Orientadores: Ricardo Jannini Sawaya, Denise de Cerqueira Rossa Feres / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T18:39:56Z (GMT). No. of bitstreams: 1 CorreaFilho_DecioTadeu_M.pdf: 2723996 bytes, checksum: 128827025a31fdb66d41e2abeb742135 (MD5) Previous issue date: 2013 / Resumo: Anfíbios anuros possuem ciclo de vida complexo e as fases larvais e adultas podem ocupar ambientes totalmente distintos. Isso faz com que cada uma das fases esteja sujeita a diferentes pressões ambientais. Desta forma, girinos e adultos podem seguir caminhos evolutivos diferentes, ainda que apresentem as mesmas relações filogenéticas. O objetivo deste estudo foi investigar os aspectos ecológicos e evolutivos que atuam na estruturação de uma metacomunidade de anuros nas fases adulta e larval. Realizamos o estudo em uma região de Cerrado no sudeste do Brasil. O trabalho está dividido em dois capítulos. No primeiro, testamos se as comunidades de adultos e girinos são concordantes, e analisamos a influência das variáveis ambientais e espaciais na abundância e composição de espécies em cada fase ontogenética. No segundo capítulo, verificamos como a diversidade fenotípica se distribui ao longo da filogenia e como os corpos d'água influenciam a diversidade fenotípica e filogenética das espécies. Além disso, verificamos a evidência de filtros ambientais na montagem das comunidades estudadas a partir da associação entre atributos fenotípicos, relações filogenéticas e variáveis ambientais. Nossos resultados do primeiro capítulo indicam que as comunidades de adultos e girinos são concordantes, ou seja, são distribuídas de maneira similar entre os habitats. As variáveis ambientais foram mais importantes do que as espaciais, sendo a área da superfície e o hidroperíodo dos corpos d'água as características que melhor explicaram a distribuição dos adultos e girinos entre os corpos d'água. A maioria das espécies esteve associada aos habitats temporários de média a longa duração. Locais temporários não apresentam predadores importantes como peixes e retém água por tempo suficiente para a metamorfose dos girinos. No segundo capítulo, verificamos que os atributos fenotípicos nos adultos são mais conservados do que nos girinos. A diversidade fenotípica dos adultos é concentrada em poucos nós da filogenia, enquanto que nos girinos é dispersa pela filogenia. A metacomunidade de adultos é estruturada por filtros ambientais relacionados principalmente aos microhabitats de vocalização. Espécies da família Hylidae que vocalizam empoleiradas, por exemplo, são associadas aos locais com maior diversidade de vegetação na margem dos corpos d'água. Para os girinos não foi observada evidência de filtro ambiental. Além disso, não houve relação clara entre os atributos fenotípicos dos girinos e características ambientais como observado para os adultos. Entretanto, a maioria dos girinos esteve associada a locais que podem oferecer maior disponibilidade de recursos alimentares e menor risco de predação, como corpos d'agua temporários, de dossel aberto e com muita vegetação em seu interior. Concluímos que os adultos determinam a distribuição dos girinos nas comunidades. Entretanto, a escolha do habitat de reprodução é baseada em parte pelos atributos dos adultos, mas também ponderada por locais de melhor desenvolvimento e sobrevivência de sua larva. Nossos resultados ressaltam a complexidade da organização das comunidades de anuros, principalmente no que diz respeito às relações entre as fases ontogenéticas, e contribuem de forma inédita para melhor compreensão da organização de comunidades de animais de ciclo de vida complexo como os anuros / Abstract: Anuran amphibians have complex life cycles, and the larval and adult stages can occupy completely different environments. Thus, each stage is subject to different environmental pressures. Tadpoles and adults can follow different evolutionary paths even though they show the same phylogenetic relationships. The aim of this study was to investigate the ecological and evolutionary aspects structuring an anuran metacommunity in both larval and adult stages. We conducted this study in a savanna region in southeastern Brazil. The study comprises two chapters. In the first, we tested if tadpole and adult communities show community concordance. Then we analyzed the influence of environmental and spatial variables on the abundance and composition of species in each ontogenetic stage. In the second chapter, we verified how the phenotypic diversity is distributed throughout the phylogeny, and how water bodies affect phenotypic and phylogenetic diversity of species. Additionally, we verified the evidence of environmental filters acting in the community assembly based on the association among phenotypic traits, phylogeny, and environmental variables. Our results in the first chapter indicated that communities of adults and tadpoles are concordant, because they have a similar distribution across the set of water bodies. Environmental variables were more important than space, because area and hydroperiod of the water bodies were the variables that best explained the distribution of species for both ontogenetic stages. Most species were associated with medium and long-term temporary habitats. Temporary habitats have no important predators like fish and could retain water long enough for tadpoles to achieve metamorphosis. In the second chapter, we find that adult traits are more conserved, which was not observed for tadpoles. The phenotypic diversity of adults is concentrated in a few nodes, while in tadpoles it is widespread throughout phylogeny. The adult metacommunity is regulated by environmental filters related to vocalization microhabitats. Hylidae species that vocalize perched on vegetation, for instance, are associated with greater vegetation diversity on the edge of the