Dissertations / Theses on the topic '060299 Ecology not elsewhere classified'

This practice-based project articulates the notion of an autoethnographic transect using Walking Home, a particular journey that I made in 2009, as its foundation. Borrowing key terms from the fields of ethnography and ecology, the project articulates a new contribution to knowledge by expanding the notion of a transect and using methods appropriated from autoethnography to generate visual arts practice in the wake of a long distance walk. Walking from London, England to St. Gallen, Switzerland the journey was undertaken in the wake of my father’s death. The key principle this project takes from autoethnography is that the position of the emotive self, as researcher and researched, can offer unique insights into a given field. Methods borrowed from autoethnography and ecology are re-employed throughout a transdisciplinary practice and body of research that, through the development of an ecological from of subjectivity, articulates an autoethnographic transect. The project expands the scale of a transect, from a line drawn across a field, to a journey taken across Europe; one that is drawn, walked and talked into being. Walking Home is presented in a holistic form whereby contextual and critical work is interwoven with and within practice: writing, image making, performance and installation. This interwoven process, whereby the practice and research become an inherent part of each other, is exemplified through a body of work called Fondue, a performance, taking place as a dinner party, which has evolved out of my engagement with autoethnography. An exhibition took place in Spring 2015, the outcomes of which are folded into this thesis. Articulating the notion of an autoethnographic transect as a new method within the field of visual arts practice this thesis will be of interest to performance practitioners, artists and writers engaged with the field of walking as a form of practice or process.

The ecological importance of introduced mammalian predators is well acknowledged in New Zealand, however, little research has focused on the ecology of native avian predators and their role in communities. This study investigated the ecology of moreporks (Ninox novaeseelandiae) on Ponui Island, Hauraki Gulf, New Zealand between August 2007 and April 2008. The primary aim was to investigate the functional response of moreporks to availability of their prey. The contents of regurgitated morepork pellets were compared with relative abundance of prey taxa (invertebrates, small birds and rodents) over the study period. The diet consisted primarily of a range of invertebrate prey, particularly weta (Anostostomatidae and Raphidophoridae) and beetles (Coleoptera). Small numbers of vertebrate prey were recorded including rodents and birds. A positive relationship between the percentage contribution to pellet samples of certain taxa and their relative availability was found, and there were peaks in the occurrence of seasonally abundant taxa including cicadas (Cicadidae), and huhu beetles (Prionoplus reticularis). The tendency of moreporks to prey on abundant taxa indicates that they are unlikely to depress prey populations to low levels, and may have some degree of stabilising influence. A significant increase in the rodent component of the diet in April indicated that the risk to moreporks of secondary poisoning during mammalian pest control operations may vary considerably with the time of year. The secondary aims were to collect data on roost site characteristics and breeding success. Moreporks roosted at a mean height of 4m, and foliar cover at the 4-6m height tier appeared to be the most important characteristic of roost sites when compared with control sites. These findings suggested that moreporks were selecting roost sites with high overhead cover. Possible reasons for this include predator avoidance, avoidance of mobbing passerines, and the microclimate provided. None of three established pairs and two other birds were observed to establish a nest or breed successfully. Additionally, only three juvenile moreporks were sighted or heard across the 90ha study area suggesting low breeding success in 2007-08. This may have been influenced by a range of factors including 1), predation by the high densities of ship rats on Ponui, or other predators 2), a lack of suitable nest sites such as tree hollows in some areas or 3), competition for invertebrate prey with high densities of ship rats and North Island brown kiwi (Apteryx mantelli).

