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Current Research

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Members of the FAR Lab work on a variety of topics. Often, we are working on more than one project at a time. Here are just a few of the topics that we are currently conducting research on.

Size selectivity of midwater trawls used in pollock acoustic abundance surveys

Kresimir Williams

Acoustic surveys are an important component of resource management effort for walleye pollock (Theragra chalcogramma), the largest fishery in the US. During the course of the survey, conducted by NOAA research ships, fish aggregations seen by the echosounders are sampled using survey trawls. The trawl catches are expected to correctly represent the species composition and size distribution of the fish in the aggregation sampled. However, trawls usually do not catch all sizes and species of fish with equal efficiency, resulting in potential errors in survey results. My research focuses on determining how fish of different sizes interact with the trawl, and what the effect of size�dependent escapement from the trawl has on the estimates of pollock abundance.

One way to sample escaping fish is to recapture them using small nets attached to the outside of the survey trawl as they try to escape. These samples are used in a model to predict total escapement from the trawl, which is used together with the retained catch to determine the length dependent selectivity characteristics of the trawl. Knowing the selectivity of the trawl and its variability allows us to estimate the effect of biased trawl catches on the acoustic survey abundance estimates.

Nets on Deck of the NOAA Ship Miller Freeman Attachment of the Pocket nets onto the outside trawl
left) Nets on deck of the NOAA ship Miller Freeman
right) Attachment of the pocket nets onto the outside trawl
  Nets on Deck of the NOAA Ship Miller Freeman
left) Deployment of trawl with pocket nets from NOAA Ship Oscar Dyson.
right) Fish caught in recapture nets.

I am also interested in the underlying causes for selective retention of fish by trawls. This requires making observations of fish behavior, specifically their reactions to the trawl components during the capture process. Fish behavior was studied using a dual-frequency identification sonar (DIDSON) to track the movements of individual fish as they encounter the trawl along with stereo-cameras to determine their size, position, and orientation. These observations provide insight into size specific behaviors of pollock, and will aid in making modifications to the trawl to reduce fish escapement.

Adult and juvenile Walleye Pollock within the midwater trawl.  Notice the mesh opening size is larger than the juvenile fish. Adult and juvenile Walleye Pollock within the midwater trawl.  Notice the mesh opening size is larger than the juvenile fish.

left) Adult and juvenile Walleye Pollock within the midwater trawl. 
right) Individual fish tracks from the DIDSON data. 

left) Track of escaping fish from the DIDSON data. 
right) Walleye pollock escaping the trawl.  Notice the mesh opening size is larger than the juvenile fish. 

This research has been sponsored by the Midwater Assessment and Conservation Engineering program, part of the NOAA Fisheries Alaska Fisheries Science Center.

Hood Canal dissolved oxygen studies (2006-2008 field work)

Sandy Parker-Stetter

A combination of 4 different projects, this work is evaluating the effect of hypoxia (i.e. low dissolved oxygen) on pelagic nekton (fish and large invertebrates). A common thread among the projects is an evaluation of vertical and horizontal distribution of nekton before, during, and after hypoxia. Another particular interest in this project is whether the development of a midwater oxygen minimum layer (M-OML) affects the nighttime vertical migration of predators (fish) and/or prey (invertebrates), potentially disrupting the transfer of energy in this system. Although the acute effects of hypoxia on fish (i.e. fish kills) have been observed in Hood Canal, this work is evaluating chronic or episodic changes in distribution or ecology such as feeding or species composition. As part of the Hood Canal Dissolved Oxygen Program (HCDOP) these projects have been in collaboration with researchers at the University of Washington (School of Aquatic and Fishery Sciences & School of Oceanography), Washington Department of Fish and Wildlife, and the Hood Canal Salmon Enhancement Group.  

On left: Dissolved oxygen profile in September, with low DO between 10-35 m.
On right: Acoustic echogram nighttime image of same site, showing lack of nekton in low DO zone.

Bering Sea squid (2007 field work)

Sandy Parker-Stetter

This project is evaluating the utility of multifrequency acoustics to separate squid (primarily Berryteuthis magister, the Magistrate armhook squid) from other groups (walleye pollock, euhausiids) in the SE Bering Sea. We are testing the ability of existing analytic approaches, and combinations of approaches, to identify squid within mixed assemblages, using midwater trawling results as a measure of the potential �true� assemblage composition. After having selected the best approach, we are comparing our estimated acoustic distribution of squid with direct trawl results (from our survey) and bycatch estimates from the walleye pollock fishery (joint with NOAA-NMFS-Alaska Fisheries Science Center (AFSC, Seattle, WA)). Finally, this project is also contributing to a better understanding of B. magister life history through morphometric evaluation (including sex and maturity stage) of specimens.