water body. Tadpoles were not affected by environmental filters. Furthermore, there was not clear relationship between tadpole traits and environmental characteristics as observed for adults. However, most of the tadpoles were associated with sites that may offer greater availability of food resources and low predation risk, such as open canopy and temporary water bodies with vegetation inside. We conclude that adults determine the distribution of tadpoles. However, even if environmental filters affect adults, the choice of the breeding habitat is based in part by adult traits and also weighted for habitats that promote better development and survival of their larvae. Our results underscore the complexity involved in frog community assembly, particularly regarding the relationship between ontogenetic stages, and thus, contribute to a better understanding of the assembly of complex life cycle communities / Mestrado / Ecologia / Mestre em Ecologia

Ecosystems in the modern world face a vast array of disturbances, from globally shifting abiotic conditions, to increasingly variable extreme natural events, to high intensity discrete human-caused disturbances. Well-developed, applicable theoretical frameworks on how ecosystems can respond to and withstand these disturbances are needed for adequate management of valued ecological systems. To date, the most promising theoretical development for understanding ecological response to complex sets of disturbances is resilience. Ecological resilience acknowledges non-linear ecosystem behavior, incorporates the role of slowly changing environmental parameters in ecological dynamics, and offers one of the few potential methods to predict, and avoid, impending ecological collapse. However, as ecological resilience has evolved conceptually to include social, political, and economic fields, it has become increasingly difficult to clearly define in, and apply to, managed ecosystems. This dissertation pairs ecological resilience with other, well-established attributes of ecological response to disturbance, namely resistance, persistence, and recovery. By doing so, we can clearly define and quantify each attribute in a range of ecosystem types and over a variety of ecological scales. In Chapter 1, we use microcosm communities to test the relationship between one potential mechanism, landscape connectivity, and multiple attributes of ecological response to disturbance including resistance, resilience, and recovery. We find that each attribute responds uniquely to connectivity, and that generalizing the role of connectivity over all three may give an inaccurate prediction of how ecosystems may respond to individual disturbances. In Chapter 2, we experimentally investigate the presence of early warning indicators of approaching critical thresholds. Using water table drawdown treatments in bog, we test for critical slowing and increased autocorrelation as the bog approaches a transition to forest. We find that critical slowing is clear in composition and moss cover, but that autocorrelation is not apparent. The decoupling of critical slowing and increased autocorrelation could be due to a number of complex ecosystem dynamics, all of which are common in ecosystem management globally. Thus, early warning indicators likely need further development if they are to become applicable. In Chapter 3, we observationally study how conservation management actions may increase or decrease ecological resilience. In particular, we explore how invasive species management intensity correlates with changes in functional redundancy, response diversity, and spatial occurrence of regime shifts in Garry oak meadows. We find that more intense management correlates with less area lost to woody encroachment and increases in functional redundancy through time. However, the relationship was strongly mediated by individual landscape settings. Finally, in Chapter 4, we scale up to a provincial study, investigating persistence of ecosystems and large mammal species in the face of the continuous pressures of land use change. In the results from all four chapters, it is clear that individual attributes of ecological response to disturbance, i.e. resistance, persistence, resilience, or recovery, all play unique roles in ecosystem dynamics. Additionally, the metric chosen to quantify each attribute can play a pivotal role in how we interpret observed dynamics. The work in this dissertation highlights that we cannot understand or predict ecological response to disturbance without clear, measurable concepts. Around a single state of interest, resilience is only one among a suite of attributes that are important to understand. Its additional strength, of potentially predicting the occurrence of ecological thresholds, is still being developed as we explore methods of quantification and application in individual ecosystems. / Graduate

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Studies of biodiversity surveys and habitat requirements are essential in landscapes threatened by anthropogenic conversion, such as those that make up the Pampa biome. In the present study we determined the spatial distribution of richness of anurans at the Área de Proteção Ambiental (APA) do Ibirapuitã, the largest protected federal area within the Pampa biome in Brazil. Thus we: (1) describe the composition of anuran community regarding species richness, abundance, constancy of occurrence and reproductive modes; (2) compare the frogs composition with other localities of grassland southernmost of South America; (3) tested whether local variables of waterbodies, space and landscape are determinants of species richness, and (4) tested whether environmental heterogeneity influences the structure of anuran community. Sampling was carried from October to November 2012 and at November 2013, the