Although watershed land use effects on in-stream fish habitat and fish-macrohabitat associations have been widely studied in the past, low-gradient, coastal Louisiana streams have been poorly described in the literature. In this thesis, I report the results of a two-year study exploring relationships among regional land use, in-stream physical habitat, and headwater stream fish assemblages. In chapter two, I examined in-stream habitat variables such as depth, flow, and substrate combined with three-pass electrofishing depletion estimates at thirteen 100-m stream sites. I used a combination of principle component analysis and structural equation modeling to determine if trends were present in the habitat, fish composition, and species trait data. I found that a species-based structural equation model was a better predictor of relationships among fish, land use, and in-stream habitat variables, when compared to species grouped by functional traits. In addition, it appears that the amount of agricultural land may not have as detrimental effects on fishes in these coastal streams as has been reported in other aquatic systems and substrate type may be the most important manageable habitat parameter. In chapter three, I measured various in-stream habitat variables (i.e. dominant substrate, depth, flow) for two dominant macrohabitats (pools vs glides). I collected fish from each macrohabitat via point-electrofishing and compared these data using canonical correlation analysis (CCorA) to determine if trends were present in macrohabitat, fish composition, and species trait data. I found that species- and functional trait-based CCorAs were able to determine correlations with various macrohabitats and variables within macrohabitats. Results indicate that species traits may be better measures of assemblage structure when macrohabitat-scale management, conservation, or restoration is the goal. Although I expected land use to heavily influence in-stream habitat and fish assemblage composition, my research indicated that in-stream habitat was be more influential than land use in determining species composition of Louisiana headwater stream fish assemblages. I also expected species- and trait-based models to successfully predict fish-macrohabitat associations. The findings of this study confirmed my predictions that multiple techniques for assessing fish-macrohabitat associations exist, although the most appropriate method may depend on specific management, restoration, or conservation goals.

Riverine fisheries management programs often do not focus on non-sport and non-commercial fishes, such as catostomids, yet many suckers have become threatened or endangered throughout river systems in the United States because of habitat alterations. In the Pearl River, sedimentation, dam construction, and other hydrologic modifications have negatively impacted habitats used by southeastern blue suckers Cycleptus meridionalis, a species of concern in both Louisiana and Mississippi. The principal objective of this project was to investigate habitat use of likely historically abundant southeastern blue suckers in the lower Pearl River. During electrofishing surveys in 2010 and 2011, we observed no southeastern blue suckers in the west branch of the Pearl River, and significantly lower catch rates in the main branch of the Pearl River (Mean Catch Per Unit Effort (CPUE) = 0.053/minute) relative to three other common benthic Pearl River fishes, including smallmouth buffalo Ictiobus bubalus (P< 0.0018), channel catfish Ictalurus punctatus (P< 0.0001) and flathead catfish Pylodictus olivaris (P< 0.0017). However, CPUE for southeastern blue suckers was similar to quillback Carpiodes cyprinus (P=0.999) and highfin carpsucker Carpiodes velifer (p=0.999). A mark and recapture population analysis was unable to generate a reasonable population estimate for southeastern blue suckers in this section of the Pearl River. The low CPUE values for other non-buffalo catostomids indicates that the availability of suitable habitat may be limiting populations of benthic suckers in the southern portions of the river. Habitat use of radio-tagged southeastern blue suckers indicated a strong affinity for deeper, outside river bends with accumulations of large woody debris and gravel, with high habitat specificity indicated by extended periods of little movement from these areas. Limited movements suggest a low potential for colonization of new areas or recolonization of abandoned habitats within the river. Raising the threat status for southeastern blue suckers, both globally and in Louisiana, may be warranted given their high habitat specificity, low recolonization potential, and susceptibility to the continuing degradation of their preferred habitats from sedimentation.

