With the ongoing advance of the agricultural frontier in the Amazon basin, it is inevitable that heterogeneous landscapes will play a key role in conservation. These landscapes are mostly composed of patchworks of small forest fragments, secondary forests and roads. Conservation, however must take species interactions into consideration as they play a pivotal part the maintenance of several biological processes in the tropics. One of the most conspicuous interspecific interactions are seen in mixed-species flocks of birds, which in the Amazon, represent one of the best organized systems of bird aggregations. In this research, I assess how flock spatial behavior and species compositions are affected by changes in habitat structure. I followed 29 mixed-species flocks in different landscapes types such as secondary forests, forest fragments of 10 and 100 ha, and mixes of primary and secondary forest patches. As flocks foraged through their territories, I recorded their species composition every 30 minutes and georeferenced their movements every 30 seconds. Flocks spatial behavior was severely affected by anthropogenic features such as forest edges and secondary forests as flocks respond strongly to vegetation height. Using step-selection models, it was possible to reproduce flock movements and show that they prefer taller vegetation and lower areas of topography such as stream valleys. Due to this behavior, flocks avoided areas where canopy height was below 15 meters, and extensive areas of secondary below this height hold unstable flocks that do not persist for long periods. The ones that persisted showed home ranges that were much larger than what was observed in primary forest. Time spent in secondary forest was dependent on vegetation height, but not area, which seems to be shaped by intraspecific interactions. Flock social structure is also severely affected by habitat structure. Flock species richness did not show a predictable pattern, but participation was negatively affected. In fact, our data indicates that flock social structure may take longer to recover than spatial behavior. Assessing a 30-year mist-net capture dataset, we were able to determine that indeed, decreased species participation seems to be a more important driver in flock dissolution than local extinction.

Bioelectrical impedance analysis (BIA) has been proposed as an easy and accurate technique for a non-lethal index of condition in fish; however, factors affecting its accuracy have yet to be properly identified. The technique uses the resistance (R) and reactance (Xc) of water and lipids in contiguous tissues to estimate lipid content. Studies have investigated the use of BIA on fish, but with mixed results, possibly caused by unrecognized sources of influences. Our study explored possible sources of variance for BIA measurements in gulf killifish, Fundulus grandis, through laboratory feeding and fasting experiments, and experimental exposures to acute changes in temperature and salinity. In our feeding and fasting experiments, wild caught F. grandis were held in recirculating tanks and either fed ad libitum or withheld food for 28 days and sampled every 7 days. In the fed and fasted experiments, BIA measurements, plasma osmolarity, Lecrens Kn, and % organ lipid were significantly different by day with most variables showing a gradual change over time (ANOVA, p <.05). However, in the fasted experiment BIA measurements did not follow the trends of declining condition indicated by Kn and % organ lipid In our experiments with environmental factors, fish acclimated to 24⁰C and 12 ppt salinity where exposed to tanks randomly assigned treatments of salinities 2, 12, 24 and temperatures 2, 12, 24⁰C. Reactance was consistently significantly higher at salinity 2 ppt, and R significantly decreased as temperature increased (ANOVA,Tukey-Kramer p <.05). Our results indicate additional possible sources of variance including sex, size, temperature and changes in body chemistry. Some of the mixed results from other studies may be explained by these sources of variance. If these sources of variance are shown to be easily correctable, BIA may prove to be an effective index of condition.

Anthropogenic regulation of the Middle Rio Grande (MRG) of New Mexico has altered the hydrogeomorphology of the system and led to a rapid decline in breeding riparian-obligate birds as native riparian forests are replaced by exotic tamarisk stands. In this study, I evaluated the relationships among hydrogeomorphology, vegetation structure and composition, and avian communities of the San Acacia Reach (SAR) of the MRG. I conducted avian point count surveys and collected habitat data to determine avian community structure and abundance, geomorphic feature, surface flooding, and vegetation structure and composition along 44 transects throughout the SAR. A total of 999 point count surveys and 1,801 vegetation plots were completed throughout the 2012 and 2013 breeding season. Sixty-nine land bird species were detected over the two breeding seasons. Avian guilds responded differently to various hydrogeomorphic conditions. Ground-nesting birds and low shrub-nesting birds were insensitive to hydrogeomorphic changes as they do not rely on native understory, but can use exotic understory or woody debris. In contrast, canopy-nesting birds required native overstory; therefore, they were sensitive to hydrogeomorphic changes as native overstory species, such as cottonwood (Populus deltoides) and Gooddings willow (Salix gooddingii), require surface floods to germinate and establish. Similarly, water-obligate species were also sensitive to hydrogeomorphic changes as they require close proximity to surface water. I also evaluated hydrogeomorphic relationships with the habitat of the Western Yellow-billed Cuckoo (Coccyzus americanus occidentalis), a candidate species under the Endangered Species Act, using cuckoo presence/absence survey data, spatial statistics in ArcGIS 10, and vegetation and hydrology data. Results indicated that management of riparian forests that promotes overbank floods and regeneration and survival of cottonwood and Gooddings willow overstory, with a mixed understory of Gooddings willow, coyote willow (Salix exigua), and New Mexico olive (Forestiera pubescens) would provide long-term habitat for Western Yellow-billed Cuckoos. I also quantified the amount of variability within Hink and Ohmart vegetation structure classes, a vegetation classification scheme widely used throughout the MRG. Results indicated that including woody stem density classes in conjunction with the current Hink and Ohmart classification methodology will better inform songbird habitat management prescriptions.