searching at breeding sites method, tadpole collecting and examination of specimens housed in herpetological collections. A total of 64 waterbodies (40 ponds and 24 streams) were sampled for the anuran amphibians, as well as were recorded environmental descriptors in three scales: local, space, and landscape. We recorded the occurrence of 33 anuran species at the APA Ibirapuitã. The registered anurans are typical of open areas, and at least 10% of them are restricted of the grassland areas to the subtropical region of South America, including two endangered species at the global and state levels. Pseudopaludicola falcipes was the most abundant species and Hypsiboas pulchellus was the species most frequently recorded. Five reproductive modes were recorded, and the deposition and the development of exotrophic tadpoles in lentic waterbodies was the most common mode (57.5%). Cluster analysis revealed five groups with more than 50% similarity, whose structure was influenced by geographic distance, but can be partially interpreted by regional peculiarities. We used generalized regression models considering the set of descriptors as predictors of anuran species richness. Subsequently, we use a partition of variance to evaluate the independent and shared explicability between different sets of predictors. Finally, we use a Canonical Redundancy Analysis to explore the role of environmental descriptors on the species abundance of frogs in ponds and streams. The richness in ponds was influenced by the local variable representing the area of waterbodies. Already the abundance was correlated with the percentage of vegetation on the shores and the water temperature. In streams, the species richness of anurans was correlated with a local variable (number of strata of emergent vegetation) and a landscape variable (distance in relation to human residences). Species abundance was affected by higher vegetation strata (> 200 cm) on the shores and by water electrical conductivity. The combined contribution of local and landscape variables have important implications for understanding how amphibians are distributed in the grassland environment. Our work shows the importance of conserving grassland biomes which are increasingly threatened by human activities. / Studies of biodiversity surveys and habitat requirements are essential in landscapes threatened by anthropogenic conversion, such as those that make up the Pampa biome. In the present study we determined the spatial distribution of richness of anurans at the Área de Proteção Ambiental (APA) do Ibirapuitã, the largest protected federal area within the Pampa biome in Brazil. Thus we: (1) describe the composition of anuran community regarding species richness, abundance, constancy of occurrence and reproductive modes; (2) compare the frogs composition with other localities of grassland southernmost of South America; (3) tested whether local variables of waterbodies, space and landscape are determinants of species richness, and (4) tested whether environmental heterogeneity influences the structure of anuran community. Sampling was carried from October to November 2012 and at November 2013, the searching at breeding sites method, tadpole collecting and examination of specimens housed in herpetological collections. A total of 64 waterbodies (40 ponds and 24 streams) were sampled for the anuran amphibians, as well as were recorded environmental descriptors in three scales: local, space, and landscape. We recorded the occurrence of 33 anuran species at the APA Ibirapuitã. The registered anurans are typical of open areas, and at least 10% of them are restricted of the grassland areas to the subtropical region of South America, including two endangered species at the global and state levels. Pseudopaludicola falcipes was the most abundant species and Hypsiboas pulchellus was the species most frequently recorded. Five reproductive modes were recorded, and the deposition and the development of exotrophic tadpoles in lentic waterbodies was the most common mode (57.5%). Cluster analysis revealed five groups with more than 50% similarity, whose structure was influenced by geographic distance, but can be partially interpreted by regional peculiarities. We used generalized regression models considering the set of descriptors as predictors of anuran species richness. Subsequently, we use a partition of variance to evaluate the independent and shared explicability between different sets of predictors. Finally, we use a Canonical Redundancy Analysis to explore the role of environmental descriptors on the species abundance of frogs in ponds and streams. The richness in ponds was influenced by the local variable representing the area of waterbodies. Already the abundance was correlated with the percentage of vegetation on the shores and the water temperature. In streams, the species richness of anurans was correlated with a local variable (number of strata of emergent vegetation) and a landscape variable (distance in relation to human residences). Species abundance was affected by higher vegetation strata (> 200 cm) on the shores and by water electrical conductivity. The combined contribution of local and landscape variables have important implications for understanding how amphibians are distributed in the grassland environment. Our work shows the importance of conserving grassland biomes which are increasingly threatened by human activities.