Plusieurs études à grande échelle ont identifié la modification ou la perte d’habitats comme menace principale à la conservation des communautés de poissons d’eau douce. Au Canada, « aucune perte nette dans la capacité productive des habitats » (NNL) est le principe directeur de la politique de gestion des habitats du ministère des Pêches et Océans. Le respect du NNL implique l’avancement des connaissances au niveau des relations entre les poissons et leurs habitats, de même que des outils pour quantifier l’impact de la modification des habitats sur les poissons. Les modèles d’utilisation de l’habitat des poissons (FHUM) sont des outils qui permettent d’améliorer nos connaissances des relations poissons – habitat, de prédire la distribution des espèces, mais aussi leurs densités, biomasses ou abondances, sur la base des caractéristiques de l’environnement. L’objectif général de mon mémoire est d’améliorer la performance des FHUM pour les rivières des basses Laurentides, en suggérant des perfectionnements au niveau de 2 aspects cruciaux de l’élaboration de tels modèles : la description précise de la communauté de poissons et l’utilisation de modèles statistiques efficaces. Dans un premier chapitre, j’évalue la performance relative de la pêcheuse électrique et de l’échantillonnage en visuel (plongée de surface) pour estimer les abondances des combinaisons d’espèces et de classes de taille des poissons en rivière. J’évalue aussi l’effet des conditions environnementales sur les différences potentielles entre les communautés observées par ces 2 méthodes d’échantillonnage. Pour ce faire, 10 sections de rivière de 20 m de longueur ont été échantillonnées à l’aide de ces 2 méthodes alors qu’elles étaient fermées par des filets de blocage. 3 plongeurs performèrent l’échantillonnage en visuel en se déplaçant de l’aval vers l’amont des sections, tout en dénombrant les espèces et classes de taille. Par la suite, nous avons fait 3 passages de pêcheuse électrique et les abondances furent estimées grâce à un modèle restreint de maximum de vraisemblance, basé sur la diminution des abondances observées. De plus grandes abondances de poissons furent observées en visuel qu’avec la pêcheuse électrique à tous les sites. La richesse spécifique observée en visuel était plus élevée (6/10) ou égale (4/10) à celle observée avec la pêcheuse électrique. Les différences entre les communautés de poissons observées à l’aide de ces 2 méthodes ne purent être reliées aux conditions environnementales. Les résultats de cette expérience sont contraires à ceux de toutes les études comparant ces 2 méthodes d’échantillonnage, lesquels suggèrent une supériorité de la pêcheuse électrique. Les conditions environnementales de notre expérience étaient distinctes de celles observées dans les autres études (absence d’arbres tombés dans l’eau, très peu de substrats grossiers), mais la différence la plus marquante était en terme de communauté de poissons observée (dominance des cyprinidés et des centrarchidés plutôt que des salmonidés). Je termine ce chapitre en suggérant que les caractéristiques comportementales favorisant l’évitement de la capture (formation de bancs) et facilitant l’observation en visuel (curiosité) sont responsables de la supériorité de la plongée de surface pour échantillonner les communautés dans les rivières des basses Laurentides. Dans un deuxième chapitre, je développe des FHUM pour des communautés de poissons de rivière ayant plusieurs espèces. Dans le but de simplifier la modélisation de telles communautés et d’améliorer notre compréhension des relations poissons – habitat, j’utilise les concepts de guilde écologique et de filtre environnemental pour explorer les relations entre les guildes formées sur la bases de différents types de traits (reproducteurs, taxonomiques, éco-morphologiques et alimentaires) et les conditions environnementales locales à l’échelle du méso-habitat. Les modèles d’habitats basés sur les guildes reproductrices ont clairement surpassé les autres modèles, parce que l’habitat de fraie reflète l’habitat de préférence en dehors de la période de reproduction. J’ai également utilisé l’approche inverse, c’est à dire définir des guildes d’utilisation de l’habitat et les mettre en relation avec les traits des espèces. Les traits reliés à l’alimentation des poissons ont semblés être les meilleurs pour expliquer l’appartenance aux groupes d’utilisation de l’habitat, mais le modèle utilisé ne représentait pas bien la relation entre les groupes. La validation de notre modèle basé sur les guildes reproductrices avec un jeu de données indépendant pourrait confirmer notre découverte, laquelle représente une manière prometteuse de modéliser les relations poissons – environnement dans des communautés de poissons complexes. En conclusion, mon mémoire suggère d’importantes améliorations aux FHUM pour les communautés de poissons des basses Laurentides, en suggérant de prendre en compte les caractéristiques biologiques des cours d’eau dans le choix d’une méthode d’échantillonnage, et également en utilisant une méthode prometteuse pour simplifier les FHUM de communautés de poissons complexes : les guildes reproductrices. / Many large scale studies have identified habitat modification or habitat losses as primary threats for the conservation of freshwater fish communities. In Canada, No Net Loss (NNL) of the productive capacity of habitats is the guiding principle of the Department of Fisheries and Oceans’ policy for the management of fish habitat. To respect NNL, a better understanding of fish-habitat relationships is required, as well as tools to quantify the impact of habitat modifications on fish. Fish habitat use models (FHUM) are tools that can improve our understanding of fish-habitat relationships, predict species occurrences, densities or biomass on the basis of habitat descriptors and quantify habitat requirements. They consist in relationships between biological descriptors of fish and habitat descriptors. The general objective of my thesis is to improve the performance of FHUM for the lower Laurentian streams by suggesting refinements on 2 crucial aspects in the development of these models: a precise description of the fish community and the use of efficient statistical models. In the first chapter, I evaluate the relative performance of electrofishing and visual surveys (snorkeling) for estimating the abundance of combinations of fish species and size classes in rivers. I also assessed the effect of environmental conditions on potential differences between the results obtained using these two sampling methods. Sampling sites consisted in 10 river