Habitat and Fish Population Dynamics: Advancing Stock Assessments of Highly Migratory Species

Fisheries sustainability is inherently linked to an understanding of the population-level effects of fishing. With an accurate characterization of historical fish and fishery dynamics, management agencies are more equipped to create regulations that sustain fishery resources over the long term. The overarching goal of this dissertation is to contribute to the advancement of fisheries stock assessment and promote resource sustainability. My research focused on highly migratory species (HMS), particularly fishes that reside in the open ocean. These species constitute some of the highest valued global fisheries; however, numerous factors compromise HMS stock assessment and management. These challenges are fully described in Chapter 1, which also includes corresponding research and management recommendations. A key limitation in HMS assessments underlying my research is the lack of independent scientific monitoring programs. In the absence of research surveys, HMS stock assessments must rely on fishery catch and effort data. Therefore, special care is required to infer population dynamics from entities that were not established to monitor populations. In particular, the habitat in which fishing occurs largely dictates the amount and composition of fishes captured. Unfortunately, habitat effects on fishery-dependent data are not commonly accounted for in HMS assessments. Chapter 2 presents the results of a performance evaluation of methods used for estimating HMS abundance trends, including traditional generalized linear models (GLMs), an existing method that considers habitat (statHBS), and a proposed method that hybridizes traditional and habitat-based approaches (HabGLM). I demonstrate that HabGLM was most accurate of those evaluated, while exhibiting minimal sensitivity to errors in input data. I recommend the use of HabGLM in future HMS stock assessments; however, despite being most accurate, there were scenarios where HabGLM still did not sufficiently capture the true abundance pattern. In Chapter 3, the HabGLM was applied to 35 HMS in the Atlantic Ocean using fisher logbook data from the US pelagic longline fishery. This comprehensive analysis portrays an HMS community in the Atlantic as generally depleted, with current abundances of 76% of the species at less than half of their 25-year observed maxima. However, despite these depletions, 26% of the species exhibited population growth, suggesting recent fishing intensities may be adequate for sustaining or rebuilding certain populations. While interpretations of abundance trends can be informative, fisheries management is more often guided by the output of stock assessments. Thus, in Chapter 4, I present the results of a study that evaluated the effects of abundance index quality on the performance of a stock assessment model (Stock Synthesis), with a focus on Atlantic blue marlin (Makaira nigricans). In general, assessment model performance was superior when based on abundance indices estimated using HabGLM; however, the management quantities derived from this best case scenario were still overly optimistic, and when the fisheries were regulated accordingly, population biomass was projected to be well below the management target level. Overall, my research emphasizes that (1) habitat should be directly incorporated into HMS stock assessments, and (2) independent stock monitoring programs are essential for effective fisheries management

Distribution and Natural History of Amphibians and Reptiles in Western Nebraska with Ecological Notes on the Herpetiles of Arapaho Prairie

Introduction: The distribution and natural history of amphibians and reptiles have been little studied in the northern states of the great plains. Relative to other vertebrate groups, the herpetofauna of grasslands is depauperate particularly at higher latitudes where temperature becomes a limiting factor to poikilotherms. Nevertheless, certain species of amphibians and reptiles are common in specific habitats and thus form a conspicuous component of the prairie fauna. The purposes of the present study were to document the distributions of herpetiles in a specified region of western Nebraska and to describe general aspects of their natural history. We hope such information will stimulate additiona} work as well as provide a baseline reference for future studies on the herpetofauna of the northern great plains. Previous work on herpetiles in western Nebraska are either in need of updating (e.g. Hudson, 1942) or are anecdotal or not comprehensive (Heyl and Smith, 1957; Gehlbach and Collette, 1959; Iverson, 1975; Lynch, 1978). Summary: The herpetofauna of the seven county study area in western Nebraska may be characterized in general by a preponderance of organisms exhibiting both wide geographical and wide ecological distributions and tolerances. Species exhibiting little microhabitat specificity and which are found widely throughout the region include the tiger salamander, spadefoot toad, rocky mountain toad, striped chorus frog, lesser earless lizard, fence lizard, racerunner, common racer, bullsnake, red-sided garter snake, plains garter snake, snapping turtle and painted turtle. Those ecologically restricted species that enter the area include the plains leopard frog, common water snake, black-headed snake, yellow mud turtle, Blanding\u27s turtle, and spiny soft-shelled turtle

