Individual niche variation is increasingly being demonstrated in animal populations in a wide variety of species and taxa. Niche variation among individuals has important implications for the ecology, evolution and management of animal populations and is a subject of increasing interest. However, despite its widespread occurrence the causes and consequences of individual niche variation remain poorly understood. In this thesis I use the European badger (Meles meles), a well studied species of high ecological interest, as a model system to investigate individual niche variation. In order to achieve this I combine information on individual foraging niches derived via stable isotope analysis (SIA) of badger vibrissae with detailed life history and ecological data from a long-term study population to investigate the incidence, cause and consequence of individual niche variation within badger social groups. First I use the biomarker Rhodamine B to investigate vibrissae growth rates and patterns in badgers and demonstrate that the isotopic composition of a single vibrissa likely reflects diet over several months (Chapter 2). Next I explore the use of SIA as a tool to investigate badger diet, by comparing isotopic patterns to seasonal changes in diet measured using faecal analysis (Chapter 3). My results provide validation that SIA is powerful tool for investigating foraging variation in this species, and suggest that within badger populations substantial dietary variation may occur among individuals. Further investigation of isotopic variation Indicates that individuals within social groups differ markedly and consistently in their isotopic signature, independent of age and sex effects and that in some instances these differences are remarkably consistent across year (Chapter 4).This suggesting long term individual specialisation (Chapter 4). I find that the degree of this individual specialisation, and the relationship between specialisation and body condition is influenced by competition for resources (Chapter 5). Social groups with higher levels of competition exhibit greater specialisation and specialised individuals within these highly competitive environments are in better condition. Finally, I discuss the implications of these results for individual niche variation, for the application of SIA to study this behaviour and for badger ecology generally (Chapter 6). I also outline future directions for further research.

Among-individual variation in resource use is pervasive and may have ecosystem-wide effects. This variation between individuals can affect population niche breadth. My study determined if niche breadth was best explained by dispersal of individuals from locations with different prey resources driven by ecosystem level disturbance regimes or competition among individuals inhabiting a site, resulting in dietary partitioning. I used structural equation modeling to examine the direct and indirect effects of several environmental variables spanning gradients of disturbance, competition strength, and food availability on niche breadth of the Eastern Mosquitofish (Gambusia holbrooki). I evaluated two complementary models 1) allowing for only direct effects of disturbance on niche breadth and 2) limiting effects of disturbance on niche breadth to indirect effects via food availability and competitor densities. The partitioning hypothesis excluding direct effects of disturbance on niche breadth was best supported by my data.

The Hutchinsonian niche is the n dimensional hyper volume that allows for the persistence of a species. Castor canadensis, a large semi-aquatic rodent, is an ecosystem engineer and often a keystone species for many ecosystems. I examined the effect of multiple spatial scales on hierarchical habitat selection byC. canadensis using presence-only modeling techniques. I also determined individual trophic niche specialization in C. canadensis utilizing stable isotope analysis. I concluded that C. canadensis displayed scale independent habitat selection when comparing landscape and fine spatial scales. Individual trophic niche specialization occurred in colonies of the same resource availability. Also, individual trophic niches varied substantially between wetlands. These results have implications for the management of “generalist” species because populations can be composed of specialized individuals. Studies of niche across spatial and organizational scales are required for successful conservation and management strategies.

