Remedies for pseudoreplication

Pseudoreplication is the failure of a statistical analysis to properly incorporate the true structure of randomness present in the data. It has been well documented and studied in the ecological literature but has received little attention in the fisheries literature. Avoiding pseudoreplication in analyses of fisheries data can be difficult due to the complexity of the statistical procedures required. However, recent developments in statistical methodology are decreasing the extent to which pseudoreplication has to be tolerated. Seven examples are given here, beginning with simple design-based remedies and progressing to more challenging examples including the model-based remedies of mixed-effects modelling, generalized linear mixed models, state-space models, and geostatistics.     

Investigation of the nutritional requirements of Australian snapper Pagrus auratus (Bloch & Schneider 1801): digestibility of gelatinized wheat starch and clearance of an intra-peritoneal injection of d-glucose

Two experiments were performed to investigate the digestibility and utilization of carbohydrate sources by Australian snapper Pagrus auratus. In the first experiment, snapper of two different size classes (110 and 375 g) were fed a reference diet containing no starch (REF) or diets containing 150 (PN15), 250 (PN25), 350 (PN35) or 450 g kg^?1 (PN45) of 100% gelatinized wheat starch to investigate the interactive effects of fish size and starch inclusion level on apparent organic matter (OM) or gross energy (GE) digestibility (ADC), post‐prandial plasma glucose concentration, hepatosomatic index (HSI) and liver or tissue glycogen content. A second experiment used a 72 h time course study to investigate the ability of larger snapper (300–481 g) to clear an intra‐peritoneal injection of 1 g d ‐glucose kg^?1 body weight (BW). Organic matter and GE ADCs declined significantly in both fish sizes as the level of starch increased (PN45energy small fishenergy large fish). There was no interaction between fish size and inclusion level with respect to GE or OM ADCs. Gross energy ADC for both sized fish was described by the linear function GE ADC=104.97 (±3.39)–0.109 (±0.010) × inclusion level (R²=0.86). Hepatosomatic index, liver and muscle glycogen concentrations were significantly elevated in both small and large snapper‐fed diets containing gelatinized starch compared with snapper fed the REF diet. Three‐hour post‐prandial plasma glucose concentrations were not significantly affected by fish size, inclusion level or the interaction of these factors (REF=PN15=PN25=PN35=PN45), and ranged between 1.60 and 2.5 mM. The mean±SD resting level of plasma glucose (0 h) was 2.4±1.1 mM. Circulating levels of plasma glucose in snapper peaked at 18.9 mM approximately 3 h after intra‐peritoneal injection and fish exhibited hyperglycaemia for at least 12–18 h. There were no significant differences between the plasma glucose concentrations of snapper sampled 0, 18, 24, 48 or 72 h after injection (0=18=24=48=72<12< 1<3=6 h), indicating snapper required almost 18 h to regulate their circulating levels of glucose to near‐basal concentrations. Australian snapper are capable of digesting moderate levels of gelatinized wheat starch; however, increasing the dietary content of starch resulted in a reduction in OM and GE digestibility. Smaller snapper appear to be less capable of digesting gelatinized starch than larger fish, and levels above 250 and 350 g kg^?1 of diet are not recommended for small and large fish respectively. Snapper subjected to an intra‐peritoneal injection of d ‐glucose have prolonged hyperglycaemia; however, the post‐prandial response to the uptake of glucose from normally digested gelatinized starch appears to be more regulated.     

Fish and flows: Abiotic drivers influence the recruitment response of a freshwater fish community throughout a regulated lotic system of the Murray-Darling Basin,Australia

1. Fish assemblages in dryland rivers have life-history strategies that have evolved in response to environmental conditions and triggers, particularly water temperatures and flow regimes. The regulation of rivers through the construction of dams, weirs and other water diversion structures has altered natural flow regimes and the associated ecological processes of river systems worldwide.
2. Over a 3-year period, using standardized fish sampling and daily otolith ageing, the recruitment of eight freshwater fish species was monitored in response to various abiotic drivers, including hydrology and water temperatures, throughout the Macquarie River, a large regulated river system of the Australian Murray-Darling Basin.
3. A data-driven statistical classification system is provided that groups species into reproductive guilds, based on their recruitment response to hydrology and water temperature, specifically designed for use in environmental flow management.
4. The eight species were grouped into three distinct reproductive guilds that showed similar recruitment responses to the abiotic drivers. Murray-Darling rainbowfish, Murray cod, and eel-tailed catfish were considered as a single guild, characterized by seasonal recruitment during a relatively narrow thermal window under low to moderate stable discharges. The second group included common carp, bony herring, and golden perch, which recruited primarily in association with larger flow events. Un-specked hardyhead and Australian smelt formed a more differentiated guild, recruiting over a broad range of temperatures and discharges. Limitations associated with using a reproductive guild approach to simplify water management are discussed.
5. This study highlighted important relationships among hydrology, water temperatures, and successful recruitment that can, in turn, be used to inform development of adaptive flow management plans and effective use of environmental water for the conservation management of native fish communities. Important considerations in the design of studies that aim to examine relationships between recruitment and abiotic drivers are also discussed.