Top - An aggregation that contained walleye pollock and shrimp.
Bottom - An aggregation that contained walleye pollock, shrimp, and squid
Top - An aggregation that contained walleye pollock and shrimp.
Bottom - An aggregation that contained walleye pollock, shrimp, and squid
Female B. magister internal detail photo credit: J. Nomura
Female B. magister internal anatomy
Photo Credit: J. Nomura

Beaufort Sea pelagic fish (2008 field work)

Sandy Parker-Stetter

Prior to this 2008 effort (joint with NOAA-NMFS-AFSC and the University of Alaska Fairbanks, Fairbanks, AK), there had been no systematic survey of pelagic fish in the U.S. portion of the Beaufort Sea. Using acoustics and midwater trawling, we are quantifying the density distribution of age-1+ Arctic cod and age-0 fish (Arctic cod, sculpin (Cottidae family), and eelblenny (Lumpenus sp.)) within the ~20-500 m region of the Beaufort Sea shelf and slope habitats. Statistical models are being used to evaluate linkages between fish distributions (age-1+ Arctic cod and age-0 fish) and habitat characteristics (e.g., bottom depth, surface temperature, mixed layer depth). Finally, this project is also comparing acoustic results for age-1+ Arctic cod (density and distribution) with those derived from the bottom trawl portion of the study. More information can be found at the AFSC website for the project.


ice in Beafort Sea study area
Picture credit: S. Parker-Stetter

Bering Sea age-0 and forage fish (2008-2010 field work)

Sandy Parker-Stetter

Through this work we are characterizing the density distribution of age-0 (walleye pollock, Pacific cod) and forage (capelin, herring) fish species in the Bering Sea. In collaboration with NOAA-NMFS Ted Stevens Marine Research Institute (TSMRI, Juneau, AK) we are collecting acoustic and midwater trawl data during the BASIS surface trawl/oceanography survey that takes place in August-September. The combination of acoustics, midwater trawling, surface trawling, and oceanography provides us with a powerful tool to evaluate vertical and horizontal distribution of target species and to evaluate changes in distribution related to oceanography. As part of the Bering Sea Integrated Ecosystem Research Program (BSIERP) we will combine this information with other investigators to evaluate patterns in marine bird and mammal distributions and to inform individual- and ecosystem-level models.


forage fish distribution

Age-0 walleye pollock distribution (2010 field work)

Sandy Parker-Stetter

This new project will build on the observation that we made during our BSIERP-BASIS surveys (see Bering Sea age-0 and forage fish above) that between 2008 and 2009, the vertical and horizontal distribution of age-0 walleye pollock completely changed. Using a high-resolution survey nested within the BASIS survey, we will evaluate whether age-0 walleye pollock distribution is related to specific oceanographic properties or whether vertical distribution is better explained by differences in age-0 walleye pollock size.


Acoustic echograms (38 kHz) from 2008 (left) and 2009 (right) BASIS regional surveys showing differences in age-0 walleye pollock vertical distribution. Maximum vertical extent in both echograms is 110 m.

Gulf of Alaska forage fish (upcoming 2012-2013 field work)

Sandy Parker-Stetter

As part of the Gulf of Alaska Integrated Ecosystem Research Program (GOA IERP), this project will evaluate the density distribution of age-0 and forage fish species in the Gulf of Alaska.

Opportunistic Acoustic Data in Fisheries Management:  Southeastern Bering Sea Alaska pollock (Theragra chalcogramma)

Steve Barbeaux

Commercial fishing vessels have long been used as sampling platforms for scientific studies and many national, state, and provincial agencies contract fishing vessels to conduct scientific research to support fisheries management objectives.

Echosounders capable of collecting scientific quality acoustic data have recently become available to the commercial fishing industry and researchers around the world have begun to use acoustic data collected from commercial fishing vessels in a broad range of fisheries research applications (Stanley 2000; Dorn et al 2002; Barbeaux et al 2005; O�Driscoll and Macaulay 2005). In the North Pacific the use of scientific quality echosounders by the Alaska pollock (Theragra chalcogramma) fishing fleet has provided an opportunity to collect acoustic data opportunistically during normal fishing operations. Collecting opportunistic acoustic data from commercial fishing vessels allows researchers to inexpensively obtain data from multiple platforms during a single time period.

The costs of collecting acoustic data opportunistically is restricted to the price of the digital media used to record the data (~$220 US for 120GB), and the staff time to install and collect media from the vessels. A multiple platform approach potentially offers a more synoptic view of a population than a survey conducted on a single vessel. Although opportunistic data are not collected on a systematic grid and may not be used to obtain population abundance estimates directly, the broad temporal extent and high spatial resolution of the opportunistic data may facilitate investigations on the distribution and behavior of fished aggregations. Due to the unstructured �sampling design� and the multiple platforms from which these data are collected there are significant challenges to its use as a quantitative tool for fisheries managers. The project I am working on will investigate the appropriate use of these data and develop methods for over-coming obstacles intrinsic to this potentially valuable data source.

This research has been sponsored by the Alaska Fisheries Science Center.