Endophytes are a unique group of microorganisms that spend at least part of their life cycle within plant tissues. These microbes are increasingly being recognized for their potential to improve the health and productivity of their host plants. Recent studies indicate that endophytes could also influence human health by altering the composition of chemical compounds within plants, thereby affecting their nutritional quality and flavor. In addition, the presence of endophytes in edible plant tissues could directly affect human health by introducing microbes that can stimulate the immune system or act as opportunistic pathogens in people with compromised immune systems. However, despite their potential importance for plant and human health, these plant-associated microbes have been understudied due to a lack of visible symptoms associated with their presence and difficulty in isolating them from plant tissues. In the present studies, we hypothesized that endophytes play an important role in carrot, one of the most important vegetable crops in the world.

Carrot is well known as an important source of vitamins, antioxidants and other nutrients in the human diet, and carrot taproots are often consumed raw. Carrot crops are slow to establish and are subject to assault by a wide range of pests that negatively affect the health and productivity of this crop, as well as the storage potential of its taproots. Consequently, the aim of these studies was to examine endophyte dynamics in carrot. Studies were carried out in field, greenhouse and laboratory trials using a diverse set of carrot genotypes with broad genetic backgrounds and physiological characteristics. Endophyte communities were studied using traditional culture-based techniques, along with low and high throughput sequencing technologies.

Results of these studies demonstrate that carrot seeds and taproots are colonized by an abundant and diverse set of endophytic microbial taxa. Many of these endophytes could solubilize phosphorous, fix atmospheric nitrogen, produce siderophores and auxin and suppress infection by a key carrot pathogen, Alternaria dauci, demonstrating their potential importance for maintaining carrot health and productivity. Some of the endophytes identified in these trials were vertically transmitted to progeny inside carrot seeds, indicating that they could be part of a core microbiome that evolved alongside carrot plants, and are likely to be critical in early seedling establishment. We also determined that carrot endophytes could be acquired via horizontal transmission from soil with greater soil health in an organic relative to a conventionally managed system resulting in greater populations of endophytes with antagonistic activity against A. dauci. Finally, endophyte communities varied among the genotypes evaluated in this study, with some being more responsive to the presence of greater populations of beneficial endophytes in their environments. This indicates that it could someday be possible to begin selecting for these beneficial plant microbial relationships in breeding programs.

Based on the results of these studies, we conclude that endophytes do indeed play an important role in carrot. Additional research aimed at determining how these microbes functionally interact with carrot plants and identifying practical approaches to manipulate these communities to enhance the productivity and quality of carrot taproots, are recommended. A new isolation technique identified in these trials will aid in these efforts.

The population genetics of species occupying formerly glaciated regions are not only impacted by glacial retreat but also agricultural land use that is typical of such regions. Areas which have experienced glaciation often display a lowered amount of genetic variability and minimal population structure, and these effects become more predominant with increasing distance from a potential refugial population. Meanwhile, agricultural land use over the recent past has also been demonstrated to disrupt population structure distribution through disturbance regimes. The purpose of this study was to assess potential post-glacial and agricultural effects on populations of creek chub (Semotilus atromaculatus) in two agricultural watersheds that differ in the glacial history. The Saint Joseph River (SJR) watershed, Indiana and Michigan, USA was entirely glaciated during the last glacial maxima, while the Little Miami River (LMR) watershed in Ohio, USA, is situated on the boundary of the glacier. The degree of agricultural land use also varies between and within the two watersheds. Using eight microsatellite loci, 312 individuals were genotyped from 13 sites in SJR and 2,318 individuals from 29 sites in LMR. Measures of genetic differentiation showed that there was strong differentiation between watersheds. Analyses within watersheds recovered additional but weaker differentiation that was mostly associated with the geography of sub-watersheds and isolation by distance. Proximity to the glacial boundary appeared to play a minimal role in genetic differentiation and genetic variation. Differentiation among localities was not directly associated with the glacial boundary within LMR, and localities in this watershed had lower allelic richness and heterozygosity than those in the fully glaciated SJR. After accounting for the positive correlation of stream distance in LMR using partial Mantel test, both glacial history and agricultural land use were positively correlated with genetic differentiation. However, these predictor variables were also strongly correlated with one another which prevented disentangling the two potential effects. Within SJR, no 10 relationship of genetic differentiation with agricultural land use was recovered. My study shows that there is not a simple relationship between glacial history, contemporary land use, and genetic differentiation in creek chub. Rather, it appears that the patterns of genetic variation observed may be more closely linked to the dispersal behavior of creek chub within and among watersheds, and the history of effective population size within watersheds.

