Several hypotheses from community ecology were tested using habitat and diet patterns for six catostomid fishes of the Assiniboine River, Manitoba. Specifically, I examined expected assemblage patterns based on the equilibrium-nonequilibrium continuum that are based on competition as a structuring mechanism. The catostomid assemblage showed characteristics of both equilibrium and nonequilibrium assemblages. Habitat utilization was not proportional to habitat availability for depth, velocity, and substrate indicating habitat selection occurs. These patterns are influenced by the distributions of soft Lake Agassiz deposits and harder glacial till-plain habitats and therefore localized. Species co-occurred in relation to abundance indicating negative associations assumed in competition-based theory were not apparent. In addition, species from the same subfamily co-occurred more often than expected by chance, indicating positive within-group comparisons, except for silver redhorse, which did not co-occur differently than random. Species from the same feeding group co-occur most frequently with conspecifics, indicating species have specific habitat patterns. Benthic invertebrate distributions and fish distributions were positively correlated with fish diet. Within-feeding-group comparisons indicated species that co-occurred frequently consumed the same food items, but showed subtle differences in abundance of diet items. The most common diet items varied among white sucker, silver redhorse, golden redhorse, and shorthead redhorse, indicating that, although these species co-occur, subtle differences in feeding behavior may account for differences in relative abundance and frequency of diet items. Quillback and bigmouth buffalo shared a few core food items, but co-occurred infrequently. Inter-specific interactions showed silver redhorse diets were a subset of white sucker diets, white sucker diets were a subset of golden redhorse diets, shorthead redhorse diets were a subset of silver redhorse and golden redhorse diets, while bigmouth buffalo diets were a subset of quillback diets. Lower richness and prevalence of organisms in quillback and bigmouth buffalo diets were due to highly aggregated prey items. Benthic invertebrate distributions were aggregated and dependent on the predictable patterns of substrates, based on hydraulic sorting in the meandering along the river. Large-scale redundancy of species-habitat associations was correlated with historical (phylogenetic) or adaptive (morphological) constraints on habitat selection. Stream habitats are constrained by regional factors of slope and sediments, but also determined by stable, repetitive and predictable local processes of erosion, transport, and deposition (meandering). The fish-habitat associations of catostomids in the Assiniboine River provide an example of interaction between the abundance of the component species, the phylogenetic constraints on the niche, and the deterministic nature of the spatial distribution of habitats. Within-feeding-group pairs showed that local habitat overlap is positively correlated with geographic overlap, while local diet overlap is negatively correlated with geographic overlap. Two species pairs (silver redhorse and golden redhorse and bigmouth buffalo and quillback) were concluded to have symmetric overlaps at the geographic scale and stable interactions. Using the functional niche concept ecological theory provides a link between ecology and biogeography of sympatric species. The multi-analytical approaches in this study provide insights into the structuring of north temperate prairie river fish communities, through hypothesis testing and correlation that have application beyond Prairie Rivers.

Several hypotheses from community ecology were tested using habitat and diet patterns for six catostomid fishes of the Assiniboine River, Manitoba. Specifically, I examined expected assemblage patterns based on the equilibrium-nonequilibrium continuum that are based on competition as a structuring mechanism. The catostomid assemblage showed characteristics of both equilibrium and nonequilibrium assemblages. Habitat utilization was not proportional to habitat availability for depth, velocity, and substrate indicating habitat selection occurs. These patterns are influenced by the distributions of soft Lake Agassiz deposits and harder glacial till-plain habitats and therefore localized. Species co-occurred in relation to abundance indicating negative associations assumed in competition-based theory were not apparent. In addition, species from the same subfamily co-occurred more often than expected by chance, indicating positive within-group comparisons, except for silver redhorse, which did not co-occur differently than random. Species from the same feeding group co-occur most frequently with conspecifics, indicating species have specific habitat patterns. Benthic invertebrate distributions and fish