sections of 20 m in length distributed in the Laurentian region of Québec. Both methods were used while sections were blocked. Three snorkelers that swam the river sections upstream while identifying and counting fish of each species and size-classes performed visual surveys. Three-pass electrofishing was performed and abundances were estimated with a maximum likelihood depletion model. Greater abundances of fish were observed by snorkeling than by electrofishing at all sites. Snorkeling species richness was higher (6/10) or equal (4/10) to electrofishing richness. Differences in the fish communities observed by both sampling methods were not related to environmental conditions. The results of our work are therefore contrary to that of most published studies that suggested the superiority of electrofishing on visual surveys. Compared to the conditions found in previous studies, our sampling sites had different environmental characteristics (no fallen trees, insignificant cover of large cobble and boulder) but the most striking dissimilarity was in terms of fish communities (dominance of cyprinids and centrarchids instead of salmonids). Behavioural characteristics favouring capture avoidance (schooling) and facilitating underwater observation (curiosity) may be responsible for the superiority of visual surveys in our study rivers. Survey methods should be selected based on fish community composition. In the second chapter, I develop FHUM for complex stream fish communities. In order to simplify the modelling of such communities, as well as improve our understanding of fish – habitat relationships, I used the ecological guild concept and the niche filtering hypothesis to explore the relationships between guilds based on different types of traits (eco-morphological, reproductive, alimentary and taxonomic) and local environmental descriptors, at the coarse meso-habitat scale. Reproductive guilds led to FHUM that clearly outperformed the other 3 approaches, because of the close relationship between preferred spawning grounds and non spawning habitat preferences, and also because reproductive traits are linked to habitat characteristics at the reach or coarse mesohabitat scale. We also defined guilds based on habitat-use and related them to species traits. Traits related to the feeding biology of fishes seemed to be the best at explaining the habitat-use guilds, but our model did not correctly represent the among-guild relationships. Validation of our reproductive trait model on an independent dataset would confirm our finding, which represents a promising way of modelling fish - habitat relationships in complex fish communities. In conclusion, my thesis suggests important improvements to FHUM models in the Laurentian streams by giving new insights on the choice of a sampling method that take into account the biological characteristics of the streams targeted, and by using a promising way of simplifying FHUM for species rich communities: reproductive guilds.

The savanna woodlands of Southern Africa, colloquially termed the miombo, are poorly described in terms of biodiversity compared to other biomes. They have therefore been underrepresented in the wider understanding of how land use intensification is shaping global biodiversity. Land use change is known to reduce biodiversity and disrupt intactness of ecological communities with consequences for ecosystem functioning, resilience, and services. Miombo woodlands are described as biodiversity hotspots due to a high endemism of species and the presence of megafauna. At the same time, they are also considered dynamic socio-ecological systems shaped by disturbances and the land use activities of people. The patterns of biodiversity change in these tropical ecosystems may, therefore, have their own unique contexts, understanding of which will be essential for biodiversity and land use management in these ecosystems. In this thesis, I identified the patterns of biodiversity change in response to the two major land use practices in the two dominant woodland types in southern African woodlands: the selective logging due to charcoal production in the mopane woodlands, and agricultural expansion in the miombo. I also examined the impact of two main disturbance agents, humans and elephants, on habitat structure and biodiversity in mopane woodlands. Across all chapters in this thesis, I investigated the effects of land use change and habitat modification on biodiversity empirically using chronosequences. To understand biodiversity change, I employed a hierarchical multilevel modelling approach making inferences at the three levels of ecological communities: species, community, and meta-community (set of ecological communities at different sites). I selected six villages in the charcoal production hotspot of southern Mozambique and carried out field surveys for three taxonomic groups: trees, mammals and ground beetles. I modelled the counts of trees and beetles and incidence of mammals using meta-community occurrence models in a Bayesian framework with the intensity class of the villages, above-ground biomass and land cover type as predictors. The results suggested that the species richness of trees and mammals declined by 12 and 8.5 % respectively while that of beetles increased by 3.5%, albeit non-significantly. In addition, the beta diversity of trees decreased while that of mammals increased. The results show that while both trees and mammals reduced in richness, they responded differently to charcoal production in terms of community organisation. The trees underwent subtractive homogenisation (decrease in alpha and beta diversities) primarily because of deterministic processes induced by selective harvesting of tree stems for charcoal. Mammal communities, on the other hand, showed subtractive heterogenization (decrease in alpha, but increase in beta diversity) mainly due to random extinctions. In the agriculture frontier of miombo-dominated northern Mozambique, I investigated the effects of fragmentation and habitat loss caused by agricultural expansion on diversity and composition of trees and mammals. I modelled the occurrences of trees and mammals using occupancy models with the fragmentation and quantity of woodland cover as predictors. The model showed that most tree species (n=10), mainly the timber and firewood species, linearly declined in population size as fragmentation increased. Mammals, on the other hand, showed a nonlinear response. Seven mammal species increased at the lower levels of fragmentation. However, at the higher levels, none of the mammal species increased while two