Freshwater diversions are a relatively recently utilized tool in wetland loss mitigation that stimulate an organic accretion response in marsh vegetation, which is based in root production and thus belowground biomass. The effectiveness of freshwater diversions in slowing marsh loss probably varies across a gradient of the factors they supply: decreased salinity, increased nutrient concentrations, and increased inundation. Flooding stress is commonly thought to be the overriding factor limiting wetland vegetation growth, however its influence may vary across salinity and nutrients. Therefore, plugs of Spartina patens were planted in four marsh organs consisting each of 36 sediment-filled PVC pipes of incremental heights that created a range of growth elevation and thus flooding stress. The organs were located in mean salinities from 2.6-14.7 ppt and two of them fertilized at 22 g N m-2, 11 g P m-2, and 5.5 g K m-2. Twice during the growing season below- and aboveground biomass was harvested, sorted, dried, weighed, and analyzed for relationships between variables. Flooding stress was found to be primary, with a secondary interactive effect between salinity and fertilization that suggests fertilization may help plants resist relatively higher salinity levels. Variations in salinity and nutrient concentrations associated with freshwater diversions, which can differ in intensity and extent, might also be linked to increased nutria herbivory. Therefore, nutria preference for fertilized versus unfertilized vegetation was also tested in a controlled setting on Panicum hemitomon, Sagittaria lancifolia, and S. patens, representative dominant plant species of fresh, fresh-brackish, and brackish marsh. Nutria showed a significant preference for fertilized vegetation within species. It is therefore possible that benefits derived from nutrient-rich fresh floodwater could potentially be negatively impacted by increased preferential herbivory.

Research on blue crab diseases, parasites, and symbionts has been sporadic in the Gulf of Mexico. Understanding the prevalence of diseases, parasites, and symbionts is important for managers to set informed regulations for the commercial industry and to understand the impacts of environmental disasters on aquatic animal health. The objective of this research was to determine the prevalence of Lagenophrys callinectes, Urosporidium crescens, Hematodinium perezi, Loxothylacus texanus, reo-like virus (RLV), shell rot, and Vibrio spp. in crabs collected from four coastal locations and four shedding facilities in 2013 and the beginning of 2014. Additionally, I determined the prevalence of white spot syndrome virus (WSSV) in the wild populations. I also recorded infections by non-Vibrio bacteria and by Ameson michaelis. H. perezi, L. texanus, WSSV, and RLV were detected by polymerase chain reactions. Shell rot and U. crescens were detected by gross visual detection. L. callinectes and A. michaelis were identified by microscopy and Vibrio spp. and non-Vibrio spp. bacteria were detected by standard microbiological culture techniques and biochemical testing. No samples were infected with H. perezi, L. texanus, or WSSV. Based on the low salinities sampled, these results were expected for H. perezi and L. texanus. Shell rot and Vibrio spp. were moderately prevalent in the wild and captive crabs, but infections were more common in the captive crabs. U. crescens was never found in crabs from Lake Pontchartrain, the lowest salinity field site. It was also rare in crabs from the low salinity shedding facilities, indicating that this hyperparasite may be limited to moderate to high salinities. L. callinectes was ubiquitous with over 90% prevalence in wild and captive crabs. Reo-like virus infections were found in wild and captive crabs in the summer of 2013, and A. michaelis was present in two shedding facility pre-molt crabs. Overall, Louisianas blue crab nearshore populations appear to be healthy with no parasitization by the two most ecologically and economically detrimental parasites, H. perezi and L. texanus. However, in the future, RLV needs to be extensively studied because it is also capable of decimating blue crab populations.