distributions were positively correlated with fish diet. Within-feeding-group comparisons indicated species that co-occurred frequently consumed the same food items, but showed subtle differences in abundance of diet items. The most common diet items varied among white sucker, silver redhorse, golden redhorse, and shorthead redhorse, indicating that, although these species co-occur, subtle differences in feeding behavior may account for differences in relative abundance and frequency of diet items. Quillback and bigmouth buffalo shared a few core food items, but co-occurred infrequently. Inter-specific interactions showed silver redhorse diets were a subset of white sucker diets, white sucker diets were a subset of golden redhorse diets, shorthead redhorse diets were a subset of silver redhorse and golden redhorse diets, while bigmouth buffalo diets were a subset of quillback diets. Lower richness and prevalence of organisms in quillback and bigmouth buffalo diets were due to highly aggregated prey items. Benthic invertebrate distributions were aggregated and dependent on the predictable patterns of substrates, based on hydraulic sorting in the meandering along the river. Large-scale redundancy of species-habitat associations was correlated with historical (phylogenetic) or adaptive (morphological) constraints on habitat selection. Stream habitats are constrained by regional factors of slope and sediments, but also determined by stable, repetitive and predictable local processes of erosion, transport, and deposition (meandering). The fish-habitat associations of catostomids in the Assiniboine River provide an example of interaction between the abundance of the component species, the phylogenetic constraints on the niche, and the deterministic nature of the spatial distribution of habitats. Within-feeding-group pairs showed that local habitat overlap is positively correlated with geographic overlap, while local diet overlap is negatively correlated with geographic overlap. Two species pairs (silver redhorse and golden redhorse and bigmouth buffalo and quillback) were concluded to have symmetric overlaps at the geographic scale and stable interactions. Using the functional niche concept ecological theory provides a link between ecology and biogeography of sympatric species. The multi-analytical approaches in this study provide insights into the structuring of north temperate prairie river fish communities, through hypothesis testing and correlation that have application beyond Prairie Rivers.

Un des objectifs majeurs de l'Ecologie est de comprendre les mécanismes qui facilitent la coexistence des espèces. L'hypothèse de la complémentarité des niches prédit qu'afin de coexister, deux espèces sympatriques doivent différer dans les conditions nécessaires à leur survie pour une des trois principales dimensions écologiques, la dimension spatiale, la dimension temporelle et la dimension alimentaire. Les mécanismes qui permettent la syntopie chez les mammifères terrestres sont complexes et variés et, parmi les méso-carnivores, la sélection d'habitat différentielle est un phénomène très répandu permettant la coexistence. La martre Européenne (Martes martes) et la fouine (Martes foina) sont les deux espèces carnivores sympatriques les plus similaires en termes de phylogénie, morphologie, régime alimentaire et rythme d'activité. Dans une région rurale française (la Bresse) où les deux espèces sont présentes en sympatrie, nous avons montré une sélection de l'habitat différentielle qui pourrait expliquer leur coexistence. En utilisant des suivis télémétriques, nous avons montré que les deux espèces diffèrent dans leur patron d'utilisation des gîtes de repos diurnes (nombre de gîtes, surface couverte par les gîtes, principal habitat utilisé pour le gîte). De plus, à partir d'un nombre important d'individus génotypés, nous avons montré que les différences dans l'utilisation de l'habitat n'ont que de faibles conséquences sur les éléments du paysage qui influent sur les flux de gènes. En effet, alors que nous avons montré un impact négatif de la pression de piégeage plus important pour la fouine que pour la martre, la connectivité pour les deux espèces est principalement assurée par le couvert végétal alors que les routes, le bâti humain et le milieu ouvert la réduisent partiellement. Ces résultats, collectivement avec une comparaison morphométrique et une approche en dynamique de population, fournissent des éléments de réponse quant à ce patron de coexistence et ses conséquences sur ces deux espèces sympatriques / One of the major goals of ecology is to understand the mechanisms which promote species coexistence. The niche-complementarity hypothesis predicts that two sympatric species must differ in their requirements for one of the three main ecological dimensions, i.e. habitat use, diet and activity time, to coexist. Mechanisms that allow for synthopy in terrestrial mammals are complex and varied