Environmental DNA (eDNA) is being used increasingly for biomonitoring of communities (e.g., microbes, macroinvertebrates, fish species) across terrestrial and aquatic ecosystems. Developing methods that combine eDNA approaches with metagenomic barcoded amplicon sequencing (eDNA-metabarcoding) are now providing a powerful noninvasive and cost-effective means for comprehensively surveying biodiversity in a wide range of habitats. Invasive species have a substantial impact on the ecology and economics of the Great Lakes region, and eDNAmetabarcoding methods have recently been applied in monitoring non-native, as well as native, fish populations in the freshwater systems there. In this research, we validated an eDNAmetabarcoding approach that uses established platforms, the MiFish/MitoFish pipeline, for fish community monitoring on Lake Michigan. For validation, we compared survey results from our eDNA-metabarcoding approach to those obtained using traditional surveys (e.g., electrofishing and seining). We also sampled a closed 180,000-gallon freshwater fish tank system to see how well our methods characterized a known native fish population that resided in the tank. Finally, we applied the approach to monitoring invasive and native fish populations in southern Lake Michigan at a site that is currently undergoing restoration to improve the aquatic habitats.. We were able to reliably capture the fish community structure of the native fish tank as well as those of open waters on the lake using our methods. Diversity patterns detected at the restoration site using our eDNA-metabarcoding approach accurately reflected those of the historical record, which have taken many years to establish by conventional means. Overall, this study suggests eDNAmetabarcoding is an efficient, credible, and powerful approach to biomonitoring.

As human activity expands across the globe, disturbance of wildlife by anthropogenic activities such as fragmentation of habitat, and wildlife-human conflicts escalate. The Pueblo of Santa Ana is receiving pressure from road expansion and urban development and is concerned with the impacts of those activities upon wildlife populations. Specifically, mule deer is a species of concern for their Department of Natural Resources (DNR). Mule deer are important economically, culturally, and for recreational purposes. The DNR understands the need for better understanding mule deer ecology to manage for potential conflicts in their interactions with expanding human infrastructure. My objectives were first to model mule deer habitat use in and around the Pueblo of Santa Ana during the summer and winter at different times of the day. My second objective was to understand the relative impacts of different scenarios for road development in the Pueblo of Santa Ana upon the disturbance of mule deer using an Individual Based Modeling (IBM) framework.

Using Geospatial Positioning System telemetry collar data collected on mule deer I used proximity based habitat predictors in a general linear mixed model to create resource selection functions. Generally I found that the season had a greater impact on mule deer habitat use than the time of day. Female and male mule deer select for similar habitat but sexually segregate in their summer distributions. My findings are consistent with results from other locations where mule deer studies have been conducted. In chapter two, I used the Simulation of Disturbance Activities (SODA) modeling framework to investigate the impact of vehicles on mule deer disturbance response behaviors, alert and fleeing. Using this framework I compared a baseline scenario to road expansion scenarios (DamRoad, ByPass, DeerCrossing) estimating the frequency of disturbance behavior of mule deer for each such scenario. My results show that mule deer were disturbed most in the baseline model. There were no significant differences in the frequency of disturbance for female mule deer across scenarios. Male mule deer did have some significant differences in alert and fleeing behavior across scenarios. My results may be a function of assumptions made in my modeling. Specifically, I assumed that mule deer would shift their areas of activity to new portions of the Pueblo of Santa Ana in response to altered habitat quality caused by new roads. If mule deer did not shift their areas of activity accordingly, my models may provide inaccurate assessments of disturbance patterns.