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The present study aimed to analyze the tree compartment of the riverside forest in Vacacaí river and investigate the relationship between the species and the characteristics of soil and topographic variables in an environmental gradient. The regeneration, stratification and dispersion guilds for two sectors of the tree community were also analyzed.A plot of 100 x 100 m was installed in the fragment, subdivided into 100 sampling units (SU) of 10 x 10 m. Each SU has been ranked sector Upper Sites (US) or Low Sites (LS). The SUs that had good drainage were considered in US, totaling 72 SUs, and where there was evidence of possible environmental disturbances such as periodic flooding and elevation of groundwater, were classified as LS, totaling 28 SUs. All individuals with diameter at breast height ≥ 5 cm were inventoried. In each SU were collected samples of soil and topographic variables, such as elevation range and average elevation. To verify the relationships between environmental variables and the distribution of individual trees, we used the canonical correspondence analysis (CCA) was used. The survey recorded 1729 individual trees belonging to 41 species from 34 genera and 20 botany families. The species highlighted in Importance Value for the survey were Actinostemon concolor (Spreng.) Müll. Arg. (51%), Sebastiania commersoniana (Baill.) LB Sm. & Downs (46,7%), Inga vera Willd. (31%), Pouteria gardneriana (A. DC.) Radlk. (29,7%) and Casearia sylvestris Sw. (21,3%), accounting for 59,9% of this index. A canonical correspondence analysis (CCA) indicated that there is a correlation between soil and topographic variables with woody vegetation. Only four variables: the CCA were significant, average elevation, elevation range, pH and CEC. Thus, these variables stood out as good indicators of floristic and structural variations, being responsible, in part, the explanation of the formation of the two sectors. These were differences in wealth, in the structure and composition of guilds and this may be due to a different historical process of environmental change in each sector. / O presente estudo objetivou analisar o compartimento arbóreo da mata ribeirinha no rio Vacacaí e investigar a relação das espécies com as características de solo e variáveis topográficas num gradiente ambiental. Também foram analisadas as guildas de regeneração, estratificação e dispersão para dois setores da comunidade arbórea. Para o levantamento da vegetação foi instalada uma parcela de um hectare, subdividida em 100 unidades amostrais (UA) de 10 x 10 m. Cada UA foi classificada em setor Terreno Alto (TA) ou Terreno Baixo (TB). As UAs que tinham boa drenagem foram consideradas em TA, totalizando 72 UAs, e onde havia possíveis evidências de perturbações ambientais, como inundações periódicas e elevação do lençol freático, foram classificadas em TB, perfazendo 28 UAs. Todos os indivíduos com diâmetro à altura do peito ≥ 5 cm foram inventariados. Em cada UA coletou-se amostras de solo e variáveis topográficas, como cota média e desnível. Para verificar as relações entre as variáveis ambientais e a distribuição de indivíduos arbóreos, empregou-se a análise de correspondência canônica (CCA). O levantamento registrou 1729 indivíduos arbóreos, pertencentes a 41 espécies, de 34 gêneros e 20 famílias. As espécies com destaque no Valor de Importância para o levantamento foram Actinostemon concolor (Spreng.) Müll. Arg. (51%), Sebastiania commersoniana (Baill.) L. B. Sm. & Downs (46,7%), Inga vera Willd. (31%), Pouteria gardneriana (A. DC.) Radlk. (29,7%) e Casearia sylvestris Sw. (21,3%), perfazendo 59,9% do total deste índice. A ordenação das UAs nos eixos da CCA indica a existência de um gradiente ambiental no qual existe uma mudança composição de espécies e na estrutura da vegetação. Apenas quatro variáveis foram significativas na CCA, cota média, desnível, pH e CTC. Deste modo, estas variáveis se destacaram como bons indicadores das variações florísticas e estruturais, sendo responsáveis, em parte, pela explicação da formação dos dois setores. Estes setores. Estes tiveram diferenças na riqueza, na estrutura e na composição das guildas e isto pode ser consequência de um processo histórico diferenciado de alterações ambientais em cada setor

How do newly established species interact with existing assemblage members to alter local biodiversity? This question is especially topical given growing concerns about increased temporal turnover levels relative to background rates. My PhD thesis concerns young, isolated pines Pinus elliottii invading the Cerrado (Brazilian savanna) as a study system to test the hypothesis that the impact of newly established individuals varies across habitat layers. I sampled both vegetation layers (shrub and grass) of two distinct habitats, the shrub-dominated campo sujo and the grass-dominated campo úmido. My results show that the pine is changing α diversity in the dominant vegetation layer of each habitat: the shrub layer of campo sujo and the grass layer of campo úmido. The shape of the diversity v. establishment time relationship is habitat dependent; there is a hump shaped relationship between diversity and pine size in the grass layer but a linear one in the shrub layer. β diversity metrics – which take species composition into account - reveal marked differences in species composition between the habitats in the shrub layer, whereas the corresponding pair of invaded and control sites of the same habitat and layer is more similar than expected (in both vegetation layers). The degree of similarity between sites also changes as the invasion proceeds. In the campo sujo habitat, sites become more compositionally distinct, whereas in the grass layer of campo úmido sites get more similar. This suggests that the timing of changes in species composition is habitat-dependent and reinforces the need to remove the invader individuals from the area. My results show that, though complex, the consequences for local biodiversity of non-native species establishment are not haphazard. As such they contribute to the understanding of species coexistence and help explain why species invasion can lead to very different biodiversity outcomes.

