Terrance J. Quinn

Incorporating Spatial Structure in Stock Assessment: Movement Modeling in Marine Fish Population Dynamics

Investigations into population structure have been at the forefront of fisheries research for decades, yet it is generally ignored in stock assessment models. As the complex nature of marine population structure has been uncovered, models have attempted to accurately portray it through the development of spatially explicit assessments that allow for movement between sub-populations. Although current tag-integrated movement models are highly complex, many arose from the relatively simple models of Beverton and Holt (1957). This article traces the historical development of these models and compares their features. Originally estimation of movement utilized only tag-recapture models, but now tag-integrated assessment models incorporate several sources of fishery, survey, and tag-recapture information to inform movement estimates. As spatial management measures become more widely used, it is increasingly important that assessment models include the spatial complexities of population structure and patterns of fishery removals, in order for more reliable monitoring of population rebuilding to take place. A generalized metapopulation model is proposed for use in fisheries stock assessment, which allows for adult movement among spatially discrete sub-populations. The input requirements for the model include region-specific catch-at-age, a tag-recapture dataset, and auxiliary information, such as a fishery-independent abundance index.

Relationship of farm salmon, sea lice, and wild salmon populations.

Increased farm salmon production has heightened concerns about the association between disease on farm and wild fish. The controversy is particularly evident in the Broughton Archipelago of Western Canada, where a high prevalence of sea lice (ectoparasitic copepods) was first reported on juvenile wild pink salmon (Oncorhynchus gorbuscha) in 2001. Exposure to sea lice from farmed Atlantic salmon (Salmo salar) was thought to be the cause of the 97% population decline before these fish returned to spawn in 2002, although no diagnostic investigation was done to rule out other causes of mortality. To address the concern that sea lice from fish farms would cause population extinction of wild salmon, we analyzed 10–20 y of fish farm data and 60 y of pink salmon data. We show that the number of pink salmon returning to spawn in the fall predicts the number of female sea lice on farm fish the next spring, which, in turn, accounts for 98% of the annual variability in the prevalence of sea lice on outmigrating wild juvenile salmon. However, productivity of wild salmon is not negatively associated with either farm lice numbers or farm fish production, and all published field and laboratory data support the conclusion that something other than sea lice caused the population decline in 2002. We conclude that separating farm salmon from wild salmon—proposed through coordinated fallowing or closed containment—will not increase wild salmon productivity and that medical analysis can improve our understanding of complex issues related to aquaculture sustainability.

Sustainability in single–species population models

In this paper, we review the concept of sustainability with regard to a single–species, age–structured fish population with density dependence at some stage of its life history. We trace the development of the view of sustainability through four periods. The classical view of sustainability, prevalent in the 1970s and earlier, developed from deterministic production models, in which equilibrium abundance or biomass is derived as a function of fishing mortality. When there is no fishing mortality, the population equilibrates about its carrying capacity. We show that carrying capacity is the result of reproductive and mortality processes and is not a fixed constant unless these processes are constant. There is usually a fishing mortality, FMSY, which results in MSY, and a higher value, Fext, for which the population is eventually driven to extinction. For each F between 0 and Fext, there is a corresponding sustainable population. From this viewpoint, the primary tool for achieving sustainability is the control of fishing mortality. The neoclassical view of sustainability, developed in the 1980s, involved population models with depensation and stochasticity. This view point is in accord with the perception that a population at a low level is susceptible to collapse or to a lack of rebuilding regardless of fishing. Sustainability occurs in a more restricted range from that in the classical view and includes an abundance th reshold. A variety of studies has suggested that fishing mortality should not let a population drop below a threshold at 10–20% of carrying capacity. The modern view of sustainability in the 1990s moves further in the direction of precaution. The fishing mortality limit is the former target of FMSY (or some proxy), and the target fishing mortality is set lower. This viewpoint further reduces the range of permissible fishing mortalities and resultant desired population sizes. The objective has shifted from optimizing long–term catch to preserving spawning biomass and egg production for the future. The use of discount rates in objective functions involving catch is not a suitable alternative to protecting reproductive value. As we move into the post–modern time period, new definitions of sustainability will attempt to incorporate he economic and social aspects of fisheries and/or ecosystem and habitat requirements. These definitions now involve ‘warm and fuzzy’ notions (healthy ecosystems and fishing communities, the needs of future generations, diverse fish communities) and value judgements of desired outcomes. Additional work is needed to make these definitions operational and to specify quantitative objectives to be achieved. In addition, multiple objectives may be incompatible, so trade–offs in what constitutes sustainability must be made. The advances made under the single–species approach should not be abandoned in the post–modern era, but rather enhanced and combined with new approaches in the multi–species and economic realms.

