Chemical signatures imprinted on tiny stones that form inside the ears of fish show that two of Alaska’s most productive salmon populations, and the fisheries they support, depend on the entire watershed.

Sockeye and Chinook salmon born in the Nushagak River and its network of streams and lakes in southwest Alaska use the whole basin as youngsters when searching for the best places to find prey, shelter and safety from predators. From birth until the fish migrate to the ocean a year later is a critical period for young salmon to eat and grow.

By analyzing each fish’s ear stone — called an — scientists have found that different parts of the watershed are hot spots for salmon production and growth, and these favorable locations change year to year depending on how climate conditions interact with local landscape features like topography to affect the value of habitats.

The new , led by the ÌìÃÀÓ°ÊÓ´«Ã½, appears online May 23 in Science.

“We found that the areas where fish are born and grow flicker on and off each year in terms of productivity,” said lead author , a postdoctoral researcher at the UW School of Aquatic and Fishery Sciences. “Habitat conditions aren’t static, and optimal places shift around. If you want to stabilize fish production over the years, the only strategy is to keep all of the options on the table.”

The Nushagak River watershed is the largest river basin in the Alaska’s , which supports the biggest sockeye salmon fishery in the world and provides about 50 percent of wild sockeye globally. It is also known for its large run of Chinook salmon.

The new study coincides with renewed efforts to gain permits for the Pebble Mine, a proposed copper and gold excavation near the headwaters of the Nushagak River. The U.S. Army Corps of Engineers’ considered only two or three years of fish counts in specific locations in proximity to the proposed mine. It states that fish habitat lost to the mine could be recreated elsewhere.

But the new Science study shows that key salmon habitat shifts year to year, and how productive one area is for a short period might not represent its overall value to the fish population or larger ecosystem.

“The overall system is more than just the sum of its parts, and small pieces of habitat can be disproportionately important,” said senior author , a professor at the UW School of Aquatic and Fishery Sciences. “The arrows point to the need to protect or restore at the entire basin scale if we want rivers to continue to function as they should in nature.”

The research team reconstructed the likely geographic locations of nearly 1,400 adult salmon, from their birth in a Nushagak stream until they migrated to the ocean. By looking at each fish’s otolith — which accumulates layers as the animal grows — researchers could tell where the fish lived by matching the chemical signatures imprinted on each “growth ring” of the otolith with the chemical signatures of the water in which they swam.

These chemical signatures come from isotopes of the trace element strontium, found in bedrock. Strontium’s isotopic makeup varies geographically from one tributary to another, particularly in the Nushagak basin, making it easy to tell where and when a fish spent time.

“The otolith is this natural archive that basically provides a transcript of how a fish moved downstream through the river network,” Schindler said. “Essentially, we’re sampling the entire watershed and letting the fish tell us where the habitat conditions were most productive in that year.”

The researchers noticed significant patterns when comparing where fish lived year to year. For example, in 2011 the northwest portion of the watershed in the Upper Nushagak was highly productive for Chinook, meaning more fish were born and gained body mass in that region. But by 2014 and 2015, the population had shifted eastward to utilize resources in the Mulchatna River and its tributaries — several that are downstream of the Pebble deposit.

Similar types of shifts have been documented in a number of land- and water-based animal populations, but this is the first study to show the phenomenon at a watershed-wide scale, the authors said.

“The big thing we show is these types of dynamics are critical for stabilizing biological production through time. When you have a range of habitat available, the total production from the system tends to be more stable, reliable and resilient to environmental change,” Brennan said.

The public comment period for the Pebble Mine draft environmental impact statement recently was extended to June 29 to provide more time for groups to weigh in on the 1,400-page document.

The authors of the new study said they hope it can be used to inform the scientific analysis of the proposed mine’s impact on fish.

“Results like those we’re presenting in this paper hopefully will get people to think about what they stand to lose by starting to develop and eliminate habitat in places like the Nushagak River,” Schindler said. “The Pebble Mine environmental impact statement, which is supposed to be a mature, state-of-the-science assessment of risks, really does a poor job of assessing risks of this specific project.”

Other co-authors are at the University of Utah; and , both former UW graduate students who are now postdoctoral researchers at the University of Michigan and Utah State University, respectively; and at the Alaska Department of Fish and Game.

The study was funded by Bristol Bay Regional Seafood Development Association, the Bristol Bay Science Research Institute and the Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative.

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For more information, contact Brennan at srbrenn@uw.edu and Schindler at deschind@uw.edu.

