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Fish Stock Assessment 101 Series: Part 3—Ecosystem Factors and Assessments

June 17, 2013

Learn more about what factors other than fishing can have an influential role in determining the health and abundance of fish stocks.



In Part 1 of our Fish Stock Assessment 101 series, we presented the three primary types of data used in fish stock assessments—catch, abundance, and biology data. These data feed into mathematical models that represent the factors causing changes in harvested fish stocks.


In Part 2, we took a more detailed look at how stock assessment models work. The models produce estimates of the fishery management factors needed for managers to make informed decisions about how to best regulate a fishery. When possible, stock assessment models include information on ecosystem and environmental effects to improve the interpretation of historical information and the precision of forecasts.

Ecosystem Factors and Stock Assessments

Factors other than fishing can have an influential role in determining the health and abundance of fish stocks. These factors are not only important to fish populations; by including them in the analysis of fishing effects, we can better interpret stock assessment results. Ecosystem factors such as species interactions, habitat, and large-scale climate patterns may be important.

  • Food Web: All species within an ecosystem are connected to each other by the things that they eat, and the things that eat them. Tiny photosynthetic cells that capture carbon using energy from sunlight form the base of marine food webs, and provide the energy that ultimately powers top level carnivorous fish, marine mammals, and seabirds. The amount of primary productivity generated by plants and algae determines the number of fish that can be supported by an ecosystem. Because of these connections, the population dynamics of one species can affect the dynamics of many other species. A food web describes the connections between different species in an ecosystem through predator and prey relationships. Understanding these interactions can provide context for interpreting stock assessment results. Output from food web and predator-prey models can provide input to a single species assessment models, for example, the time series of natural mortality, providing improved stock assessment outputs.
  • Competition and Other Species Interactions: Species interactions other than predator-prey relationships can also influence population dynamics. Because resources within marine ecosystems are limited, animals must compete for food and space. Competition within and between species, as well as symbiotic and other types of species relationships can all be important. In Part 2 of this series, we noted how the natural mortality rate of fish is an important piece of information in order to accurately estimate the level of fishing mortality. Because of competition, the total production of a system may be more limited than one might expect if each species is considered alone.
  • Habitat: Healthy habitats sustain marine and coastal species, communities, and economies. Marine habitats may be altered in a number of ways, including through development, dredging, pollutants, or natural disasters. In turn, these alterations impact food sources, cover, refugia, and breeding grounds which are vital for reproduction, growth, metabolism, and other vital rates of marine species. Because habitat plays such a large role in structuring populations, understanding fish interactions with their habitat is important to stock assessment. One way that habitat information can improve stock assessments is by designing and analyzing fish abundance surveys according to habitat maps rather than simple geographic boundaries. Habitat quality and quantity may be assessed using habitat surveys—using multibeam sonars, echosounders, and underwater robots. These surveys map and document the physical, chemical, and biological system and help scientists understand complex interactions between fish and their habitats. Habitat features can be considered in these surveys to change the parameters and covariates affecting fish population dynamics. Habitat studies may also provide important information on species’ vital rates, which are important inputs for stock assessments and can affect the accuracy and precision of assessment results.
  • Physical Environment: In addition to physical habitat (e.g., bottom type), variability in ocean and climate patterns should also be taken into account when examining fish stocks. Many fish species have a relatively narrow range of temperature, chemical and other physical tolerances. Disruptions in the physical environment, due to climate or other perturbations, can impact natural stock behaviors such as spawning and migration. One effect of fluctuations in ocean conditions is on the numbers of young fish that survive from eggs to juveniles each year. For a fish stock like Pacific hake, the annual recruitment levels can be over 100 times different from year to year. Assessments can measure and track these changes in recruitment, but they cannot accurately forecast current and upcoming fluctuations without additional information. To improve forecasts, we need both better climate forecasts and better understanding of the effect of ocean climate on the factors that control fish recruitment.  Incomplete understanding of the impact of climate and other physical parameters on populations can lead to a mismatch between seasonal fisheries regulations, migration patterns, and population distributions, leading to unintended impacts to fishery stocks.

A Holistic Approach

Traditionally, fish stock assessments have relied on direct measurement of fish stocks and catch to determine a stock’s abundance and potential catch levels. This approach is effective for looking at present and historical conditions, but limited when trying to understand why changes occurred because it only accounts for the effects of fishing. This approach is also limited when trying to make accurate forecasts of sustainable catch levels because it does not account for changing ecosystem factors that could impact fish abundance.

The integrated analysis models described in Part 2 of this series allow environmental and ecosystem factors to be included in a stock assessment model, which can help scientists better understand historical stock changes and improve forecasts. For example, research indicates that the annual catchability of several stocks of flatfish in the Bering Sea is affected by bottom water temperatures. For these species, colder water influences the timing of spawning migrations and also slows activity, making the fish less likely to be caught in survey trawls. Modeling the relationship between annual bottom temperatures and survey catchability for these species improves the fit of survey biomass estimates and reduces overall uncertainty in the model results. Ecosystem food web studies can also provide more accurate values for important fish assessment parameters, such as natural mortality. For example, several species of forage fishes like the Atlantic herring assessments have begun to include estimates of predation removals. Modeling the dynamics of Atlantic herring inclusive of predation has provided a more accurate accounting of what has been removed from the stock each year, and hence a more realistic understanding of how that stock behaves, consistent with scientific and fisher observations on the water.

More research is needed to determine which factors are most important to fish populations so these factors can be included in stock assessment models appropriately. It is clear that very often more than just catch can affect fish stocks. Fish stock assessment results often feed back into holistic ecosystem studies by providing long time series of information on historical fish abundance and productivity. NOAA Fisheries is committed to supporting science and research to move us toward effective ecosystem-based management. Developing tools and approaches for incorporating ecosystem factors will allow us to deal with the impacts of climate and other environmental change on our marine trust species.


Why study food webs?

Studying a particular fish’s prey and predators helps scientists understand how that fish is connected to other marine resources in the ocean. Fish, marine mammals, sea turtles, seabirds, and plankton all live in a balance known as the food web. Researching food web dynamics helps NOAA Fisheries scientists better understand the important factors to be considered in stock assessments. These stock assessments are used as tools for setting catch limits. 


What is ecosystem data?

Factors other than fishing can have an important role in determining the health and abundance of fish stocks. Ecosystem factors such as interactions among species in the marine food web, changes in marine coastal habitat, and constantly changing ocean environmental factors may be important. Examples of ecosystem data that may inform stock assessments include:


Last updated by Office of Communications on May 07, 2021

Fish Stock Assessments