declined. Similarly, the species richness of trees linearly declined, while that of mammals increased up to a fragmentation level of 55-65% and declined above this limit. The beta diversity of trees increased with fragmentation while that of mammals decreased. The results suggest that, although fragmentation reduces species richness of both trees and mammals, it affects their species compositions in different ways. Trees undergo subtractive heterogenization due to random species losses while mammals experience subtractive homogenisation mainly due to the combined effects of fragmentation-led habitat loss and intensified hunting. Finally, this study concludes that, above 75% fragmentation or below 26% habitat quantity, both taxonomic groups endure biodiversity loss. The threshold results here corroborate similar habitat quantity thresholds (20-30%) observed elsewhere in different ecosystems. However, they differ with the widespread notion that above 30% habitat quantity, the effect of fragmentation is non-existent. The results here emphasize that taxonomic groups respond differently, the diversity and population size of mammals reduced only after the habitat threshold, whereas, those of trees showed linear decrease with fragmentation most likely due to fragmentation-led habitat loss. Lastly, I examined the effects of disturbance by humans and elephants on habitat structure and bird diversity by conducting a space for time substitution comparison in the mopane woodlands of Zambia. To examine the woodland structure, I modelled the structural attributes of habitat (stem diameter, stand density, and basal area) using mixed models with the proportion of affected stems by humans and elephants as explanatory variables. I found that elephant disturbance was associated with higher stem diameters, low stand densities, but no change in basal area. Human disturbance, on the other hand, was related to reductions in stand density and basal area, but no change in the stem diameter. Further, I tested species and functional diversity of birds against the covariates of habitat structure and disturbance. I found that bird communities reduced in species richness in both, human as well as elephant disturbed areas. However, the functional diversity did not change with elephant disturbance. I concluded that human disturbance reduces woody biomass (basal area is correlated with woody biomass) of mopane woodlands and functional diversity of birds whilst elephants do not. In this thesis, I conclude that human driven land use change in the miombo woodlands erodes alpha diversity of all taxonomic groups. However, increases in beta diversity of mammals with charcoal land use and trees in agricultural land use may maintain their diversities at the meta-community level.

Biodiversity is determined by a myriad of complex processes acting at different scales. Given the current rates of biodiversity loss and change, it is of paramount importance that we improve our understanding of the underlying structure of ecological communities. In this thesis, I focused on Species Abundance Distributions (SAD), as a synthetic measure of biodiversity and community structure, and on Beta (β) diversity patterns, as a description of the spatial variation of species composition. I systematically assessed the effect of scale on both these patterns, analysing a broad range of community data, including different taxa and habitats, from the terrestrial, marine and freshwater realms. Knowledge of the scaling properties of abundance and compositional patterns must be fully integrated in biodiversity research if we are to understand biodiversity and the processes underpinning it, from local to global scales. SADs depict the relative abundance of the species present in a community. Although typically described by unimodal logseries or lognormal distributions, empirical SADs can also exhibit multiple modes. However, the existence of multiple modes in SADs has largely been overlooked, assumed to be due to sampling errors or a rare pattern. Thus, we do not know how prevalent multimodality is, nor do we have an understanding of the factors leading to this pattern. Here, I provided the first global empirical assessment of the prevalence of multimodality across a wide range of taxa, habitats and spatial extents. I employed an improved method combining two model selection tools, and (conservatively) estimated that ~15% of the communities were multimodal with strong support. Furthermore, I showed that the pattern is more common for communities at broader spatial scales and with greater taxonomic diversity (i.e. more phylogenetically diverse communities, since taxonomic diversity was measured as number of families). This suggests a link between multimodality and ecological heterogeneity, broadly defined to incorporate the spatial, environmental, taxonomic and functional variability of ecological systems. Empirical understanding of how spatial scale affects SAD shape is still lacking. Here, I established a gradient in spatial scale spanning several orders of magnitude by decomposing the total extent of several datasets into smaller subsets. I performed an exploratory analysis of how SAD shape is affected by area sampled, species richness, total abundance and taxonomic diversity. Clear shifts in SAD shape can provide information about relevant ecological and spatial mechanisms affecting community structure. There was a clear effect of area, species richness and taxonomic diversity in determining SAD shape, while total abundance did not exhibit any directional effect. The results supported the findings of the previous analysis, with a higher prevalence of multimodal SADs for larger areas and for more taxonomically diverse communities, while also suggesting that species spatial aggregation patterns can be linked to SAD shape. On the other hand, there was a systematic departure from the predictions of two important macroecological theories for SAD across scales, specifically regarding logseries distributions being selected only for smaller scales and when species richness and number of families were proportionally much smaller than the total extent. β diversity quantifies the variation in species composition between sites. Although a fundamental component of biodiversity, its spatial scaling properties are still poorly understood. Here, I tested if two conceptual types of β diversity showed systematic variation with scale, while also explicitly accounting for the two β diversity components, turnover and nestedness (species replacement vs species richness differences). I provided the first empirical analysis of β