Relatively little is known about either the biological (i.e., predation) or physical (i.e., current, sedimentation) effects that artificial reefs may have on surrounding benthic infaunal communities. Following deployment of artificial reefs (concrete boulders) between the first and second reefs off Fort Lauderdale, Florida, on 30 October 2009, sediment cores were taken at 4 distances along three replicate 10-m transects on 13 and 26 September 2013, and 24 and 25 May 2014 at each of four artificial reef sites and four of their adjacent natural reef sites using SCUBA. Infauna (>0.5mm) were extracted from the sediment and identified to the lowest possible taxonomic level. Statistical analysis (PRIMER, PERMANOVA, SIMPER) focused on four main variables: type of reef, year, site, and distance. Type of reef, year, and site was significantly different between samples, while distance did not affect density. There is a clear separation of communities between the artificial and natural reefs. From 2013 to 2014, a slight shift occurred between communities suggesting the artificial reef community composition became slightly more similar to the natural reef. All four artifical reef sites were more taxonomically distinct at the phylum and class level then the natural reef, which had higher diversity, higher species richness and more low-density taxa. This two year study provides insight on infauna communities four and five years out from deployment, but follow up monitoring in 3-5 years could shed light on whether these patterns of shift to more similar assemblages between reefs will continue as the artificial reef matures. Environmental data collection including longer time-series datasets, longer transects, and physical and geological data could provide more knowledge of how the artificial reef infaunal communities are changing over time.

La destruction de l'habitat, les invasions biologiques et leur interaction sont des menaces majeures pour la biodiversité. La Nouvelle-Calédonie est menacée à la fois par des feux d'origine humaine, et par des fourmis invasives : il est important de comprendre leur impact sur ce biotope unique. Pour ce faire, une approche hiérarchique intégrant différents aspects de la biodiversité (composition, structure et fonction) a été adoptée. Les fourmis ont une grande importance écologique, en particulier en milieu tropical, et leur classification en groupes fonctionnels facilite l'interprétation de leur réponse aux perturbations environnementales. Les objectifs de cette étude étaient donc d'évaluer les impacts des feux, des fourmis invasives, et de leur interaction, sur les fourmis natives de Nouvelle-Calédonie, et ce à différentes échelles spatiales (globale, régionale, locale) et temporelles (court et long terme), ainsi qu'à divers niveaux d'organisation biologique (communautés, espèces, gènes). L'étude contribue à une meilleure connaissance de la myrmécofaune calédonienne, en révélant l'absence de fourmis souterraines spécialisées, et en documentant la distribution et composition des communautés de fourmis à l'échelle de l'île, en lien avec l'habitat et les fourmis exotiques. Les mécanismes par lesquels les feux impactent les fourmis natives, y compris en association avec les fourmis invasives, sont révélés. Le feu, en créant les conditions de micro- et macrohabitat favorisées par les fourmis invasives, facilite l'invasion, qui cause ensuite d'avantage de perte de diversité, soit quelques années après un incendie ou dans le contexte de la fragmentation à long terme. L'approche hiérarchique a permis de détecter des réponses contrastées au niveau des espèces et de la génétique, liées à différents traits d'histoire de vie, en plus des réponses mesurées au niveau des communautés. Cette étude souligne l'avantage d'une approche holistique pour adresser des problèmes liés à la biodiversité. / Habitat destruction, biological invasions and their interaction are global drivers of biodiversity loss. The New Caledonian hotspot of biodiversity is threatened by both anthropogenic fires and invasive ants: it is important to understand their impacts on its biota. Because biodiversity spans several levels of organisation (from genes to communities) and relates to different attributes (compositional, structural and functional), this thesis takes a hierarchical approach to address this issue. Ants are of great ecological importance, especially in tropical biomes, and their classification into functional groups provides a global framework for analysing their response to disturbance. My aims were therefore to investigate the impacts of anthropogenic fires and invasive ants, and their interaction, on the native New Caledonian ant fauna at different spatial (global, regional, local) and temporal (short and long term) scales, and at different levels of biological organisation (community, species, genes). The study contributes to an improved knowledge of the New Caledonian ants, by revealing the lack of specialised subterranean species, and by investigating island-scale patterns of ant communities, in relation to habitat and invasion. The mechanisms by which fire impacts native ants, either as a standalone process or in association with invasion could be identified. In particular, I show that fire, by creating macro- and microhabitats favoured by invasive ants, facilitates invasion, which then causes further diversity declines, either in the short- (post-burning) or long-term (forest fragmentation). The hierarchical approach used enabled the detection of contrasting trait-derived responses at the species and genetic level, in addition to responses measured at the community level. This study highlights the advantage of a holistic approach to investigating biodiversity-related issues.

