Over the past few decades, it has become increasingly apparent that host-associated microbial communities play an integral role in the development, physiology, and health of their host organisms. All hosts have evolved mechanisms to filter the microbial taxa that comprise their resident intestinal microbial community, or gut microbiota. Utilizing the zebrafish as a model host organism, we documented the development of the gut microbiota through time, and found a significant shift in the composition of the gut microbiota after the onset of adaptive immunity. This led us to hypothesize that adaptive immunity is an important determinant of gut microbiota composition. We tested this hypothesis using wild type and rag1-/- zebrafish, which lack a functional adaptive immune system. Additionally we tested the robustness of the effects of adaptive immunity to dispersal of microbes between immune-compromised and immune-competent genotypes. We found that adaptive immunity had less of an effect on the composition of the gut microbiota than we expected, although there were intriguing differences in the nature of selection imposed when adaptive immunity was present than when it was absent. Because “westernization”, or market-integration, has been associated with significant changes in the human microbiota and certain health risks, we used similar analyses to those we applied to the zebrafish system to determine whether market-integration alters the filtering effects of inflammation and intestinal helminth parasites on the intestinal microbial community. We found that market-integration increased inter-subject dissimilarity and reduced inter-subject dispersal. Even small changes in the inflammation marker, CRP, were associated with differences in the gut microbiota, but these effects were reduced in the presence of helminth infection, which has been hypothesized to affect the microbiota by reducing inflammation. In total, this dissertation provides evidence for the nature and importance of host filters of the gut microbiota across two vertebrate species, as well as providing a framework for future studies of the effects of such filters on the assembly of the gut microbiota. This dissertation includes previously published, and unpublished, co-authored material.

The movement of organisms and resources within ecosystems are essential elements in the productivity, stability, and distribution of communities. This thesis examines how water velocity, a defining factor of lotic systems, influences the dispersion of benthic organisms and particulate organic matter in small stream ecosystems. Variation in movement-related behaviours in two rheophilous (‘flow-loving’) mayflies (Epeorus and Baetis) and two rheophobic (‘flow-avoiding’) mayflies (Ameletus and Paraleptophlebia) were compared to determine how benthic organisms disperse between and within habitat patches in hydrodynamically complex landscapes. The degree to which water velocity and particle shape influence the retention of organic matter (including deciduous leaves, conifer needles, red-cedar fronds, and branch fragments) was examined to determine how physical factors determine detrital resource availability in streams. Although water velocity did not influence the crawling rates of Baetis and Ameletus in daylight conditions, both mayflies dispersed rapidly upstream in low-velocity flows in dark conditions. Drift rates of both mayflies were lower in daylight than dark conditions, and were generally inversely related to their habitat preferences. Escape responses in grazing Epeorus, Baetis, and Ameletus larvae in a range of flow conditions showed that retreat distance was more sensitive than flight initiation distance to variation in water velocity, suggesting that hydrodynamics mediate the risks of predation and the costs of flight in stream systems. Comparisons of the transport distances of live larvae, dead larvae, and passive tracer particles in low and high water velocities showed that drift distance varied substantially among taxa, and that behavioural control over drift distance generally declined as water velocity increased. While organic matter particles generally travelled further in high-velocity reaches, leaves were retained in riffles when they impacted on protruding clasts, while ‘stiff’ particles were retained when they settled into streambed interstices. Leaves placed in high-velocity microhabitats were broken down more slowly than leaves in low-flow areas, likely due to the exclusion of large-bodied detritivores. In conclusion, this thesis supports the view that hydrodynamic forces control trophic interactions and local population dynamics in stream ecosystems by directly altering the physical – and sometimes behavioural – processes of particle entrainment, transport, and deposition.

In this thesis I investigated the importance of plant-animal mutualisms to the reproductive success of three West African mistletoe species in two genera, Globimetula braunii, Agelanthus brunneus and A. djurensis, in Ngel Nyaki Forest Reserve, Nigeria. The flowers of all three mistletoes were visited by 3 - 4 species of sunbird. Agelanthus flowers were also visited by honeybees (Apis mellifera) and a small social wasp species (Vespinae). A. mellifera appeared to be robbing nectar from the flowers of A. brunneus. To investigate the relative role of pollinators, I compared flower opening and fruit set amongst bagged, caged, natural, hand-selfed and hand-crossed treatments. The flowers of G. braunii were able to selfopen on average 66% of the time when pollinators were excluded, whereas pollinators were essential to the flower opening mechanism of both Agelanthus spp. Insects were as effective at opening the flowers of Agelanthus spp. as sunbirds. However, flower opening ability did not translate directly into pollination effectiveness, as insect access alone did not result in significantly higher fruit set than that observed under the bagged condition. There was no significant evidence for autonomous selfing within any of the three mistletoes and thus reproduction was almost entirely reliant on 3 – 4 species of sunbird. Hand-pollinations of all three species indicated a high level of self-compatibility, and in one species, G. braunii, pollen limitation was evident (PLI = 0.504). To investigate dispersal mutualisms amongst the three mistletoe species, fruit ripening and removal were monitored. The fruits of all three mistletoe species appeared to be removed rapidly from plants as they ripened, with few ripe or overripe fruits present on the branches at any time. Dispersal efficiency, or the total proportion of fruit crop removed across the fruiting season, was also very high (>90%) for the Agelanthus spp. but lower in G. braunii, for which almost a third of the total fruit crop was recorded undispersed in fruit nets beneath plants. Mistletoes are an important component of West African montane forests. Disruption to mistletoe reproductive mutualisms may affect not only mistletoes and their mutualists directly, but also an entire network of species, all linked within a web of interactions. To protect these ecosystems from further degradation, increased community involvement and greater enforcement of laws set out to manage montane forest habitat across the region is essential. Without this support, the future of these ecosystems and the web of interacting species within remains tenuous.

