The presence of nonnative trout and the recent introduction of Myxobolus cerebralis in the Logan River drainage pose a threat to the native Bonneville cutthroat trout population (Oncorhynchus clarki Utah). The variability in the response of susceptible trout populations to M. cerebralis, causing agent of whirling disease, suggests that environmental factors may influence the effects of the parasite in infected environments. I investigated the relationship between temperature, discharge, substrate size, nutrient concentration (nitrogen and phosphorus), periphyton (chlorophyll a), and the relative abundance of Tubifex tubifex to the distribution, and prevalence of M. cerebralis in wild salmonid populations and sentinel fish in the mainstem of the Logan River and two of its tributaries. In addition, I investigated the potential influence of biotic (e.g., food availability, M. cerebralis prevalence) and abiotic factors (e.g., temperature) on the distribution abundance, and condition of salmonid fishes. Differences in mean temperature and discharge across sites explained most (>70%) of the variability in prevalence of M. cerebralis observed along the Logan River. However, the prevalence of the parasite was not related to other factors that can influence its life cycle, such as productivity and substrate composition. The results also indicate that the fish fauna presents a longitudinal change reflected in a zonation pattern. Cutthroat trout dominates the headwaters and high-elevation reaches, while reaches at lower elevations of the mainstem and tributaries were dominated by brown trout. The transition between these species was consistent with changes in environmental characteristics. Cutthroat trout dominates the fish community in mainstream reaches with the lowest average minimum temperature and highest diel temperatures, and where small boulders and small cobbles are the predominant substrate. This study provides insights of the abiotic and biotic factors that affect the distribution, abundance, and condition of salmonid populations along the Logan River. Identifying these factors is crucial to effectively manage this and other trout streams, where ensuring the conservation of native cutthroat trout populations is a priority. Further, I present baseline information of the potential linkages between environmental factors and M. cerebralis distribution and prevelance, which could be used to develop plans to minimize the potential negative effects of this parasite on wild salmonid populations.

Non-native species are increasing globally, and with this increase, it is likely that there will be new, unique relationships found among non-natives as well as additional impacts on native species. Rats and mongooses have been introduced to islands throughout the world where they impact native species, including birds, reptiles, and amphibians. The coqui frog was introduced to Hawaii in the 1980’s, where there were already abundant rat and mongoose populations. Previous research suggests that the high densities of coqui frogs may provide enough of a new food source for mongooses and rats that their populations would grow larger than they would without coqui frogs, and that this would exacerbate the negative effects that these predators have on native birds. We investigated whether there are relationships between coqui presence, and the local abundance of introduced rats and mongoose on the island of Hawaii. We also investigated at these 12 sites whether there were indirect effects of coquis on bird nest predation rates using camera traps on artificial nests. Finally, we interpret our results in light of an analysis of the stomach contents of mongooses and rats, and data collected from remote cameras monitoring scavengers of dead coqui frogs. We compared abundances of mammals in coqui invaded plots and uninvaded plots. In areas where coquis were present, we found a greater number of mongooses, and less Pacific rats. Both predators consume coquis, but mongooses were more important consumers of live and dead coquis. Shifts in mongoose and rat diets were observed in coqui invaded and uninvaded plots. It may be that coqui frogs are competing with rats because we found more fruit in rat stomachs collected in coqui invaded compared to uninvaded plots. We did not observe any difference in nest predation rates with and without coquis. Our results show that the coqui may serve as novel prey and/or competitors to non-native mammals.

Users of the Instream Flow Incremental Methodology CTFIM) commonly assume that there is a positive linear relationship between available habitat (WUA) and stream fish biomass. However, several studies have shown a lack cf correlation between WUA and biomass. Such poor relationships may occur if other factors limit fish abundance. Food availability is a potentially important factor limiting abundance of stream fishes and can affect blomass by influencing fish condition (individual weight). I collected rainbow trout (Oncorhynchus mykiss) exposed to different levels of invertebrate-drift density to determine if condition was greater where food was more abundant. I also examined whether size-selective predation and gut fullness varied with drift density. Size-selective predation was not related to drift density. However, condition and gut fullness were both significantly correlated with drift density. Furthermore, changes in drift density appeared to have a stronger influence on small-trout condition than large-trout condition. The results of this study and others support the contention that the reliability of the IFIM might be improved if food availability were incorporated into models.