In conclusion my findings are similar to results from other locations. Specifically, the inferences that roads and road development are important to consider for mule deer management transcends variation associated with the unique characteristics of the Pueblo of Santa Ana mule deer population. Finally, my results suggest that the use of an IBM modeling framework has the potential to provide insights into the disturbance of mule deer by vehicular traffic even if my conclusions were constrained by study design.

Elucidation of habitat and resource use patterns is important for facilitating sustainable management of fisheries. Discrete habitats in large aquatic ecosystems may offer distinct resources and differentially affect performance. Movement of organisms and organic materials links these habitats and potentially leads to spatially complex trophic pathways between basal resources and consumers. Habitat and resource use are commonly explored via two common methods: stable isotopes and morphometric analysis. The first research chapter of this thesis employed both methods to investigate seasonal habitat use of yellow perch Perca flavescensin eastern Lake Michigan and connected waterbodies known as drowned river mouth (DRM) lakes. Landmark-based geometric morphometrics was used to compare shape differences among habitats. Stable isotopes of ambient water, otoliths, and soft tissues were compared to differentiate among habitats. Both methods provided evidence of resident nearshore Lake Michigan fish, resident DRM lake fish occupying the littoral zone, and transient Lake Michigan fish occupying the profundal zone of DRM lakes. The majority of transient Lake Michigan fish moved into the profundal zone of DRM lakes in the fall. These results support previously published genetic data of distinct populations of yellow perch in eastern Lake Michigan and connected waterbodies. The second research chapter of this thesis also employed stable isotopes and morphometric analysis, but to investigate the consistency of resource use of age-0 yellow perch in Saginaw Bay, Lake Huron. These methods served as long-term diet indicators, as compared to short-term stomach contents analysis. Both stable isotopes of soft tissues and morphometric analysis showed spatial consistency in variation among sites. Fish from the two sites closer to the tributary input had higher δ¹⁵N values and more fusiform bodies, while fish from the third site further away from the tributary had lower δ¹⁵N values and were deeper-bodied. This spatial variation supports stomach content analysis of age-0 yellow perch from a previously published study. δ¹³C ratios displayed annual variation, and while inconsistent with stomach content analysis, was consistent with available prey items. The findings from this study suggest that young yellow perch in Saginaw Bay have limited movement and forage in a similar area to where they were collected. Previous studies have found discrepancies among indicators and have cautioned generalization of trophic relationships when only relying on a single metric. Agreement between complementary techniques provided additional support to previously-published genetic results and stomach content data, and thereby helped more fully describe habitat use by yellow perch in these systems.

Disturbance regimes like freezing and thawing (FT) can have potentially significant impacts on nutrient release from soil and are predicted to increase with climate change. This is particularly important in biogeochemical hotspots like floodplains that can both remove and release nutrients to surface waters during flooding. Connection between the river and floodplain can improve water quality by reducing nutrient loads through microbial processes and sedimentation. However, conditions during flooding can also lead to phosphorus (P) release from pools that are not normally bioavailable. Disturbance events like FT can also lead to changes in bioavailable P due to microbial cell lysis. This study investigates differences in P chemistry and flux during flooding from intact soil cores that have undergone a FT cycle compared to soils that have not undergone freezing. Floodplain soils were collected from four sites along the Wabash and Tippecanoe Rivers in Indiana. We hypothesized that (i) the primary pools of P within the soil would change with freezing (ii) and flooding; (iii) frozen treatment cores would release more P during flood incubations than unfrozen control cores; and (iv) processes controlling P release during flood incubations would change after FT due to changes in the primary pools of P in the soil cores.