Hydrologic alterations frequently lead to vegetation changes in floodplain ecosystems. In Louisiana, there has been an expansion of water-elm (Planera aquatica) and to a lesser extent baldcypress (Taxodium distichum) at Catahoula Lake, a Ramsar Wetland of International Importance. Water-elm and baldcypress both are flood tolerant species; baldcypress growth is known to be influenced by hydrologic conditions more than climate. The expansion of these woody trees has reduced herbaceous vegetation valuable for waterfowl. In this study, I tested two hypotheses that establishment of water-elm trees into the lake increased after the construction of water control structures in the nearby Black River and a diversion canal and water-control structure on the lake in 1971; and that growth rates of water-elm and baldcypress are more correlated with hydrologic regimes than with local climate. Water-elm trees have been found in the lake for at least 140 years, but most (171 of 219) sampled trees were established in the period following the construction of water-control. In addition, 48 of 67 plots consisted of trees established entirely in the post-control period. Hydrologic conditions in the lake changed with the modifications, including reduced variability in June and August lake levels and reduced fall flooding. These changes coincided with apparently increased establishment of water-elm trees during the post-control period. Finally, there are several sources of uncertainty that prevent clear interpretation of the effects of water control on water-elm establishment including prevailing climatic conditions, control measures by Louisiana Department of Wildlife and Fisheries and cattle grazing. My second hypothesis that growth of water-elm and baldcypress would be more correlated with hydrologic regimes than with climate was partially supported. Growth of water-elm was more related to climatic variables than with lake levels, whereas baldcypress radial growth was more correlated with lake levels than with climatic variables. The response of water-elm radial growth to lake hydrology was limited to a negative relationship with late spring lake levels in the pre-control period; baldcypress had a consistent positive response with lake levels during several seasons in both the pre-and post-control periods.

The goal of this dissertation was to integrate multiple disciplines for application of high-throughput sperm cryopreservation to aquatic species. The blue catfish Ictalurus furcatus was selected for research due to its role in production of hybrid catfish with eggs from channel catfish Ictalurus punctatus. A high-throughput cryopreservation pathway was developed by systematically evaluating each process factor and using automated processing systems. Large quantities of cryopreserved sperm produced from this protocol were evaluated in commercial-scale hatcheries in cooperation with aquaculture producers. To develop production for commercial requirements, quality characteristics of materials and products were identified and recorded during processing and analyzed using industrial engineering methods to regulate quality. More than 1 million channel catfish eggs from 300 females were fertilized with thawed sperm, which was larger than any previous large-scale fertilization trial performed in fish. This demonstrated that the fertilization capability of cryopreserved sperm was equivalent to fresh sperm in production of hybrid fry. Quality regulation was presented within a quality assurance plan designed specifically for this process using quality standards (specifications) and quality variation data (quality control). This quality assurance plan is potentially the first of its kind for cryopreserved sperm of any species. After being scaled up by automation and standardized by the quality assurance plan, the cryopreservation process produced reliable products for hatcheries. Proper use of these products (i.e., as a dose of 3704 eggs/straw) can provide a basis for industry standards for artificial spawning. A quantitative evaluation was developed based on the defined dose and the production efficiency. To increase the efficiency for large-scale production, simulation model computing was used to create a virtual process. The simulation model was validated based on the existing process, and provides a valuable tool for future improvements. This dissertation took the initiative to apply high-throughput cryopreservation in aquaculture and expand the process from planning to operation at the production line, to terminal use of products by customers. This enables cryopreserved sperm to become a practical form of genetic resources applicable for aquatic genetic improvement and conservation.

Alternative or supplemental management activities may be necessary to restore and enhance oyster production on Louisiana public oyster reefs. The production of wild oysters is variable due to anthropogenic and environmental factors that affect recruitment, growth and survival. The availability and structure of cultch material for larval recruitment and survival is particularly important to maintain oyster production. Beginning in 2011, the Sea Grant Oyster Hatchery on Grand Isle, LA and the Louisiana Department of Wildlife and Fisheries (LDWF) collaborated to test the survival of hatchery-produced spat and hatchery-produced larvae deployed on public oyster grounds and cultch plant sites. In 2011, a preliminary study was conducted on hatchery-produced spat survival in Hackberry Bay, LA, where 100% mortality of hatchery-produced spat was observed. Survival of hatchery-produced spat was also tested in Mississippi Sound, LA (Round Island site) and California Bay, LA, where sampling took place in September and November 2012 and January 2013. No hatchery-produced spat were collected at either of these sites, suggesting 100% mortality. No significant differences were observed between the numbers of wild spat oysters on treated plots, plots with hatchery-produced spat, to untreated plots (P>0.05). In 2012, LDWF released hatchery-produced larvae at four sites at Calcasieu Lake and the sites were monitored monthly using standard LDWF sampling procedures. For most of the sites, few to no spat existed. Possible causes of hatchery-produced spat and larval mortality are sedimentation, predation, water quality and absence of suitable settling material. To increase survival, future studies should focus on ways to minimize causes of hatchery-produced spat and larval mortality.

