Contributions à l'étude des patrons spatiaux de biodiversité dans les paysages complexes

Les patrons spatiaux issus de processus écologiques naturels et anthropiques constituent une mosaïque complexe dans la nature. Ceci combiné aux conséquences parfois colossales des perturbations anthropiques sur la biodiversité et les services écosystémiques, fait de l'écologie spatiale une science à la fois complexe et urgente dans un contexte de changement global rapide. Dans cette thèse, j’ai essayé de contribuer à notre compréhension de comment la structure spatiale des paysages influence la dynamique des populations, en utilisant des approches innovantes. Dans ce but, j'ai étudié différentes perturbations et différents aspects de la dynamique des populations dans trois chapitres. Les deux premiers chapitres d’analyse portent sur un biome qui fournit de nombreux services écosystémiques. La forêt boréale présente une exploitation en plein développement potentiellement non durable, et est aussi actuellement menacée par des perturbations naturelles sans précédents et exacerbées. J'ai d'abord examiné comment l’habitat naturel et les nombreuses altérations du paysage causées par l'homme influencent une communauté de mammifères de la forêt boréale. Ensuite, je me suis concentré sur une autre perturbation à grande échelle de la forêt boréale en identifiant les éléments du paysage qui limitent la propagation d’un des ravageurs forestiers les plus destructeurs au monde. Enfin, j'ai complété les approches utilisées dans les deux chapitres précédents, en me concentrant sur l'aspect temporel du changement de la dynamique des populations. Je l'ai fait en construisant et en évaluant une méthode capable de détecter des changements de diversité génétique locaux et atypiques, malgré les changements aléatoires omniprésents apportés par la dérive génétique et le flux de gènes. Mes trois chapitres d’analyse ont des implications claires en matière de conservation. Bien que deux d'entre eux soient concentrés sur des systèmes spécifiques, ils peuvent s'appliquer à d'autres paysages, ou du moins fournir une piste pour de futures recherches. Pour conclure ma thèse, j'ai suivi la synthèse de mes chapitres par une discussion sur comment l'interdisciplinarité des disciplines associées à l'écologie spatiale est une force essentielle que nous devrions cultiver. Je termine ma thèse en identifiant certaines des directions de recherche futures les plus excitantes et prometteuses.Natural and anthropogenic spatial patterns create an intricate mosaic. This fact, combined with the sometimes colossal consequences of anthropogenic disturbances on biodiversity and ecosystem services, makes spatial ecology a science of both complexity and urgency in a context of rapid global change. In this thesis, I have tried to contribute to our understanding of how the spatial structure of landscapes influences population dynamics through innovative approaches. Towards this goal, I have investigated different perturbations and different aspects of population dynamics in three chapters. The first two analysis chapters focus on a biome which is a large provider of ecosystem services and resources, featuring rapidly increasing and possibly unsustainable exploitation, but which is also currently under threat from unprecedented and exacerbated natural disturbances. First, I delved into how a community of boreal forest mammals is driven by its natural habitat and the many man-made alterations to the landscape. Then, I focused on another large-scale perturbation of the boreal forest by identifying what elements of the landscape constrain the spread of one of the most destructive forest pests in the world. Finally, I complemented the approaches used the previous two chapters, by focusing on the temporal aspect of population dynamics change. I did this by constructing and evaluating of a method capable of detecting local atypical change in genetic diversity despite the ever-present random changes brought by genetic drift and gene flow. My three analysis chapters have clear conservation implications which, although two of them focused on specific systems, may translate to other landscapes, or at least provide a pipeline for future research. To conclude my thesis, I followed the synthesis of my chapters by a discussion about how the interdisciplinarity of disciplines associated with spatial ecology is an essential strength we should cultivate. I end my thesis by identifying some of the most exciting and promising future research directions

A new giant nautilid species from the Middle Jurassic of Luxembourg and Southwest Germany

Abstract In comparison to other cephalopods such as ammonites and belemnites, nautilid shells are relatively rare fossils in Jurassic marine deposits and knowledge of their taxonomy is therefore still patchy. We describe herein a new species of Cenoceras, C. rumelangense, from the early Bajocian Humphriesianum Zone of Luxembourg and Southwest Germany. In Luxembourg, the type material occurs in the ‘Marnes sableuses d’Audun-le-Tiche’ unit, which yields other large-sized cephalopods, such as the largest known belemnite genus, Megateuthis. The new species reaches a remarkable size, with diameters up to 610 mm. Thus, it is amongst the largest known post-Triassic nautilids worldwide, together with Paracenoceras giganteum and Paracenoceras ingens from the Upper Jurassic. Additionally, we discuss some aspects of the taphonomy of these large shells deposited in a shallow marine setting

Modelling landscape genetic connectivity of the mountain pine beetle in western Canada

The current mountain pine beetle (MPB; Dendroctonus ponderosae Hopkins, 1902) outbreak has reached more than 25 million hectares of forests in North America, affecting pine species throughout the region and substantially changing landscapes. However, landscape features that enhance or limit dispersal during the geographic expansion associated with the outbreak are poorly understood. One of the obstacles in evaluating the effects of landscape features on dispersal is the parameterization of resistance surfaces, which are often constructed based on biased expert opinion or by making assumptions in the calculation of ecological distances. In this study, we assessed the impact of four environmental variables on MPB genetic connectivity across western Canada. We optimized resistance surfaces using genetic algorithms and models of maximum likelihood population effects, based on pairwise genetic distances and ecological distances calculated using random-walk commute-time distances. Unlike other methods for the development of resistance surfaces, this approach does not make a priori assumptions about the direction or shape of the relationships between environmental features and their cost to movement. We found highest support for a composite resistance surface including elevation and climate. These results further the understanding of MPB movement during an outbreak. Additionally, we demonstrated how to use our results for management purposes.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

The role of dispersal, selection, and timing of sampling on the false discovery rate of loci under selection during geographic range expansion

Identifying adaptive loci is important to understand the evolutionary potential of species undergoing range expansion. However, in expanding populations, spatial demographic processes such as allele surfing can create spatial patterns of neutral genetic variation that appear similar to those generated through adaptive processes. As a result, the false discovery rate of adaptive loci may be inflated in landscape genomic analyses. Here, we take a simulation modelling approach to investigate how range expansion affects our ability to correctly distinguish between neutral and adaptive genetic variation, using the mountain pine beetle outbreak system as a motivating example. We simulated the demographic and population genetic dynamics of populations undergoing range expansion using an individual-based genetic model CDMetaPOP. We investigated how the false discovery rate of adaptive loci is affected by (i) dispersal capacity, (ii) timing of sampling, and (iii) the strength of selection on an adaptive reference locus. We found that a combination of weak dispersal, weak selection, and early sampling presents the greatest risk of misidentifying loci under selection. Expanding populations present unique challenges to the reliable identification of adaptive loci. We demonstrate that there is a need for further methodological development to account for directional demographic processes in landscape genomics.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Geo-referenced microsatellite data from <i>Triturus cristatus</i> in Luxembourg

Microsatellite genotypes (15 loci) and geographical locations of 897 samples from the northern crested newt (Triturus cristatus) in Luxembourg. Provided coordinates are based on the Luxembourg 1930 (EPSG: 2169) projection. The data were analysed in the context of the article: "Robustness of resistance surface optimisations: sampling schemes and genetic distance metrics affect inferences in landscape genetics".</p