Biochemistry Biology Coastal Management Conservation Fisheries Genetics

Protecting Hometown Herring


Turner, S.M., K.E. Limburg, & E.P. Palkovacs, 2015. Can different combinations of natural tags identify river herring natal origin at different levels of stock structure?. Canadian Journal of Fisheries and Aquatic Sciences,72(999): 1-10.


River herring is a common name used to refer to two different species of fish: alewife and blueback herring. These fish live most of their adult life in the ocean, but spawn in freshwater rivers and streams each spring. These fish represent an incredibly important link in the food chain as many species of fish, birds, and mammals rely on river herring as a high quality protein source (Figure 1). Historically, these schooling fish were harvested in large numbers along the Atlantic coast. As the fish migrate into shallow freshwater streams to lay their eggs, they become very easy to catch. Overtime, a combination of over-harvesting and a reduction in available spawning habitats led to a crash in the river herring population (Figure 2).

Figure 1 – Examples of animals that like to eat river herring.


Figure 2 - Herring landings (catch) each year in metric tons of fish caught. The population began to crash around 1970 and has not yet recovered (from
Figure 2 – Herring landings (catch) each year in metric tons of fish caught. The population began to crash around 1970 and has not yet recovered (from

Since the population crash, most states on the East coast made all harvesting of river herring illegal. This strategy has protected river herring while they are in freshwater for spawning; however, adult river herring are only in rivers for about one month out of each year. The rest of the year they are in the ocean where they are at risk of being caught as bycatch in other commercial fisheries. Previously, when a school of river herring were captured as bycatch in a commercial fishery, scientists were largely unable to tell which river those herring originated from. If we were able to identify the stream of origin of herring removed as bycatch, we may be able to identify certain streams that are disproportionately affected by certain commercial fisheries. This would give managers an opportunity to intervene to better protect those populations. The research done by Sara Turner and Karin Limburg of SUNY College of Environmental Science and Forestry and Eric Palkovacs of UC Santa Cruz may help us do just that.

The Study:

A total of 26 watersheds from 14 different states from Florida to Maine were included in the study. Samples from each watershed were analyzed and their spawning location was estimated using the model developed by the researchers and the estimated location was compared to the known location to determine how accurately they could estimate an unknown fish’s spawning location.

Turner et al. tested “natural tags” to see if they could accurately identify the spawning location of river herring. “Natural tags” refers to naturally occurring features of the fish that allows researchers to distinguish groups or individual fish, as opposed to an artificial tag that can be implanted in or on fish for identification purposes. In this study, the researchers looked at both. So, what were they actually measuring? Otoliths are small ear bones inside of fish that are part of the hearing and balance systems. These structures are formed by absorbing elements from the water and calcifying a new layer of otolith as the fish ages, similar to tree rings. Once the layer of otolith is calcified, it becomes chemically inert, meaning its chemical makeup does not change. That means scientists can tap into these otoliths to find chemical signals that are unique to certain environments (like the particular spawning river of a given fish). The concentrations of these elements in the water depend on the type of bedrock under the body of water which differs slightly along the Atlantic coast. However, some environments have similar chemical signals, making it difficult to accurately estimate the exact stream that a fish may have come from. That is where genetic markers come in.

Because river herring, like salmon, tend to return to the area that they were born to spawn as adults, genetic patterns tend to be localized by region. Based on this, genetic markers were used first to determine which general geographic region a fish was from, then examined chemical signals from otolith chemistry to more precisely identify the specific stream within that region the fish likely spawns in.


Using otolith chemistry alone, the researchers were able to correctly identify the natal origins of 70% of river herring. Certain regions, like the St. John’s River in Florida, have very unique chemical signals and therefore have a higher success rate. However, other regions, like the upper portions of the Chesapeake Bay and the Delaware River in New Jersey, were more difficult to distinguish because fish born in the Delaware River sometimes pass through the canal into the Chesapeake Bay on their way to the ocean, picking up upper Chesapeake Bay chemical signals on the way.

Using genetic markers in combination with otolith chemistry increases classification accuracy to 80%. This method of classifying a fish based on its spawning stream requires researchers to know genetic sequences of herring from all possible spawning locations. This is obviously very difficult to accomplish. Expanding the database would likely improve accuracy; however, classification accuracy will likely never reach 100% because the composition of elements in the water changes slightly from year to year and some river herring stray from their natal spawning grounds.


Figure 3 - Signs alerting citizens about the moratorium on river herring harvest in MA.
Figure 3 – Signs alerting citizens about the moratorium on river herring harvest in MA.

River herring are an incredibly valuable component of marine and freshwater ecosystems. The crash in their numbers has been caused in part by bycatch in commercial harvest as well as reduced access to spawning grounds. River herring are now fairly well protected when they are in freshwater rivers, however we still know very little about where they go once they are in the ocean. Do river herring from Maine mix with river herring from Florida and everywhere in between forming large, mixed schools? Do certain regions group together? We now have the tools to begin to understand these questions which may be able to help protect river herring spawning populations from commercial harvests while at sea. Once researchers understand where river herring go while at sea, regulations could be placed on the commercial harvest of other fish species in order to better protect river herring in the marine environment.

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