Research » Modeling

Category: Modeling

This is my intro to the category.

Salmon experts predict more wild coho but fewer Chinook in Puget Sound this year

Greater numbers of wild coho salmon are expected to return to Puget Sound later this year, according to forecasts released last week, but threatened Puget Sound Chinook stocks are likely to see another decline.

Graph: Washington Department of Fish and Wildlife

The 2021 salmon forecasts were announced Friday during an online video conference with sport and commercial fishers and other interested people (TVW telecast). The annual meeting serves to launch negotiations that, when completed in April, will prescribe fishing seasons for the coming summer and fall.
Protecting so-called “weak stocks” from fishing pressure continues to be a challenge. Salmon managers with the Washington Department of Fish and Wildlife will consult with representatives of area tribes to identify times and places for fishing that will still allow adequate numbers of spawning salmon to get back to their home streams.
Low numbers of salmon predicted for some areas of Puget Sound will force managers to make some tough choices, said Fish and Wildlife Director Kelly Susewind.
Graph: Washington Department of Fish and Wildlife

“If every salmon run across the state was healthy, our jobs would be easy,” he said in a news release. “But the unfortunate truth is that some stocks just won’t be able to support fisheries and are likely to impact fisheries even for healthier runs. We’ll work hard alongside the co-managers to stay within our shared conservation goals while still offering chances to get out and fish this year whenever possible.”
Some 246,000 wild coho are expected to return to Puget Sound this year, up about 51 percent from last year but still 15 percent below the 10-year average, said Chad Herring, a fishery policy analyst for Fish and Wildlife. In contrast, hatchery coho are expected to increase by 8 percent.
Graph: Washington Department of Fish and Wildlife

While fishing opportunities could come from the increased coho run, managers must be careful to protect wild Chinook, which remain at risk of extinction. This year’s total Chinook run size (hatchery and wild, not including spring Chinook) is estimated to be down 11 percent from last year’s forecast of 233,000 fish and 2 percent below the recent 10-year average. Keep in mind that the recent 10-year average for wild Chinook is 24 percent below the 10-year average recorded when Puget Sound Chinook were placed on the Endangered Species List back in 1999 — so things are not looking good for Chinook.
The Department of Fish and Wildlife recently began increasing production of Chinook at some hatcheries in an effort to help the Southern Resident Killer Whales, which frequent Puget Sound and consume a lot of salmon, primarily Chinook. The result of that increased production could be seen in coming years, although the effects on wild Chinook have been hotly debated.
Graph: Washington Department of Fish and Wildlife

Wild Chinook make up just 12 percent of the total run size, with hatchery Chinook making up the remainder, so one strategy for increasing fishing opportunities while protecting wild fish is to shift fishing efforts to “terminal areas” closer to the hatcheries during carefully timed periods.
To protect wild Chinook and coho, anglers may be allowed to keep only hatchery fish while releasing wild fish. Young hatchery Chinook and coho are typically marked by removing their adipose fins before release. During the COVID-19 pandemic, marking equipment housed in special mobile units went into operation around the clock to get the work done while limiting the number of staffers working in confined spaces, according to Kelly Cunningham. director of the Fish Program for WDFW. The marking program successfully handled between 140 million and 160 million juvenile salmon with no delay in their scheduled release, he said.
Graph: Washington Department of Fish and Wildlife

Chum salmon, largely taken by commercial fishers, have been in a general decline since their historical peak in 2002, research biologist Mickey Agha said during Friday’s conference.
“Last year, I noted that in 2019 we had the lowest Puget Sound return since 1979,” Agha said. “Unfortunately, preliminary estimates for 2020 are revealing a return only slightly higher.”
The graph showing the chum forecast, shown on this page, includes a year-old forecast of a higher run last year, because the hard data about the actual run size are still being compiled. That goes for the other species as well.
“As many of you in the chum industry are aware, it was a rather poor year fishing for the limited opportunity that was available,” Agha said. “South Puget Sound and Hood Canal returned poorly, as compared to the long-term averages. Nevertheless, there were some bright spots where we met conservation goals head-on and reached our escapement goals (for the number of spawners reaching their home streams). That was along the coast for a few populations and for a few populations in the Central to North Puget Sound.”
Graph: Washington Department of Fish and Wildlife

