Small herds of cows were observed and spatially mapped over continuous twenty-four hour periods. Treatments were implemented that investigated the effect of water site and supplementation on animal distribution patterns. A series of six observation periods constituted each observation series. Observation series were repeated winter (January) and summer (July) for two years. Forage conditions varied considerably between years and seasons. Three regression models for different periods related forage variables to animal use with R�� values ranging from 0.51 to 0.77. A spatial point analysis, Ripley's K, also discerned differences in spatial point arrangements related to differences in forage and season. It detected and quantified changes caused by locating a high-protein supplement in the pasture. Swale sites and slopes of less than 10 percent were preferred for grazing in all seasons. Water sources and shade trees were distribution focal points for three observation series. In the winter of 1998, animals spent more time on warmer sites. We recorded more cow activity and movement at night than other researchers. Resting areas had aspect and elevation attributes that relate to temperature regulation. Animal positions were analyzed to determine cattle subgroups. Forage availability and thermoregulatory needs influenced the distance between associated members. Social dominance and subgroup membership were closely related to the age of individual animals. A geographic information system based technique called multi-criteria evaluation was used to develop temporal/spatial models predicting cattle distribution across the landscape. Summer models worked better than winter models because water sources and shade sites were more consistent as focal points for cattle activities. / Graduation date: 2002

Riparian zones are critical habitats for management because of their importance for both cattle production and wildlife, and a high potential for resource conflicts. Riparian management should address habitat and microhabitat features that sustain both livestock production and wildlife diversity. I conducted a study to determine how small mammal distributions and abundance differ among 3 structurally different riparian habitats in eastern Oregon. The 3 habitat types, herbaceous, discontinuous willow, and continuous willow, represent a range of habitats typical of riparian zones in central and eastern Oregon. I estimated small mammal population sizes in 9 trap grids placed in riparian zones using capture-recapture techniques. Four species of small mammals were captured during 7 trapping periods from August 1994 to September 1995. Small mammal distributions and population sizes of each species varied both within and among riparian pastures. Montane voles (Microtus montanus) were the most abundant species in all grids. Deer mice (Peromyscus maniculatus) had high population sizes in grids with low montane vole populations and moderate to high willow cover. Competition with voles appeared to occur in riparian habitats of Bear Valley, and influenced the distribution and numbers of deer mice. Western jumping mice (Zapus princeps) were captured at relatively low numbers and almost exclusively in continuous willow habitats. Vagrant shrews (Sorex vagrans) were captured on all grids, and population sizes were small. Haying negatively affected survival rates of voles. Biomass, vegetation height, and percent ground cover were the habitat variables most frequently associated with occurrence of montane voles in Bear Valley. The probability of occurrence of this species was positively correlated with these habitat variables. Deer mice probability of occurrence was positively correlated with percent ground cover, plant biomass, and soil moisture. Most deer mice captures occurred in continuous willow habitats, and the number of captures increased with willow basal cover (R��=0.7579, P<0.001). Western jumping mice occurrence was positively correlated with plant biomass and soil moisture, and negatively correlated with distance from willow and percent ground cover. Western jumping mice also were more frequently captured in willow than nonwillow vegetation associations (P=0.054) within continuous willow habitats. Vagrant shrews were positively associated with plant biomass, vegetation height, and soil moisture. Small mammal habitat associations from my study sites in Bear Valley are in agreement with the literature, suggesting relatively consistent patterns in species-habitat associations. Distribution of small mammal species differed among pastures probably as a result of historical management practices. Alterations of riparian zone structure from historical management practices were evident in the study area, including elimination or decreased willow density, channel entrenchment, and invasion of riparian areas by xeric vegetation. Western jumping mice are apparently the most sensitive species in this area, requiring dense willow stands, suggesting that jumping mice could serve as an indicator species for riparian habitat condition. / Graduation date: 1997

