facies in space and time

The end-Permian mass extinction greatly affected the sedimentary record, but the sedimentary response was not limited to the Permian-Triassic boundary interval. This transformation extended to sedimentation that spanned the entire Early Triassic. Calcimicrobialites play an important role throughout this time interval, and at least four main events of anomalous carbonate deposition can be shown. A post-extinction calcimicrobial unit occurs above the extensive Permian skeletal carbonate platform exposed in the Taurus Mountains (southern Turkey), in south Armenia, north-west north and Central Iran along the Zagros Mountains. The calcimicrobial unit formed during the flooding of the platform that took place during the earliest Triassic. A similar calcimicrobialite formed during late Griesbachian to Dienerian time atop the shallow Permian skeletal carbonate platform largely exposed in south China. A third event occurred during the Early Olenekian on the first Mesozoic isolated pelagic plateau (Baid seamount, Oman Mountains). Here the change in carbonate sedimentation is reflected in the occurrence of thrombolites and carbonate seafloor fans. Near the end of Early Triassic time, unusual carbonate deposition is recorded both on an isolated pelagic plateau of the Western Tethys (Halstatt limestone of Dobrogea, Romania) and on the eastern Panthalassa margin of the western United States. In the western United States, the event is represented by stromatolites and thrombolites in the Virgin Limestone of the Moenkopi Formation and by seafloor fans in the middle and upper members of the Union Wash Formation. These unusual episodes of anomalous carbonate deposition illustrate a fundamental change in sedimentation that occurred in the aftermath of the end-Permian mass extinction.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.

Gliotransmitters Travel in Time and Space.

The identification of the presence of active signaling between astrocytes and neurons in a process termed gliotransmission has caused a paradigm shift in our thinking about brain function. However, we are still in the early days of the conceptualization of how astrocytes influence synapses, neurons, networks, and ultimately behavior. In this Perspective, our goal is to identify emerging principles governing gliotransmission and consider the specific properties of this process that endow the astrocyte with unique functions in brain signal integration. We develop and present hypotheses aimed at reconciling confounding reports and define open questions to provide a conceptual framework for future studies. We propose that astrocytes mainly signal through high-affinity slowly desensitizing receptors to modulate neurons and perform integration in spatiotemporal domains complementary to those of neurons.

Artificial evolution on network structures : how time and space influence dynamics

