Review of size- and age-dependence in batch spawning: implications for stock assessment of fish species exhibiting indeterminate fecundity

Most assessments of fish stocks use some measure of the reproductive potential of a population, such as spawning biomass. However, the correlation between spawning biomass and reproductive potential is not always strong, and it likely is weakest in the tropics and subtropics, where species tend to exhibit indeterminate fecundity and release eggs in batches over a protracted spawning season. In such cases, computing annual reproductive output requires estimates of batch fecundity and the annual number of batches—the latter subject to spawning frequency and duration of spawning season. Batch fecundity is commonly measured by age (or size), but these other variables are not. Without the relevant data, the annual number of batches is assumed to be invariant across age. We reviewed the literature and found that this default assumption lacks empirical support because both spawning duration and spawning frequency generally increase with age or size. We demonstrate effects of this assumption on measures of reproductive value and spawning potential ratio, a metric commonly used to gauge stock status. Model applications showed substantial sensitivity to age dependence in the annual number of batches. If the annual number of batches increases with age but is incorrectly assumed to be constant, stock assessment models would tend to overestimate the biological reference points used for setting harvest rates. This study underscores the need to better understand the age- or size-dependent contrast in the annual number of batches, and we conclude that, for species without evidence to support invariance, the default assumption should be replaced with one that accounts for age- or size-dependence.

Seasonal and interannual variation in juvenile salmonids and associated fish assemblage in open waters of the lower Columbia River estuary

The transition between freshwater and marine environments is associated with high mortality for juvenile anadromous salmonids, yet little is known about this critical period in many large rivers. To address this deficiency, we investigated the estuarine ecology of juvenile salmonids and their associated fish assemblage in open-water habitats of the lower Columbia River estuary during spring of 2007–10. For coho (Oncorhynchus kisutch), sockeye (O. nerka), chum (O. keta), and yearling (age 1.0) Chinook (O. tshawytscha) salmon, and steelhead (O. mykiss), we observed a consistent seasonal pattern characterized by extremely low abundances in mid-April, maximum abundances in May, and near absence by late June. Subyearling (age 0.0) Chinook salmon were most abundant in late June. Although we observed interannual variation in the presence, abundance, and size of juvenile salmonids, no single year was exceptional across all species-and-age classes. We estimated that >90% of juvenile Chinook and coho salmon and steelhead were of hatchery origin, a rate higher than previously reported. In contrast to juvenile salmonids, the abundance and composition of the greater estuarine fish assemblage, of which juvenile salmon were minor members, were extremely variable and likely responding to dynamic physical conditions in the estuary. Comparisons with studies conducted 3 decades earlier suggest striking changes in the estuarine fish assemblage—changes that have unknown but potentially important consequences for juvenile salmon in the Columbia River estuary.

Fish consumption by harbor seals (Phoca vitulina) in the San Juan Islands, Washington

The harbor seal (Phoca vitulina) is a large-bodied and abundant predator in the Salish Sea ecosystem, and its population has recovered since the 1970s after passage of the Marine Mammal Protection Act and the cessation of bounties. Little is known about how this large predator population may affect the recovery of fish stocks in the Salish Sea, where candidate marine protected areas are being proposed. We used a bioenergetics model to calculate baseline consumption rates in the San Juan Islands, Washington. Salmonids (Oncorhynchus spp.) and herring (Clupeidae) were the 2 most energetically important prey groups for biomass consumed by harbor seals. Estimated consumption of salmonids was 783 (±380 standard deviation [SD]) metric tons (t) in the breeding season and 675 (±388 SD t in the nonbreeding season. Estimated consumption of herring was 646 (±303 SD) t in the breeding season and 2151 (±706 SD) t in the nonbreeding season. Rockfish, a depressed fish stock currently in need of population recovery, composed one of the minor prey groups consumed by harbor seals (84 [±26 SD] t in the nonbreeding season). The variables of seal body mass and proportion of prey in seal diet explained >80% of the total variation in model outputs. Prey groups, such as rockfish, that are targeted for recovery may still be affected by even low levels of predation. This study highlights the importance of salmonids and herring for the seal population and provides a framework for refining consumption estimates and their confidence intervals with future data.

Shifts in the estuarine demersal fish community after a fishery closure in Puget Sound, Washington

Puget Sound is one of the largest and most ecologically significant estuaries in the United States, but the status and trends of many of its biological components are not well known. We analyzed a 21-year time series of data from standardized bottom trawl sampling at a single study area to provide the first assessment of population trends of Puget Sound groundfishes after the closure of bottom trawl fisheries. The expected increase in abundance was observed for only 3 of 14 species after this closure, and catch rates of most (10) of the abundant species declined through time. Many of these changes were stepwise (abrupt) rather than gradual, and many stocks exhibited changes in catch rate during the 3-year period from 1997 through 2000. No detectable change was recorded for either temperature or surface salinity over the entire sampling period. The abrupt density reductions that were observed likely do not reflect changes in demographic rates but may instead represent distributional shifts within Puget Sound.