and, among mesocarnivores, differential habitat selection is a widespread evidenced phenomenon facilitating coexistence. Plus, this differential habitat selection must have consequences on the landscape elements influencing gene flow. It is thus important to gather information on species life history traits in terms of habitat use and selection and in terms of demographic and genetic responses to environmental perturbations. The European pine marten (Martes martes) and the stone marten (Martes foina) are the most similar sympatric carnivores in Europe taking into account phylogenetic relationships, morphology, foraging behaviour, and activity pattern. In a French rural region (Bresse, eastern France) where both species are present in sympatry, we evidenced differential habitat use which could theoretically explain their sympatry. Using telemetry data set, we shown that both species differed in their resting site patterns (number of resting sites, area over which they are distributed, main habitat type used for resting). Additionally, using large data set of genotyped individuals, we found that these habitat use differences have slight consequences on the landscape elements influence on gene flow. Indeed, while we shown a differential negative impact of the trapping pressure on the spatial genetic variation, connectivity in both species is mainly provided by vegetation cover while roads human buildings and open area partially impede it. These results, collectively with morphometric comparison and population dynamics approaches, provided better insights on the pattern and the consequences of the coexistence of the two sympatric species

La première partie de ma thèse est une revue donnant un aperçu du répertoire génomique des bactéries intracellulaires et de leurs symbiotes. L'objectif de cette étude est d'explorer le processus permettant aux bactéries intracellulaires d'acquérir leur mode de vie spécifique. Nous avons commencé par examiner les données à propos de l'existence ancienne de bactéries intracellulaires, leur adaptation à leur hôte et les différences entre sympatrie et allopatrie. Une comparaison du contenu génomique de plusieurs bactéries avec différents modes de vie a révélé la capacité des bactéries à échanger des gènes à des degrés différents, en fonction de l'écosystème. La deuxième partie de ma thèse porte sur la séquence du génome de la souche Diplorickettsia massiliensis 20B qui est une bactérie intracellulaire obligatoire à Gram négatif isolée à partir des tiques de Slovaquie Ixodes ricinus. Dans ma troisième et dernière partie, nous exploré le répertoire du génome de Diplorickettsia massiliensis en le comparant aux génomes de bactéries phylogénétiquement très proches de Diplorickettsia massiliensis, issues de différentes niches. Ceci a permis de révélé son mode de vie allopatrique. Dans cette étude, nous avons comparé les caractéristiques du génome de Diplorickettsia massiliensis avec vingt-neuf espèces séquencées de Gammaproteobacteria (Legionella, Coxiella burnetii, Francisella tularensis et Rickettsiella grylli) en utilisant l'approche pangénomique multi-genre. Ce travail de thèse fournit des données originales et permet d’apporter plus de lumière sur la diversité des bactéries intracellulaires. / The initial purpose of my thesis is to understand with the help of comparative genomics, genomic variations based on coexistence, by examining data on the ancient existence of intracellular bacteria, their host adaptation and the differences between sympatry and allopatry. The first part of my thesis is a review giving insight into intracellular bacterial genome repertoire and symbionts. The goal of this review is to explore how intracellular microbes acquire their specific lifestyle. Due to their different evolutionary trajectories, these bacteria have different genomic compositions. We reviewed data on the ancient existence of intracellular bacteria, their host adaptation and the differences between sympatry and allopatry. A comparison of the genomic contents of bacteria with certain lifestyles revealed the bacterial capacity to exchange genes to different extents, depending on the ecosystem. The second part of my thesis present about the genome sequence of Diplorickettsia massiliensis strain 20B which is an obligate intracellular, gram negative bacterium isolated from Ixodes ricinus ticks collected from Slovak. In the third part, we investigated the genome repertoire of Diplorickettsia massiliensis compared to closely related bacteria according to its niche, revealing its allopatric lifestyle. In this study, we compared the genomic features of Diplorickettsia massiliensis with twenty-nine sequenced Gammaproteobacteria species (Legionella strains, Coxiella burnetii strains, Francisella tularensis strains and Rickettsiella grylli) using multi-genus pangenomic approach. This thesis work provides original data and sheds light on intracellular bacterial diversity.