diversity scaling patterns for different taxa, revealing remarkably consistent scaling curves. Total β diversity and turnover exhibit a power law decay with log area, while nestedness is largely insensitive to scale changes. For the distance decay of similarity analysis, while area sampled affected the overall dissimilarity values, rates of similarity were consistent across large variations in sampled area. Finally, in both these analyses, turnover was the main contributor to compositional change. These results suggest that species are spatially aggregated across spatial scales (from local to regional scales), while also illustrating that substantial change in community structure might occur, despite species richness remaining relatively stable. This systematic and comprehensive analysis of SAD and community similarity patterns highlighted spatial scale, ecological heterogeneity and species spatial aggregation patterns as critical components underlying the results found. This work expanded the range of scales at which both theories deriving SAD and community similarity studies have been developed and tested (from local plots to continents). The results here showed strong departures from two important macroecological theories for SAD at different scales. In addition, the overall findings in this thesis clearly indicate that unified theories of biodiversity (or assuming a set of synthetic minimal assumptions) are unable to accommodate the variability in SADs shape across spatial scales reported here, and cannot fully reproduce community similarity patterns across scales. Incorporating more realistic assumptions, or imposing scale dependent assumptions, may prove to be a fruitful avenue for ecological research regarding the scaling properties of SAD and community similarity patterns. This will allow deriving new predictions and improving the ability of theoretical models to incorporate the variability in abundance and similarity patterns across scales.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-07-15T14:44:30Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Elâine_Ribeiro_TESE_PPGBV.final_V2.pdf: 8805946 bytes, checksum: 49c5072b57c8b0d0264ac0e02e425dc3 (MD5) / Made available in DSpace on 2016-07-15T14:44:30Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Elâine_Ribeiro_TESE_PPGBV.final_V2.pdf: 8805946 bytes, checksum: 49c5072b57c8b0d0264ac0e02e425dc3 (MD5) Previous issue date: 2015-02-25 / FACEPE / Este estudo teve como objetivo investigar quais os efeitos de perturbações antrópicas crônicas (e.g. coleta de madeira e de produtos florestais não madeireiros, pastoreio extensivo, caça e danos causados à vegetação pela introdução de espécies exóticas que ocorrem em áreas remanescentes de floresta) sobre a diversidade taxonômica e filogenética da flora lenhosa da Caatinga. Inicialmente, investigamos como se dá a questão da perturbação crônica da flora e seus efeitos sobre a biodiversidade através da revisão de 51 artigos que tratam do tema. Verificamos que estes estudos, em sua maioria, foram realizados em países em desenvolvimento, cujas populações humanas utilizam a floresta para subsistência e comércio. Os efeitos da perturbação foram acessados principalmente ao nível de populações e comunidades, sendo a coleta de produtos florestais não madeireiros a fonte de impacto mais analisada. Os efeitos sobre a biodiversidade foram em geral negativos, mas efeitos neutros e positivos também foram registrados. O segundo capítulo traz um estudo de caso que verifica a influência das perturbações humanas crônicas sobre a diversidade e composição taxonômica da flora lenhosa da Caatinga, realizado em várias propriedades privadas na cidade de Parnamirim-PE, Brasil. Neste estudo foram amostradas comunidades lenhosas de adultos, jovens e plântulas, e como preditores da perturbação crônica utilizaram-se a densidade de pessoas e animais domésticos (caprinos e bovinos), além de indicadores de acessibilidade às áreas, como a distância ao centro urbano mais próximo, à estrada mais próxima e à propriedade rural mais próxima às parcelas amostradas. Esses preditores tiveram em geral efeitos negativos sobre a diversidade taxonômica independente do estágio ontogenético, sendo a densidade de pessoas e de animais os preditores mais importantes desses efeitos. Verificouse ainda que a composição das espécies nas áreas perturbadas foi distinta, sendo pouco representada pela abundância de espécies de madeira densa nas áreas mais perturbadas. O terceiro e último capítulo verificou como as comunidades lenhosas de adultos, jovens e plântulas da Caatinga, amostradas no capítulo anterior, são afetadas pela perturbação crônica do ponto de vista de diversidade e estrutura filogenética. Neste capítulo, utilizaram-se os mesmos preditores da perturbação citados anteriormente, porém agora combinados em um índice de perturbação crônica. A diversidade de famílias esperadas para história evolutiva da região e a distância média entre os indivíduos dessas comunidades, medida em anos, foi reduzida em ambientes mais perturbados e para todos os estágios ontogenéticos. As comunidades de jovens e de plântulas apresentaram maior grau de parentesco em áreas mais perturbadas, sendo os táxons Euphorbiaceae e Cnidoscolus responsáveis por esse aumento de parentesco. Os resultados desta tese demonstram que as perturbações antrópicas crônicas na Caatinga não podem ser negligenciadas, pois conferem efeitos negativos importantes à diversidade taxonômica e filogenética da flora lenhosa. Dessa forma, estratégias de manejo que conciliem o uso dessas florestas e a manutenção da biodiversidade da Caatinga são urgentes. / The aim of this study was to investigate the effect of chronic anthropogenic disturbances (e.g. harvesting of timber and non-timber forest products, hunting, livestock, and damage to vegetation caused by exotic species that occur in natural remnant forests) on the taxonomic and phylogenetic diversity of wood flora from Brazilian Caatinga. Initially, 51 scientific papers were revised in order to investigate how chronic anthropogenic disturbances affect the flora of natural ecosystems. Most studies were conducted at developing countries, where human populations use forest resources for subsistence and commerce. Chronic disturbance effects were accessed mainly at population and community levels, and harvesting of nontimber forest products was the disturbance source more frequently analyzed in those papers. Effects of the chronic disturbances were in general negative, however positive and neutral effects were also documented. The second chapter brings a case study that evaluates the