     

Chemical profiling with modeling differentiates wild and farm-raised salmon

Classifications of fish production methods, wild or farm-raised salmon, by elemental profiles or C and N stable isotope ratios combined with various modeling approaches were determined. Elemental analysis (As, Ba, Be, Ca, Co, Cd, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, P, Pb, Sr, Ti, and Zn) of wild and farm-raised salmon samples was performed using an inductively coupled plasma atomic emission spectroscopy. Isotopic and compositional analyses of carbon and nitrogen were performed using mass spectrometry as an alternative fingerprinting technique. Each salmon (king salmon, Oncorhynchus tshawytscha ; coho salmon, Oncorhynchus kisutch ; Atlantic salmon, Salmo salar ) was analyzed from two food production practices, wild and farm raised. Principal component analysis (PCA) and canonical discriminant analysis (CDA) were used for data exploration and visualization. Five classification modeling approaches were investigated: linear discriminate function, quadratic discriminant function, neural network, probabilistic neural network, and neural network bagging. Methods for evaluating model reliability included four strategies: resubstitution, cross-validation, and two very different test set scenarios. Generally speaking, the models performed well, with the percentage of samples classified correctly depending on the particular choice of model and evaluation method used.     

A Dynamic, Stochastic Model of a Land-Based Summer Flounder Paralichthys dentatus Aquaculture Firm

Exploring the possibilities for commercial aquaculture has historically concentrated on reducing production uncertainty by focusing on an animal's biology and the engineering of the production facility. However, the aquaculturist faces both production and market uncertainty, both of which may significantly affect the economic feasibility of a production facility. We developed a dynamic stochastic model to compare alternative production and marketing scenarios and used the net present value of returns to evaluate the scenarios. Based on the model and the scenarios we examined, firms producing summer flounder Paralichthys dentatus are unlikely to be profitable unless they locate near and use a source of salt-water, sell their product predominately to sushi chefs (or other premium market outlets) who desire medium-sized live fish, and engage in strategies that account for market dynamics.     

Neospora-like protozoal infections associated with bovine abortions

Eighty bovine fetuses with presumed protozoal infections from a previous 2-year retrospective study were examined by immunohistochemistry using antisera against Neospora caninum. In 66 (83%) of the fetuses, protozoa were found that reacted positively with anti-N. caninum sera. In three (4%) additional fetuses, protozoa identified as Sarcocystis species did not react, and in two fetuses (3%) single protozoal clusters were found only in hematoxylin and eosin-stained slides. A group of 20 fetuses were chosen for further evaluation. They included 14 fetuses from the first group of 80 fetuses plus six additional fetuses that had large numbers of protozoa in the fetal brain. The 20 fetuses were examined immunohistochemically with antisera to N. caninum, Hammondia hammondi, and Toxoplasma gondii. Protozoa from 3/20 fetuses, identified as Sarcocystis species, failed to react with any antisera. In 16/20 fetuses protozoa reacted positively to antisera against N. caninum, and in most cases reacted to H. hammondi, and weakly to one or more of the antisera against T. gondii. Thick-walled protozoal tissue cysts were found in the brain of four of these 16 fetuses by transmission electron microscopy. The cyst wall morphology was comparable to N. caninum. The results suggested that a single protozoal parasite of unknown identity was responsible for most of the bovine abortions. By immunohistochemistry, the unknown protozoon reacted most strongly and consistently to N. caninum antisera, but was antigenically distinct from N. caninum. Ultrastructurally, tissue cysts found in four fetuses most closely resembled Neospora caninum.     

Phagocytosis and erythrocyte antibody-rosette formation by three populations of mononuclear phagocytes obtained from dogs treated with glucocorticoids

The effect of systemic administration of glucocorticoids was evaluated on 3 populations of macrophages obtained from healthy dogs. Phagocytic and Fc-receptor activities were determined for mononuclear phagocytes from blood and pulmonary and peritoneal lavage fluids. Samples were collected from 12 dogs before treatment and again on the same dogs after glucocorticoid administration. Thirty or more days were allowed between treatment periods. Twelve hours after combined prednisolone sodium succinate and dexamethasone sodium phosphate administration, the percentage of phagocytosing cells decreased for blood monocytes and increased for pulmonary macrophages. The percentage of pulmonary macrophages positive for erythrocyte antibody-rosette formation (Fc-receptor activity) increased. After 7 days of oral administration of prednisone, the percentage of phagocytosing peritoneal macrophages increased, whereas the percentage of blood monocytes with Fc-receptor activity increased. Results indicate that significant (P less than 0.05) changes in macrophage function occur after systemic administration of the glucocorticoid doses used in this study. Also, the effect of systemic administration of glucocorticoids on mononuclear phagocytes varies, depending on the specific cell location.