Observer Accuracy and Precision in Aerial and Foot Survey Counts of Pink Salmon in a Southeast Alaska Stream

Abstract Within- and between-observer variability and bias in aerial and foot survey estimates of spawning abundance of pink salmon Oncorhynchus gorbuscha were determined for survey counters from Chaik Bay Creek on southern Admiralty Island, Southeast Alaska, in 1992–1994. Multiple counts of pink salmon escapement in predetermined sections of the creek were made. At the same time, a mark–recapture experiment was performed to estimate the actual number of pink salmon and chum salmon O. keta. Observer counting abilities were also examined by using computer images that simulated aerially observed fish; four object types aggregated at predetermined numbers were tested. Observers tended to undercount the actual number of salmon present, and accuracy decreased nonlinearly with an increase in actual salmon escapements. On average, observers counted between 25% and 68% of the salmon present. Correction factors determined for each observer can be used to reduce bias in estimates of total abundance and make counts ...

Failure of population recovery in relation to disease in Pacific herring

Following an estimated 60% decline in population abundance in early 1993, recovery of the Pacific herring Clupea pallasii population of Prince William Sound, Alaska, USA, has been impaired by disease. Comprehensive epidemiological study from 1994 through 2002 validated an age-structured assessment (ASA) model of disease and population abundance; from 2003 to 2006, the impact of disease was modeled by analyzing only 2 lesions: ulcers and white foci in the heart. The ASA model identified increased natural mortality since 1993 that can be explained by (1) epidemics associated with ulcers (prevalence about 3%) and the North American strain of viral hemorrhagic septicemia virus (VHSV Type IVa; prevalence up to 14%) in 1994 and 1998 and (2) relatively high prevalence of the mesomycetozoean Ichthyophonus hoferi from 1994 through 2006, including epidemics with the greatest sample prevalence in 2001 (38%, by histopathology) and 2005 (51%, estimated histopathology prevalence). Fourteen other parasites occurred at prevalence > 10%, but none were considered significant contributors to fish mortality. We predict that if natural mortality after 1994 had returned to background levels that best fit the model from 1980 to 1992 (0.25 yr(-1)), population biomass in 2006 would have been 3 times the best estimate, despite relatively poor recruitment since 1994. In conclusion, disease information can be used to explain and predict changes in populations that have confounded traditional fisheries assessment.

A multispecies age-structured assessment model for the Gulf of Alaska

Predation is the largest source of mortality for marine fish and may be an important process in regulating population size. Recent population models have attempted to quantify predation separately from other sources of natural mortality. Building upon such work, a multispecies age-structured assessment model (MSASA) for the Gulf of Alaska was developed, which included arrowtooth flounder (Atheresthes stomias), Pacific cod (Gadus macrocephalus), and walleye pollock (Theragra chalcogramma). Predation mortality was a flexible function of predator and prey abundances that was fitted to stomach-content data. A proof of concept illustration is presented here, assessing model outputs against a set of single-species models. The MSASA model was able to successfully estimate predation between species and integrate it into total mortality. Significant predation occurred on younger pollock and flounder. Results indicate a significant change in predation over time on pollock as a function of increased arrowtooth floun...

