Richard Routledge

Temporal Patterns of Sea Louse Infestation on Wild Pacific Salmon in Relation to the Fallowing of Atlantic Salmon Farms

Abstract We report on a 3-year study of the infestation rates of the sea louse, Lepeophtheirus salmonis, on wild juvenile pink salmon Oncorhynchus gorbuscha and chum salmon O. keta in the Broughton Archipelago, British Columbia. In 2002, the British Columbia Ministry of Agriculture, Fisheries, and Food ordered farm fallowing (i.e., the removal of farmed Atlantic salmon Salmo salar from net-cages) along the presumed migration route of wild juvenile Pacific salmon in this area. The goal was to protect wild juvenile fish from sea louse infestation. We assessed the effectiveness of this decision by comparing sea louse infestation rates on wild juvenile salmon near three Atlantic salmon farm sites prior to, during, and after fallowing. Overall, L. salmonis levels were significantly reduced (P < 0.0001) at the study sites during fallowing but returned to the original level after fallowing. The decline was age specific. While the abundance of the earliest attached sea louse phase (the copepodid stage) declined b...

Bent-Cable Regression Theory and Applications

We use the so-called “bent-cable” model to describe natural phenomena that exhibit a potentially sharp change in slope. The model comprises two linear segments, joined smoothly by a quadratic bend. The class of bent cables includes, as a limiting case, the popular piecewise-linear model (with a sharp kink), otherwise known as the broken stick. Associated with bent-cable regression is the estimation of the bend-width parameter, through which the abruptness of the underlying transition may be assessed. We present worked examples and simulations to demonstrate the regularity and irregularity of bent-cable regression encountered in finite-sample settings. We also extend existing bent-cable asymptotics that previously were limited to the basic model with known linear slopes of 0 and 1. Practical conditions on the design are given to ensure regularity of the full bent-cable estimation problem if the underlying bend segment has nonzero width. Under such conditions, the least-squares estimators are shown to be consistent and to asymptotically follow a multivariate normal distribution. Furthermore, the deviance statistic (or the likelihood ratio statistic, if the random errors are normally distributed) is shown to have an asymptotic chi-squared distribution.

Sea Louse Infestation in Wild Juvenile Salmon and Pacific Herring Associated with Fish Farms off the East-Central Coast of Vancouver Island, British Columbia

Abstract Reports of infestations of sea lice Lepeophtheirus salmonis and Caligus clemensi in juvenile salmonids in Pacific Canada have been restricted to pink salmon Oncorhynchus gorbuscha and chum salmon O. keta from one salmon-farming region, the Broughton Archipelago of British Columbia. Here, we report on 2 years of sea louse field surveys of wild juvenile pink and chum salmon, as well as wild sockeye salmon O. nerka and larval Pacific herring Clupea pallasii, in another salmon farming region, the Discovery Islands region of British Columbia. For pink and chum salmon we tested for the dependency of sea louse abundance on temperature, salinity, sampling period, host species, and farm exposure category. For both louse species, farm exposure was the only consistently significant predictor of sea lice abundance. Fish exposed to salmon farms were infected with more sea lice than those in the peripheral category. Sea louse abundance on sockeye salmon and Pacific herring followed the same trends, but sample ...

Estimating the Size of Criminal Populations

The estimation of total population size for various phenomena of crime is an important factor critical for criminal justice policy formulation and criminological theory development. In this paper, methods are discussed for estimating the size of a criminal population from police records. Capture-recapture analysis techniques, borrowed from the biological sciences, are used to predict the size of population for migrating (or fleeing) fugitives and for street prostitutes. Heterogeneity and behavioral responses to previous police encounters are identified as major complicating factors. The basic problem is that the police records are virtually unaffected by a potentially large pool of cryptic criminals. It is shown how independently collected auxiliary data can address this problem.

Reducing Gill-Net Mortality of Incidentally Caught Coho Salmon

Abstract The abundance of coho salmon Oncorhynchus kisutch has declined dramatically over much of the southern part of its range along the Pacific Coast of North America. This decline has created the need to reduce fishing mortalities, including bycatch mortalities in fisheries that are targeting other species. Traditional gill-net fishing causes an estimated 35–70% mortality rate on incidentally caught coho salmon. A reduction in this high mortality rate is necessary if gill nets continue to be used in fisheries that inadvertently intercept depressed coho salmon stocks while fishing other species. By using modified gear, short net soak times, careful handling of fish on removal from the gill net, and a newly designed recovery box, the short-term mortality rate on incidentally caught coho salmon can be reduced to as little as 6%, possibly even lower in some circumstances. This substantial reduction in mortality on nontargeted species expands the possible role of gill nets in the development of selective f...

