The Laguna Madre is a hypersaline lagoon. Despite harsh conditions, the upper Laguna Madre (ULM) is a highly productive ecosystem and a popular sportfishing area, especially for spotted seatrout and red drum. It is also the most important Texas bay for commercial fishing of black drum. TPWD’s Coastal Fisheries division began conducting routine monitoring of coastal fishery resources in 1977 to guide management. The goal of the present study was to improve understanding of spatiotemporal trends in relative abundance of selected fish and macro-invertebrate species in the upper Laguna Madre. I used TPWD’s bag-seine and water-quality data from the years 1985-2004 to examine variation in species’ relative abundances and relationships to several environmental factors. I hypothesized that one or more of these variables, alone or in combination, were related to spatial and temporal trends in community composition. I used detrended correspondence analysis (DCA) to measure species turnover (beta diversity) and to determine which model (linear or unimodal) of species response along a gradient to apply. I used canonical correspondence analysis to relate species abundances directly to explanatory variables. The explanatory variables were tested for significance and the variance partitioned among three groupings: temporal, spatial and environmental. DCA indicated complete species turnover along two dimensions: seasonal and spatial. It also indicated that a unimodal method such as CCA was appropriate for further analysis. The CCA model included 39 variables. The included variables explained 14% of the variation in species abundance in the data set. Since the first four axes explained 67% of the variation contained in the first two DCA axes, the chosen explanatory variables were sufficient to explain the majority of the tractable variation in species abundance. The variance partitioning procedure indicated that temporal effects were the most important in explaining species variation in the Upper Laguna, followed by the spatial component. The pure environmental component explained the least amount of variation. In this study, much of the variability in species abundance was due to the spawning patterns of estuary-dependent species, most of which spawn in the spring and summer months, leading to higher abundances from spring through fall.

This paper presents the R package anacor for the computation of simple and canonical correspondence analysis with missing values. The canonical correspondence analysis is specified in a rather general way by imposing covariates on the rows and/or the columns of the two-dimensional frequency table. The package allows for scaling methods such as standard, Benzécri, centroid, and Goodman scaling. In addition, along with well-known two- and three-dimensional joint plots including confidence ellipsoids, it offers alternative plotting possibilities in terms of transformation plots, Benzécri plots, and regression plots.

Bayesian Model Averaging (BMA) is a new area in modern applied statistics that provides data analysts with an efficient tool for discovering promising models and obtaining esti-mates of their posterior probabilities via Markov chain Monte Carlo (MCMC). These probabilities can be further used as weights for model averaged predictions and estimates of the parameters of interest. As a result, variance components due to model selection are estimated and accounted for, contrary to the practice of conventional data analysis (such as, for example, stepwise model selection). In addition, variable activation probabilities can be obtained for each variable of interest. This dissertation is aimed at connecting BMA and various ramifications of the multivari-ate technique called Reduced-Rank Regression (RRR). In particular, we are concerned with Canonical Correspondence Analysis (CCA) in ecological applications where the data are represented by a site by species abundance matrix with site-specific covariates. Our goal is to incorporate the multivariate techniques, such as Redundancy Analysis and Ca-nonical Correspondence Analysis into the general machinery of BMA, taking into account such complicating phenomena as outliers and clustering of observations within a single data-analysis strategy. Traditional implementations of model averaging are concerned with selection of variables. We extend the methodology of BMA to selection of subgroups of observations and im-plement several approaches to cluster and outlier analysis in the context of the multivari-ate regression model. The proposed algorithm of cluster analysis can accommodate re-strictions on the resulting partition of observations when some of them form sub-clusters that have to be preserved when larger clusters are formed. / Ph. D.

Tidal freshwater forest restoration after dam removal has been unexplored to date. This study elucidated pre-dam forest composition, as well as post-dam edaphic and microtopographical attributes and woody species recruiting along a narrow ecotone of a 29.3-ha tidal freshwater wetland. The ≈65-year-old historical forest (15 species, 200 stems ha-1) and ≈7-year-old contemporary forest (40 species and 11,009 stems ha-) community dominants were dissimilar (Fraxinus spp. vs. Liquidambar styraciflua, respectively). Pre-dam environmental conditions were unknown. Post-dam edaphic water content, organic matter, redox potential and microtopography differed significantly across tidal sites but were less variable in non-tidal sites. Shifts in the contemporary woody community composition and the concomitant increase in stem density and seedling:sapling ratios with elevation likely owed to significant changes in microtopography and edaphic attributes. Developing ecotones that contain variable microtopography may be extremely important for successful natural woody recruitment after dam removal from a tidal freshwater system.

Human activities, such as agricultural activity, housing construction, forest logging, etc., play an important role in vegetation changes. Any disturbance to the ecosystem by a severe change in landscape patterns may reduce the survival capacity of certain plant species. In recent years, many studies have used a geographic information system to establish spatial data on vegetation changes; this information includes both the plant species and their spatial structure. Therefore, the aim of this study is to investigate the trends and patterns of vegetation changes and the degree of correlation with the particular environmental features at Wangan Island and Chimei Island in the Penghu Islands, from 1979 to 2009. Both islands have very similar natural features, including geographic location, natural environment, and economic development, but the spatial structures of the land use type are different. The study makes use of geographic information systems, detrended correspondence analysis, canonical correspondence analysis and landscape ecological indicators as study tools. The results are expected to promote our understanding of the spatial distribution patterns of vegetation types and plant species. The results can be divided into three areas. First, both islands follow the same trend with regard to changes in land cover, but the rates of change are different. And the spatial structure of land use types affects the location of land cover types. Example, the centralized and decentralized villages both impact the distribution of the woodland. The mesh and ring road both impact the location of agricultural land. Second, the grassland plant species are correlated with the environmental factors, but the forest plant species are not. The major woodland specie is Leucaena leucocephala on both islands, whose physiological habits may reduce the degree of the correlation. Third, compared to the two islands, Chimei Island is more significant about that the vegetation types are correlated with the neighboring land use types. Finally, the plant species of the local vegetation types could be predicted by changes in the type of land use. In addition, this study has built a trend scheme of the spatial structure changes on Wangan Island and on Chimei Island, which can be used in the island¡¦s future environmental planning.