influence of chronic disturbances on the taxonomic diversity and composition of Caatinga wood flora from private propreties at the municipality of Parnamirim-PE, Brazil. Adult, sapling and seedling of wood plant communities were sampled, and the density of people and livestock (goats and catle) near the plot were used as predictors of chronic disturbance, as well as the distances to the nearest urban centre, road and rural property. In general, these disturbance predictors showed negative effects on taxonomic diversity irrespective to ontogenetic stage. Moreover, the density of people and livestock near the plot were the main predictors of these negative effects. Species composition differed between plots with low and high level of disturbance, especially in relation to hard wood species, which were rare in the plots highly disturbed. The third and last chapter analyzed how the adult, sapling and seedling communities, surveyed previously, were affected by chronic disturbances from the viewpoint of the phylogenetic diversity and structure. In this chapter the chronic disturbance predictors described above were combined into a chronic disturbance index. The diversity of families expected to the local evolutionary history and the mean phylogenetic distance between the individuals were reduced in plots with higher level of disturbance for all ontogenetic stages. Sapling and seeedling communities had higher degree of relatedness in most disturbed sites, being Euphorbiaceas and Cinidoscolus taxa responsible for this increasing in the relatedness degree. Overall, this thesis demonstrates that chronic anthropogenic disturbance at Caatinga could not continue to be neglected, as it imposes deleterious effects to the taxonomic and phylogenetic diversity of wood plant assemblages. Management strategies conciliating forest use and the maintenance of Caatinga biodiversity are urgent.

Attempts to quantify the effects of ocean acidification and warming (OAW) on scleractinian corals provide a growing body of response measurements. However, placing empirical results into an ecological context is challenging, owing to variations that reflect both natural heterogeneity and scientific bias. This study addresses the heterogeneity of climate change induced changes in coral recruitment and calcification. To discern scientific bias and identify drivers of the remaining heterogeneity, 100 publications were analyzed using a combination of weighted mixed effects meta-regression and factorial effect size meta‑analysis. A linear model was applied to quantify the variation caused by differing stress levels across studies. The least squares predictions were then used to standardize individual study outcomes and effect size meta-analysis was performed on original and standardized outcomes separately. On average, increased temperature significantly reduces larval survival, while ocean acidification impedes settlement and calcification. Coral resistance to OAW is likely governed by biological traits (genera and life cycle stage), environmental factors (abiotic variability) and experimental design (feeding regime, stressor magnitude, and exposure duration). Linear models suggest that calcification rates are driven by carbonate and bicarbonate concentrations, which act additively with warming. Standardizing outcomes to linear model predictions proved useful in discerning strong sources of scientific bias. The approach used in this study can improve modelling projections and inform policy and management on changes in coral community structure associated with the expected future intensification of OAW.

L'urbanisation croissante de ces dernières décennies nécessite une connaissance approfondie de la dynamique de la biodiversité en milieu urbain afin d’aider à la mise en place de politiques de développement urbain favorisant le maintien de cette biodiversité. Ce travail de doctorat a évalué l'homogénéisation taxonomique et la composition fonctionnelle des communautés de flore spontanée le long d’un gradient d’urbanisation en prenant comme unité d’étude le jardin privatif, ainsi que la structure génétique d’une espèce de plante, Parietaria judaica.L'homogénéisation taxonomique varie le long du gradient d’urbanisation. Les jardins privatifs des centres villes étudiés seraient moins riches, mais favoriseraient la diversité taxonomique au regard de la composition spécifique des communautés de par leurs expositions, aménagements et pratiques. L'étude des traits des communautés met en évidence des variations de la composition fonctionnelle le long du gradient d’urbanisation. Les zones de forte densité de bâti filtrent des traits, notamment liés à la dispersion et à la persistance des espèces. L'endozoochorie pourrait permettre le franchissement des bâtis qui entourent les jardins.Enfin, l’absence de structure génétique de Parietaria judaica à l’échelle locale des villes suggère des échanges génétiques quelle que soit la densité de bâti, tandis qu’une structure génétique marquée est observée à l’échelle régionale, entre les trois sites.Le jardin privatif qui à l’instar des autres habitats du milieu urbain, présentent des communautés végétales qui peuvent participer aux dynamiques de la végétation urbaine. / Increasing urbanization in recent decades requires a thorough understanding of the dynamics of urban biodiversity to aid in the establishing of urban development policies to promote the biodiversity. This doctoral work evaluated the taxonomic homogenization and functional composition of spontaneous flora communities along a gradient of urbanization taking as the unit of study the private garden, and the genetic structure of a plant species, Parietaria judaica.Taxonomic homogenization varies along the urbanization gradient. The private gardens of the centers studied cities are less rich but would enhance taxonomic diversity in terms of species composition of communities through their exposure, planning and practices.The study of traits communities highlights changes in the functional composition along the urbanization gradient. High built-up density areas filter traits, in particular linked to the dispersion and persistence of species. The endozoochorie could allow the crossing of built around the gardens.Finally, the lack of genetic structure of Parietaria judaica at local scale suggests genetic exchange regardless of the built-up density, while a significant genetic structure was observed at the regional level between the three sites.The private gardens, which like the other green patchs in urban areas, have plant communities that can participate in the dynamics of urban vegetation.