Abstract The main objective of this work is to show how the choice of the temporal dimension and of the spatial structure of the population influences an artificial evolutionary process. In the field of Artificial Evolution we can observe a common trend in synchronously evolv¬ing panmictic populations, i.e., populations in which any individual can be recombined with any other individual. Already in the '90s, the works of Spiessens and Manderick, Sarma and De Jong, and Gorges-Schleuter have pointed out that, if a population is struc¬tured according to a mono- or bi-dimensional regular lattice, the evolutionary process shows a different dynamic with respect to the panmictic case. In particular, Sarma and De Jong have studied the selection pressure (i.e., the diffusion of a best individual when the only selection operator is active) induced by a regular bi-dimensional structure of the population, proposing a logistic modeling of the selection pressure curves. This model supposes that the diffusion of a best individual in a population follows an exponential law. We show that such a model is inadequate to describe the process, since the growth speed must be quadratic or sub-quadratic in the case of a bi-dimensional regular lattice. New linear and sub-quadratic models are proposed for modeling the selection pressure curves in, respectively, mono- and bi-dimensional regu¬lar structures. These models are extended to describe the process when asynchronous evolutions are employed. Different dynamics of the populations imply different search strategies of the resulting algorithm, when the evolutionary process is used to solve optimisation problems. A benchmark of both discrete and continuous test problems is used to study the search characteristics of the different topologies and updates of the populations. In the last decade, the pioneering studies of Watts and Strogatz have shown that most real networks, both in the biological and sociological worlds as well as in man-made structures, have mathematical properties that set them apart from regular and random structures. In particular, they introduced the concepts of small-world graphs, and they showed that this new family of structures has interesting computing capabilities. Populations structured according to these new topologies are proposed, and their evolutionary dynamics are studied and modeled. We also propose asynchronous evolutions for these structures, and the resulting evolutionary behaviors are investigated. Many man-made networks have grown, and are still growing incrementally, and explanations have been proposed for their actual shape, such as Albert and Barabasi's preferential attachment growth rule. However, many actual networks seem to have undergone some kind of Darwinian variation and selection. Thus, how these networks might have come to be selected is an interesting yet unanswered question. In the last part of this work, we show how a simple evolutionary algorithm can enable the emrgence o these kinds of structures for two prototypical problems of the automata networks world, the majority classification and the synchronisation problems. Synopsis L'objectif principal de ce travail est de montrer l'influence du choix de la dimension temporelle et de la structure spatiale d'une population sur un processus évolutionnaire artificiel. Dans le domaine de l'Evolution Artificielle on peut observer une tendence à évoluer d'une façon synchrone des populations panmictiques, où chaque individu peut être récombiné avec tout autre individu dans la population. Déjà dans les année '90, Spiessens et Manderick, Sarma et De Jong, et Gorges-Schleuter ont observé que, si une population possède une structure régulière mono- ou bi-dimensionnelle, le processus évolutionnaire montre une dynamique différente de celle d'une population panmictique. En particulier, Sarma et De Jong ont étudié la pression de sélection (c-à-d la diffusion d'un individu optimal quand seul l'opérateur de sélection est actif) induite par une structure régulière bi-dimensionnelle de la population, proposant une modélisation logistique des courbes de pression de sélection. Ce modèle suppose que la diffusion d'un individu optimal suit une loi exponentielle. On montre que ce modèle est inadéquat pour décrire ce phénomène, étant donné que la vitesse de croissance doit obéir à une loi quadratique ou sous-quadratique dans le cas d'une structure régulière bi-dimensionnelle. De nouveaux modèles linéaires et sous-quadratique sont proposés pour des structures mono- et bi-dimensionnelles. Ces modèles sont étendus pour décrire des processus évolutionnaires asynchrones. Différentes dynamiques de la population impliquent strategies différentes de recherche de l'algorithme résultant lorsque le processus évolutionnaire est utilisé pour résoudre des problèmes d'optimisation. Un ensemble de problèmes discrets et continus est utilisé pour étudier les charactéristiques de recherche des différentes topologies et mises à jour des populations. Ces dernières années, les études de Watts et Strogatz ont montré que beaucoup de réseaux, aussi bien dans les mondes biologiques et sociologiques que dans les structures produites par l'homme, ont des propriétés mathématiques qui les séparent à la fois des structures régulières et des structures aléatoires. En particulier, ils ont introduit la notion de graphe sm,all-world et ont montré que cette nouvelle famille de structures possède des intéressantes propriétés dynamiques. Des populations ayant ces nouvelles topologies sont proposés, et leurs dynamiques évolutionnaires sont étudiées et modélisées. Pour des populations ayant ces structures, des méthodes d'évolution asynchrone sont proposées, et la dynamique résultante est étudiée. Beaucoup de réseaux produits par l'homme se sont formés d'une façon incrémentale, et des explications pour leur forme actuelle ont été proposées, comme le preferential attachment de Albert et Barabàsi. Toutefois, beaucoup de réseaux existants doivent être le produit d'un processus de variation et sélection darwiniennes. Ainsi, la façon dont ces structures ont pu être sélectionnées est une question intéressante restée sans réponse. Dans la dernière partie de ce travail, on montre comment un simple processus évolutif artificiel permet à ce type de topologies d'émerger dans le cas de deux problèmes prototypiques des réseaux d'automates, les tâches de densité et de synchronisation.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

Time and space: genetic structure of the common sea urchin paracentrotus lividus in the south-eastern iberian coast

Spatio-temporal variability in settlement and recruitment, high mortality during the first life-history stages, and selection may determine the genetic structure of cohorts of long-lived marine invertebrates at small scales. We conducted a spatial and temporal analysis of the common Mediterranean Sea urchin Paracentrotus lividus to determine the genetic structure of cohorts at different scales. In Tossa de Mar (NW Mediterranean), recruitment was followed over 5 consecutive springs (2006-2010). In spring 2008, recruits and two-year-old individuals were collected at 6 locations along East and South Iberian coasts separated from 200 to over 1,100 km. All cohorts presented a high genetic diversity based on a fragment of mtCOI. Our results showed a marked genetic homogeneity in the temporal monitoring and a low degree of spatial structure in 2006. In 2008, coupled with an abnormality in the usual circulation patterns in the area, the genetic structure of the southern populations studied changed markedly, with arrival of many private haplotypes. This fact highlights the importance of point events in renewing the genetic makeup of populations, which can only be detected through analysis of the cohort structure coupling temporal and spatial perspectives.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.