Bear Lake, a large oligotrophic lake (282 km2), was studied from October 1986 to December 1987 to determine the temporal changes in the zooplankton assemblage at one site in the pelagic zone and one in the littoral area. In this study, species composition, abundance, biomass, and size frequency distribution were determined. Additionally, chlorophyll a, water transparency, and temperature and oxygen profiles were measured to help interpret zooplankton changes during the study. The zooplankton species assemblage comprised eight species of cladocera, seven species of copepods, and five species of rotifers. The abundance and biomass of the zooplankton assemblage, particularly that of crustaceans, were very low and comparable with those of oligotrophic systems. Mean densities of crustaceans in the pelagic zone, excluding copepod nauplii, varied from 250 to 1,700 organisms/m3. The analysis of the size structure of the zooplankton indicated the dominance of small organisms and the scarcity of large organisms, particularly cladocera. The zooplankton assemblage in the littoral zone was similar in species composition, abundance, and size structure to that in the pelagic zone. Many results suggest the littoral zooplankton assemblage is an extension of the pelagic assemblage. Low zooplankton food resources and interference of calcium carbonate particles in the feeding behavior of crustaceans are suggested as the primary factors controlling the low abundance and biomass of zooplankton in Bear Lake. Size-selective fish predation probably causes the assemblage to be dominated by small species. The analysis of Epischura nevadensis, the dominant species in the system, indicated that this species is bivoltine in Bear Lake. In the spring and summer, adult E. nevadensis were more abundant in the littoral zone, whereas copepodites were more abundant offshore. The low density, biomass, and small size structure of the zooplankton in Bear Lake limits its importance as a source of food for fishes.

Climate change is expected to continue to cause large increases in temperature in Arctic and sub-Arctic ecosystems which has already resulted in changes to plant communities; for example, increased shrub biomass and range. It is important to understand how warmer temperatures could affect the plant community in a wetland system because this region provides crucial high-quality forage for migratory herbivores during the breeding season. One mechanism by which warming could cause change is directly, where warming influences the vital rates of a species; these effects may be either positive or negative. Warmer temperatures may also affect a species indirectly, by impacting neighboring plants which compete with, or facilitate that species. Altering interspecific interactions may affect the abundances of the surrounding species. Recent research shows these ‘indirect’ effects which are mediated by biotic interactions may be important enough to reverse ‘direct’ effects of climate change in some plant communities. Furthermore, herbivores have been shown to mediate the effects of warming, in some systems, even preventing shrub expansion. However, the abundance of herbivores may change because of climate change so it is important to understand the role of herbivores in mitigating climate change effects to inform management strategy. Therefore, we aimed to determine the importance of direct and indirect effects of warming on this plant community while considering changing herbivore pressures. We conducted a two-year field experiment in the coastal wetlands of western Alaska to investigate how warming and herbivory will impact the abundances of two common species, a sedge and a dwarf shrub. We used the results from the experiment to predict the equilibrium abundances of the two species under different climate and herbivory scenarios and determine the contribution of direct and indirect effects to predicted community change. The sedge, Carex ramenskii, remained dominant in under ambient conditions, but the dwarf shrub, Salix ovalifolia, became dominant in warmed treatments. Herbivory mediated some of the effects of warming; where grazing was present community composition did not change as much as where it was not grazed. Results suggest that in the absence of goose herbivory, a 2°C increase could cause a shift from sedge to woody plant dominance on the coast of western Alaska. However, if grazing pressure by geese continues at the present rate, it may help retain the current community composition, though herbivory pressure was not sufficient to entirely reverse the effect of warming. Finally, we found that direct effects were more important than indirect effects in causing changes to this plant community.