Denna uppsats ämnar att undersöka den språkliga och visuella utformningen av White Guide- restaurangers menyer med avsikt att få en djupare förståelse för vissa återkommande drag som kan kopplas till restauranger med denna höga kvalitetsklassificering. Forskningsfrågorna för studien lyder: Vilka visuella skillnader och likheter, när det kommer till typografi, färgsättning, användning av ikoner samt placering av text, finns det mellan de utvalda restaurangernas menyer? Finns det några språkliga skillnader och likheter ifråga om beskrivningar av tillagningsmetod, sensoriska uttryck samt uttryck för ursprung, mellan menyerna? Materialet som analyseras har avgränsats till sex olika menyer tillhörande restauranger inom kategorin mycket god klass i White Guide 2020. Menyerna analyseras dels genom en visuell analys med hjälp av sociosemiotisk teori samt genom en språklig analys som bygger på traditionell lexikal taxonomisk semantik. I den visuella analysen undersöks typografi, färgsättning, ikoner samt textens placering i menyerna och i den språkliga analysen undersöks olika uttryck för tillagningsmetoder, sensoriska uttryck samt uttryck för ursprung i menyernas maträttsbeskrivningar. Resultatet visar att menyer inom denna kategori i White Guide skiljer sig mycket åt både språkligt och visuellt även om vissa likheter har påfunnits. Alla analyserade menyer innehåller ord som betecknar tillagningsmetoder och trots att antalet skiljer sig mycket åt mellan menyerna är tillagningsmetoderna ändå flest till antalet bland samtliga språkliga analyskategorier. Många typsnittsvarianter förekommer i de olika menyerna även om typsnittsantalet inom en meny vanligen är mellan ett till tre. Marginaljusterad eller centrerad text är det absolut vanligaste i menyerna och en stor majoritet av alla menyer har en ljus bakgrund med en mörk text, där få färger och dova färger är vanligast. Att använda ikoner som fotografier eller andra symboler förekommer även om det sker sparsamt.

MSc (Zoology) / Department of Zoology / The concept of taxonomic diversity has been widely used to investigate diversity patterns and the mechanism underlying community assembly. However, functional and trait diversity can further explain the factors driving community assembly because they capture different aspects of species ecological roles such as habitat requirements and resource use. To investigate the factors shaping community assembly along the elevational Soutpansberg transect, ants were used as a model study organism because they are widely distributed geographically, ubiquitous and play several important roles in ecosystems. Functional and taxonomic diversity patterns along the elevation, their drivers (seasonality, soil properties, temperature and habitat structure) were examined using a long-term dataset (8 years) collected seasonally. Morphological and physiological traits at a community level are quantified and their relationship to temperature, soil properties and habitat structure modelled. Traits were used to test the size-grain hypothesis, Janzen’s rule and Brett’s rule. Functional and taxonomic diversity had a humped-shaped pattern on the northern and a decreasing pattern on the southern aspect. However, taxonomic diversity did not decrease monotonically on the southern aspect. Functional diversity was mainly related to habitat structure and temperature while taxonomic diversity was explained by seasonality, soil properties and temperature. Functional and taxonomic diversity were positively related at a larger scale but habitat specific at a smaller scale. Taxonomic diversity explained more variation in functional diversity than habitat structure and their interactions. The results supported the size-grain hypothesis and Janzen’s rule but not the Brett’s rule. Patterns in taxonomic and functional diversity mirrored each other but were the result of different mechanisms. Temperature was however important for both measures. Incorporating functional diversity analysis into taxonomic diversity contributed significantly in understanding the different mechanisms underlying community assembly along the Soutpansberg transect. This together with trait responses to environmental variables such as a decrease in size with increased temperature could be used to model the responses of ant communities to global change drivers such as climate and land use change / NRF

Le langage est dans son ensemble bien préservé pendant le vieillissement (Meyer & Federmeier, 2010) tandis que la mémoire sémantique peut même s'améliorer (Kavé, Samuel-Enoch, & Adiv, 2009; Prinz, Bucher, & Marder, 2004; Salthouse, 2009; Verhaegen & Poncelet, 2013 ; Wingfield & Grossman, 2006), malgré de nombreux changements neurophysiologiques se produisant dans le cerveau (Grady, Springer, Hongwanishkul, McIntosh, & Winocur, 2006 ; Kemper & Anagnopoulos, 1989 ; Wingfield & Grossman, 2006). Cette thèse se concentre sur la préservation de la mémoire sémantique dans le vieillissement, « l'acte cognitif d'accéder aux connaissances stockées sur le monde » (Binder, Desai, Graves et Conant, 2009) à travers une tâche de jugement sémantique manipulant le contrôle sémantique avec deux niveaux de demande (faible et élevé) et deux types de relations sémantiques (taxonomique et thématique). Nous avons développé une nouvelle tâche variant les niveaux de demande (faible et élevé) chez 39 adultes jeunes et 39 adultes âgés. Plus précisément, les objectifs de notre étude étaient 1) d'identifier si le vieillissement affecte l'activité cérébrale liée à la mémoire sémantique conformément aux prédictions du modèle CRUNCH, à travers une tâche de jugement sémantique à deux niveaux d'exigences. 