Demographic characteristics of juvenile Dover sole (Microstomus pacificus) were examined in relation to physical and biotic factors to develop a hypothesis explaining annual variations in recruitment. Surveys were conducted along the Oregon continental shelf at depths between 50-400 m bimonthly during 1989 and annually (in March) between 1990 and 1993. To determine settlement timing, growth, and mortality, daily growth increments were validated, as was position of the first post-settlement annulus. A method of estimating precision of otolith elemental composition with the electron microprobe was developed; otolith microstructure and microchemistry were used to identify a landmark associated with settlement. Mean density of 0-group settlers varied annually, with 1989 and 1990 high, 1991 and 1992 low, and 1993 intermediate. 0-group abundance was correlated with fall offshore divergence one year before settlement and with southward geostrophic velocity during the summer before settlement. These conditions may be related to production of prey available to pelagic larvae. Density of 0-group Dover sole was highest between 100-119 m, but deeper areas were also utilized in years of highest abundance. Density was not correlated with spawning stock biomass or density of older juveniles. It was correlated with rex sole (Glyptocephalus [Errex] zachirus) density. Growth rate was positively correlated with mean April-October upwelling and was not related to density or mortality of Dover sole. First-year mortality was positively correlated with early settlement of 0-group larvae, possibly due to an advantage of settling and migrating to the primary nursery area well in advance of the spring transition. A multiple regression model predicting density of 1-group Dover sole from three physical environmental factors was applied to an independent time series of Dover sole "age-5" recruitment estimates (Turnock and Methot 1992). The model was a poor predictor of annual recruitment to fisheries but a good predictor of trends based on five-year running averages. Results suggest that multi-year trends in Dover sole recruitment to fisheries can be explained by a small set of density-independent physical factors. / Graduation date: 1995

The Sultanate of Oman has 1700 km of coastline extending from the Arabian Gulf south to the Arabian Sea. The demersal fish distributions and assemblages have not previously been well defined. In winter, variations in the oceanography of the area are minimal. In summer, however, the Arabian Sea is strongly influenced by the southwest monsoon. For this study the continental shelf off Oman was divided into eight regional areas and research trawl data on the distribution of demersal fish assemblages was studied using two forms of multivariate statistical analysis: two-way indicator species analysis and detrended correspondence analysis. The study was carried out to examine the influence on the species assemblages of geographical zonation, seasonal variation, and factors such as depth, time of day, and distance from untrawlable ground. There was seasonal variation in the fish assemblages and this variation was greatly influenced by the summer monsoon. Within each regional area depth appeared to be the major factor determining species distribution. In addition to the multivariate analyses, univariate techniques were applied to the catch rate data for forty commercial species to study in detail the influence of time of day and distance from untrawlable ground, factors which could potentially influence stock assessment estimates of fish biomass. Because the data were highly unbalanced, they were analyzed using General Linear Model with five factors, two continuous variables, and ten interaction terms to examine variation in the log-transformed catch rates. The factors time of day and distance from untrawlable ground, in combination with other factors, had significant effects on the catch rates for half of the species. / Graduation date: 1995

Pendent Usnea species were collected in western Oregon and examined. Character states, such as cortex-medulla-axis ratio; fibril length; papilla diameter; branching patterns; and presence or absence of fibrils, papillae, soredia, isidia; plus chemistry, were recorded and analyzed by inspection for differences. Historical names were researched in the literature. A comparison was made between species concepts used in these accounts, with many conflicting concepts encountered. Selected morphological characters were examined by scanning electron microscope, or dissecting microscope, described, and illustrated. The characters reviewed included articulate fissures; isidia and soredia; cortex-medulla-axis ratio; papillae; and foveate pits. Species determinations were made for field collections. Names were found for all specimens inspected without introducing new names at this time. Eight pendent species were found in western Oregon; they are Usnea cavernosa, Usnea ceratina, Usnea fillpendula, Usnea hesperina subsp. liturata, Usnea inflata, Usnea leucosticta, Usnea longissima, and Usnea merrillii. A practical key to taxa with descriptions is provided and geographic distributions are recorded in tables and maps. / Graduation date: 1995

The purpose of my research was to test the hypothesis that the availability of fresh, naturally occurring water may limit the distribution of Florida Key Deer (Odocoileus virginianus clavium). More specifically, I was trying to determine if there was enough fresh, drinkable water for the deer on each of the islands. To test the hypothesis, I developed a model that simulated likely seasonal fluctuations in fresh water availability in naturally occurring waterholes within the Key Deer range. I estimated 60 scenarios representing different weather (precipitation and evaporation) conditions, different literature estimates of the daily water requirement of Key Deer and also different upper salinity thresholds for drinkable water. Results showed that 1) even under the most favorable conditions in terms of fresh water availability, there was not enough fresh, drinkable water for the deer on any of the islands. Results also showed that 2) high salinity was important in determining the fresh water availability to the deer, in addition to the lack of water volume. Although these results suggest a prolonged seasonal shortage of fresh, naturally occurring water on each of the islands, deer were present on all of the islands during all seasons. One possible reason for the lack of correlation between Key Deer distribution and naturally occurring waterholes is the availability of man-made water sources (e.g. birdbaths, swimming pools).