This research has been sponsored by the Alaska Department of Fish and Game

Spatio-temporal patterns of near-surface acoustic backscattering in the eastern Bering Sea based on multi-frequency analysis and geostatistical methods

Mathieu Woillez

Fisheries acoustic surveys often collect multi-frequency data to help classify the species composition of the echosign. Because fishes are usually the primary target species, relatively little ground truthing efforts are spent to confirm the identity of the other scatterers. However, methods to characterize spatio-temporal patterns of these other scatterers based solely on the acoustic data can provide important insight to understand ecological relationships among these assemblages and those of the target species. In my work, I conduct an analysis of multi-frequency acoustic data collected in the eastern Bering Sea (EBS) during summers 2004, 2006-2008 to describe the spatio-temporal characteristics of a persistent, near-surface acoustic backscattering layer that exists throughout most of the EBS during summer. Analysis methods include unsupervised clustering, which takes into account the spatial context of these data. My approach initially focuses on the large scale-patterns in the frequency response, and then integrates small-scale patterns (i.e. echogram morphology) by using selected variogram-based textural indices. Categorical maps of each identified class of scatterers are produced and significant changes in their spatial patterns are tracked over time. Results will be used to optimize a field sampling plan to identify the species composition of this unique large-scale, near-surface feature as well as to identify important bio-physical forcing mechanisms that influence its spatial distribution and abundance.

Keywords: Spatial patterns, geostatistics, clustering, multi-frequency acoustics, inter-annual variability, eastern Bering Sea.

This research has been sponsored by the Alaska Fisheries Science Center.

Emily Runnells

Efforts to quantify marine bird population trends in the San Juan Archipelago have indicated regional declines in the majority of species during the past 30 years. Diving birds that specialize on schooling pelagic fish have shown the most severe declines (80-95%) (Bower 2007). The causes of these declines are unknown, but possible explanations include natural or anthropogenically forced variability in food supply. As top predators in marine ecosystems, seabirds may function as important indicators of ecological change because they are visible, abundant and relatively easy to study; however, seabirds� usefulness as indicators is dependent on our ability to understand the factors underlying their variation over different temporal and spatial scales (Piatt et al. 2007).

My research will offer a decadal comparison of seabird activity and abundance, forage fish abundance and distribution, and the zooplankton community in Cattle Pass (San Juan Islands, WA) and examine how seabird foraging activity reflects forage fish abundance by quantifying co-variation of seabirds and forage fish. A current estimate of forage fish availability will be acquired via acoustic surveys to determine the distribution and abundance of forage fish species. Land based seabird surveys, targeting detection of multi-species foraging aggregations, provide a proxy for feeding success and relate seabird presence and behavior to prey population data. Zooplankton sampling will provide data on food availability for forage fish. All of this information will be compared to research carried out by Jen Zamon in Cattle Pass during the summers of 1994 - 1997 (Zamon 2003), which offers a comprehensive data set on seabird abundance, seabird foraging activity, forage fish abundance and distribution, and the zooplankton community.

Responses of walleye pollock early life stages to varying environmental conditions.

Tracey Smart

The walleye pollock fishery in Alaskan waters comprises one of the largest single species fisheries in the world. Yearly catch limits on pollock are determined from modeled predictions derived from age-1 year class strength and each subsequent year before recruiting to fishing gear. The economic stability of the coastal communities greatly depends on the success of these predictions in minimizing fluctuations to quotas. We are interested in abundance patterns of walleye pollock in their first year, from spawning to metamorphosis to juvenile fish prior to their first winter. The success of the larval stages, and the age-1�s produced from these year classes, is highly dependent on varying oceanographic conditions acting upon survival of larvae through feeding ability, physiology, and predation.

Currently, we are using generalized additive models (or non-linear regression) to examine the responses of eggs, larvae, and juveniles to changes in temperature, wind-driven mixing, and zooplankton prey availability. These analyses have revealed important ontogenetic differences to varying environments that can greatly impact our predictions of age-1 year classes when we only take into consideration the abundance of a single stage prior to the first winter. We are also working to quantify the effects of varying suites of environmental conditions (i.e. warm and calm vs. cool and stormy) on the spatio-temporal distribution and success of each stage.

Temporal variability of pelagic fauna and bio-physical coupling in a coastal upwelling system with long-term measurements from a sonar observatory

Sam Urmy

The deep ocean is the largest habitat on Earth. It is, unfortunately, very difficult to know what goes on there, and even harder to know what goes on there for any extended period of time. We typically use some combination of nets, sonar, and cameras to piece together a picture the underwater world. This works, but we have to stop using them once the research cruise ends. As a result, we tend to have a better idea of the ocean�s What and Where than its How and When. There is a growing movement in oceanography to supplement ship-based research with ocean observatories. These are collections of instruments deployed for extended periods, preferably supplied with electrical power and communications via a cable.

My research uses DEIMOS, a deep-water acoustics package at the MARS observatory on the continental slope in Monterey Bay, California (read more about it here) to describe the distribution and density of animals through the entire water column through time. I am trying to describe changing patterns in this density distribution using a variety of metrics and indicators derived from the raw data, with the aim of gaining a clearer picture of how this system behaves, especially at time scales that are hard to resolve with ship-based sampling. Ultimately, I will try to connect the biological record from DEIMOS with other physical and biological time series available from Monterey Bay, such as water temperature, upwelling, currents, and chlorophyll concentration.

©2010 Fisheries Acoustics Research