The niche concept provides a tractable measure of the ecological roles and requirements of organisms, which can inform our understanding of the patterns of biodiversity, and subsequently, direct conservation policy. Although niche is most commonly considered for species, variation nested within lower hierarchies of biological organization (i.e., phenotypes, genotypes) also contributes to maintaining biodiversity. Herein I examine spatial and dietary niche variation among and within species in a consumer–resource system where resources and competition are structured by a heterogeneous environment. An underlying theme of this dissertation was developing research through a community-engaged approach that not only contributed to conceptual advancements in niche theory but also to applied conservation priorities. The marine archipelago of the central coast of British Columbia, Canada structures salmon (Oncorhynchus spp.) resources and the inter- and intraspecific competitive context for coastal grizzly (Ursus arctos) and black bears (Ursus americanus). This assembly of ursids represents nested levels of biological organization (i.e., species, phenotypes (white vs black-coated morphs of black bears) and genotypes (dominant homozygote black-coated black bears, heterozygote black-coated black bears, recessive homozygote white-coated ‘Spirit’ black bears)), which allows for investigation into niche variation across and within species. I investigated niche variation using a suite of non-invasive methods. Local and Traditional Ecological Knowledge (LEK/TEK) provided complementary information to genetic and stable isotope (13C and 15N) data from hair samples. First, I investigated changes in the spatial niche of coastal grizzly bears. By combining western scientific approaches with TEK/LEK interviews I found the range of coastal grizzly bears has expanded westward onto several coastal islands. The economic, cultural, and ecological impacts of this shift in spatial niche are not yet understood. Second, I tested hypotheses related to variation in the foraging niche of black bears in response to the competitive environment and salmon resource availability. I found that grizzly bear presence reduced the proportion of salmon in black bear diets by ~40%. I also found that salmon species diversity, and not biomass abundance, was positively correlated to salmon in black bear diets. This highlights the importance of resource diversity to consumers beyond the consideration of abundance. Third, I explored spatial niche patterns of Spirt bears in relation to protected areas. I found that landscape-level Spirit bear allele frequency and population estimates were lower than previously reported. Approximately ~50% of Spirit bear allele hotspots corresponded to protected areas. This finding suggests Spirit bears are rarer and less protected than previously assumed. Finally, I tested hypotheses related to niche variation between phenotype and genotypes of Spirit bear populations. I found both phenotypes and genotypes diverged in foraging niche, with Spirit bears and black-coated heterozygotes having elevated stable isotope signatures compared to black-coated homozygotes. This result supports the role of ‘multi-niche’ mechanisms in maintaining this rare polymorphism. Results from all chapters contributed to land- and marine-use stewardship efforts of collaborating First Nations. Collectively, this dissertation offers novel contributions towards understanding how niche variation at multiple levels of biological organization can contribute to conservation planning. / Graduate / 2020-04-04

Submitted by Jean Medeiros (jeanletras@uepb.edu.br) on 2016-05-17T12:56:17Z No. of bitstreams: 1 PDF - Maria Rita Nascimento Duarte.pdf: 2708130 bytes, checksum: 83ff7c3f4dd9638f2a12090069b8a8e8 (MD5) / Approved for entry into archive by Secta BC (secta.csu.bc@uepb.edu.br) on 2016-07-21T20:42:27Z (GMT) No. of bitstreams: 1 PDF - Maria Rita Nascimento Duarte.pdf: 2708130 bytes, checksum: 83ff7c3f4dd9638f2a12090069b8a8e8 (MD5) / Made available in DSpace on 2016-07-21T20:42:27Z (GMT). No. of bitstreams: 1 PDF - Maria Rita Nascimento Duarte.pdf: 2708130 bytes, checksum: 83ff7c3f4dd9638f2a12090069b8a8e8 (MD5) Previous issue date: 2016-02-02 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In the Neotropical zone the generalist habit is common among fish populations, especially in semi-arid rivers. In these systems, where the availability of food items varies spatially and temporally, it is expected that a more generalist strategy dominates. However, populations classified as generalist may actually be composed of relatively specialist individuals. This study aims at quantifying the use of food resources and understanding the individual contribution to population niche of Hoplias malabaricus, Geophagus brasiliensis and Prochilodus brevis. Four collections were performed at four sites along the Ipanema (PE) River, in April and July 2007 (wet season) and October 2007 and January 2008 (dry season). Sampling was performed at daylight, using gillnets, manual trawls and cast nets. The specimens collected were fixed in 4% formalin and preserved in 70% ethanol. The diet was quantified using the indirect volumetric method, frequency of occurrence and numeric frequency. Spatial patterns of variation in food items between species were