Change points detection in crime-related time series: an on-line fuzzy approach based on a shape space representation

The extension of traditional data mining methods to time series has been effectively applied to a wide range of domains such as finance, econometrics, biology, security, and medicine. Many existing mining methods deal with the task of change points detection, but very few provide a flexible approach. Querying specific change points with linguistic variables is particularly useful in crime analysis, where intuitive, understandable, and appropriate detection of changes can significantly improve the allocation of resources for timely and concise operations. In this paper, we propose an on-line method for detecting and querying change points in crime-related time series with the use of a meaningful representation and a fuzzy inference system. Change points detection is based on a shape space representation, and linguistic terms describing geometric properties of the change points are used to express queries, offering the advantage of intuitiveness and flexibility. An empirical evaluation is first conducted on a crime data set to confirm the validity of the proposed method and then on a financial data set to test its general applicability. A comparison to a similar change-point detection algorithm and a sensitivity analysis are also conducted. Results show that the method is able to accurately detect change points at very low computational costs. More broadly, the detection of specific change points within time series of virtually any domain is made more intuitive and more understandable, even for experts not related to data mining.

Characterizing major avalanche episodes in space and time in the twentieth and early twentyfirst centuries in the Catalan Pyrenees

With the aim of better understanding avalanche risk in the Catalan Pyrenees, the present work focuses on the analysis of major (or destructive) avalanches. For such purpose major avalanche cartography was made by an exhaustive photointerpretation of several flights, winter and summer field surveys and inquiries to local population. Major avalanche events were used to quantify the magnitude of the episodes during which they occurred, and a Major Avalanche Activity Magnitude Index (MAAMI) was developed. This index is based on the number of major avalanches registered and its estimated frequency in a given time period, hence it quantifies the magnitude of a major avalanche episode or winter. Furthermore, it permits a comparison of the magnitude between major avalanche episodes in a given mountain range, or between mountain ranges, and for a long enough period, it should allow analysis of temporal trends. Major episodes from winter 1995/96 to 2013/14 were reconstructed. Their magnitude, frequency and extent were also assessed. During the last 19 winters, the episodes of January 22-23 and February 6-8 in 1996 were those with highest MAAMI values,followed by January 30-31, 2003, January 29, 2006, and January 24-25, 2014. To analyze the whole twentieth century, a simplified MAAMI was defined in order to attain the same purpose with a less complete dataset. With less accuracy, the same parameters were obtained at winter time resolution throughout the twentieth century. Again, 1995/96 winter had the highest MAAMI value followed by 1971/72, 1974/75 and 1937/38 winter seasons. The analysis of the spatial extent of the different episodes allowed refining the demarcation of nivological regions, and improving our knowledge about the atmospheric patterns that cause major episodes and their climatic interpretation. In some cases, the importance of considering a major avalanche episode as the result of a previous preparatory period, followed by a triggering one was revealed.

Space and time characterization of laser-induced plasmas for applications in chemical analysis and thin film deposition