Dérivants ou submergés, les débris grossiers dérivés de plantes terrestres fournissent de l'énergie et des nutriments pour les écosystèmes marins. En considérant cette matière organique allochtone, l'objectif de ma thèse est de décrire le processus d'assemblage d'une communauté autour d'une ressource trophique et de considérer en retour l'effet de la diversité et de la composition observée au sein de cette communauté sur la dynamique d'exploitation de la ressource. Pour ce faire, j'ai combiné des expériences in situ et la modélisation avec l'intention de parvenir à une description cohérente et quantitative du lien écogéochimique entre la biodiversité et le fonctionnement des écosystèmes. En utilisant de la litière de feuilles et du bois mort, cette approche a permis: (i) de montrer l'importance des interactions biotiques dès le début du processus d'assemblage de la communauté, (ii) de faire le lien explicite entre la consommation des ressources et la dynamique de populations des consommateurs, et (iii) de tester comment la transformation des ressources est affectée par la diversité observée au sein des communautés. / Either adrift or submerged, coarse debris derived from terrestrial plants provide energy and nutrients for marine ecosystems. By considering this allochtonous organic material, the goals of my PhD were to describe the assembly process of macrobenthic communities around food sources and to consider the feedback effect of the observed communities on the geochemical fate of the resource. To do so, I combined in situ experiments and modelling with the intention to build a consistent, quantitative description of the ecogeochemical link between biodiversity and ecosystem functioning. Using leaf litter and dead wood, this approach allowed: (i) to show the importance of biotic interactions from the beginning of the community assembly process, (ii) to make the explicit connection between the resource consumption and the population dynamics of the consumers, and (iii) and to test how resource processing is affected by the specific diversity of the communities.

Les milieux agricoles constituent des habitats essentiels pour de nombreuses espèces mais l’intensification agricole des dernières décennies a provoqué un fort déclin de la biodiversité. Cette intensification a des conséquences tant à l’échelle locale de la parcelle (engrais, pesticides, labour, perte de diversité des espèces cultivées) qu’à l’échelle du paysage (homogénéisation, perte des éléments semi-naturels) et a des dimensions tant spatiales que temporelles (simplification des rotations culturales). L’objectif général de cette thèse est donc (i) d’identifier les processus structurant les communautés dans le temps et l’espace en milieu changeant et hétérogène ; (ii) de tester l’influence de l’hétérogénéité des cultures en terme de composition et de configuration, (iii) ainsi que l’influence des pratiques agricoles plus extensives (agriculture biologique) sur la diversité et la stabilité des communautés. Nous avons premièrement évalué la part relative de l’environnement vs de la dispersion dans les processus d’assemblage des communautés d’oiseaux. Nos résultats mettent en avant un fort effet de la dispersion dans les milieux agricoles ouverts, par opposition à un effet dominant de l’environnement dans les milieux plus bocagers. Nous concluons que les communautés seraient plus structurées par des processus de type « mass effect » en milieu changeant et par des processus de type « species sorting » en milieux stables. Dans un deuxième temps, nous avons étudié l’effet de la composition et de la configuration des cultures à travers une analyse inter-sites (comparaison entre 8 sites d’étude en Europe et Canada) nous permettant de vérifier la généralité des effets observés. Nous avons testé si l’effet de l’hétérogénéité était dépendant du niveau d’intensification global de la région ou de sa composition en éléments semi-naturels. Nos résultats montrent globalement un effet positif de la composition en culture agissant en interaction avec les éléments boisés du paysage et dépendant du niveau d’intensification (plus de diversité dans les paysages complexes, boisés et de faible niveau d’intensification).Troisièmement, nous avons cherché à évaluer l’importance relative des composantes spatiales et temporelles et à mettre en évidence d’éventuels facteurs stabilisant les communautés d’oiseaux face à l’instabilité et l’imprédictibilité des milieux agricoles. Notre hypothèse était que l’hétérogénéité des milieux agricoles pourrait jouer un rôle d’assurance en stabilisant les communautés localement. Nos résultats montrent un turnover important des espèces dans le temps et