The purpose of my research was to test the hypothesis that the availability of fresh, naturally occurring water may limit the distribution of Florida Key Deer (Odocoileus virginianus clavium). More specifically, I was trying to determine if there was enough fresh, drinkable water for the deer on each of the islands. To test the hypothesis, I developed a model that simulated likely seasonal fluctuations in fresh water availability in naturally occurring waterholes within the Key Deer range. I estimated 60 scenarios representing different weather (precipitation and evaporation) conditions, different literature estimates of the daily water requirement of Key Deer and also different upper salinity thresholds for drinkable water. Results showed that 1) even under the most favorable conditions in terms of fresh water availability, there was not enough fresh, drinkable water for the deer on any of the islands. Results also showed that 2) high salinity was important in determining the fresh water availability to the deer, in addition to the lack of water volume. Although these results suggest a prolonged seasonal shortage of fresh, naturally occurring water on each of the islands, deer were present on all of the islands during all seasons. One possible reason for the lack of correlation between Key Deer distribution and naturally occurring waterholes is the availability of man-made water sources (e.g. birdbaths, swimming pools).

In this study, annual variations in biochemical composition of seston and zooplankton community were investigated to characterize the nutritional environment of zooplankton in the Mersin Bay, NE Mediterranean Sea. For this goal, seawater and zooplankton samples were collected at monthly intervals from two stations / one representing coastal and other representing open waters characteristics from November 2004 to January 2006. Seawater samples were collected with Niskin bottles from the sea surface. Zooplankton samples were collected both in the horizontal and vertical plane by towing a Nansen net (70 cm mouth diameter with 112 &micro / m mesh). Surface seston chl-a, lipid, protein and carbohydrate concentrations were measured by fractionating seawater into three different size groups, 0.7-2.7, 2.7-18 and &gt / 18 &micro / m representing pico, nano and micro particulates in the seston. Zooplankton biomass and abundance were determined at four size fractions: 112-200, 200-500, 500-1000 and &gt / 1000 &micro / m / dry and organic weights were measured by gravimetric method and major taxonomic groups of zooplankton was identified under stereo-microscope. The nearshore station was always more productive than the offshore station in terms of chl-a, particulate organic matter (POM: protein+lipid+carbohydrate), zooplankton abundance and biomass. Chl-a maxima occured in spring and autumn at both stations. Very low chl-a concentrations at the offshore station (0.02-0.35 &micro / g L-1) confirmed oligotrophic character of the Northeastern Mediterranean. The highest chl-a concentration (2.4 &micro / g L-1) was observed in March 2005 at the nearshore station due to the input of Lamas River nearby. POM varied from 42.1 &micro / g L-1 (in January 2006) to 1082 &micro / g L-1 (in March 2005) and 53.7 &micro / g L-1 (in January 2006) to 246 &micro / g L-1 (in May 2005) at the nearshore and offshore stations, respectively. The oligotrophy of this system was indicated by the extremely low particulate lipid, protein and carbohydrate concentrations (1-3 times lower than in more productive systems). The most evident characteristic of this oligotrophic environment was the dominance of pico-POM throughout the study period, accounting for 31&ndash / 65 % of the total carbohydrates, proteins, lipids and chl-a. The prt:cho ratio was generally lower than 1 (low in organic nitrogen). Carbohydrate was the dominant biochemical component at both stations. Zooplankton varied during the sampling period, and they showed two peak abundances, in spring and autumn, with small increase in summer. The higher biomasses of zooplankton were observed in summer and autumn in the entire water column, but in spring and autumn periods in the surface water. Zooplankton data showed that 200-500 and 112-200 &micro / m size fractions were dominant in abundance at both stations. However, 200-500 &micro / m size fraction was dominant in zooplankton biomass at nearshore, whereas &gt / 1000 &micro / m size fraction was at offshore station. Copepods were the most abundant zooplankton group and dominated the distribution of total zooplankton, followed by crustace nauplii, appendicularia, cladocera and pteropoda.