Herbivore abundances are determined by a set of interacting factors that vary among different habitat types. Specifically, herbivore abundances in monocultures and polycultures may be governed by the same set of factors but with varying influences in the different habitats. In addition, monophagous and polyphagous herbivores may respond differently to the same set of influencing factors. I examined several abiotic and biotic factors in manipulated monocultures and polycultures of Borrichia frutescens in a west central Florida salt marsh. The experimental plots differed in both plant diversity and aboveground habitat structure to see how each component of diversity contributed to variability in the abiotic and biotic factors and how those factors were related to differences in herbivore abundances. The monoculture treatment involved clipping all above ground non-host plant material to achieve a host plant monoculture. The polyculture treatments involved pinning all non-host plant material to achieve a polyculture with reduced above ground habitat structure. The second polyculture treatment was a control in which the naturally diverse plots were unmanipulated. Two monophagous and one polyphagous herbivores were chosen for this study because of their abundance and availability in the field. The two monophagous herbivores on the host plant Borrichia frutescens were Pissonotus quadripustulatus (Homoptera:Delphacidae) and Asphondylia borrichiae (Diptera: Cecidomyiidae) both of which have been well studied in the field where the current experiment took place. The polyphagous herbivore was Cyarda acutissima (Homoptera: Flatidae), a poorly known invasive from Cuba. Soil salinity and host plant leaf nitrogen content were the abiotic factors measured. Herbivore abundances, percent egg and gall parasitism by parasitoids, spider abundances on host plant stems and ground spider abundances were the biotic factors measured. Both salinity and host plant leaf nitrogen were significantly different among the different treatments with clipped plots having the highest salinity and leaf nitrogen content. Population densities of both of the monophagous herbivores were not significantly different between treatments. The polyphagous herbivore had significantly higher abundances in the pinned and control plots than in the clipped plots. Stem spider abundances were not significantly different among treatments. Ground spiders, however, were significantly more abundant in control and pinned plots than clipped plots. Parasitism of both monophagous herbivores was not significantly different between treatments but was generally higher in the control plots. The results suggest that for monophagous herbivores bottom-up and top-down factors act antagonistically in monocultures but for the polyphagous herbivore, the presence of multiple host plants is more influential in diverse plots even given the higher abundances of generalist predators.

Biological processes like species interactions and patterns such as abundance and distribution observed in nature can vary depending on the scale at which the subject of interest is evaluated. Knowing that there is no single natural scale at which systems should be studied, in this thesis, I conducted a series of basic and applied ecological approaches in order to examine the phenomena that can occur at different scales of space, time, and ecological organization. Species abundances can vary over large spatial and temporal scales. By studying the habitat use of an abundant species, which uses a wide range of habitats, insights can be gained into how seascape-scales might influence population-level patterns. Similarly, temporal scales might affect the dynamics of species that have complex life cycles where migration is involved. Therefore, in the first study I used an eight-year dataset to conduct a population-level study at broader time- and seascape- scales of an abundant species in Tampa Bay, Florida. The goal of this study was to provide the first in-depth study on the habitat use of Pinfish on the eastern Gulf of Mexico and to provide insights on how seascape-scales can influence their abundance and distribution. Predator-prey interactions can be influenced by habitat at different spatial scales. In seagrass systems, blade density can provide prey refugia at local scales, which are further embedded within the seascape-scale effect of turbidity. In the second study, I used a combination of in situ field experiments and laboratory-controlled experiments to examine and separate the effects of habitat across these local and seascape scales on the relative predation rates of tethered Pinfish (Lagodon rhomboids). The broad-scale analyses indicated that population-level differences, such as abundance patterns and distribution can be influenced by temporal and spatial scales. Field- studies showed that habitat can influence ecological interactions at local- and seascape- scales. Overall, this research demonstrates the importance of using multiple spatial and temporal scale approaches when studying ecology, especially of those organisms that move over large distances and have complex life histories.