Practicing safe statistics with the mid-p*

The mid-p-value is the standard p-value for a test minus half the difference between it and the nearest lower possible value. Its smaller size lends it an obvious appeal to users - it provides a more significant-looking summary of the evidence against the null hypothesis. This paper examines the possibility that the user might overstate the significance of the evidence by using the smaller mid-p in place of the standard p-value. Routine use of the mid-p is shown to control a quantity related to the Type I error rate. This related quantity is appropriate to consider when the decision to accept or reject the null hypothesis is not always firm. The natural, subjective interpretation of a p-value as the probability that the null hypothesis is true is also examined. The usual asymptotic correspondence between these two probabilities for one-sided hypotheses is shown to be strengthened when the standard p-value is replaced by the mid-p.

Sea louse infection of juvenile sockeye salmon in relation to marine salmon farms on Canada's west coast.

Background Pathogens are growing threats to wildlife. The rapid growth of marine salmon farms over the past two decades has increased host abundance for pathogenic sea lice in coastal waters, and wild juvenile salmon swimming past farms are frequently infected with lice. Here we report the first investigation of the potential role of salmon farms in transmitting sea lice to juvenile sockeye salmon (Oncorhynchus nerka). Methodology/Principal Findings We used genetic analyses to determine the origin of sockeye from Canadas two most important salmon rivers, the Fraser and Skeena; Fraser sockeye migrate through a region with salmon farms, and Skeena sockeye do not. We compared lice levels between Fraser and Skeena juvenile sockeye, and within the salmon farm region we compared lice levels on wild fish either before or after migration past farms. We matched the latter data on wild juveniles with sea lice data concurrently gathered on farms. Fraser River sockeye migrating through a region with salmon farms hosted an order of magnitude more sea lice than Skeena River populations, where there are no farms. Lice abundances on juvenile sockeye in the salmon farm region were substantially higher downstream of farms than upstream of farms for the two common species of lice: Caligus clemensi and Lepeophtheirus salmonis, and changes in their proportions between two years matched changes on the fish farms. Mixed-effects models show that position relative to salmon farms best explained C. clemensi abundance on sockeye, while migration year combined with position relative to salmon farms and temperature was one of two top models to explain L. salmonis abundance. Conclusions/Significance This is the first study to demonstrate a potential role of salmon farms in sea lice transmission to juvenile sockeye salmon during their critical early marine migration. Moreover, it demonstrates a major migration corridor past farms for sockeye that originated in the Fraser River, a complex of populations that are the subject of conservation concern.

Fulton's Condition Factor: Is it a Valid Measure of Sea Lice Impact on Juvenile Salmon?

Abstract Condition factor formulas have been developed and are used to assist in assessing the state of fish health. Fultons condition factor has been used to measure anthropogenic impacts on fish, such as oil spills, and has provided results that, at times, are contentious. Recently, it has been used to suggest that infestation rates of sea lice Lepeophtheirus salmonis currently reported for juvenile pink salmon Oncorhynchus gorbuscha and chum salmon O. keta in the Broughton archipelago, British Columbia, may have no impact on fish health. Here, we show that Fultons condition factor values will remain high in salmon fry lethally infected with sea lice until shortly before death. Furthermore, we report that as condition factor values declined, the affected fish exhibited high predator risk behavior. We conclude that Fultons condition factor does not provide a reliable indicator of the impact of sea lice infestations on juvenile pink and chum salmon.

Fisher's Exact Test

Fishers exact test can be used to assess the significance of a difference between the proportions in the two groups. In particular, it provides a widely applicable way to assess the results of simple, completely randomized experiments leading to two-by-two contingency tables with small frequency counts, However, it has low power, especially when the standard P-value is used. The power can be increased considerably through either using the mid-P value, or carefully constructing a test based, at least in part, on a binomial model. Keywords: binomial; contingency tables; frequency data; mid-P; power

P -values from permutation and F -tests

Abstract Permutation tests present an attractive alternative to the commonly used F-tests in analysis of variance. Not only are they free of distributional assumptions, but they also relate directly to the permutation in the experimental design. Recent advances in computing power have enhanced their feasibility to the point where the researcher is often free to quote a p-value from either a permutation test or an F-test. Very large differences are shown to be possible for small experiments, with a systematic component that can be virtually eliminated through the use of the mid-p for the permutation version. Advantages of eliminating this systematic component are discussed. A mild potential for overstating significance by choosing the smaller of the two p-values is illustrated through an examination of the null-hypothesis distribution of the minimum. A subtle bias towards increased significance of marginal evidence is also shown to arise in a routine application of a naive, but very natural screening procedure.