Many of the world's tropical forests are under threat, with anthropogenic deforestation and degradation occurring at an alarming rate. Seed dispersal in an important process in forest restoration and regeneration, however seed rain is often low in degraded habitats, hindering reforestation efforts. Up to 90% of tropical fruit are dispersed by vertebrates, animal seed dispersers are incredibly important in maintaining forest health. Additionally, frugivores that disperse seeds into degraded areas may be of great importance in aiding natural reforestation. I therefore, investigated the potential role of the frugivorous monkey, Chlorocebus tantalus tantalus, in forest regeneration via seed dispersal. I assessed its patterns of habitat use, the quality and quantity of seed dispersal it provides, the effectiveness of current conservation management actions and the density of C. t. tantalus at Ngel Nyaki Forest Reserve. I found C. t. tantalus utilised forest, edge and grassland habitats, and dispersed seeds of 28 pioneer and forest edge species into these habitats. Moreover, the number of seeds dispersed per faeces was significantly higher in the grassland than the forest with means of 16.4 +/- 6.1 and 3.4 +/- 0.97 seeds >2 mm in these habitats respectively. Germination of C. t. tantalus dispersed seeds was highest in grazed grassland and lowest in grassland protected from grazing and fire, suggesting the current practice of fencing off grassland to protect from cattle grazing may not be sufficient on its own, due to seed-seedling conflict in habitat suitability. These findings combined with an estimated density of 28 +/- 10.8 C. t. tantalus individuals km⁻² suggests C. t. tantalus may benefit forest regeneration via its role as a seed disperser, provided appropriate management actions are implemented. This and other frugivorous species may play similar roles in other locations but such roles need to be investigated in order to implement management actions that ensure their seed dispersal benefits are maximised for forest restoration and regeneration.

The movement of organisms and resources within ecosystems are essential elements in the productivity, stability, and distribution of communities. This thesis examines how water velocity, a defining factor of lotic systems, influences the dispersion of benthic organisms and particulate organic matter in small stream ecosystems. Variation in movement-related behaviours in two rheophilous (‘flow-loving’) mayflies (Epeorus and Baetis) and two rheophobic (‘flow-avoiding’) mayflies (Ameletus and Paraleptophlebia) were compared to determine how benthic organisms disperse between and within habitat patches in hydrodynamically complex landscapes. The degree to which water velocity and particle shape influence the retention of organic matter (including deciduous leaves, conifer needles, red-cedar fronds, and branch fragments) was examined to determine how physical factors determine detrital resource availability in streams. Although water velocity did not influence the crawling rates of Baetis and Ameletus in daylight conditions, both mayflies dispersed rapidly upstream in low-velocity flows in dark conditions. Drift rates of both mayflies were lower in daylight than dark conditions, and were generally inversely related to their habitat preferences. Escape responses in grazing Epeorus, Baetis, and Ameletus larvae in a range of flow conditions showed that retreat distance was more sensitive than flight initiation distance to variation in water velocity, suggesting that hydrodynamics mediate the risks of predation and the costs of flight in stream systems. Comparisons of the transport distances of live larvae, dead larvae, and passive tracer particles in low and high water velocities showed that drift distance varied substantially among taxa, and that behavioural control over drift distance generally declined as water velocity increased. While organic matter particles generally travelled further in high-velocity reaches, leaves were retained in riffles when they impacted on protruding clasts, while ‘stiff’ particles were retained when they settled into streambed interstices. Leaves placed in high-velocity microhabitats were broken down more slowly than leaves in low-flow areas, likely due to the exclusion of large-bodied detritivores. In conclusion, this thesis supports the view that hydrodynamic forces control trophic interactions and local population dynamics in stream ecosystems by directly altering the physical – and sometimes behavioural – processes of particle entrainment, transport, and deposition.