On average, soil cores that underwent FT released greater amounts of P than unfrozen cores over the course of the 3-week experimental flood incubation. Phosphorus release in both unfrozen control and FT treatment cores during flooding was explained in part by soil extractable Al and Fe and redox status; however, P release was influenced by soil Ca-P in the FT cores to a greater extent than unfrozen cores. Phosphorus release in FT cores occurred faster than in control cores with overlying water concentrations peaking 2 weeks after onset of flooding, followed by lower concentrations at 3 weeks. Whereas control cores had some release and uptake early on but then released P throughout the 3-week incubation—supporting the hypothesis that drivers of P release were different after FT. Interactive effects of FT and flooding suggest that concentration gradients between soil pore water and overlying surface water could have enhanced dissolution of the Ca-P pool, highlighting the importance of floodwater chemistry to P dynamics following FT. This study provides an important link between observed winter floodplain P loss and potential drivers of release and retention, which is critical to informing floodplain restoration design and management through all seasons.

Pathogens and parasites are increasingly recognized as important components within host populations, communities, and ecosystems. Parasite contributions to ecosystem function most likely manifest as density-mediated impacts of parasites on their hosts, the direct contributions of parasite biomass to a system, and via parasite-induced changes in host behavior and physiology (trait-mediated impacts). Here, a framework was constructed that can be used to conceptualize parasite contributions to ecosystem function (Chapter 1). Then the influence of parasite attack on host movement was explored to further evince the mechanistic underpinnings of trait-mediated parasite impacts (Chapter 2). Additionally, mesocosms were created across a gradient of parasitism to examine how these mechanisms are likely to unfold at larger biological scales (Chapter 3). Lastly, a series of differential equations was created to model host-parasite-ecosystem interactions and generate theoretical predictions about how and when parasites are likely to influence ecosystem processes (Chapter 4). Parasites have many characteristics of ecosystem engineers, but their role has historically been ignored. These studies begin to explore the role that parasitism may have as one of the drivers of ecosystem processes.

Forest canopies are a critical component of forest ecosystems as they influence many important functions. Specifically, the structure of forest canopies is a driver of the magnitude and rate of these functions. Therefore, being able to accurately measure canopy structure is crucial to ensure ecological models and forest management plans are as robust and efficient as possible. However, canopies are complex and dynamic entities and thus their structure can be challenging to accurately measure. Here we study the feasibility of using lidar to measure forest canopy structure across large spatial extents by investigating the compatibility of aerial and terrestrial lidar systems. Building on known structure-function relationships measured with terrestrial lidar, we establish grounds for scaling these relationships to the aerial scale. This would enable accurate measures of canopy structural complexity to be acquired at landscape and regional scales without the time and labor requirements of terrestrial data collection. Our results illustrate the potential for measures of canopy height, vegetation area, horizontal cover, and canopy roughness to be upscaled. Furthermore, we highlight the benefit of utilizing multivariate measures of canopy structure, and the capacity of lidar to identify forest structural types. Moving forward, lidar is a tool to be utilized in tandem with other technologies to best understand the spatial and temporal dynamics of forests and the influence of physical ecosystem structure.

Tropical ecosystems play a key role in regulating the global climate and the carbon cycle thanks to the large amounts of water and carbon exchanged with the atmosphere. These biogeochemical fluxes are largely the result of high photosynthetic rates. Photosynthetic activity is highly dependent on climate and vegetation, and therefore can be easily modified along with changes in those two factors. A better understanding of what drives or alters photosynthetic activity in the tropics will lead to more accurate predictions of climate and subsequent effects on ecosystems. The seasonal pattern of photosynthetic activity is one of the main uncertainties that we still have about tropical ecosystems. However, this seasonality of tropical vegetation and its relationship to climate change and land cover is key to understanding how these ecosystems could be affected and have an effect on climate.