This study focuses on a secondary contact zone between two sister species of woodrat, Neotoma fuscipes (dusky-footed woodrat) and N. macrotis (big-eared woodrat). Along the Nacimiento River, on the border of southern Monterey and northern San Luis Obispo counties, the ranges of these sister species of woodrats meet and overlap forming a secondary contact zone. The zone of secondary contact is estimated to include a 500-meter (~1,650 linear feet) portion of the Nacimiento River riparian corridor. This research examines quantifiable morphological change that is likely associated with heightened inter-specific competition within the contact zone. When in sympatry the sister species may compete for resources indirectly through exploitative competition, or directly through contest competition, or through a combination of these two processes. The prediction that heightened competition has resulted in distinctive morphological character shifts between allopatric and sympatric populations was tested my examining size and shape of adult woodrats along a 20-kilometer transect. It was confirmed that adults woodrats of the two sister taxa are morphologically distinct (N = 602) and that the phallus morphology was indeed a reliable means to identify adult male woodrats as to species (p < 0.0001, N = 331). A two model approach was used to examine convergence and divergence in size and shape of woodrats across the transect. Neotoma fuscipes exhibited a statistically significant divergerence from N. macrotis with regard to breadth of rostrum (p < 0.0001, N = 414) in a region of sympatry along the Nacimiento River. Based on the results on one statistical model, N. macrotis exhibited a statistically significant convergence with regard to body-size (p = 0.0240, N = 587) and length of hind foot (p < 0.0001, N = 563) towards those of N. fuscipes between zones of sympatry and allopatry. Alternatively, based on the results of a second statistical model that accounted for environmental variation within the system both species exhibited a statistically significant divergence with regard to body-size (p = 0.0054, N = 587) and towards that of N. fuscipes between zones of sympatry and allopatry. Also, N. macrotis exhibited a statistically significant convergence with regard to length of ear (p = 0.0022, N = 563) towards that of N. fuscipes. Based on the results of both models, detectable re-patterning of size-independent traits was observed to varying degrees. The morphological character shifts between sympatric populations and allopatric populations of woodrats suggest that ecological interactions between the species are occuring. Specifically, across the contact zone, patterns of variation in body-size and other morphological character traits are consistent with expectations of a combination of contest and exploitative competition.

Made available in DSpace on 2014-12-17T14:33:05Z (GMT). No. of bitstreams: 1 BrunnoFDO_DISSERT.pdf: 1072437 bytes, checksum: ca0f1130c794e389077757530d1d5b66 (MD5) Previous issue date: 2012-02-13 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Based on climate data and occurrence records, ecological niche models (ENM) are an important opportunity to identify areas at risk or vulnerable to biological invasion. These models are based on the assumption that there is a match between the climatic characteristic of native and invaded regions predicting the potential distribution of exotic species. Using new methods to measure niche overlap, we chose two exotic species fairly common in semi-arid regions of South America, Prosopis juliflora (Sw.) D.C. and Prosopis pallida (H. ; B. ex. Willd) HBK, to test the climate matching hypothesis. Our results indicate that both species occur with little niche overlap in the native region while the inverse pattern is observed in the invaded region on South America, where both species occur with high climatic overlap. Maybe some non-climate factor act limiting the spread of P. pallida on the native range. We believe that a founder effect can explain these similarities between species niche in the invaded region once the seeds planted in Brazil came from a small region on the Native range (Piura in Peru), where both species occur sympatric. Our hypothesis of a founder effect may be evident when we look at the differences between the predictions of the models built in the native and invaded ranges. Furthermore, our results indicate that P. juliflora shows high levels of climate matching between native and invaded ranges. However, conclusions about climate matching of P. pallida should be taken with caution. Our models based on climatic variables provide multiple locations suitable for occurrence of both species in regions where they still don t have occurrence records, including places of high interest for conservation. / Baseados nas informa??es clim?ticas e nos registros de ocorr?ncia, modelos de nicho ecol?gico (MNE) s?o uma importante oportunidade de identificar ?reas sob risco ou vulner?veis ? invas?o biol?gica. Estes modelos se ap?iam na suposi??o de que existe congru?ncia entre os climas das regi?es nativa e invadida para prever a distribui??o potencial de esp?cies ex?ticas. Utilizando m?todos recentes para medir sobreposi??es entre MNE, escolhemos duas esp?cies invasoras bastante comuns em regi?es semi-?ridas da Am?rica do Sul, Prosopis juliflora (Sw.) D.C. e Prosopis pallida (H. ; B. ex. Willd) H.B.K., para testar a hip?tese da congru?ncia clim?tica. Nossos resultados indicam as duas esp?cies ocorrem com pouca sobreposi??o de nicho na regi?o nativa, enquanto que o inverso se observa na regi?o invadida na Am?rica do Sul, onde as duas esp?cies ocorrem com elevada sobreposi??o de nicho. Algum fator n?o clim?tico pode atuar limitando a dispers?o de P. pallida na ?rea nativa. Acreditamos que um efeito fundador pode explicar estas semelhan?as de nicho encontradas na regi?o invadida uma vez que as sementes plantadas no Brasil vieram de uma pequena regi?o da ?rea nativa (Piura, Peru), onde ambas esp?cies ocorrem em simpatria. Diferen?as entre as previs?es dos modelos constru?dos na regi?o nativa e projetados para a regi?o nativa evidenciam nossa hip?tese do efeito fundador. Al?m disso, nossos resultados indicam que P. juliflora ocorre nas regi?es nativas e invadidas em condi??es clim?ticas bastante congruentes. Entretanto, conclus?es sobre congru?ncia clim?tica entre regi?es nativas e invadidas por P. pallida devem ser tomados com cautela. Os modelos prev?em v?rios locais favor?veis para a ocorr?ncia de ambas as esp?cies em regi?es onde ainda n?o existem registros de ocorr?ncia, inclusive locais de elevado interesse para conserva??o.