The movement of organisms and resources within ecosystems are essential elements in the productivity, stability, and distribution of communities. This thesis examines how water velocity, a defining factor of lotic systems, influences the dispersion of benthic organisms and particulate organic matter in small stream ecosystems. Variation in movement-related behaviours in two rheophilous (‘flow-loving’) mayflies (Epeorus and Baetis) and two rheophobic (‘flow-avoiding’) mayflies (Ameletus and Paraleptophlebia) were compared to determine how benthic organisms disperse between and within habitat patches in hydrodynamically complex landscapes. The degree to which water velocity and particle shape influence the retention of organic matter (including deciduous leaves, conifer needles, red-cedar fronds, and branch fragments) was examined to determine how physical factors determine detrital resource availability in streams. Although water velocity did not influence the crawling rates of Baetis and Ameletus in daylight conditions, both mayflies dispersed rapidly upstream in low-velocity flows in dark conditions. Drift rates of both mayflies were lower in daylight than dark conditions, and were generally inversely related to their habitat preferences. Escape responses in grazing Epeorus, Baetis, and Ameletus larvae in a range of flow conditions showed that retreat distance was more sensitive than flight initiation distance to variation in water velocity, suggesting that hydrodynamics mediate the risks of predation and the costs of flight in stream systems. Comparisons of the transport distances of live larvae, dead larvae, and passive tracer particles in low and high water velocities showed that drift distance varied substantially among taxa, and that behavioural control over drift distance generally declined as water velocity increased. While organic matter particles generally travelled further in high-velocity reaches, leaves were retained in riffles when they impacted on protruding clasts, while ‘stiff’ particles were retained when they settled into streambed interstices. Leaves placed in high-velocity microhabitats were broken down more slowly than leaves in low-flow areas, likely due to the exclusion of large-bodied detritivores. In conclusion, this thesis supports the view that hydrodynamic forces control trophic interactions and local population dynamics in stream ecosystems by directly altering the physical – and sometimes behavioural – processes of particle entrainment, transport, and deposition. / Applied Science, Faculty of / Civil Engineering, Department of / Graduate

Simulation models are valuable for making predictions that may be tested in natural systems and for understanding observed patterns. The simulation model developed for this thesis evaluates the effects of spatial network architecture, including organism dispersal patterns and isolation of habitats, on metapopulations. Two fields were merged throughout this project: metapopulation biology and small-world network theory. Small-world networks are characterized in their extremes as scale-free or single-scale. These models potentially simulate the networks of habitats and corridors in which metapopulations operate. Small-world network theory has been used to describe systems as diverse as rivers, the world-wide-web, and protein interactions, but has not been used as an experimental treatment for metapopulation dynamics. I tested the effects of growth rate, dispersal pattern, network architecture (scale-free and single-scale), attack type (targeted or random), and attack severity (0, 5, 10, 20, or 40% attacked populations) on metapopulation size and inter-population variation in a simulated system designed to be relevant to conservation biology and ecology. Metapopulation size and inter-population variation changed due to combinations of dispersal pattern, growth rate, and attack severity. Specifically, metapopulations were most affected by a combination of unidirectional dispersal and low growth rate in both metapopulation number and inter-population variation. However, a significant difference between scale-free and single-scale metapopulations was not found due to a low connectivity in the modeled networks as well as limitations of experimental assumptions. However, future studies that alter the model's assumptions could improve understanding of the influence of landscape structure on at-risk metapopulations.

No description available.

Dispersal, especially long-distance dispersal, is an important component in many disciplines within biology. Many species are passively dispersed by wind, not least spore-dispersed organisms. In this thesis I investigated the dispersal capacity of bryophytes by studying the colonization patterns from local scales (100 m) to landscape scales (20 km). The dispersal distances were measured from a known source (up to 600 m away) or inferred from a connectivity measure (1–20 km). I introduced acidic clay to measure the colonization rates over one season of a pioneer moss, Discelium nudum (I–III). I also investigated which vascular plants and bryophytes that had colonized limed mires approximately 20–30 years after the first disturbance (IV). Discelium effectively colonized new disturbed substrates over one season. Most spores were deposited up to 50 meters from a source but the relationship between local colonization rates and connectivity increased with distance up to 20 km (I–III). Also calcicolous wetland bryophyte species were good colonizers over similar distances, while vascular plants in the same environment colonized less frequently. Common bryophytes that produce spores frequently were more effective colonizers, while no effect of spore size was detected (IV). A mechanistic model that take into account meteorological parameters to simulate the trajectories for spores of Discelium nudum fitted rather well to the observed colonization pattern, especially if spore release thresholds in wind variation and humidity were accounted for (III). This thesis conclude that bryophytes in open habitats can disperse effectively across landscapes given that the regional spore source is large enough (i.e. are common in the region and produce spores abundantly). For spore-dispersed organisms in open landscapes I suggest that it is often the colonization phase and not the transport that is the main bottle-neck for maintaining populations across landscapes. / <p>At the time of the doctoral defence the following papesr were unpublished and had  a status as follows: Paper 2: Epubl ahead of print; Paper 3: Manuscript; Paper 4: Manuscript</p>

No description available.