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Long-term population dynamics across heterogeneous environments can be a major factor in determining species’ ability to expand their ranges and persist in novel environments. Whether and how the relative performance of populations in different microsites over time impacts invasion into new microsites is poorly understood. Though largely restricted to disturbed semi-shaded microhabitats in its home range, the invasive herb Alliaria petiolata (garlic mustard) successfully invades intact forest understories – a novel microhabitat – in its introduced range, where it is known to impact above and below ground community composition. To test the hypothesis that source-sink metapopulation dynamics may be promoting A. petiolata’s incursion into the forest understory, I utilized two multi-season field surveys – approximately a decade apart – to evaluate trait variation, biomass allocation, and long-term population demographics of A. petiolata growing at the forest edge, within the intact forest understory, and in the intermediate transition zone between the two. My results show that adult plants in the edge were taller and branchier, produced more fruits, and had higher total and reproductive biomass than plants in the intermediate and forest microhabitats. Over time, seedling density remained highest in the edge microhabitat compared to the forest and intermediate microhabitats, which had similar densities. Reproductive adult densities were similar among all microhabitats at the beginning of the study, but a decade later, all microhabitats exhibited a decline in the number of adult plants they supported. Populations in the intermediate microhabitat displayed the steepest decline in reproductive adults between sampling periods but still supported more adult plants than the forest microhabitat. Populations in all microhabitats were predicted to grow (λ>1) at the onset of the study. A decade later, declines in population size were only predicted in the forest understory (λ1). Since edge and intermediate patches had higher densities of adult plants which produced the most fruit and had larger reproductive biomass, it appears that the edge populations, and possibly the intermediate populations, have sustained the low-density forest populations through source-sink dynamics at my study sites.

La daurade royale (Sparus aurata) est une espèce de sparidé dont l’aire de répartition s’étend des côtes du Sénégal à l’Irlande, et est commune en mer Méditerranée. Elle est considérée comme rare en limite nord de répartition (Manche, mer d’Irlande et mer du Nord). Depuis une dizaine d’années, l’abondance d’individus pêchés en limite nord ne cesse d’augmenter. Ce phénomène peut être expliqué par l’évolution septentrionale de son aire de répartition, en lien avec le réchauffement climatique. Aucune donnée écologique sur les populations de cette espèce en limite nord de répartition, devenues une ressource de pêche en Manche, n’est actuellement publiée dans la littérature. Les traits de vie de S. aurata ont été étudiés face à la modification spatio-temporelle de son aire de répartition, via l’analyse du régime alimentaire, de la croissance et des déplacements côtiers. D’autre part, l’étude a conduit à l’analyse de la structure de ces populations septentrionales par une approche multi-marqueur couplant la génétique et la microchimie des otolithes.L’analyse des contenus stomacaux des populations de S. aurata en limite nord de répartition confirme un régime opportuniste, avec une forte proportion d’espèces-proies du genre Mytilus. Malgré un régime alimentaire similaire, la croissance des individus est, quant à elle, plus faible que celle observée sur des individus de mer Méditerranée, ce phénomène étant conditionné par les paramètres du milieu (température, salinité). Les variations élémentaires des otolithes ont permis de caractériser les migrations côtières lors des premières années de vie des poissons avec un passage en mer en hiver et la fréquentation de zones côtières. Cela suggère la présence de zones de nourricerie le long du pourtour atlantique et de la Manche. Une variabilité inter-individuelle a été mise en évidence