A general growth model for mark-recapture data

Abstract The general four-parameter size-age growth model of Schnute incorporates many classical formulations, such as the von Bertalanffy, Gompertz, and Richards, as submodels. The general model has different submodels depending on the values of two model parameters a and b. We develop here the equivalent model representations for mark-recapture data, consisting of size measurements at the times of marking and recapture and the times at large. The general mark-recapture model for these data contains only three distinct parameters, because actual fish age is not included in the data set. Thus, mark-recapture data can be used to determine a general growth model only if one of the parameters, most likely size at the starting age, is specified beforehand. The model is applied to two data sets with both size-age and mark-recapture data: Arctic char in the Wood River system, Alaska and rainbow trout in the Kenai River, Alaska. Different growth formulations are isolated for the two data sets, illustrating the versatility of Schnutes formalism of growth. In only one instance is the ubiquitous von Bertalanffy growth model selected, suggesting that alternative growth models should be considered more frequently. We discuss how growth variations of individuals may be incorporated into the general model.

Long-term growth dynamics of young Pacific halibut: evidence of temperature-induced variation

Abstract The first five otolith growth zones of 744 Pacific halibut from 26 year-classes (1953–1978) were analyzed to identify patterns of annual growth and the sources of temporal variation. Sexual differences in growth appeared at an early age, and size selectivity of the gear types was shown to influence the perception of past growth. We adjusted the growth record for these two effects by removing variation in annual otolith growth that was linearly related to the size of the fish at capture. Correlation patterns of the otolith zones at the youngest ages suggested a general uncoupling of individual growth from one year to the next. Temporal variation was examined by developing a linear model to partition growth at different ages into both year and year-class effects. Randomization tests indicated that both effects are significant when all five ages are included, but when subsets of the data are examined, the year effect is strongest for youngest juveniles, whereas the year-class effect is significant for older juveniles. The year effect is probably attributable to interannual temperature changes, as indicated by a strong linear relationship between sea surface temperature (SST) and otolith growth from ages 0 to 2 years. However, analysis of residuals indicated a remaining year effect, suggesting that SST is an imperfect measure of the actual environment that regulates juvenile growth. The year-class effect observed in older juveniles was not present in the data adjusted for size selectivity, suggesting that this effect could be influenced by sampling bias, though intrinsic influences cannot be ruled out. Density-dependent growth did not appear to be a factor accounting for growth variation; instead, there appeared to be a slight positive correlation between otolith growth at ages 1 and 2 years and estimated year-class abundance (at age 8 years), suggesting that early growth is a factor in determining year-class strength.

The effect of organohalogen contaminants on western Steller sea lion survival and movement in the Russian Far East.

The western stock of Steller sea lions (Eumetopias jubatus) have experienced dramatic declines since the 1960s, particularly in the western Alaskan and Asian portions, which have continued to decline or stabilized at low levels. Multiple causes for this decline have been proposed and may include anthropogenic contamination from organohalogen contaminants (OCs). These include polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDT), which have not been ruled out as a potential cause for the lack of recovery. The objective of this study was to determine the effects of OCs on survival and movement probabilities estimated in program MARK using resighting data collected from 2003 to 2009. PCBs and DDTs were measured in whole blood from 136 (74 males and 62 females) individually marked, free-ranging pups from four Russian Far East rookeries. The mean concentration of ∑PCB and ∑DDT was 4.25±5.12 and 3.22±4.28 ng g(-1) ww (n=136), respectively, and the average ∑PCB and ∑DDT concentration for those above the aggregate mean (n=44) was 9.25±6.55 and 7.65±5.21 ng g(-1) ww, and those below the aggregate mean (n=92) the concentration was 1.86±0.89 and 1.11±0.65 ng g(-1) ww, respectively. The lowest estimated probabilities of survival occurred in the first year, ranging from 38% to 74%, but increased for ages 1-9, ranging from 82% to 94%. The greatest movement occurred from Medny Island west toward the Kamchatka Peninsula (33%) and to Bering Island (18%), and low movement estimates for other natal rookeries was largely due to minimal resighting effort. The estimated probabilities of resighting varied by location (48%-87%), but had greater precision than survival or movement parameters. Survival and movement were most affected by age and location rather than OCs.