This bone, called an , accumulates layers as a fish grows, similar to trees. These “growth rings” are produced throughout a salmon’s life. Scientists can tell where the fish lived by matching the chemical signatures of the otolith with the chemical signatures of the water in which they swim, according to a published May 15 in the online, open-access journal .

“Each fish has this little recorder, and we can reveal the whole life history of the fish from the perspective of the otolith. Each growth ring is a direct reflection of the environment the fish was swimming in at the time it was formed,” said lead author Sean Brennan, who completed the study as a doctoral student at the University of Alaska Fairbanks. He is now a postdoctoral researcher in the ÌìÃÀÓ°ÊÓ´«Ã½’s .

This chemical signature comes from isotopes of the trace element , found in bedrock. Strontium’s chemical makeup varies geographically. As rushing water weathers the rocks, the element is dissolved and released into the water. The dissolved strontium ions get picked up by fish, either through the gills or gut lining, then are deposited onto the otolith.

As strontium makes its way from rocks into the otoliths of fish swimming in the rivers, its chemical signature does not change, and so it serves as a robust tag that can tie each fish as being in a specific location in the river at a specific time.

“This particular element and its isotopes are very strongly related to geography,” said Matthew Wooller, director of the Alaska Stable Isotope Facility at University of Alaska Fairbanks and a co-author of the paper. “It is a really good marker for where animals have been and whether they move around in their environment.”

This process relies on a river system that has been mapped extensively for its strontium isotope variation. In general, watersheds that are diverse in the types and ages of rocks will also have a lot of variation in strontium isotope signatures – and thus are good candidates for using this technique, Brennan said.

“Alaska is a mosaic of geologic heterogeneity,” he added. “As long as you can look at a geologic map and see rocks that are really different, that’s a good potential area.”

The Bristol Bay region in Alaska produces some of the last remaining wild salmon runs in the world. The area is perhaps best known for its sockeye salmon commercial fishery, but Chinook salmon, particularly those in the where this study took place, supply important subsistence and sport fisheries for the region. The Nushagak Chinook salmon are also the third biggest run in Western Alaska, ranking it as one of the largest worldwide.

About 200,000 Chinook make their way each summer from the ocean to spawn in the river’s upper tributaries and streams. When their eggs hatch in the spring, young Chinook salmon spend a whole year in the river, feeding and growing before migrating to the Bering Sea and the Pacific Ocean.

Scientists need a way to determine the birth streams of adult Chinook when they are caught in coastal fisheries. Once they have that information, they can begin to understand how freshwater habitat, the movement of fish and environmental factors can affect fish survival. Alaska’s Chinook salmon populations have declined dramatically in the past decade, and scientists are still trying to determine why.

“This is science responding to a societal issue and need,” said co-author , U.S. Geological Survey ecologist and chief of water and interdisciplinary studies at the USGS Alaska Science Center in Anchorage. “Using this approach, we will be able to map salmon productivity and determine how freshwater habitats influence the ultimate number of salmon. With declines in Chinook salmon in Western Alaska, fishery and land-use managers need better information about freshwater habitats to guide conservation.”

Using data collected from adult salmon in 2011, the researchers not only determined which parts of the river produced the most fish but also found that the majority of Chinook salmon in the Nushagak watershed stayed in the same place for their entire first year before they migrated to the ocean. About 20 percent left their birthplace for short forays in the river’s lower main stem before swimming to the ocean.

Brennan now works with at the UW, where they will expand this work to include sockeye salmon in the same river. They will collect three years of Chinook data and two years of sockeye by end of the project, which will help determine whether birth and life history patterns in Alaskan rivers vary across years, or remain consistent.

The techniques used in Brennan’s study can also help scientists understand the behavior of other animal populations. Strontium also accumulates in things like bird feathers and teeth and also survives even after being fossilized. This allows researchers to study the movements of a wide range of animals including seals, whales, bison, ancient human populations and even dinosaurs.

Other co-authors are Diego Fernandez and Thure Cerling at the University of Utah, where all of the analyses for this research were conducted, and Megan McPhee at the University of Alaska Fairbanks.

This research was funded by Alaska Sea Grant and the U.S. Geological Survey National Institute of Water Resources program.

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For more information, contact Brennan at srbrenn@uw.edu or 801-633-7906; Zimmerman at czimmerman@usgs.gov or 907-786-7071; Cerling at thure.cerling@utah.edu or 801-581-5558; and Wooller at mjwooller@alaska.edu or 907-474-6738.

Grant numbers: R/100-02 (Alaska Sea Grant); 2012AK108B (U.S. Geological Society)