Abundance trends of highly migratory species in the Atlantic Ocean: accounting for water temperature profiles

Relative abundance trends of highly migratory species (HMS) have played a central role in debates over the health of global fisheries. However, such trends have mostly been inferred from fishery catch rates, which can provide misleading signals of relative abundance. While many biases are accounted for through traditional catch rate standardization, pelagic habitat fished is rarely directly considered. Using a method that explicitly accounts for temperature regimes, we analysed data from the US pelagic longline fishery to estimate relative abundance trends for 34 HMS in the Atlantic Ocean from 1987 through 2013. This represents one of the largest studies of HMS abundance trends. Model selection emphasized the importance of accounting for pelagic habitat fished with water column temperature being included in nearly every species’ model, and in extreme cases, a temperature variable explained 50–60% of the total deviance. Our estimated trends represent observations from one fishery only, and a more integrated stock assessment should form the basis for conclusions about stock status overall. Nonetheless, our trends serve as indicators of stock abundance and they suggest that a majority of HMS (71% of analysed species) are either declining in relative abundance or declined initially with no evidence of rebuilding. Conversely, 29% of the species exhibited stable, increasing, or recovering trends; however, these trends were more prevalent among tunas than either billfishes or sharks. By estimating the effects of pelagic habitat on fishery catch rates, our results can be used in combination with ocean temperature trends and forecasts to support bycatch avoidance and other time-area management decisions

Effect of Pre-and Post-weaning Nutrition and Management on Performance of Weaned Pigs to circa 35 kg.

End of Project ReportThe objective of this project was to examine the factors affecting performance (growth rate, appetite, feed conversion efficiency) of pigs in the stage from weaning to 35 kg liveweight. The study involved three stages, creep feeding during the suckling period, management during the first weaner stage (c. 4 weeks from weaning or 6 kg to 15 kg liveweight) and management during the second weaner stage (c. 15 kg to 35 kg liveweight. Creep feed intake before weaning was low c. 2.5 to 3.0 kg per litter but where it was consumed the response in terms of feed conversion efficiency was good with litter weight increasing in weight by about 1.1 kg for each 1 kg creep consumed. Milk replacer in liquid form was very readily consumed but its preparation and feeding is very laborious. Weaning weight was poorly related to post weaning performance and weaning age seemed to be more critical which is probably a reflection of the greater maturity of older animals. In the first weaner stage, feeding of cooked cereal containing diets was found to have little benefit in pig performance. Acidification of feeds is likely to have only a minor influence on pig performance. An experiment on choice feeding of starter and link feeds did not confirm that smaller pigs require a higher quality diet and, in a choice situation will eat a greater proportion of the more nutrient dense diet. In the second weaner stage, comparison of three commercial weaner feeds with a cereal based control diet showed good performance on all four diets. Pigs fed a high lysine weaner diet grew better in the weaner stage but by slaughter those pigs fed the low lysine weaner diet, after all pigs were fed a common finisher diet, had overtaken them. The high lysine group did, however, have leaner carcasses. Residual effects of early nutrition need to be investigated in more detail including the effect of pregnancy feeding on prenatal development and the relationship between prenatal growth and postnatal growth, in particular development of muscle.European Union Structural Funds (EAGGF

The Lavic Lake Fault: A Long-Term Cumulative Slip Analysis via Combined Field Work and Thermal Infrared Hyperspectral Airborne Remote Sensing