2) de combler le vide de la littérature sur l'existence et l'évolution des hubs sémantiques dans le vieillissement, à la lumière des théories single hub et dual-hub, en évaluant l'effet du vieillissement sur le rôle des lobes temporaux antérieurs (ATL) et du jonction temporo-pariétale (TPJ) en tant que représentations neuronales des centres sémantiques responsables respectivement du traitement taxonomique et thématique. Une soumission par rapport pré-enregistré (registered report) a été utilisée pour ce projet de recherche. Nos participants, adultes plus jeunes et plus âgés, étaient globalement appariés en termes de réserve cognitive, plus précisément en ce qui concerne le niveau d'éducation et comme le montrent les questionnaires évaluant l'engagement dans des activités cognitivement stimulantes, les tests MoCA et WAIS-III. Les résultats comportementaux ont confirmé que la tâche varie correctement la difficulté de la tâche puisque les taux d'erreur et les temps de réponse (RT) augmentent de manière linéaire avec l'augmentation des exigences de la tâche, à savoir dans la condition de forte demande. Nous avons constaté que la participation à des activités stimulantes sur le plan cognitif avait un impact positif à la fois sur les RT de référence et sur la précision. Nous n’avons pas observé de différence statistiquement significative dans la précision entre les participants jeunes et plus âgés, quelle que soit la condition. Nous avons constaté que des scores plus élevés aux tests WAIS-III et PPTT étaient positivement corrélés avec la précision chez les personnes âgées. En termes de RT, nous avons observé une différence statistiquement significative entre les participants jeunes et plus âgés pour la tâche et les conditions de référence, les adultes plus âgés étant plus lents à répondre en général. Les RT augmentent linéairement avec l'âge du participant. En tant que telle, la tâche de mémoire sémantique a réussi à a) manipuler la difficulté de la tâche sur deux niveaux d'exigences et b) démontrer une performance comportementale invariante selon l'âge pour le groupe plus âgé, comme l'exige le test du modèle CRUNCH (Fabiani, 2012 ; Schneider-Garces et al., 2010). Pour l'objectif n°1, les tests cruciaux du modèle CRUNCH, l'interaction IRMf groupe par difficulté, n'étaient pas cohérents avec les prédictions du modèle. Malgré nos résultats comportementaux, lorsque nous avons comparé directement la condition de faible demande avec la condition de forte demande, il n'y avait pas de différence statistiquement significative dans l'activation entre les conditions de faible et de forte demande. Nous n'avons pas non plus obtenu d'interaction entre tranche d'âge et difficulté. Nous avons obtenu des interactions significatives en comparant les conditions de demande faible et élevée avec la ligne de référence. Au niveau neuronal, indépendamment de l'âge, la tâche de jugement de similarité sémantique a activé un large réseau bilatéral fronto-temporo-pariétal. Pour l'objectif n°2 concernant l'effet de relation sémantique, le contraste de la condition taxonomique avec la condition thématique directement n'a pas trouvé d'activation robuste à un seuil corrigé. La condition taxonomique a donné des résultats intéressants par rapport à la condition de base. Sept groupes distincts dans le cortex fronto-temporo-pariétal ont été activés dans les deux hémisphères, y compris les lobes temporaux antérieurs (ATL) et la jonction temporo-pariétale gauche (TPJ). De plus, l'activation était significative dans le gyrus supérieur frontal gauche, le gyrus angulaire gauche (AG) et le gyrus frontal inférieur (partie orbitale) sur l'hémisphère droit. Cette découverte pourrait être en partie conforme à la théorie du double-hub, qui propose que les ATL bilatéralement et le TPJ agissent comme des hubs sémantiques. Bien que nous n'ayons pas trouvé d'activation significative dans les ATL pendant la condition taxonomique et dans le TPJ pendant la condition thématique, nous avons cependant constaté que dans la condition taxonomique parmi les sept clusters significativement activés, l'activation dans le gyrus frontal supérieur gauche était significativement corrélée avec la performance dans la condition taxonomique pour les deux groupes d'âge. L'activation dans le gyrus temporal moyen droit était également corrélée à l'amélioration des performances, mais cela n'était pas significatif dans le groupe plus âgé. En ce qui concerne la condition thématique, par contraste avec condition de référence, dix groupes distincts ont été activés, y compris la jonction temporo-pariétale (TPJ), alors que les ATL n'ont pas été activés de manière robuste pendant la condition thématique. Plus précisément, les régions activées comprenaient bilatéralement le gyrus angulaire, le gyrus temporal moyen, le gyrus frontal inférieur (partie triangulaire) et le gyrus frontal moyen. Nous visons à poursuivre des analyses supplémentaires pour explorer la relation entre les exigences de la tâche, le type de relation sémantique et la réorganisation neurofonctionnelle liée à l'âge. Cependant, ces résultats relatifs à la préservation avec l'âge des capacités à traiter les différentes relations sémantiques de mots sont associés à un certain nombre de réorganisations neurofonctionnelles. Celles-ci peuvent être spécifiques au traitement de différentes relations sémantiques et de différentes demandes de tâches. Il reste à déterminer si cette réorganisation est induite par les changements structurels du cerveau avec l'âge, ou par l'utilisation accrue de telles relations sémantiques tout au long de la trajectoire de la vie. / Language overall is well preserved in aging (Meyer & Federmeier, 2010) whereas semantic memory may even improve (Kavé, Samuel-Enoch, & Adiv, 2009; Prinz, Bucher, & Marder, 2004; Salthouse, 2009; Verhaegen & Poncelet, 2013; Wingfield & Grossman, 2006), despite numerous neurophysiological changes taking place in the brain (Grady, Springer, Hongwanishkul, McIntosh, & Winocur, 2006; Kemper & Anagnopoulos, 1989; Wingfield & Grossman, 2006). The present study focuses on the preservation of semantic memory in aging, the ‘cognitive act of accessing stored knowledge about the world’ (Binder, Desai, Graves, & Conant, 2009) by means of a semantic judgment task manipulating semantic control with two demand levels (low and high) and two types of semantic relations (taxonomic-thematic). We used a novel task that varied task demands (low versus high) in 39 younger and 39 older adults. More specifically, the aims of this study was 1) to identify whether aging affects the brain activity subserving semantic memory in accordance with the CRUNCH predictions, through a semantic judgment task with two levels of demands (low and high). 