The processes that control species composition and structure in wetland ecosystems are complex and controlled by many factors including seasonality, depth and duration of flooding, and nutrient dynamics. Catahoula Lake is a floodplain lake that has existed with seasonally fluctuating water levels for at least 4,000 years. The herbaceous vegetation that attracts these waterfowl is slowly being outcompeted by woody vegetation, most notably water-elm (Planera aquatica). Our general goal is to understand the processes that cause this shift, focusing on the role of sediments. Our first objective was to use historical aerial imagery to detect historical changes in plant communities at Catahoula Lake, focusing on timing and rates of expansion of woody vegetation. Aerial imagery indicated woody vegetation has been encroaching into the lake bed and the rate of this expansion has increased 249% since major hydrologic alterations in the 1960s. There are three local patterns to this expansion: continuous expansion of woody vegetation, long-term stability of the tree line, and complex patterns of tree establishment. Second, we used 137Cs in lakebed sediments to calculate rates of sedimentation. Results indicated sedimentation was 0.26 cm yr-1, which is increased 225% from the pre-settlement rate of 0.08 cm yr-1. Peaks of 137Cs were muted and deposition rates were similar around the lake, suggesting redistribution of sediments is common. Third, we investigated elemental concentrations in sediment which revealed little spatial variation in recent sediment, but a shift from mixed coastal-plain and Mississippi Alluvial Valley sediments to dominance by acidic, coastal-plain sediments in the past ~60 yr. Sediments are low in organic matter, and carbon and nitrogen concentrations decrease with depth and are being sequestered at low rates (840 t yr-1 and 120 t yr-1, respectively). Compared to its condition prior to hydrologic alterations beginning in the 1920s, Catahoula Lake is about 15 cm shallower and the chemical composition of sediments is more acidic. Although these results are not sufficient to link these differences directly to ecological changes, it is likely the altered sedimentary and hydrologic environment is contributing to the increased dominance of woody vegetation.

Changes in the timing and interaction of seasonal high temperatures and low salinity as predicted by climate change models could dramatically alter oyster population dynamics. Little is known explicitly about how low salinity and high temperature combinations affect spat (<25 mm), seed (26-75 mm), and market (>75 mm) oyster growth and mortality. Using lab and field studies, this project quantified the combined effects of extremely low salinities (< 5) and high temperatures (>30 oC) on growth and survival of spat, seed, and market-sized oysters. In 2012 and 2013, hatchery-produced oysters were placed in open and closed bags at three sites in Breton Sound, LA, along a salinity gradient which typically ranges from 5 to 20. Growth and mortality were recorded monthly. Regardless of size class, oysters at the lowest salinity site (annual mean = 4.8) experienced significantly higher mortality and lower growth than oysters located in higher salinity sites (annual means = 11.1 and 13.0); furthermore, all oysters in open bags at the two higher salinity sites experienced higher mortality, likely due to predation. To explicitly examine oyster responses to extreme low salinity and high temperature combinations, a series of laboratory experiments were conducted. Oysters were placed in 18 tanks in a fully crossed temperature (25oC, 32oC) by salinity (1, 5, 15) experiment with 3 replicates, and repeated twice for each oyster size class. Regardless of temperature, seed and market oysters held in low salinity tanks (salinity 1) experienced 100% mortality within seven days. In contrast, at salinity 5, temperature significantly affected the mortality rate; all size class oysters experienced > 50% mortality at 32 oC, and < 40% mortality at 25 oC. In higher salinity tanks (15), only market-sized oysters held at 32 oC experienced significant mortality (>60%). These experiments demonstrate that high water temperatures (> 30 oC) and low salinities (< 5) negatively impact oyster growth and survival, and that high temperatures alone may negatively impact market-sized oysters. It is critical to understand the potential impacts of climate and anthropogenic changes on oyster resources in order to better adapt and manage for long-term sustainability.

The population of Bald Eagles (Haliaeetus leucocephalus) nesting in Louisiana reached precariously low numbers in the early 1970s, and although the population has since increased markedly, resident eagles remain a species of conservation concern in Louisiana. Using statewide aerial nest survey data from 19752008, I documented the history and quantified the recovery of the nesting population in Louisiana. Known active nests increased exponentially from 7 to 387 during this period, exhibiting a mean annual rate of increase of 11.1 ± 0.3% per year with no indications of slowing. By 1990, the nesting population in Louisiana had exceeded all goals of the Southeastern States Bald Eagle Recovery Plan. I used nest location and status data from the most recent year (20072008) of the nest monitoring program to examine landscape level nest site selection and success. Success of a nest was not greatly influenced by the physical characteristics around a site, whereas the initial selection of a nest site was most influenced by distance to the historical nest centroid and the proportion of open water and agricultural land within 3 km. Bald Eagles nest during the winter in Louisiana, but they are rarely observed in the state during summer. Therefore, I used satellite GPS transmitters to provide evidence of their undocumented summer migrations and examined parameters such as timing of departure and arrivals, stopover use, routes used, and seasonal and annual variations in these parameters. Marked eagles flew relatively direct routes, exhibiting high route fidelity going between Louisiana and their summering areas, which were spread out across much of Canada and south to Illinois. Using locations from their winter and summering areas, I estimated home range and core area size. Home ranges varied from 19.71,997.7 km2, but nesting Bald Eagles had smaller home ranges, on average, than did non-nesting birds. The sex of an individual can play an important role when considering variations in movements, home ranges, and habitat use. Accordingly, I evaluated the published field technique for sex determination of Bald Eagles, and upon documenting misclassifications, I developed a new formula applicable to Louisiana and other southern regions.