In this study, the hydrology and physical, chemical and biological variables of a shallow lake system including the Lakes Mogan and Eymir between 1997-2005 were evaluated. In Lake Eymir, a biomanipulation study was conducted between August, 1998 &ndash / December, 1999. Upon biomanipulation, Lake Eymir shifted to clearwater state with submerged vegetation domination during 2000-2003. However, in 2004, the lake shifted back to algae-dominated turbid state since the buffer mechanisms provided by submerged plants were absent. In the summer of 2005, fish kills were observed due to algal bloom. However, due to increasing hydraulic residence time in the lake, internal processes became more important for nutrients. Lake Mogan faces seasonal and interannual water level fluctuations. During the low water levels experienced in 2001 and 2005, which coincided with the high hydraulic residence times, the in-lake phosphorus amount was controlled by internal processes rather than external loading. Moreover, results revealed that hydrology and submerged plants were important in the ecology of Lake Mogan. Furthermore, the relationship between the phytoplankton, zooplankton and the environment in Lakes Eymir and Mogan, which was predicted via Canonical Corresponding Analysis, revealed that nutrients and water transparency were both important for plankton communities. Both the top-down and bottom up effects were valid in Lake Eymir, while only the bottom-up effect and submerged plants were important for Lake Mogan. Finally, the present study provided a good example for the submerged plant dominated clearwater state triggered by biomanipulation, and the impact of hydrology on the ecology of shallow lakes.

This project was designed to correlate environmental variables with the development of Pierce’s Disease (PD), an infection caused by the gram negative bacterium Xylella fastidiosa (Xf), in grapes (Hopkins et al. 2002). PD is one of the most difficult crop pathogens to manage because it is vectored by insects and its continued presence in the vine is usually fatal. PD is influenced by the interaction of host, disease and vector, and probably many other environmental variables. The general objective was to study and identify the most important variables involved in the expression of Pierce’s Disease. Over a two year period, from a total of eight sites in northern and southern California data was collected on forty-five environmental variables including those relating to soil moisture, soil chemistry, soil nutritional status, vine nutritional status, vine water status, in-season and dormant season climate, incidence of Xf in adjacent vineyard vegetation, sharpshooter species and abundance at each location, and proximity of vineyard field sites to citrus or riparian areas. The environmental variables were analyzed with canonical correspondence analysis (CCA) to determine significance of each as they correspond with increased disease severity. The significance of environmental variables produced by CCA indicates increased soil moisture as the leading cause for increased PD incidence; several other environmental variables positively correlate with increased disease presence. Conversely, vineyard factors identified by CCA as not conducive to disease formation may play an inhibitory role in PD severity. We undertook polymerase chain reaction (PCR) to test for the presence of PD in vegetative samples, using a 733 base pair probe specific to Xf. These samples indicate alternative hosts in adjacent locations which act as reservoirs of Pierce’s Disease as well as verifying diseased vines within the vineyard locations.

The occurrence of phytoplankton taxa, with special focus on harmful algal bloom (HAB) taxa, was monitored for one year off the central coast of California to examine both their co-occurrence and physical and chemical variables influencing their temporal patterns. Bi-weekly samples were taken from October 6, 2008 to October 5, 2009 in San Luis Obispo Bay, CA. Canonical correspondence analysis (CCA) of weekly samples indicated that 46.1% of the variability in species abundance was explained by the variables in the model, higher than previous reports. Cluster analysis divided phytoplankton communities into HAB and non-HAB groups of species, while shared distribution analysis identified specific co-occurring species of HABs. The HAB dinoflagellate group consisted exclusively of HAB taxa, including Cochlodinium polykrikoides Margalef, Dinophysis acuminata Claparède & Lachmann, and Alexandrium spp., and was correlated with a homogeneous water column and high nitrate concentration during the fall and winter seasons. The domoic acid producing diatoms Pseudo-nitzschia seriata (Cleve) H. Peragallo complex and Pseudo-nitzschia delicatissima (Cleve) Heiden complex grouped with several other non-HAB diatoms, and were correlated with warm, thermally stratified waters of the summer season. These results contradict the classic diatom / dinoflagellate succession theory and suggest that event-scale processes influencing water column stability within seasons may influence the distribution of HAB species in near shore upwelling dominated regions.

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This study investigated the impact of three edaphic factors on the distribution of forest plants in Sweden. Based on 2657 plots with 22 common species, Canonical Correspondence Analysis (CCA) and Generalized-linear-model (GLM) were performed with pH measurements in the top layer of the soil, latitude and deciduous tree proportion as explanatory variables. Variation of the species occurrence could to a substantial degree be explained by pH, latitude and proportion of timber volume of deciduous tree species. Furthermore, the majority of species were affected by the studied environmental variables. Therefore, these factors have an important role in the ecological interactions in the forest. All species also showed broad pH-niches with many occurrences spread out within the species entire pH-range. Finally, the study relates to educational science through designing a meaningful excursion for secondary school when teaching ecology.