Changes in species abundance and richness, stand structure, and species responses to habitat characteristics including disturbance intensity, were investigated in 28 permanent sample plots (PSP) covering a total area of about 6.2 hectares of subtropical rainforests in north-east New South Wales, Australia. The disturbance that occurred over 36 years previously varied from unlogged (controls), through single-tree selection (light), moderate selection and repeated single-tree selection to intensive (heavy) logging. Multivariate and univariate approaches were used to investigate changes in various plant groups, including all vascular plants, regenerating species (trees and understorey species > 1.3 m in height and < 10 cm diameter at 1.3 m above the ground level (dbh)), juvenile trees (regenerating species capable of attaining at least 10 cm dbh), and trees ¡Ý 10 cm dbh. In addition, dynamic parameters (recruitment, growth and mortality) were estimated using hierarchical multilevel modelling and parameter estimates used to simulate behaviour of the subtropical rainforest tree species in unlogged and logged stands, both within and beyond the range of available data.Chronological post-disturbance responses and changes in species abundance and richness as well as stand structure for trees ¡Ý 10 cm dbh were investigated using 20 PSP in a bid to better understand rainforest post-disturbance regeneration. The results portrayed minor and gradual ecological changes in the undisturbed controls analogous with natural forest dynamics where the changes were not significant. In logged sites, initial gradual changes were followed with more rapid and significant changes.In both unlogged and logged stands, the changes proceeded through three clearly identifiable stages. The first two stages lasted between 5 and 15 years each. In the initial stage, the number of individuals decreased in species with high frequency mainly in the shade tolerant species, with little or no change in species richness. In the second stage, species abundance and richness changed due to localised species turnover, replacement and losses with very little recruitment, and the numbers of both speciesand individuals declined to minima. In the third stage, due to recruitment beyond the 10 cm dbh, the net loss of species and trees ¡Ý 10 cm dbh were halted and reversed, and species diversity and abundance began to return to pre-disturbance levels.Species abundance and diversity for both shade tolerant and intolerant species in less intensively logged sites (single-tree selection logging) have recovered to levels comparable with that observed in the controls, but more intensively logged sites have not recovered to similar levels. Increased logging intensity was associated with increased and decreased densities in the shade intolerant and ¨Ctolerant species respectively. It was evident that stand structure in logged sites had yet to recover to levels comparable with that of unlogged controls. It appears the restoration of floristic diversity to levels similar to that of intact primary forest takes considerably less time than structural recovery. Changes in regeneration patterns in a subtropical rainforest in north-east New South Wales were investigated for a 13-year period during the 3rd and 4th decades following repeated single-tree selection logging. Multivariate and univariate analyses results showed that there were no significant differences in floristic assemblages within and between censuses; however, two contrasting trends of changes in plant groups were detected. In trees ¡Ý 10 cm dbh, the stem density and species richness increased in shade tolerant group, and while stem density increased in the shade intolerant group, species richness decreased during the study period. Amongst smaller sized species including trees (< 10 cm dbh), a general decrease in species richness was observed along with significant changes in stem densities (P = 0.03) with the number of individuals in the shade tolerant species increasing, while that of both shade intolerant and vine species decreased. Excluding the vines and understorey species from the broader regenerating species group, revealed a decrease in species richness in juvenile canopy tree, and a significant change in densities (P = 0.004) with the number of individuals in shade tolerant increasing, while that of shade intolerant trees decreased. A comparison between the canopy trees ¡Ý 10 cm dbh and juvenile canopy trees group showed that these groups were tending towards similar floristic assemblages. These results suggest gradual replacement of shade intolerant by shade tolerant species as stands were tending toward later stages of recovery within the regeneration. The results also show that the inclusion of regenerating species in long-term studies is both complementary to the larger plant component and more revealing of both trends and changes.Species-specific estimates of shade tolerance and size structure at maturity derived from observations on 23 plots were used to intuitively group 277 vascular plant species into 3 main groups including full floristic (all together), shade tolerant and intolerant groups. The shade tolerant and intolerant groups were further grouped into smaller plants