Two phylogenies of Phalaenopsis (Orchidaceae) are presented, one from combined chloroplast DNA data and one from a nuclear actin gene. We used these phylogenies to assess and modify the classification of Phalaenopsis and to examine several morphological characters and geographical distribution patterns. Our results support Christenson’s (2001) treatment of Phalaenopsis as a broadly defined genus that includes the species previously placed in the genera Doritis and Kingidium. Some of Christenson’s subgeneric groups needed to be recircumscribed to reflect a natural classification. We recognized four subgenera and six sections, subgenera Aphyllae, Parishianae (with sections Conspicuum, Delisiosae, Esmeralda, and Parishianae), Phalaenopsis, and Polychilos (with sections Fuscatae and Polychilos). In order to find a set of universally amplifiable, phylogenetically informative, single-copy nuclear regions, we conducted a whole genome comparison of the rice (Oryza sativa) and Arabidopsis thaliana genomes. We constructed a database of both genomes and searched for pairs of sequences using criteria we felt would ensure primers that would reliably amplify using standard PCR protocols. We tested the most promising 142 primer pairs in the lab on eighteen taxa and found four potentially informative markers in Phalaenopsis and one in Helianthus. Our results indicated that it will be difficult to find universal nuclear markers, however our database provides an important tool for finding informative nuclear markers within specific groups. The full set of primer combinations is available online at, “The Conserved Primer Pair Project,” http://aug.csres.utexas.edu:8080/cpp/index.html. We used fourteen Phalaenopsis species and seven horticultural hybrids to create a real dataset with which to test phylogenetic network reconstruction methods. We tested the performance of Neighbor-Net, implemented in SplitsTree, under four different categories of complexity: one hybrid, two independent hybrids (hybrids with no parents in common), three independent hybrids, and two non-independent hybrids (one parent was shared between hybrids). Neighbor-Net was able to predict accurately the parents of hybrids in only about half of the datasets we tested, and there were so many false positives that it was impossible to distinguish the hybrids from the species. We plan to use this dataset to test methods, such as RIATA and RGNet, when they become available. / text

The paradigm of aquatic food webs has undergone fundamental revision over the past twenty years. Research suggests that a significant proportion of organic material and energy in aquatic ecosystems flows through a "microbial loop" before passage into the classic aquatic food web. Unique Antarctic conditions mean such "bottom-up" control can be of extreme importance during the austral winter. In order to investigate this, the microbial communities and physico-chemical properties of three saline lakes in the Vestfold Hills, eastern Antarctica, Ace, Highway and Rookery, were investigated between December 1995 and February 1997 . The lakes of the Vestfold Hills were formed approximately 8000 years ago following a period of post-glacial marine transgression, which isolated seawater in glacially scoured basins. Post-formation, the chemistry and biology of this isolated seawater underwent significant changes creating a suite of lakes and ponds with highly varied chemical and biological compositions. This study was concerned with meromictic Ace Lake in particular. Physico-chemical results demonstrated that the lake was highly stratified. An upper, nutrient-poor mixolimnion was separated by a thermoclinelhalocline from a lower, nutrient-replete monimolimnion. The monimolimnion was further stratified in terms of oxygen; an oxycline separated an oxic upper stratum from an anoxic lower stratum. At the oxycline, organic substrate sedimenting from above and inorganic nutrients diffusing from below were entrained. This stable stratification exerted a profound influence on the microbial dynamics of Ace Lake. Over the course of its evolution the microbial food web of Ace Lake was truncated and a simple, low diversity community of bacteria, algae and Protozoa, with a paucity of metazoan zooplankton, now dominates. This evolutionary process was illustrated by the intermediate diversity of the protozoan community in recently formed, Rookery Lake. The most dominant micro-organisms in Ace Lake were those which were highly motile and employed versatile nutritional strategies, such as mixotrophy, to remain physiologically active during the austral winter. Ace Lake is an oligotrophic system which receives negligible allochthonous inputs of organic carbon and inorganic nutrients. However, a simple model of the carbon flux within Ace Lake highlighted the fact that autotrophic production within the plankton was insufficient alone to maintain the level of heterotrophic activity observed. Instead, the microbial plankton were dependent on regenerative fluxes of inorganic nutrients and slow-turnover autochthonous carbon, consistent with the concept of the microbial loop.