The continental scaup population (lesser [Aythya affinis] and greater scaup [A. marila] combined) has declined markedly during the past 20 years, and has remained below the population goal of the North American Waterfowl Management Plan since 1985. One hypothesis explaining the scaup population decline states that reproductive success has decreased because females presently are arriving on breeding areas in poorer condition than that historically (Spring Condition Hypothesis [SCH]). I tested the SCH by comparing fresh body masses (FBMs) and nutrient reserves (lipid, protein, and mineral) of lesser scaup at 4 locations (Louisiana, Illinois, Minnesota, and Manitoba) in the Mississippi Flyway between decades of the 1980s and 2000s. I found that mean FBMs of females were 58.5 g and 58.9 g lower in the 2000s than were those in the 1980s in northwestern Minnesota and near Erickson, Manitoba, respectively; mean FBMs of males similarly were 40.7 g lower in Minnesota. Mean lipid reserves of females in the 2000s were 28.8 g lower than those in the 1980s in northwestern Minnesota and 27.8 g lower near Erickson, Manitoba. Mean mineral reserves of females in the 2000s were 3.2 g lower than those in the 1980s near Erickson, Manitoba. Consequently, females arriving to breed near Erickson, Manitoba in the 2000s had accumulated lipid reserves for 4.1 fewer eggs and mineral reserves for 1 fewer egg than had those arriving to breed in the 1980s. Accordingly, my results clearly are consistent with predictions of the SCH and indicate that there has been a long-term decline in female body condition, reflected by declines in FBMs, lipids and mineral reserves, which could significantly reduce reproductive success.

Nearly 35,000 ha are used to grow crawfish in southwest and south-central Louisiana, and many of these ponds discharge into impaired water bodies. In 2002, proposed guidelines were published by the United States Environmental Protection Agency (USEPA) assigning effluent limitations and standards for some aquaculture production systems and exempting others (e.g. crawfish ponds). This research had three objectives relative to crawfish ponds: develop water discharge models; final drawdown effluent quality and seasonal mass loading of solids and nutrients; and identification of Best Management Practices (BMPs) that could reduce effluent discharge and improve effluent quality. Models for south-central and southwest Louisiana with a 15 cm storage capacity showed that excess precipitation overflow (final drawdown not included) can be decreased by 28% for a high precipitation year, 61% for an average precipitation year, and 100% for a low precipitation year. The major sources of effluent from crawfish ponds are (1) overflow during winter when precipitation exceeds evaporation, evapotranspiration, and infiltration and (2) discharge during the summer drawdown period. Pond evaporation and evapotranspiration combined are the greatest sources of water loss (68%) during a crawfish production cycle. During final drawdown, solids were high during the first 5% of pond water discharge due to poorly consolidated sediment in and around the drain and high during the last 20% of pond water discharge due to the poorly consolidated pond bottom sediments. During final drawdown: total suspended solids were reduced over a distance of 268 m by 28% at the Aquaculture Research Station (wide, shallow, non-vegetated ditch); total suspended solids increased over a distance of 268 m by 15% at the Rice Research Station (narrow, non-vegetated ditch); and total suspended solids were reduced over a distance of 268 m by 80% at the University of Louisiana at Lafayette Model Sustainable Agricultural Complex (deep vegetated ditch). To reduce solid and nutrient mass loading in crawfish pond discharge, ponds should be slowly drained from the top of the water column and avoid draining the last 20% of the pond volume. If that is not possible, then it is recommended to treat the last 20% of the pond volume by sending the discharge through deep vegetated ditches, settling basins, or constructed wetlands with a residence time of 4 d to 14 d.