Après des décennies de développement, l'ablation laser est devenue une technique importante pour un grand nombre d'applications telles que le dépôt de couches minces, la synthèse de nanoparticules, le micro-usinage, l’analyse chimique, etc. Des études expérimentales ainsi que théoriques ont été menées pour comprendre les mécanismes physiques fondamentaux mis en jeu pendant l'ablation et pour déterminer l’effet de la longueur d'onde, de la durée d'impulsion, de la nature de gaz ambiant et du matériau de la cible. La présente thèse décrit et examine l'importance relative des mécanismes physiques qui influencent les caractéristiques des plasmas d’aluminium induits par laser. Le cadre général de cette recherche forme une étude approfondie de l'interaction entre la dynamique de la plume-plasma et l’atmosphère gazeuse dans laquelle elle se développe. Ceci a été réalisé par imagerie résolue temporellement et spatialement de la plume du plasma en termes d'intensité spectrale, de densité électronique et de température d'excitation dans différentes atmosphères de gaz inertes tel que l’Ar et l’He et réactifs tel que le N2 et ce à des pressions s’étendant de 10‾7 Torr (vide) jusqu’à 760 Torr (pression atmosphérique). Nos résultats montrent que l'intensité d'émission de plasma dépend généralement de la nature de gaz et qu’elle est fortement affectée par sa pression. En outre, pour un délai temporel donné par rapport à l'impulsion laser, la densité électronique ainsi que la température augmentent avec la pression de gaz, ce qui peut être attribué au confinement inertiel du plasma. De plus, on observe que la densité électronique est maximale à proximité de la surface de la cible où le laser est focalisé et qu’elle diminue en s’éloignant (axialement et radialement) de cette position. Malgré la variation axiale importante de la température le long du plasma, on trouve que sa variation radiale est négligeable. La densité électronique et la température ont été trouvées maximales lorsque le gaz est de l’argon et minimales pour l’hélium, tandis que les valeurs sont intermédiaires dans le cas de l’azote. Ceci tient surtout aux propriétés physiques et chimiques du gaz telles que la masse des espèces, leur énergie d'excitation et d'ionisation, la conductivité thermique et la réactivité chimique. L'expansion de la plume du plasma a été étudiée par imagerie résolue spatio-temporellement. Les résultats montrent que la nature de gaz n’affecte pas la dynamique de la plume pour des pressions inférieures à 20 Torr et pour un délai temporel inférieur à 200 ns. Cependant, pour des pressions supérieures à 20 Torr, l'effet de la nature du gaz devient important et la plume la plus courte est obtenue lorsque la masse des espèces du gaz est élevée et lorsque sa conductivité thermique est relativement faible. Ces résultats sont confirmés par la mesure de temps de vol de l’ion Al+ émettant à 281,6 nm. D’autre part, on trouve que la vitesse de propagation des ions d’aluminium est bien définie juste après l’ablation et près de la surface de la cible. Toutefois, pour un délai temporel important, les ions, en traversant la plume, se thermalisent grâce aux collisions avec les espèces du plasma et du gaz.

Remaking place and securitising space: Urban regeneration and the strategies, tactics and practices of policing in the UK

Urban regeneration programmes in the UK over the past 20 years have increasingly focused on attracting investors, middle-class shoppers and visitors by transforming places and creating new consumption spaces. Ensuring that places are safe and are seen to be safe has taken on greater salience as these flows of income are easily disrupted by changing perceptions of fear and the threat of crime. At the same time, new technologies and policing strategies and tactics have been adopted in a number of regeneration areas which seek to establish control over these new urban spaces. Policing space is increasingly about controlling human actions through design, surveillance technologies and codes of conduct and enforcement. Regeneration agencies and the police now work in partnerships to develop their strategies. At its most extreme, this can lead to the creation of zero-tolerance, or what Smith terms 'revanchist', measures aimed at particular social groups in an effort to sanitise space in the interests of capital accumulation. This paper, drawing on an examination of regeneration practices and processes in one of the UK's fastest-growing urban areas, Reading in Berkshire, assesses policing strategies and tactics in the wake of a major regeneration programme. It documents and discusses the discourses of regeneration that have developed in the town and the ways in which new urban spaces have been secured. It argues that, whilst security concerns have become embedded in institutional discourses and practices, the implementation of security measures has been mediated, in part, by the local socio-political relations in and through which they have been developed.

Risk of foot and mouth disease associated with proximity in space and time to infected premises and the implications for control policy during the 2001 epidemic in Cumbria

An analysis was made that calculated the risk of disease for premises in the most heavily affected parts of the county of Cumbria during the foot-and-mouth disease epidemic in the UK in 2001. In over half the cases the occurrence of the disease was not directly attributable to a recently infected premises being located within 1.5 km. Premises more than 1.5 km from recently infected premises faced sufficiently high infection risks that culling within a 1.5 km radius of the infected premises alone could not have prevented the progress of the epidemic. A comparison of the final outcome in two areas of the county, south Penrith and north Cumbria, indicated that focusing on controlling the potential spread of the disease over short distances by culling premises contiguous to infected premises, while the disease continued to spread over longer distances, may have resulted in excessive numbers of premises being culled. Even though the contiguous cull in south Penrith appeared to have resulted in a smaller proportion of premises becoming infected, the overall proportion of premises culled was considerably greater than in north Cumbria, where, because of staff and resource limitations, a smaller proportion of premises contiguous to infected premises was culled