evaluated using the Nonmetric Multidimensional Scaling (NMS). The Multi-Response Permutation Procedure (MRPP) was used to test the significance of differences in diet composition between species, sites and sampling periods. The degree of specialization of each individual was calculated using a proportional similarity index. The amplitude and niche overlap ratios were calculated using the Levins and Bolnick indexes. The graphical analysis of Amundsen was performed in order to correlate the diet composition with the selection of specific prey. The species showed a pattern of distribution and segregation in diet between the sampling sites. The MRPP showed that there were significant differences in the diet composition between species (MRPP, A= 0, 61; p= 0, 00). Geophagus brasiliensis specie showed significant differences between site 1 and site 4 (MRPP, A = 0.14; p = 0.03) and site 2 and site 4 (MRPP, A = 0.16 p = 0, 03), the Prochilodus brevis specie between site 1 and site 3 (MRPP, A = 0.28 p = 0.02) and site 1 and site 4 (MRPP, A = 0.11; p = 0.04). The three species present individual specialization in all sampling sites and in both periods of the hydrological cycle. The species Hoplias malabaricus has a population with most experts individuals, with rest of fish as the dominant item, however, with other individuals in the population consuming a high abundance of specific prey. However Geophagus brasiliensis presented a generalist population, with individuals of the population consuming a variety of items, displaying a relatively high component within phenotype. Prochilodus brevis showed a population with varied feeding strategy, presenting degrees of specialization with the contribution of Cyclotela item and generalization, where food items were consumed by more than half of the population. It was observed that individual specialization is highly correlated with niche overlap, indicating that the smaller the overlap the larger the degree of individual specialization. It is important to emphasize that the greatest degree of individual specialization was observed where there was a greater availability of food resources consumed by the populations. / Na região neotropical o hábito generalista é comum em populações de peixes, especialmente em rios do semiárido. Nesses sistemas onde a distribuição dos itens alimentares varia espacial e temporalmente, espera-se que a estratégia generalista predomine entre as espécies. Este estudo objetiva quantificar a utilização de recursos alimentares e compreender a contribuição individual para o nicho populacional em três espécies de peixes, Hoplias malabaricus, Geophagus brasiliensis e Prochilodus brevis. Foram realizadas coletas em quatro pontos ao longo do rio Ipanema (PE) nos meses de abril e julho de 2007 (período chuvoso) e outubro de 2007 e janeiro de 2008 (período seco). As amostragens foram feitas durante o dia, usando redes de arrasto, espera e tarrafa. Os espécimes coletados foram fixados em formol 4% e preservados em álcool 70%. A dieta foi quantificada usando o método volumétrico indireto, frequência de ocorrência e a frequência numérica. Padrões espaciais de variação de itens alimentares para as espécies foram avaliados por meio Escalonamento Multidimensional Não- Métrico (NMS). O Procedimento de Permutações Múltiplas (MRPP) foi utilizado para testar diferenças na composição da dieta entre as espécies, pontos e períodos de amostragem. O grau de especialização de cada indivíduo foi calculado utilizando um índice de similaridade proporcional. A amplitude e sobreposição de nicho foram calculadas utilizando os índices de Levins e Bolnick. Foi realizada a análise gráfica de Amundsen a fim de relacionar a composição da dieta com a seleção de presas específicas. O MRPP mostrou que houve diferenças significativas na composição da dieta entre as espécies (A = 0,61; p = 0,005). Entre os pontos de coleta a espécie Geophagus brasiliensis apresentou diferenças significativas entre o ponto 1 e ponto 4 (MRPP, A = 0,14 e p = 0,03) e ponto 2 e ponto 4 (MRPP, A = 0,16 e p = 0,03), a espécie Prochilodus brevis entre o ponto 1 e ponto 3 (MRPP, A = 0,28 e p = 0,02) e ponto1 e ponto 4 (MRPP, A = 0,11 e p = 0,04). As três espécies apresentaram especialização individual em todos os pontos de coletas e em ambos os períodos de regime hidrológico. A espécie Hoplias malabaricus apresentou uma população com a maioria dos indivíduos especialistas, apresentando resto de peixe como item dominante, porém, com outros indivíduos da população consumindo uma alta abundância de presas especificas. Geophagus brasiliensis apresentou uma população generalista, com indivíduos da população consumindo uma variedade de itens, exibindo um componente relativamente elevado dentre- fenótipo. Prochilodus. brevis mostrou uma população com estratégia de alimentação variada, apresentando graus de especialização com a contribuição do item alimentar Cyclotela e generalização, onde os itens alimentares tinham sido consumidos por mais da metade da população. Observou-se que a especialização individual está correlacionada com a sobreposição de nicho, indicando que, quanto menor sobreposição maior é o grau de especialização individual. É importante ressaltar que o maior grau de especialização individual foi observado onde houve uma maior riqueza de recursos alimentares consumidos pelas populações.