groups depending on the development stage and maximum size at maturity. These groups included regenerating species, juvenile trees, and trees ¡Ý 10 cm dbh. Multivariate analyses of these nominated groups revealed that floristic assemblages were significantly associated with environmental gradients based on simple site characteristics.At the landscape (larger) scale, the floristic assemblages were significantly different between low (200-400), mid (400-700) and high altitude (over 700 meters above sea level). In addition, abundance of shade tolerant species including Doryphora sassafras Endl, Orites excelsa R.Br and Caldcluvia paniculosa (F.Muell) Hoogland was positively correlated with the altitudinal gradient. At the smaller (local) scale, intensively logged sites where large gaps were created had recovered their species richness, but effects of past logging were evident in trees ¡Ý 10 cm dbh, especially trees greater than 50 cm dbh where species abundance in shade tolerant decreased significantly. Less intensively logged sites at mid altitude where a few stems were removed had recovered their species richness in respect to trees ¡Ý 10 cm dbh, but the small gaps created may have healed quickly for appreciable regeneration response to occur, as juvenile trees component was significantly different to that of the (unlogged) controls.The abundance of shade intolerant and juvenile shade tolerant tree species increased in concert with levels of disturbance and abundance of shade intolerant species such as Duboisia myoporoides R.Br, Acacia melanoxylon R.Br, Rubus moorei F.Muell and R. hilli F.Muell was positively correlated with the disturbance gradient. Increase in number of individuals of certain tree species was positively correlated with both disturbance intensity and topography (mid slope through lower slope to creek/gully), but negatively correlated with aspect (NE - NW). We concluded that logged sites are yet to recover their pre-logging stand structure and rainforest tree species were found in sites where favourable recruitment and growth conditions were the encountered. These results show that logged sites had not yet regenerated to the pre-logging stand structure. They also show that habitat characteristics including history of disturbance and topography can influence the floristic assemblages in the sub-tropical rainforests at both the small (local) and large (geographic) scales. This supports the environmental control model that states ¡°species are found at sites where they encounter favourable living conditions¡±. Site characteristics as surrogate for some of these favourable living conditions were identified as useful potential variables to investigate the rainforest dynamic parameters (growth, recruitment and mortality) in both logged and unlogged stands.A quantitative model was developed using over 3 decades of data to describe and simulate the dynamics including recruitment, growth and mortality in unlogged stands and others subjected to different silvicultural regimes in uneven-aged mixed-species subtropical rainforests of north-eastern New South Wales. Hierarchical multilevel regression analyses including Poisson, Binomial and multinomial logit regression were used to estimate the rainforest dynamic parameters based on the assumption that trees perform differently in space and time, thus there are variations at both the plot and tree by measurement levels.Variations at the tree level required the botanical identity of trees to species level, and then the species-specific size at maturity and shade tolerance were used to classify species into 5 groups, each consisting of species with similar ecological characteristics. These groups were labelled as emergent and shade tolerant main canopy, shade tolerant mid canopy, shade tolerant understoreys, moderate shade tolerant and persistent, and shade intolerant pioneer tree species. Significant variables at the plot level including site characteristics such as topography (elevation, slope and aspect), and past disturbance were used as explanatory variables in species group models. The final model is as a classical matrix management-oriented model with an ecological touch and maximum size-dependent parameters of ingrowth and outgrowth. The model provides a tool to simulate stand performance after logging and to assess silvicultural prescriptions before they are applied in these types of forests.The simulations indicate that full recovery following a logging intensity where 47% of the overstorey basal area is removed with a checkerboard of logged and unlogged patches (group selection) on a 120-year cycle could enable sustainable timber production without compromising the ecological integrity in these forests. Following single-tree selection (33%), recovery takes about 150 years, and more intensive harvesting practices where 50-78% overstorey basal area is removed may take 180-220 years to recover. Pre-harvest climber cutting coupled with poisoning of non-timber species followed by intensive logging of merchantable trees would allow logging on a 300-year cycle. Shorter logging cycles may lead to changes in the forest structure and floristic composition where the overall species density is low with higher density of shade intolerant species.