Chum returns to Puget Sound this year are expected to be only slightly better than for 2019, one of the worst years on record. Hatchery fish make up roughly half the run size of fall chum salmon. The total run size this year is estimated at 526,000.
Meanwhile, 2021 will be a “pink year,” as it is called, reflecting the fact that the vast majority of pink salmon spawn in odd-numbered years. The past decade has been a period of both boom and bust for pinks, which are almost all wild salmon. This year, about 2.9 million pinks are expected to return to Puget Sound, vastly outnumbering chum. That return would be similar to 2019, following a very low year in 2017.
Elsewhere, anglers online for Friday’s presentation heard some welcome news about coho in the Columbia River. The forecast calls for 1.6 million fish among the early and late runs, a dramatic increase from last year’s 363,000, according to estimates.
Graph: Washington Department of Fish and Wildlife

Although that big number is encouraging, there is a need to protect other at-risk stocks in the region, said Kyle Adicks, intergovernmental salmon manager for Fish and Wildlife.
“All of our forecasting indicates a strong coho return to the Columbia, but a lot can change between now and when the fish start to arrive, including out in the ocean,” Adicks said in a news release. “We’ll be keeping a close eye throughout this year’s salmon-season-setting process on stocks of low abundance.”
Fishing along the Washington Coast is expected to be a mixed bag, with some stocks up and others down. Poor returns anticipated for the Queets and other coastal rivers could limit fishing off the coast, despite the large numbers of coho returning to the Columbia River.
Graph: Washington Department of Fish and Wildlife

All these forecasts are based on computer modeling that factors in many variables, from the number of juvenile salmon that leave the streams to the number of adult salmon returning in the previous cycle to the number of “jacks” that return a year before they are due. Also considered are ocean conditions, such as temperature, which have a major influence on the movement of salmon and their food supply.
Higher surface temperatures in the ocean off the West Coast in recent years are believed to be a major factor in the decline of salmon, which tend to do better in cooler waters. Global warming can affect salmon through every life stage, from the stream where they hatch out of gravel to the Pacific Ocean where they grow and mature.
Making things worse is a recurring patch of warm ocean water nicknamed “the blob” by Washington State Climatologist Nick Bond. Sometimes stretching from California to Alaska, the highest temperatures since 1982 were recorded during a period from 2014 to 2016. (See map at top of this page.) Last year, the blob’s reappearance brought temperatures nearly as high.
Lower-than-average sea surface temperatures have prevailed near the equator during February, portending better conditions for salmon in the Northwest. Map: NOAA’s Climate Prediction Center

Since then, ocean temperatures have declined to more normal conditions, which should benefit salmon, according to Marisa Litz, research scientist for Fish and Wildlife who spoke during Friday’s meeting. Other good news is the current mountain snowpack of between 95 and 150 percent of normal, which should help provide adequate flows of cool water during the critical spring period for young salmon, she said.
The Pacific Ocean currently remains in a cooler phase called La Niňa, which has resulted in below-normal ocean temperatures from the west-central Pacific Ocean to our region along the coast, according to a report released yesterday by NOAA’s Climate Prediction Center (PDF 3.3 mb).
“In the last week, negative anomalies strengthened across most of the equatorial Pacific Ocean,” the report says, providing additional atmospheric evidence of La Niña conditions.
The federal forecasters say there is a 60-percent chance that our current ocean conditions will transition by June to neutral — that is more average conditions midway between the cooler La Niña and the warmer El Niño. These more normal conditions are likely to persist into fall, according to most models.
These cooler ocean temperatures should help with the growth and survival of salmon that return to Puget Sound in the next couple years, although many other factors also play a role in the lives of salmon.
The latest salmon forecasts, a list of upcoming public meetings, and other information, can be seen on the North of Falcon webpage on the Department of Fish and Wildlife’s website.

Salmon experts predict more wild coho but fewer Chinook in Puget Sound this year

Greater numbers of wild coho salmon are expected to return to Puget Sound later this year, according to forecasts released last week, but threatened Puget Sound Chinook stocks are likely to see another decline.