The development of cointegration theories and the presence of nonstationarity in time series raised serious concerns about possible spurious estimations in forest products models. Based on the results of Hsiao (1997a, 1997b), all the virtues of two-stage least square (2SLS) hold if there are sufficient cointegration relations. Stationary null and nonstationary null unit root tests and monthly seasonal unit root tests were applied to the time series used in this dissertation. Cointegration tests with exogenous variables were performed to justify the 2SLS. A regional error correction model (ECM) with four regional lumber supply and demand equations and a U.S.-Canada supply and demand ECM were estimated. CUSUM tests did not find any structural changes. Both estimated models showed that the imported Canadian lumber and the U.S. lumber are substitutes. The estimated long-run and short-run own-price elasticities for demand and supply are inelastic for all the equations but the short-run supply equation for the West Coast. The long-run lumber supply equations have significant trends: annually -3% for the Inland West and 2% for the other regions. The popular maximum likelihood estimation for the restricted ECM cannot pass the test for the restrictions and is, therefore, not used for the regional structural lumber model. A series of univariate and multi-equation models were used as forecasting models. A combination of univariate model were shown to be the best forecasting models for lumber prices, and a combination of univariate and multi-equation models were shown to be the best forecasting models for lumber quantities. The selected combinations of models were shown to be the best with additional observations. It was also shown that lumber quantities could be forecasted better than lumber prices.

Branch and tree sap flux density (SFD) was measured to evaluate the effects of thinning, fertilization, and throughfall exclusion treatments on water use by loblolly pine (Pinus taeda L.) trees. Variations in SFD at different radial xylem depths were also examined to improve estimates of tree water use from sap flux density measured in the outer sapwood. This study was conducted in an 18-year-old loblolly pine plantation in central Louisiana in 1999. The results revealed that SFD was higher in the outer xylem than in the inner xylem and large trees had higher SFD than small trees. Thinning increased daily tree SFD and whole tree water use four years after re-treatment, but decreased stand-level tree water use. Fertilization increased tree SFD, whole-tree water use, and stand-level tree water use within the thinned plots. Throughfall exclusion decreased mean daily water use by branches and trees. SFD and water use at different levels of scale (branch, tree, and stand) changed with available soil water and microclimatic factors. Generally, SFD was positively related to photosynthetic photon flux density and vapor pressure deficit. Branch SFD was higher in the upper crown than in the lower crown. Fertilization significantly increased daily branch water use within the thinned plots, but did not significantly affect branch transpiration per unit leaf area. This study shows that tree and stand water use is affected by spatial variation in the canopy environment as well as climatic variables and forest cultural practices. Scaling up water use, carbon dynamics and growth from needle level to branch-, tree-, and stand levels under various global scenarios should account for cultural practice differences, within canopy variation, and changes in micro-environmental factors. Cultural practices, such as thinning and fertilization, significantly increased SFD and whole tree water use by accelerating leaf area development. Correlated changes in other physiological processes eventually alter tree growth. The ability to model tree and stand growth response through monitoring of whole tree and branch water use has the potential to substantially improve our understanding of forest responses to management and climate change and should be useful in policy decision making.

Termites cause serious damage to wood and wood products. In recent years, increasing attention has been paid to extractives from naturally decay resistant trees. In this study, we compared the termiticidal and antifungal effects of extractives from Alaska yellow cedar (AYC), Port-Orford cedar (POC), and Eastern red cedar (ERC). Pentane and Hexane-Acetone extractives from YC and POC, and pentane extractives from ERC were most favorable in terms of termite protection among the extractives we got. Weight loss of strips treated with 5000 ppm pentane extractives from Eastern red cedar, was significantly lower than those treated with solutions of pentane extractive from the other two species of wood at the same concentration or lower concentrations. Wood blocks treated with pentane extractives from ERC also exhibited significantly lower weight loss than other fractions from ERC and from the other two species at 5000 ppm after 3 weeks exposure to brown rot fungi. Weight loss of blocks treated with hexane-acetone extractives was significantly lower than other treatments after 6 and 9 weeks for the white rot decay test. Comparing the chemical components in the different tree parts in ERC, some difference were found between the needles, bark and the stem of ERC. Cedrol or widdrol were not detected in the extractives from needles extracted by hexane. From the TLC spectra there were small differences between the components in callus induced from ERC and the seedlings. GC-MS spectrum showed smaller types of components and a bigger difference of the peak areas between components in the callus. A higher concentration of cedrol was detected in the callus than that in the original seedlings. Widdrol was not detected in the extractives from callus or seedlings.