l’espace et mettent en évidence que les éléments pérennes du paysage (haies) ainsi qu’une configuration complexe contribuent à stabiliser les communautés locales dans le temps. Enfin nous avons testé l’effet de pratiques agricoles moins intensives (agriculture biologique) à l’échelle du paysage sur la diversité des communautés d’adventices. Nous avons cherché à vérifier l’hypothèse que les parcelles gérées en agriculture biologiques pouvaient constituer des zones refuges et maintenir la diversité des adventices au sein des paysages agricoles via des phénomènes de dispersion à l’échelle de la méta-communauté. Nos résultats montrent un effet positif de l’agriculture biologique à l’échelle du paysage sur la richesse spécifique des champs conventionnels et biologiques, et principalement prononcé en bordure de champs et sur les espèces rares. En conclusion nous montrons que des solutions existent pour concilier production et biodiversité dans les agro-ecosystèmes (selon l’hypothèse de « land sharing ») via un maintien ou un rétablissement de la diversité des cultures associé à la préservation de zones semi-naturelles, ainsi que par le maintien dans les paysages d’exploitations gérées de manière moins intensives pouvant constituer des zones source de biodiversité. / Agricultural areas represent essential habitats for many species, but the agricultural intensification of the last decades has caused a significant decline in biodiversity. This intensification has consequences both at the local level in fields (fertilizer, pesticides, ploughing, decrease in cultivated crop diversity) and at the landscape level (homogenization, decrease in semi-natural habitats) and impacts both the spatial and temporal levels (decrease in crop rotation complexity). The main objective of this PhD was (i) to identify the structuring processes of bird and weed communities in space and time in changing and heterogeneous landscapes; (ii) to assess crop heterogeneity effects (composition and configuration), (iii) and the impact of more extensive agricultural practices (organic farming) on the stability and diversity of bird communities. We first assessed the role of environment as it related to dispersal and structuring of bird communities. Our results show a strong dispersal effect in open agricultural landscapes, as opposed to a dominant structuring effect of environment in more wooded agricultural landscapes. We conclude that bird communities could be more structured by a « mass effect » process in changing landscapes and by a « species sorting » process in stable landscapes.Secondly, we analyzed crop composition and configuration effects in an inter-site study (comparison between eight study sites in Europe and Canada), enabling us to check the generality of the effects we observed. We studied whether or not landscape heterogeneity was dependent on the overall intensification level or on the proportion of semi-natural habitats of the region. Our results show a positive effect of crop composition complexity, interacting with the semi-natural habitats and intensification levels (more diversity in complex landscapes with wooded areas and low intensification levels).Thirdly, we compared the relative importance of spatial and temporal components, and we tried to identify potential stabilizing factors for bird communities in response to the instability and unpredictability of agricultural landscapes. Our hypothesis is that agricultural landscape heterogeneity can act to ensure the stabilization of the local communities. Our results show a significant species turnover in space and time, and highlight the fact that perennial landscape habitats (hedgerows) as well as complex landscape configurations contribute to the stabilization of local communities over time. Finally, we assessed the effects of less intensive agricultural practices (organic farming) on weed community diversity at the landscape level. We tested the hypothesis that organic fields can constitute refuge areas and maintain weed diversity in agricultural landscapes via the dispersal processes at the meta-community level. Our results show the positive effects of organic farming on the richness of weed species for both conventional and organic fields, but positive effects were more pronounced in field boundaries and for rare species.In conclusion, this thesis shows that potential solutions exist to conciliate production and biodiversity in agro-ecosystems (according to the « land sharing » hypothesis) by the preservation or the restoration of crop diversity associated with the conservation of semi-natural habitats, and by supporting less intensive farms which can constitute source areas of biodiversity.