Orientador: Márcio Silva Araújo / Resumo: A variação individual no uso de recursos alimentares pode depender de fatores ecológicos como a competição intra e interespecífica, predação, além da diversidade e abundância de recursos. O objetivo deste trabalho foi identificar as causas da variação individual no uso de recursos alimentares em populações do peixe Characidium schubarti, conh’ecido como “charutinho” e descrito como insetívoro bentônico. O estudo foi realizado em riachos de Mata Atlântica no Parque Estadual Carlos Botelho, núcleo São Miguel Arcanjo, região sudeste do Estado de São Paulo. Os charutinhos foram coletados ao longo de transectos em 11 riachos diferentes. Foram coletadas amostras da comunidade de invertebrados bentônicos em cada riacho para a obtenção de estimativas da diversidade e abundância de recursos alimentares. Identificamos e quantificamos todas as possíveis espécies de peixes competidoras (insetívoros bentônicos). Nossos resultados sugerem significativa variação na dieta dos indivíduos de todas as populações, porém com baixo grau de especialização individual. Nós não encontramos efeito significativo da oportunidade ecológica (diversidade de recursos), produtividade secundária (biomassa de recursos) e competição (densidade de charutinhos e competidores) sobre o grau de variação na dieta nas populações estudadas. / Abstract: Individual variation in food resource use can depend on ecological factors such as intra and interspecific competition, predation, and the diversity and abundance of resources. Our main goal in this study was to identify the ecological causes of individual variation in the use of food resources in natural populations of the fish Characidium schubarti, part of a group popularly known as “South American darters”, described as benthic insectivores. The study was conducted in Atlantic Forest streams at the Carlos Botelho State Park, at São Miguel Arcanjo, in the southeast of the state of São Paulo. Specimens were collected along transects in 11 streams. We collected samples from the benthic invertebrate community in each stream to estimate the diversity and abundance of food resources. We identified and quantified all possible competing species of fishes (benthic insectivores). Our results suggest significant variation in the diet of individuals from all populations, however, with a low degree of individual specialization. We found no significant effect of ecological opportunity (resource diversity), secondary productivity (resource biomass) and competition (density of charutinhos and competitors) on the degree of dietary variation in the studied populations. / Mestre

La capacité à répondre aux changements environnementaux est cruciale pour l’établissement et la persistance des populations dans un système hétérogène. Les processus sous-jacents à cette capacité peuvent prendre différentes formes. La grande diversité génétique (et phénotypique) découlant de la reproduction sexuée est un des processus permettant à une population de répondre aux différentes conditions environnementales par la survie d’au moins quelques individus. D’autre part, les processus épigénétiques, en permettant la modification du patron d’expression des gènes, contribuent également à la variation phénotypique. Ces variations peuvent survenir accidentellement (épimutations) ou en réponse à un stimulus environnemental (plasticité). Les processus épigénétiques représenteraient ainsi une alternative à la variation génétique pouvant expliquer le succès écologique des organismes génétiquement identiques. Toutefois, les génotypes ne répondent pas tous de la même façon aux conditions environnementales ; certains génotypes sont considérés comme généralistes et peuvent s’acclimater à une vaste gamme de conditions environnementales alors que d’autres sont plutôt spécialistes et restreints à un type d’environnement donné. L’objectif général de cette thèse est de mettre en évidence certains des processus responsables de la persistance des organismes asexués en déterminant les relations entre la variation épigénétique, la variation phénotypique et les stratégies écologiques. Pour ce faire, des hybrides asexués Chrosomus eos-neogaeus, un poisson à reproduction clonale, ont servi de modèle biologique. Se reproduisant par gynogenèse, les lignées clonales (génotypes) doivent faire face aux mêmes variations environnementales que les espèces parentales sexuées. De plus, la répartition géographique de chacune des lignées suggère la présence de génotypes généralistes et spécialistes. L’analyse de ces lignées en milieux naturels et en milieux contrôlés a permis de décortiquer l’influence des variations génétique, environnementale et épigénétique sur la