In this dissertation, I present three projects to improve our understanding about tropical ecosystems and how their photosynthetic activity is affected by climate and land cover change. The lack of field-based data has been one of the main limiting factors in our study of tropical ecosystems. Therefore, in these projects I extensively use remote sensing-derived data to analyze large scale and long term patterns. In the first study, I looked at the seasonal relationship between photosynthetic activity and climate, and how model simulations represent it. Vegetation in most of the tropics is either positively correlated with both water and light, or positively correlated with one of them and negatively with the other. Ecosystem models largely underestimate positive correlations with light and overestimate positive correlations with water. In the second study, I focus on the effect of land cover change in photosynthetic activity and transpiration in a highly deforested region in the Amazon. I find that land cover change decreases tropical forests photosynthetic activity and transpiration during the dry season. Also, land cover change increases the range of photosynthetic activity and transpiration in forests and shrublands. These effects are intensified with increasing land cover change. In the last project, I quantify the amount of change in evapotranspiration due to land cover change in the entire Amazon basin. Our remote sensing-derived estimates are well aligned with model predictions published in the past three decades. These results increase our confidence in climate models representation of evapotranspiration in the Amazon.

Findings from this dissertation highlight (1) the importance of the close relationship between climate and photosynthetic activity and (2) how land cover change is altering that relationship. We hope our results can build on our knowledge about tropical ecosystems and how they could change in the future. We also expect our analysis to be used for model benchmarking and tropical ecosystem monitoring.

This thesis considers various aspects of the use of ground-based methods and remote sensing of Biological Soil Crusts (BSC). They are mostly distributed in winter rainfall dominated areas such as those at Middleback Field Centre (MFC) in South Australia. They can be used potentially as an indicator of rangeland condition by estimating grazing pressure (trampling). Two BSC based indicators for rangeland condition assessment are species composition and cover. While there is strong agreement that BSC composition is a good indicator, there is less agreement that BSC cover alone is a good indicator. Although BSC have been included in previous remotely-sensed studies, their spectral characteristics, and hence their contributions to remotely-sensed spectral signatures, are not well known. Data collection methods were refined for suitable method selection, stratification and site characterization, and morphological/ functional group classification. Cover data of BSC were collected using a 100 m line-intercept method on the stratified land units and statistical analyses were based on the cover variance analyses. Spectra of BSC groups were collected and characterized for different remote sensing indices. Five grazing gradient models based on collected spectra were developed for the evaluation of BSC effect on remotely-sensed data. Both existing and newly developed remote sensing indices were examined for BSC detection. Sampling for cover of BSC in the field showed that there is indeed a detectable change with distance from water, suggesting that BSC cover can be used as an indicator of rangeland condition, provided that appropriate stratification of the study sites is carried out prior to sampling, and spectral differences in morphological and functional groups are taken into account. Spectral analysis of BSC components showed that different classes of organisms in the crusts have different spectral characteristics, and in particular, that the (commonly-used) perpendicular vegetation index (PD54) is not suitable for detecting BSC. On the other hand, ground-level spectral modelling showed that the Normalized Difference Vegetation Index (NDVI) and Soil Stability Index (SSI) did show a distinguishable contribution from BSC. A procedure for detecting cover of BSC was developed for image taken during the period after an effective rain, in contrast to the normal practice of selecting images of dry surfaces for interpretation. The most suitable intervals appears to be 2-4 days after rain in late autumn, winter and early spring. Of the existing indices, the SSI is the best for estimating cover of BSC from Landsat images. However, eight new indices, specifically designed for detection of BSC were developed during the cource of this work. The best results were obtained for indices using using the middle-infrared bands. These results are promising for application to rangeland monitoring and suggest that BSC cover is an important indicator of rangeland condition if appropriate stratification, classification and data-collection methods are used. The effects of BSC cover on a remotely-sensed method are considerable, and thus they can not be neglected during image interpretation. There are different phenological patterns for BSC, annual and perennial elements, thus there is the possibility for the selection of imagery based on each phenological stage to detect these elements. Application of certain indices such as the PD54 may create mis-estimation of land covers. Although some of the existing and newly developed indices had significant results for BSC cover estimation, there is a requirement for a standalone remotely-sensed method to conclude the best index.