Les mesures de végétalisation ou de restauration écologique nécessitent de comprendre les mécanismes qui sous-tendent les changements de composition et de structure de la végétation au cours de la succession écologique. Des perturbations, d’intensité et fréquence variables, naturelles ou causées par l’Homme, agissent souvent en interaction sur la dynamique temporelle de la végétation. Cependant, l’influence d’une perturbation récurrente combinée aux changements écologiques au cours de la succession est restée peu étudiée jusqu’à présent.Les communautés végétales de talus routiers représentent un modèle pertinent pour étudier cette problématique. L’historique d’aménagement et de gestion des talus est particulièrement bien renseigné ; on a donc une connaissance précise de l’âge des communautés et de leur régime de perturbation par la fauche. Les talus routiers fournissent ainsi un plan quasi-expérimental in situ permettant l’étude des processus qui affectent l’assemblage des communautés au cours de la succession sous l’influence d’une perturbation récurrente.L’objectif principal de cette étude est de caractériser la dynamique successionnelle initiée par la mise en place d’un talus routier en région méditerranéenne et de déterminer les processus écologiques et les facteurs environnementaux influençant cette dynamique. On s’intéresse en particulier à l’influence de la fauche récurrente sur cette dynamique.Pour cela, nous avons étudié la composition floristique et la diversité des traits fonctionnels (traits foliaires et de phénologie de floraison principalement) de la végétation de talus routiers de l’Hérault (France). Chaque talus inclut une partie fauchée et une partie non fauchée, l’ensemble formant une chronoséquence sur près de 70 ans.L’analyse des variations taxonomiques entre les communautés végétales de talus routiers montre un large remplacement des espèces au cours de la succession. Ce turnover floristique est associé à des changements fonctionnels au sein des communautés. Ces derniers sont structurés par des filtres environnementaux qui influent (1) sur la synchronie de floraison entre espèces au sein des communautés au cours du temps et (2) sur la diversité de combinaisons de traits fonctionnels entre communautés d’âge similaire. Ces changements de filtres environnementaux au cours du temps semblent liés à des changements pédologiques et à l’augmentation de l’hétérogénéité spatiale des conditions de lumière et de température (avec la fermeture progressive de canopée). La fauche altère les trajectoires floristiques et fonctionnelles, notamment en provoquant un ralentissement du changement de stratégie d’utilisation des ressources au cours de la succession par rapport à la trajectoire naturelle, sans fauche. De plus, cette perturbation récurrente induit une augmentation de la diversité taxonomique et fonctionnelle au sein des communautés alors qu’elle la réduit entre communautés d’âge similaire. Finalement, la fauche agit comme un filtre environnemental supplémentaire sur l’assemblage des communautés au cours de la succession et induit une homogénéisation de la végétation entre communautés d’âge similaire.Les conclusions de cette étude contribuent à la connaissance écologique fondamentale. En termes d’implications pour la gestion des communautés végétales de talus routiers, nos conclusions suggèrent, entre autres, que l’association de végétation fauchée et non fauchée au sein des mêmes sites pourrait servir d’habitat pour une plus grande diversité de faune associée. Cette association permettrait de plus d’avoir un rendu paysager agréable aux usagers de la route, tout en garantissant une bonne visibilité pour la sécurité routière. / The success of revegetation or ecological restauration highly depends on our knowledge of mechanisms underlying changes in composition and structure of the vegetation along the ecological succession. Natural or human-induced disturbances of varying intensity and frequency often occur simultaneously to influence vegetation temporal dynamics. However, the influence of a recurrent disturbance combined with ecological changes along plant succession remains poorly documented.Plant communities growing on road slopes are particularly appropriate to study this issue. Construction work and management history are well documented, so that the age of the vegetation and its disturbance regime by mowing can be precisely informed. Thus, road slopes plant communities represent an in situ quasi-experimental framework particularly adapted to study processes affecting community assembly along the ecological succession under the influence of a recurrent disturbance.The principal objective of this study is to characterise the successional dynamic initiated after road slope construction in the Mediterranean area, and to identify the ecological processes and environmental factors influencing this dynamic. We particularly focused on the influence of recurrent mowing on this dynamic.We studied the floristic composition and the diversity of functional traits (mainly leaf traits and flowering phenology traits) in a 70-year long chronosequence of French Mediterranean (Hérault, France) road slopes, each including both mown and unmown vegetation.The analysis of taxonomical variations between road slopes plant communities reveals a large species turnover along the ecological succession. This floristic turnover relates with functional changes within communities. These functional changes are structured by environmental filters influencing flowering synchrony within communities on one hand, and the diversity of a combination of functional traits between communities of similar age on the other hand. These environmental filters changing along the succession relate with changing soil parameters and increasing spatial heterogeneity of light and temperature conditions with canopy closure.Mowing alters floristic and functional trajectories along the succession, notably through the decrease of speed in resource-use strategy changes along the succession in mown communities compared to unmown communities. In addition, this recurrent disturbance increases taxonomic and functional diversity within communities, while it decreases taxonomic and functional turnover between communities of the same age. Finally, mowing acts as an additional environmental filter on community assembly along the succession and homogenises vegetation between communities of the same age.The conclusions of this study provide basic knowledge in ecology. It also has implications for the management of road slopes plant communities in the perspective of their revegetation after construction work. Our conclusions suggest, amongst others, that combining mown and unmown vegetation could provide habitats for a higher diversity of associated fauna. In addition, it would allow vegetation to be pleasant to road users, while still ensuring a good visibility for road safety.