2) To bridge the gap in the literature on the existence and evolution of semantic hubs in aging, in light of the dual and single-hub theories, by evaluating the effect of aging on the role of the Anterior Temporal Lobes (ATLs) and the Temporo-parietal junction (TPJ) as neural representations of the semantic hubs responsible for taxonomic and thematic processing, respectively. A submission by registered report was opted for this research project. Our participants, younger and older adults, were overall matched in regards to level of education and as shown in questionnaires assessing engagement in cognitively stimulating activities, MoCA and WAIS-III tests. The behavioral results confirmed that the task was successful in manipulating task difficulty, with error rates and RTs increasing with increasing task demands, namely in the high-demand condition. We found that engaging in cognitively stimulating activities impacted positively on both baseline RTs and accuracy and that higher scores on the WAIS-III and the PPTT tests were positively correlated with accuracy in older adults. There was no statistical difference in accuracy between younger and older participants regardless of the condition, so there was no age effect in accuracy. In terms of RTs, there was a statistically significant difference between younger and older participants for both the task and the baseline conditions, with older adults being slower to respond in general. RTs increased the more the participant’s age increased, which is in line with findings in the literature. As such, the semantic memory task was successful in a) manipulating task difficulty across two levels of demands and b) demonstrating age-invariant behavioural performance for the older group, as requires to test the CRUNCH model (Fabiani, 2012; Schneider-Garces et al., 2010). For objective no 1, the crucial test of CRUNCH model, the fMRI age group by task demand interaction was not found. We did not find statistically significant interaction neither between task demands and age group for RTs or accuracy, nor in regards to brain activation. At the neural level, independently of age, the semantic similarity judgment task activated a large network including bilateral inferior frontal, parietal, supplementary motor, temporal and occipital brain regions, which correspond overall with the semantic network, as suggested in the literature. Region of interest analyses demonstrated task demand effect in these regions, most notably in the left and right inferior frontal gyrus, the left posterior middle temporal gyrus, the posterior inferior temporal gyrus and the pre-frontal gyrus, regions which are typically associated with semantic control requirements. We did not find any significant interactions between task demands and activation in the regions of interest either. Several possible reasons may justify the lack of findings as predicted by the CRUNCH hypothesis. For objective no 2 in regards to the semantic relation effect, the contrast of the taxonomic with the thematic condition directly did not produce any robust activation at a corrected threshold. The taxonomic condition yielded interesting results when contrasted with the baseline one. Seven distinct clusters in the fronto-temporo-parietal cortex were activated across the two hemispheres, including the anterior temporal lobes (ATLs) and the left temporo-parietal junction (TPJ). Additionally, activation was significant in the left frontal syperior gyrus, the left angular gyrus (AG) and the inferior frontal gyrus (orbital part) on the right hemisphere. This finding could be partly in line with the dual-hub theory, that proposes that the ATLs bilaterally and the TPJ act as semantic hubs. Though we did not find the expected double dissociation e.g., significant activation in the ATLs during the taxonomic condition only and in the TPJ during the thematic condition only, we found however that in the taxonomic condition among the seven significantly activated clusters, activation in the left superior frontal gyrus was significantly correlated with performance in both age groups. Activation in the right middle temporal gyrus was also correlated with improved performance, but this was not significant in the older group. During the thematic condition, when contrasted with baseline, ten distinct clusters were activated, including the temporo-parietal junction (TPJ), whereas the ATLs were not robustly activated during the thematic condition. We aim to pursue additional analyses to explore the relation between task demands, type of semantic relation and age-related neurofunctional reorganization. However, these results in relation to the preservation with age of the abiliites to process the different semantic word relations is associated with a number of neurofunctional reorganizations. These can be specific to the processing of different semantic relations and different task demands. Whether this reorganization is induced by the structural changes in the brain with age, or by the enhanced use of such semantic relations along the trajectory of life is still under exploration.

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