suggérant une plasticité comportementale des individus. Les approches de génétique, combinant l’emploi de marqueurs mitochondriaux et des microsatellites, et de microchimie des otolithes ont mis en évidence l’absence de structure au sein des populations en limite nord de répartition. Ce phénomène concorde avec la colonisation récente des populations. Cependant, une différenciation entre les individus échantillonnés le plus au sud et ceux en limite nord d’échantillonnage a été mise en évidence, suggérant peu de mélange génétique. Les allèles communs entre les individus échantillonnés évoquent une colonisation des individus de proche en proche depuis la mer Méditerranée. Des différences génétiques et de traits de vie ont été observées entre les individus échantillonnés en Manche, suggérant l’existence d’une barrière biogéographique au sein de cet environnement. La présence de conditions environnementales favorables constitue un atout majeur pour cette espèce prédatrice qui semble présenter une capacité d’acclimatation importante. L’ensemble des approches abordées dans le cadre de ces travaux ont permis d’apporter les premières données sur les traits de vie et la structure des populations d’une espèce à fort intérêt commercial dans une zone d’expansion récente en lien avec des modifications globales des conditions environnementales. / The gilthead seabream (Sparus aurata) is a sparidae species whose natural distribution stretches from Senegal to Ireland coasts, with its common habitat in the Mediterranean Sea. This species is still considered as rare in its northern limit of distribution. For a decade, the abundance of individuals caught in the northern limit (English Channel, Irish Sea and North Sea), has increased. This species is now a fishing resources in the English Channel. This phenomenon, in link with global warming, is explained by the northern expansion of its distribution range. No ecological data about this species in northern distribution range is currently published. Life history traits of S. aurata in relation to the spatio-temporal modification of its distribution range has been studied, through diet, growth and sea/coastal movement analysis. On the other hand, the population structure analysis of these northern populations has been done with a multi-marker approach coupling the genetics and otolith microchemistry.Analysis of the stomach contents of S. aurata at the northern range confirms an opportunistic diet with a high proportion of prey species from the genus Mytilus. The growth of individuals is lower than that observed on individuals in the Mediterranean Sea. This phenomenon is conditioned by environmental parameters (temperature, salinity) at the distribution range limit. Elemental composition of the otoliths allowed us to characterize the sea/coastal migrations during the first year of life, with a sea transition in winter and the occupation of coastal zones. A variability between individuals has been observed as a behavioral plasticity of individuals. This suggests the presence of nursery areas along the Atlantic and Channel Sea coasts. Otolith microchemistry and genetic approaches, combining the use of mitochondrial and microsatellites markers, have demonstrated the lack of structure within populations at the northern distribution range. This phenomenon matches with the recent population colonization. However, a differentiation was identified between the most southern individuals sampled and those at the northern sampling boundary, suggesting little genetic mixing. Common alleles between individuals suggest a “step by step” colonization of individuals from the Mediterranean Sea. Genetic and life history traits differences were observed between individuals sampled in the Channel Sea, suggesting a biogeographic barrier within this environment.Favorable environmental conditions are a major asset for this predatory species, which appears to have a huge acclimatization ability. All the various approaches discussed in this work have then made it possible to provide the first data on the life characteristics and the population structure of a species with a high commercial interest on the northern range of its distribution.