variation phénotypique. Dans un premier temps, les modèles de stratégies généraliste et spécialiste ont été testés de manière empirique : (i) des analyses génétiques ont permis d’inférer les processus historiques expliquant la diversité et la répartition actuelle des lignées clonales ; (ii) l’analyse du patron de ii méthylation de différentes lignées a permis de déterminer l’importance relative des sources de variations épigénétiques selon les fluctuations environnementales et de les associer à une stratégie écologique : une importante influence de l’environnement ou une plus grande stochasticité dans l’établissement des marques épigénétiques étant associées à la plasticité phénotypique ou au bet-hedging, respectivement ; et (iii) le rôle de la plasticité phénotypique dans la diversification de niches écologiques a été souligné par la comparaison de la variation de la morphologie trophique en milieux naturels et contrôlés. D’autre part, le second volet de cette thèse a permis d’associer un coût (détection d’une instabilité développementale) à la plasticité phénotypique et d’élaborer une hypothèse sur l’existence d’un handicap démographique nécessaire afin d’expliquer la situation contre-intuitive concernant la coexistence des organismes gynogènes et de leurs hôtes sexués. La compréhension des différents mécanismes sous-jacents au succès écologique des organismes face aux variations environnementales permet ainsi une meilleure évaluation de leur potentiel évolutif et fournit des outils supplémentaires pour leur protection face à un environnement changeant. / The capacity to cope with environmental changes is crucial to the establishment and persistence of populations. The processes underlying such a capacity can take different forms. The high genetic (and phenotypic) diversity arising from sexual reproduction is one process that allows to cope with different environmental conditions through the survival of at least a few individuals. On the other hand, epigenetic processes, allowing the modification of gene expression, are also responsible for phenotypic variation. Epigenetic changes may occur accidentally (epimutations) or in response to an environmental stimulus (plasticity). Thus, epigenetics would represent an alternative process to genetic variation to explain the ecological success of genetically identical organisms. However, genotypes are not equally capable of coping with environmental changes. Some genotypes are generalists and can acclimatize to a wide range of environmental conditions, whereas other genotypes are specialized and restricted to narrow environmental conditions. The general objective of this thesis is to highlight the processes responsible for the persistence of asexual organisms by determining the relationship between epigenetic processes, phenotypic variation and ecological strategies. To achieve this, the clonal hybrid fish Chrosomus eos-neogaeus were used as a biological model. By reproducing by gynogenesis, the clonal lineages (genotypes) are distributed among the same environments than the sexual parental species. Moreover, the geographical distribution of the lineages suggests the presence of generalist and specialist genotypes. The analysis of these lineages in natural and controlled conditions allowed to disentangling the influence of genetic, environmental and epigenetic variations on phenotypic variation. On the one hand, generalist and specialist strategies were empirically tested: (i) genetic analyses were used to infer the historical processes explaining the diversity and the current distribution of the clonal lineages; (ii) the comparison of methylation patterns in different lineages allowed to determine the dynamism of the epigenetic processes according to environmental fluctuations and to associate them with an ecological strategy: an important environmental or stochastic effect on epigenetic variation being associated with phenotypic iv plasticity or bet-hedging, respectively; and (iii) the role of phenotypic plasticity in niches diversification was highlighted by comparing individuals’ trophic morphology in natural and controlled conditions. On the other hand, the second part of this thesis has allowed to associate a cost (developmental instability) to phenotypic plasticity and to propose a hypothesis about the existence of a demographic handicap necessary to explain the paradox regarding the coexistence of sexual and asexual sperm-dependent organisms. Understanding these different mechanisms underlying the ecological success of organisms in face of environmental heterogeneity allows us to better establish their evolutionary potential and provides additional tools to protect them against changing environments.