Influence of soak time and fish accumulation on catches of reef fishes in a multispecies trap survey

Catch rates from fishery-independent surveys often are assumed to vary in proportion to the actual abundance of a population, but this approach assumes that the catchability coefficient (q) is constant. When fish accumulate in a gear, the rate at which the gear catches fish can decline, and, as a result, catch asymptotes and q declines with longer fishing times. We used data from long-term trap surveys (1990–2011) in the southeastern U.S. Atlantic to determine whether traps saturated for 8 reef fish species because of the amount of time traps soaked or the level of fish accumulation (the total number of individuals of all fish species caught in a trap). We used a delta-generalized-additive model to relate the catch of each species to a variety of predictor variables to determine how catch was influenced by soak time and fish accumulation after accounting for variability in catch due to the other predictor variables in the model. We found evidence of trap saturation for all 8 reef fish species examined. Traps became saturated for most species across the range of soak times examined, but trap saturation occurred for 3 fish species because of fish accumulation levels in the trap. Our results indicate that, to infer relative abundance levels from catch data, future studies should standardize catch or catch rates with nonlinear regression models that incorporate soak time, fish accumulation, and any other predictor variable that may ultimately influence catch. Determination of the exact mechanisms that cause trap saturation is a critical need for accurate stock assessment, and our results indicate that these mechanisms may vary considerably among species.

Estimating overall fish bycatch in U.S. commercial fisheries

Bycatch, or the unintended capture of fish, marine mammals, sea turtles, and seabirds by fishing gear, occurs to some degree in most fisheries. The recently released National Marine Fisheries Service’s (NMFS) U.S. National Bycatch Report provides information on bycatch in U.S. commercial fisheries by fishery and species. The report also provides national statistics in the form of national bycatch ratio and a national bycatch estimate. We describe the methods used to develop these statistics and compare them to similar studies. We conclude that the national bycatch ratio and national bycatch estimates developed by NMFS represent the best available information on bycatch in U.S. fisheries. However, given changes in bycatch management over time, as well as inter-annual variability in bycatch levels and a high percentage of fisheries for which data on bycatch are not currently available, we recommend that NMFS continue to support bycatch data collection and reporting efforts to improve the quality and quantity of bycatch data and estimates available to fisheries managers and scientists over time. This will enable NMFS to meet its requirements for bycatch reporting under the Magnuson-Stevens Act (MSA), as well as requirements for bycatch minimization under the MSA, Marine Mammal Protection Act, and Endangered Species Act.

Comparing autonomous underwater vehicle (AUV) and vessel-based tracking performance for locating acoustically tagged fish

Autonomous underwater vehicles (AUV’s) are increasingly used to collect physical, chemical, and biological information in the marine environment. Recent efforts include merging AUV technology with acoustic telemetry to provide information on the distribution and movements of marine fish. We compared surface vessel and AUV tracking capabilities under rigorous conditions in coastal waters near Juneau, Alaska. Tracking surveys were conducted with a REMUS 100 AUV equipped with an integrated acoustic receiver and hydrophone. The AUV was programmed to navigate along predetermined routes to detect both reference transmitters at 20–500 m depths and tagged fish and crabs in situ. Comparable boat surveys were also conducted. Transmitter depth had a major impact on tracking performance. The AUV was equally effective or better than the boat at detecting reference transmitters in shallow water, and significantly better for transmitters at deeper depths. Similar results were observed for tagged animals. Red king crab, Paralithodes camtschaticus, at moderate depths were recorded by both tracking methods, while only the AUV detected Sablefish, Anoplopoma fimbria, at depths exceeding 500 m. Strong currents and deep depths caused problems with AUV navigation, position estimation, and operational performance, but reflect problems encountered by other AUV applications that will likely diminish with future advances, enhanced methods, and increased use.

Marine Fisheries Stock Assessment Improvement Plan: report of the National Marine Fisheries Service National Task Force for Improving Fish Stock Assessments

This report argues for greatly increased resources in terms of data collection facilities and staff to collect, process, and analyze the data, and to communicate the results, in order for NMFS to fulfill its mandate to conserve and manage marine resources. In fact, the authors of this report had great difficulty defining the "ideal" situation to which fisheries stock assessments and management should aspire. One of the primary objectives of fisheries management is to develop sustainable harvest policies that minimize the risks of overfishing both target species and associated species. This can be achieved in a wide spectrum of ways, ranging between the following two extremes. The first is to implement only simple management measures with correspondingly simple assessment demands, which will usually mean setting fishing mortality targets at relatively low levels in order to reduce the risk of unknowingly overfishing or driving ecosystems towards undesirable system states. The second is to expand existing data collection and analysis programs to provide an adequate knowledge base that can support higher fishing mortality targets while still ensuring low risk to target and associated species and ecosystems. However, defining "adequate" is difficult, especially when scientists have not even identified all marine species, and information on catches, abundances, and life histories of many target species, and most associated species, is sparse. Increasing calls from the public, stakeholders, and the scientific community to implement ecosystem-based stock assessment and management make it even more difficult to define "adequate," especially when "ecosystem-based management" is itself not well-defined. In attempting to describe the data collection and assessment needs for the latter, the authors took a pragmatic approach, rather than trying to estimate the resources required to develop a knowledge base about the fine-scale detailed distributions, abundances, and associations of all marine species. Thus, the specified resource requirements will not meet the expectations of some stakeholders. In addition, the Stock Assessment Improvement Plan is designed to be complementary to other related plans, and therefore does not duplicate the resource requirements detailed in those plans, except as otherwise noted.