The rapid pace of conversion of natural areas to agronomic systems is a matter of great concern, and the consequences for conservation and pest management are not yet fully understood. We examined mitochondrial (COI and Cytb) and nuclear (ITS1) gene regions of 21 Euschistus heros populations to investigate the genetic diversity, genetic structure, and the demographic history of this emerging pest of soybean crops in South America. Two deep divergent lineages that separated in the Pliocene (4.5 My) have been found over a wide area. The northern lineage is older, more diverse, and prevalent in the Amazon and Caatinga, while the southern lineage is younger, less diverse, and prevalent in the Atlantic Forest and Chaco biomes. The secondary contact is occurring mainly in the Cerrado, an important agriculture frontier. Euschistus heros populations are expanding in size and range, but are strongly affected by environment variables. Historical changes during the Plio-Pleistocene created significant genetic differentiation between E. heros populations, which differentiated further in several biomes. The present populations are expanding at different rates, mixing highly diverse populations with less-diverse populations in regions of intensive farming. This, individuals adapted to different environmental conditions and to large monocultures might currently be combining into a panmictic and hard-to-control pest population. / O ritmo acelerado da conversão de áreas naturais em sistemas agronômicos é motivo de grande preocupação e as consequências para conservação e manejo de pragas ainda não são totalmente compreendidas. Examinamos regiões de genes mitocondriais (COI e Cytb) e nucleares (ITS1) de 21 populações de Euschistus heros para investigar a diversidade genética, a estrutura genética e a história demográfica dessa praga emergente de soja na América do Sul. Duas linhagens profundamente divergentes que se separaram no Plioceno (4.5 My) foram encontradas amplamente distribuidas na América do Sul. A linhagem norte é mais antiga, mais diversificada e predomina na Amazônia e Caatinga, enquanto a linhagem sul é mais jovem, menos diversificada e prevalente nos biomas da Mata Atlântica e Chaco. O contato secundário está ocorrendo principalmente no Cerrado, uma importante fronteira agrícola. As populações de E. heros estão se expandindo em tamanho e área, mas são fortemente afetadas pelas variáveis ambientais. As mudanças históricas durante o Plio-Pleistoceno criaram significativa diferenciação genética entre as populações de E. heros, que se encontram estruturadas nos biomas. As populações atuais estão se expandindo em diferentes taxas, misturando populações altamente diversas com populações menos diversas em regiões de agricultura intensiva. Assim, indivíduos adaptados a diferentes condições ambientais e grandes monoculturas podem combinar-se em uma população de pragas panmítica e difícil de controlar.

Bakgrund:                   För att stärka sin position på marknaden önskar Staples Sweden AB utöka sitt artikelsortiment till att omfatta 1 000 000 artiklar. För att möjliggöra sortimentsexpansionen behövs beslutsunderlag rörande hantering och kostnadsstruktur identifieras. Syfte:                          Syftet med studien är att utveckla en modell vid val och utformning av distributionssätt för att föreslå en distributionsslösning. Syftet är också att genom en kostnadsanalys identifiera orderkostnadsstrukturen för den föreslagna distributionslösningen. Metod:                        Vid genomförandet av studien tillämpades en fallstudiedesign. Det empiriska materialet samlades in genom intervjuer utförda på Staples Sweden AB. Slutsats:                      Vid tillämpningen av modellen som utvecklades i studien framkom att distributionslösningen ska utgöras av direktleveranser, konsoliderade direkleveranser, ”cross-docking”, ”cross-docking” med buffert och traditionell lagerhållning. Orderkostnaden skiljde sig mellan distributionssätten där ”cross-docking” var billigast och direktleveransvarianterna var dyrast. / Background:               To strengthen its position on the market, Staples Sweden AB seeks to expand its product range to include one million articles. The problem is that no one in the company knows how such a variety of items should be managed and how the structure of order costs would change. Based on these problems, the task for the study arose. Purpose:                      The thesis aims to develop a model for the selection and design of distribution methods for proposing a solution that can manage one million articles. It also aims to identify the structure of order cost for the proposed solution through a cost analysis. Methodology:             The study was conducted by applying a case study design. The empirical data were collected through interviews conducted at the Staples Sweden AB. Conclusion:                 In the application of the developed model showed that the distribution solution should consist of direct shipping, consolidated direct shipping, cross-docking, cross-docking with buffer and traditional warehousing. Order cost differed between distribution where "cross-docking" showed to be the cheapest and direct shipping variants were the most expensive.