In this thesis we investigate the large-scale distribution of Ly alpha forest absorption, the effect of ionizing radiation from QSOs on their surrounding intergalactic medium and the primordial abundance of deuterium. We develop a new technique for detecting structure on Mpc scales in the Ly alpha forest. This technique does not rely on identifying individual absorption lines but is rather based on the statistics of the transmitted flux. We demonstrate that the new method is significantly more sensitive to the presence of large-scale structure in the Ly alpha forest than a two-point correlation function analysis. We apply this method to 2 A resolution spectra of ten QSOs which cover the redshift range 2.2 < z < 3.4. The QSOs form a closely spaced group on the sky and are concentrated within a 1-deg^2 field. We find evidence for large-scale structure in the distribution of Ly alpha forest absorption at the > 99 per cent confidence level. Along the line of sight we find overdense Ly alpha absorption on scales of up to 1200 km s^-1. There is also strong evidence for correlated absorption across line of sight pairs separated by < 3 h^-1 Mpc. For larger separations the cross-correlation signal becomes progressively less significant. Using the same technique and dataset we confirm the existence of the proximity effect. We derive a value for the mean intensity of the extragalactic background radiation at the Lyman limit of J = (3.6^+3.5_-1.3) x 10^-22 ergs s^-1 cm^-2 Hz^-1 sr^-1. This value assumes that QSO redshifts measured from high ionization lines differ from the true systemic redshifts by Delta v = 800 km s^-1. Allowing for known QSO variability we find evidence at a level of 2.1 sigma that the significance of the proximity effect is correlated with QSO Lyman limit luminosity. From the complete sample we find no evidence for the existence of a foreground proximity effect, implying either that J > 20 x 10^-22 ergs s^-1 cm^-2 Hz^-1 sr^-1 or that QSOs emit at least a factor of 1.4 less ionizing radiation in the plane of the sky than along the line of sight to Earth. We do, however, find one counter-example where a foreground QSO apparently depletes the absorbing gas in four surrounding lines of sight. We discuss the feasibility of pre-selecting absorption systems from low resolution data for a measurement of the primordial deuterium abundance. We present a new, low resolution spectroscopic survey of 101 high redshift QSOs aimed at identifying candidate D/H systems. We further present an echelle spectrum of a Lyman limit system at z = 2.917. We find that this system is most likely heavily contaminated and does not yield an interesting limit on D/H.

<p>Climate and environmental change following the retreat of the last glacial ice sheet in the Antarctic Peninsula has been interpreted, employing diatom abundance, relative abundance of <i>Chaetoceros</i> resting spores and diatom assemblages as proxies. These together with sedimentological data and radiocarbon dating, suggest four major events that can be further subdivided.</p><p>Deglaciation ~13.2-11.5 kyr BP with ice shelf breakup and strong surface water stratification from melting ice. </p><p>Climate reversal ~11.5-9.0 kyr BP with turbulent water masses. </p><p>Climate optimum ~9.0-4.0 kyr BP with intrusions of northern ´warm` water masses. </p><p>Neoglacial ~4.0 kyr BP-present with extended periods of sea ice cover and increased storm frequency. </p><p>One aspect of climate change is the stability of marine based ice sheets, and the interaction with underlying sediment. A pilot study on characterizing sediment influenced by past ice streaming (Ross Sea) was performed using diatom, texture and chemical analysis. The results show that:</p><p>Diamictons are chemically and texturally well homogenized, whereas diatom assemblages suggest different degrees of stratigraphic mixing and reworking related to mode of glacial sediment transport. </p><p>Mud appears in different stratigraphic sections deposited in sub-ice shelf or ice edge environment, or through winnowing by currents. This is evident through stratigraphically-diverse diatom assemblages and texture. Most sediment characterized as mud is enriched in zinc (Zn). </p><p>Hemipelagic diatomaceous muds are enriched in barium (Ba) and the diatom assemblage is dominated by typical neritic post-glacial species.</p>