The blue crab (Callinectes sapidus) is a commercially, recreationally, and ecologically important species in Louisiana coastal waters. Louisiana landings account for more than 80% of Gulf of Mexico hard crab landings. In 2012, over 24 thousand metric tons of blue crab were landed in Louisiana with an economic value over $52 million. The blue crab fishery in the northern Gulf of Mexico relies heavily on Atlantic menhaden (Brevoortia tyrannus) for bait, which is a species with stock concerns resulting in approximately a 20% decrease in total allowable catch beginning in 2013. Decreased landings results in increased cost of B. tyrannus for industrial and bait uses, demonstrating a need for new cost-effective alternative bait. Large amounts of waste are produced from processing over 40 thousand metric tons of penaeid shrimp annually landed in Louisiana. Shrimp carapace accounts for approximately ¨ö to ¨ø of the total biomass and can be used an attractant in alternative bait. The objectives of this study are: 1) determine a feasible attractant utilizing seafood processing waste; 2) determine if alternative bait soak time, diffusion, and catch will perform similar to B. tyrannus; and 3) Determine fishermen opinions and preferences for an alternative bait. Crabs responded favorably to bait created with shrimp waste as the attractant in laboratory choice bioassays. Field trials in three temperature regimes demonstrate soak time of alternative bait is comparable to the current natural bait used by the industry. Additionally, the alternative bait diffuses proteins, which stimulate feeding in crabs, at levels similar to or higher than natural bait. Paired-trap field trails demonstrated alternative bait produces catch rates comparable to natural bait; shrimp alginate accounted for 41% of total catch. Additionally, reduced rates of bycatch were seen in traps baited with alternative bait. Interviews conducted with commercial fishermen indicate the industry is willing to use alternative bait. Current results show a bait created with a waste product as an attractant is feasible. Alternative bait would benefit blue crab fishermen, B. tyrannus stocks by reducing fishing pressure, and processors by creating a value added product.

The modern day Mississippi River Delta Plain and the Louisiana Chenier Plain have been greatly altered through anthropogenic changes to course and hydrological conditions of the Mississippi River and local rivers, most notably by levees that have excluded the Mississippi River from the delta plain. This has slowed accretion and increased land loss destroying vast quantities of marsh, endangering many coastal communities. This masters thesis examined long-term total suspended sediment yield of four Chenier Plain rivers, total suspended sediment yield of the Mississippi River under different flow conditions, and total suspended sediment dynamics of the Atchafalaya River in relation to Atchafalaya River Delta Complex growth and Atchafalaya River Basin sedimentation. Results estimated average annual total suspended sediment yield to coastal Louisiana of 176.3 megatonnes (MT), with the Mississippi River contributing 72% and the Atchafalaya River contributing 28%. The Chenier Plain rivers contributed a negligible amount to this total, averaging annually 342,950 tonnes, with the Sabine contributing 62% to this total (213,100 tonnes), while the Calcasieu River supplied 46,850 tonnes, Mermentau River 40,200 tonnes, and Vermilion River 42,800 tonnes. The hydrograph-based approach for quantification of actual available total suspended sediment of the Mississippi River identified the rising limb of the flood pulse during Action Stage (12.1-14.6 m) and Flood Stage (14.6-16.8 m) maximized total suspended sediment with 28.9 MT supplied. Atchafalaya River Delta Complex growth rate was 2.8 km2 yr-1 (1989-2010). Both Atchafalaya River Morgan City subdelta (ARSD) and Wax Lake Outlet Subdelta (WLSD) growth rates were influenced by large floods that helped maintain positive growth rates, and tropical systems that decreased growth rates over the period. Average annual sedimentation rate in the Atchafalaya River Basin (ARB) was estimated between 30.4-79.1 mm yr-1, while total suspended sediment retention averaged 5.3 MT yr-1 (1996-2010), but interannual variation demonstrates that the ARB has reached an equilibrium and resembles a fluvially dominated system rather than lacustrine or palustrine system. Results from this study provide an exhaustive understanding of riverine sediment availability to coastal Louisiana and the impacts on coastal evolution, providing information that land managers can use to model restoration of coastal Louisiana.