The rapid pace of conversion of natural areas to agronomic systems is a matter of great concern, and the consequences for conservation and pest management are not yet fully understood. We examined mitochondrial (COI and Cytb) and nuclear (ITS1) gene regions of 21 Euschistus heros populations to investigate the genetic diversity, genetic structure, and the demographic history of this emerging pest of soybean crops in South America. Two deep divergent lineages that separated in the Pliocene (4.5 My) have been found over a wide area. The northern lineage is older, more diverse, and prevalent in the Amazon and Caatinga, while the southern lineage is younger, less diverse, and prevalent in the Atlantic Forest and Chaco biomes. The secondary contact is occurring mainly in the Cerrado, an important agriculture frontier. Euschistus heros populations are expanding in size and range, but are strongly affected by environment variables. Historical changes during the Plio-Pleistocene created significant genetic differentiation between E. heros populations, which differentiated further in several biomes. The present populations are expanding at different rates, mixing highly diverse populations with less-diverse populations in regions of intensive farming. This, individuals adapted to different environmental conditions and to large monocultures might currently be combining into a panmictic and hard-to-control pest population. / O ritmo acelerado da conversão de áreas naturais em sistemas agronômicos é motivo de grande preocupação e as consequências para conservação e manejo de pragas ainda não são totalmente compreendidas. Examinamos regiões de genes mitocondriais (COI e Cytb) e nucleares (ITS1) de 21 populações de Euschistus heros para investigar a diversidade genética, a estrutura genética e a história demográfica dessa praga emergente de soja na América do Sul. Duas linhagens profundamente divergentes que se separaram no Plioceno (4.5 My) foram encontradas amplamente distribuidas na América do Sul. A linhagem norte é mais antiga, mais diversificada e predomina na Amazônia e Caatinga, enquanto a linhagem sul é mais jovem, menos diversificada e prevalente nos biomas da Mata Atlântica e Chaco. O contato secundário está ocorrendo principalmente no Cerrado, uma importante fronteira agrícola. As populações de E. heros estão se expandindo em tamanho e área, mas são fortemente afetadas pelas variáveis ambientais. As mudanças históricas durante o Plio-Pleistoceno criaram significativa diferenciação genética entre as populações de E. heros, que se encontram estruturadas nos biomas. As populações atuais estão se expandindo em diferentes taxas, misturando populações altamente diversas com populações menos diversas em regiões de agricultura intensiva. Assim, indivíduos adaptados a diferentes condições ambientais e grandes monoculturas podem combinar-se em uma população de pragas panmítica e difícil de controlar.

Biodiversity is being lost around the world and anthropogenic activities, like non-native species introductions and urbanization, are among the leading causes of decline. Broadening our understanding of human-driven impacts on biodiversity can lead to more effective solutions and contribute towards stemming biodiversity losses. In this thesis, I explored the impacts of non-native species introductions and urbanization on butterfly-plant communities. I evaluated potential factors influencing the range expansion of a newly introduced species (Chapter 1), examined the role of urbanization in structuring biological communities (Chapter 2), and identified important ecological interactions between native and non-native species (Chapter 3). In my first chapter, I found that the newly introduced European Common Blue butterfly (Polyommatus icarus) was more abundant in urban and disturbed habitat that was unmown and where their preferred larval host plant (Lotus corniculatus), a non-native species, was present. I also found that P. icarus was not a strong flier relative to other butterfly species, suggesting that adult dispersal may not be a driving factor in range expansion. Instead, this species could expand its range in the future by colonizing habitats in developed regions across Canada given the association I found between P. icarus and disturbed habitat. In my second chapter, I found that urbanization led to the biotic homogenization of butterfly communities around Montréal, QC, favouring a few, highly abundant, non-native species. Homogenization was detected at both the taxonomic and functional levels and was driven by increases in P. icarus abundance in the more urban sites. In my third chapter, I found that non-native plants were well integrated into native butterfly nectar diets in an at-risk oak savanna ecosystem on Vancouver Island, BC and that usage of non-native plants increased when they were more available during the season. I also found that native butterflies visited non-native plants more often than flower availability predicted on its own, suggesting that butterflies may even prefer non-native nectar. Findings from my thesis research broaden our understanding of the ways in which butterfly communities can be influenced by human activities like urbanization and the introduction of non-native species, informing conservation efforts and directing future research needs.