The 1999 Hector Mine earthquake ruptured to the surface in eastern California, with >5 m peak right-lateral slip on the Lavic Lake fault. The cumulative offset and geologic slip rate of this fault are not well defined, which inhibits tectonic reconstructions and risk assessment of the Eastern California Shear Zone (ECSZ). With thermal infrared hyperspectral airborne imagery, field data, and auxiliary information from legacy geologic maps, we created lithologic maps of the area using supervised and unsupervised classifications of the remote sensing imagery. We optimized a data processing sequence for supervised classifications, resulting in lithologic maps over a test area with an overall accuracy of 71 ± 1% with respect to ground-truth geologic mapping. Using all of the data and maps, we identified offset bedrock features that yield piercing points along the main Lavic Lake fault and indicate a 1036 +27/−26 m net slip, with 1008 +14/−17 m horizontal and 241 +51/−47 m vertical components. For the contribution from distributed shear, modern off-fault deformation values from another study imply a larger horizontal slip component of 1276 +18/−22 m. Within the constraints, we estimate a geologic slip rate of <4 mm/yr, which does not increase the sum geologic Mojave ECSZ rate to current geodetic values. Our result supports previous suggestions that transient tectonic activity in this area may be responsible for the discrepancy between long-term geologic and present-day geodetic rates

Leading-effect vs. Risk-taking in Dynamic Tournaments: Evidence from a Real-life Randomized Experiment

Two 'order effects' may emerge in dynamic tournaments with information feedback. First, participants adjust effort across stages, which could advantage the leading participant who faces a larger 'effective prize' after an initial victory (leading-effect). Second, participants lagging behind may increase risk at the final stage as they have 'nothing to lose' (risk-taking). We use a randomized natural experiment in professional two-game soccer tournaments where the treatment (order of a stage-specific advantage) and team characteristics, e.g. ability, are independent. We develop an identification strategy to test for leading-effects controlling for risk-taking. We find no evidence of leading-effects and negligible risk-taking effects

Time-evolving acoustic propagation modeling in a complex ocean environment

During naval operations, sonar performance estimates often need to be computed in-situ with limited environmental information. This calls for the use of fast acoustic propagation models. Many naval operations are carried out in challenging and dynamic environments. This makes acoustic propagation and sonar performance behavior particularly complex and variable, and complicates prediction. Using data from a field experiment, we have investigated the accuracy with which acoustic propagation loss (PL) can be predicted, using only limited modeling capabilities. Environmental input parameters came from various sources that may be available in a typical naval operation. The outer continental shelf shallow-water experimental area featured internal tides, packets of nonlinear internal waves, and a meandering water mass front. For a moored source/receiver pair separated by 19.6 km, the acoustic propagation loss for 800 Hz pulses was computed using the peak amplitude. The variations in sound speed translated into considerable PL variability of order 15 dB. Acoustic loss modeling was carried out using a data-driven regional ocean model as well as measured sound speed profile data for comparison. The acoustic model used a two-dimensional parabolic approximation (vertical and radial outward wavenumbers only). The variance of modeled propagation loss was less than that measured. The effect of the internal tides and sub-tidal features was reasonably well modeled; these made use of measured sound speed data. The effects of nonlinear waves were not well modeled, consistent with their known three-dimensional effects but also with the lack of measurements to initialize and constrain them.Netherlands. Ministry of DefenceUnited States. Office of Naval Research (Grant N00014-12-1-0944 (ONR6.2))United States. Office of Naval Research (Grant N00014-08-1-1097 (ONR6.1))United States. Office of Naval Research (Grant N00014-08-1-0680 (PLUS-SEAS)

Germline polymorphisms as modulators of cancer phenotypes

Identifying the complete repertoire of genes and genetic variants that regulate the pathogenesis and progression of human disease is a central goal of post-genomic biomedical research. In cancer, recent studies have shown that genome-wide association studies can be successfully used to identify germline polymorphisms associated with an individual's susceptibility to malignancy. In parallel to these reports, substantial work has also shown that patterns of somatic alterations in human tumors can be successfully employed to predict disease prognosis and treatment response. A paper by Van Ness et al. published this month in BMC Medicine reports the initial results of a multi-institutional consortium for multiple myeloma designed to evaluate the role of germline polymorphisms in influencing multiple myeloma clinical outcome. Applying a custom-designed single nucleotide polymorphism microarray to two separate patient cohorts, the investigators successfully identified specific combinations of germline polymorphisms significantly associated with early clinical relapse. These results raise the exciting possibility that besides somatically acquired alterations, germline genetic background may also exert an important influence on cancer patient prognosis and outcome. Future 'personalized medicine' strategies for cancer may thus require incorporating genomic information from both tumor cells and the non-malignant patient genome