The Amazon rainforest harbors the planet's highest biodiversity among terrestrial ecosystems; however, the biology and ecology of most of its species are unknown. Niche partitioning is considered a key factor allowing species co-existence, especially for morphological similar species such as spiny rats of the genus Proechimys. I examined the extent to which habitat differentiation, species body mass, and diet could explain the community composition of small mammals at a site in the southeastern Amazon. Moreover, I radio-tagged sympatric species of Proechimys spp. and Mesomys stimulax (an arboreal spiny rat) to obtain detailed autoecology information, including habitat use and use of space. I found support for niche partitioning among species and associated small mammal species with distinct successional phases of gap dynamics. I also observed among Proechimys spp. a typical polygynous organization: females appeared to be territorial against females of any species of their genus; but male territories overlapped with those of several females. Mesomys stimulax showed evidence of monogamy and possible sociality, although sample sizes were small. To identify the importance of small mammals as seed disperser of Brazil nut seeds, I conduct experiments using a combination of fluorescent powder, seed exclosures, and track plates in forests with and without Brazil nut groves, and in forests with and without Brazil nut harvesting. Among small mammals, only Proechimys spp. removed, dispersed, and preyed upon Brazil nut seeds. Proechimys spp. sometimes scatterhoarded these seeds, and hence have the potential to play a significant role in recruiting new Brazil nut trees. I also trapped small mammals and measured forest structures on the same sites used for the seed dispersal experiment, to determine the ecological effects of Brazil nut harvest on small mammal communities; however, my results showed little evidence of changes associated with the seed exploitation. My results highlight the importance of habitat heterogeneity in structuring small mammal communities, and indicate that forest management practices that alter habitats, such as partial logging, also can be expected to alter small mammal composition and diversity. Proechimys spp. have the potential to play an important role in the ecological restoration of intensive exploited Brazil nut groves.

The Amazon rainforest harbors the planet's highest biodiversity among terrestrial ecosystems; however, the biology and ecology of most of its species are unknown. Niche partitioning is considered a key factor allowing species co-existence, especially for morphological similar species such as spiny rats of the genus Proechimys. I examined the extent to which habitat differentiation, species body mass, and diet could explain the community composition of small mammals at a site in the southeastern Amazon. Moreover, I radio-tagged sympatric species of Proechimys spp. and Mesomys stimulax (an arboreal spiny rat) to obtain detailed autoecology information, including habitat use and use of space. I found support for niche partitioning among species and associated small mammal species with distinct successional phases of gap dynamics. I also observed among Proechimys spp. a typical polygynous organization: females appeared to be territorial against females of any species of their genus; but male territories overlapped with those of several females. Mesomys stimulax showed evidence of monogamy and possible sociality, although sample sizes were small. To identify the importance of small mammals as seed disperser of Brazil nut seeds, I conduct experiments using a combination of fluorescent powder, seed exclosures, and track plates in forests with and without Brazil nut groves, and in forests with and without Brazil nut harvesting. Among small mammals, only Proechimys spp. removed, dispersed, and preyed upon Brazil nut seeds. Proechimys spp. sometimes scatterhoarded these seeds, and hence have the potential to play a significant role in recruiting new Brazil nut trees. I also trapped small mammals and measured forest structures on the same sites used for the seed dispersal experiment, to determine the ecological effects of Brazil nut harvest on small mammal communities; however, my results showed little evidence of changes associated with the seed exploitation. My results highlight the importance of habitat heterogeneity in structuring small mammal communities, and indicate that forest management practices that alter habitats, such as partial logging, also can be expected to alter small mammal composition and diversity. Proechimys spp. have the potential to play an important role in the ecological restoration of intensive exploited Brazil nut groves.