Avec les changements climatiques et les perturbations humaines, de nombreuses espèces changent leurs aires de répartition. Dans ce contexte, l’identification de loci potentiellement adaptatifs chez ces populations en expansion est importante pour mieux comprendre le potentiel évolutif et la capacité d’envahissement de ces espèces. Toutefois, chez les espèces en expansion de territoire, tel le dendroctone du pin, les processus démographiques comme le surf d’allèles peuvent résulter en des patrons spatiaux de variation génétique neutre qui imitent ceux issus des processus adaptatifs. Ce phénomène gonfle le taux de faux-positif d’identification des loci adaptatifs et confond ainsi les méthodes de génomique du paysage. Dans le cadre de ce projet de maîtrise, j’ai étudié le développement des structures génétiques neutres et adaptatives lors d’une expansion de territoire. Je me suis attardé particulièrement sur l’influence de différentes conditions démographiques sur le taux de loci neutres qui imitent les patrons spatiaux de ceux adaptatifs, en menant une revue de littérature et en utilisant le système épidémique du dendroctone du pin pour paramétrer un modèle de simulations. J’ai simulé les dynamiques démographiques et génétiques des populations de dendroctones à l’aide du modèle de simulation génétique explicitement spatial CDmetaPOP. J’ai analysé les conséquences de trois facteurs sur le taux de faux-positif : 1) la capacité de dispersion; 2) le moment d’échantillonnage durant l’expansion de territoire; et 3) la force de sélection agissant sur le locus adaptatif de référence. J’ai démontré qu’une combinaison de faible capacité de dispersion, faible sélection et un échantillonnage tôt au début de l’expansion contribuent à un plus grand taux de faux-positif, alors qu’une forte capacité de dispersion conduit à de plus faibles taux de faux-positif. Lorsque les méthodes de génomique du paysage sont utilisées dans ces conditions, elles risquent d’avoir un haut taux de loci neutres identifiés comme adaptatifs et doivent donc être interprétées avec prudence. La situation démographique complexe que présente le système actuel du dendroctone (et d’autres espèces irruptives et envahissantes) rend l’identification d’allèles adaptatifs plus difficile. Les résultats de ce projet encouragent l’incorporation de ces processus démographiques dans les méthodes de génomique du paysage. / Under the actual climate changes and human perturbations global context, many species are altering their geographic range. The identification of putatively adaptive loci in those expanding populations is thus important to better understand evolutionary potential and invasiveness of these species. However, in irruptive species undergoing rapid expansion, such as the mountain pine beetle (MPB), demographic processes such as allele surfing can result in spatial patterns of neutral genetic variation that can mimic those that result from adaptive processes. This phenomenon inflates the false discovery rate of adaptive loci and thus confounds landscape genomics methods. In this thesis, I studied the development of neutral and adaptive genetic structure during a range expansion. I investigated precisely how different demographic conditions influence the rate of neutral loci mimicking the spatial patterns of adaptive loci, doing a literature review and using the mountain pine beetle outbreak system to parametrize a simulation model. I simulated the demographic and population genetic dynamics of mountain pine beetle populations undergoing range expansion using the spatially explicit, individual-based genetic model CDmetaPOP. I examined the consequences of three factors on the false discovery rate: 1) species dispersal capacity; 2) timing of sampling during the course of the expansion; and 3) the strength of selection on adaptive reference loci. I found that a combination of weak dispersal capacity, weak selection, and early sampling during expansion results in the highest rate of false positive, while strong dispersal was responsible for lower rates of false positive. Used under these conditions of dispersal capacity, strength of selection and sampling timing, landscape genomics models risk elevated false discovery rates of adaptive loci and must be interpreted cautiously. Complex demography in the current MPB system (and other irruptive and invasive species) makes identification of adaptive loci challenging. Results from this project clearly demonstrate that there is a need for further method development to include these directional demographic processes in the field of landscape genomics.

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