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.     

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.     

Soil compaction in cropping systems: A review of the nature, causes and possible solutions

Soil compaction is one of the major problems facing modern agriculture. Overuse of machinery, intensive cropping, short crop rotations, intensive grazing and inappropriate soil management leads to compaction. Soil compaction occurs in a wide range of soils and climates. It is exacerbated by low soil organic matter content and use of tillage or grazing at high soil moisture content. Soil compaction increases soil strength and decreases soil physical fertility through decreasing storage and supply of water and nutrients, which leads to additional fertiliser requirement and increasing production cost. A detrimental sequence then occurs of reduced plant growth leading to lower inputs of fresh organic matter to the soil, reduced nutrient recycling and mineralisation, reduced activities of micro-organisms, and increased wear and tear on cultivation machinery. This paper reviews the work related to soil compaction, concentrating on research that has been published in the last 15 years. We discuss the nature and causes of soil compaction and the possible solutions suggested in the literature. Several approaches have been suggested to address the soil compaction problem, which should be applied according to the soil, environment and farming system.

The following practical techniques have emerged on how to avoid, delay or prevent soil compaction: (a) reducing pressure on soil either by decreasing axle load and/or increasing the contact area of wheels with the soil; (b) working soil and allowing grazing at optimal soil moisture; (c) reducing the number of passes by farm machinery and the intensity and frequency of grazing; (d) confining traffic to certain areas of the field (controlled traffic); (e) increasing soil organic matter through retention of crop and pasture residues; (f) removing soil compaction by deep ripping in the presence of an aggregating agent; (g) crop rotations that include plants with deep, strong taproots; (h) maintenance of an appropriate base saturation ratio and complete nutrition to meet crop requirements to help the soil/crop system to resist harmful external stresses.     

Geothermal convection through oceanic crust and sediments in the Indian ocean

Closely spaced heat flow surveys at four sites on the flanks of the Central Indian Ridge and the Southeast Indian Ridge delineate a pattern of oscillatory heat flow which can only result from cellular convection of oceanic bottom water through the oceanic crust and overlying sediment. These cells have a wavelength of 5 to 10 kilometers and are presently active in sea floor 18 x 10(6), 25 x 10(6), and 45 x 10(6) years old of the Crozet Basin and in sea floor 55 x 10(6) years old of the Madagascar Basin. The precise measurement of nonlinear temperature profiles makes it possible to calculate the conductive and convective heat transfer components through the sea floor. Even in the oldest sites, geothermal convection is still a major component of heat transfer through both the crust and sedimentary layers. These observations coupled with the results of earlier oceanwide geothermal studies indicate that more than one-third of the entire surface area of the world's ocean floor contains presently active geothermal convection that is cellular in plan form.     

Potential of a recombinant antigen as a prophylactic vaccine for day-old broiler chickens against Eimeria acervulina and Eimeria tenella infections.

A genetically engineered Eimeria tenella antigen (GX3262), produced as a fusion protein with beta-galactosidase and identified with a monoclonal antibody, induced partial but significant protection in young broiler chickens against experimental E. tenella and Eimeria acervulina infections. The antigen appears to share a T-helper cell epitope with the parasite as evidenced by (a) booster inoculation with either the recombinant antigen or with a small number of live oocysts enhanced the protective immunity in GX3262 primed chickens, and (b) ability of the antigen to induce in vitro stimulation of T-cells from chickens immunized with antigen or parasite. These observations suggest the feasibility of a single vaccination of 1 or 2-day-old broilers with GX3262 to induce an acceptable degree of protective immunity. The implications of the observations reported here are far reaching in terms of a practical coccidiosis vaccine for poultry, and show for the first time that 1-day-old broiler chickens can be efficiently vaccinated with a recombinant antigen against one or more species of Eimeria.     

Dose-dependent pharmacokinetics of gentamicin in sheep

Dose-related changes in the pharmacokinetics of gentamicin sulfate were investigated in 9 sheep given 3, 10, or 20 mg/kg of body weight IV in a crossover design with a 24-day washout period. The pharmacokinetics of the 3 mg/kg single dose were compared with that of the terminal phase pharmacokinetics of 3 mg of gentamicin/kg IV every 8 hours for 7 days in 8 additional sheep. Serum concentrations were monitored for 21 to 24 days after the dose. Polyexponential equations were fit to each data set. The number of exponential terms was determined by optimizing the fit for each data set. The pharmacokinetics of the 3 mg/kg single dose were mainly described by triexponential equations. The 10 mg/kg and the 20 mg/kg single doses and the 3 mg/kg multiple-dose data were described by a tetraexponential equation. The elimination rate constant was significantly smaller (P less than 0.05) after the larger single doses, and the serum gentamicin clearance increased as the dose increased (P less than 0.05). The crossover design sequence had a significant effect on serum gentamicin clearance and the area under the curve normalized to unit dose (P less than 0.01). The final exponential phase was not detectable with the present assay sensitivity under the 3 mg/kg single dose. The triexponential equation underpredicted the terminal serum concentrations determined after the 3 mg/kg multiple dose, whereas the 4 phase equation overpredicted the same terminal serum concentrations, perhaps reflecting saturation of the tissue pools that were mirrored by the serum gentamicin concentrations after 24 hours. The present study emphasized the complexity of the terminal phase gentamicin. pharmacokinetics and acknowledged the need for a long-term washout period when using the crossover design for gentamicin pharmacokinetic studies.