Graph: Washington Department of Fish and Wildlife

The 2021 salmon forecasts were announced Friday during an online video conference with sport and commercial fishers and other interested people (TVW telecast). The annual meeting serves to launch negotiations that, when completed in April, will prescribe fishing seasons for the coming summer and fall.
Protecting so-called “weak stocks” from fishing pressure continues to be a challenge. Salmon managers with the Washington Department of Fish and Wildlife will consult with representatives of area tribes to identify times and places for fishing that will still allow adequate numbers of spawning salmon to get back to their home streams.
Low numbers of salmon predicted for some areas of Puget Sound will force managers to make some tough choices, said Fish and Wildlife Director Kelly Susewind.
Graph: Washington Department of Fish and Wildlife

“If every salmon run across the state was healthy, our jobs would be easy,” he said in a news release. “But the unfortunate truth is that some stocks just won’t be able to support fisheries and are likely to impact fisheries even for healthier runs. We’ll work hard alongside the co-managers to stay within our shared conservation goals while still offering chances to get out and fish this year whenever possible.”
Some 246,000 wild coho are expected to return to Puget Sound this year, up about 51 percent from last year but still 15 percent below the 10-year average, said Chad Herring, a fishery policy analyst for Fish and Wildlife. In contrast, hatchery coho are expected to increase by 8 percent.
Graph: Washington Department of Fish and Wildlife

While fishing opportunities could come from the increased coho run, managers must be careful to protect wild Chinook, which remain at risk of extinction. This year’s total Chinook run size (hatchery and wild, not including spring Chinook) is estimated to be down 11 percent from last year’s forecast of 233,000 fish and 2 percent below the recent 10-year average. Keep in mind that the recent 10-year average for wild Chinook is 24 percent below the 10-year average recorded when Puget Sound Chinook were placed on the Endangered Species List back in 1999 — so things are not looking good for Chinook.
The Department of Fish and Wildlife recently began increasing production of Chinook at some hatcheries in an effort to help the Southern Resident Killer Whales, which frequent Puget Sound and consume a lot of salmon, primarily Chinook. The result of that increased production could be seen in coming years, although the effects on wild Chinook have been hotly debated.
Graph: Washington Department of Fish and Wildlife

Wild Chinook make up just 12 percent of the total run size, with hatchery Chinook making up the remainder, so one strategy for increasing fishing opportunities while protecting wild fish is to shift fishing efforts to “terminal areas” closer to the hatcheries during carefully timed periods.
To protect wild Chinook and coho, anglers may be allowed to keep only hatchery fish while releasing wild fish. Young hatchery Chinook and coho are typically marked by removing their adipose fins before release. During the COVID-19 pandemic, marking equipment housed in special mobile units went into operation around the clock to get the work done while limiting the number of staffers working in confined spaces, according to Kelly Cunningham. director of the Fish Program for WDFW. The marking program successfully handled between 140 million and 160 million juvenile salmon with no delay in their scheduled release, he said.
Graph: Washington Department of Fish and Wildlife

Chum salmon, largely taken by commercial fishers, have been in a general decline since their historical peak in 2002, research biologist Mickey Agha said during Friday’s conference.
“Last year, I noted that in 2019 we had the lowest Puget Sound return since 1979,” Agha said. “Unfortunately, preliminary estimates for 2020 are revealing a return only slightly higher.”
The graph showing the chum forecast, shown on this page, includes a year-old forecast of a higher run last year, because the hard data about the actual run size are still being compiled. That goes for the other species as well.
“As many of you in the chum industry are aware, it was a rather poor year fishing for the limited opportunity that was available,” Agha said. “South Puget Sound and Hood Canal returned poorly, as compared to the long-term averages. Nevertheless, there were some bright spots where we met conservation goals head-on and reached our escapement goals (for the number of spawners reaching their home streams). That was along the coast for a few populations and for a few populations in the Central to North Puget Sound.”
Graph: Washington Department of Fish and Wildlife

Chum returns to Puget Sound this year are expected to be only slightly better than for 2019, one of the worst years on record. Hatchery fish make up roughly half the run size of fall chum salmon. The total run size this year is estimated at 526,000.
Meanwhile, 2021 will be a “pink year,” as it is called, reflecting the fact that the vast majority of pink salmon spawn in odd-numbered years. The past decade has been a period of both boom and bust for pinks, which are almost all wild salmon. This year, about 2.9 million pinks are expected to return to Puget Sound, vastly outnumbering chum. That return would be similar to 2019, following a very low year in 2017.
Elsewhere, anglers online for Friday’s presentation heard some welcome news about coho in the Columbia River. The forecast calls for 1.6 million fish among the early and late runs, a dramatic increase from last year’s 363,000, according to estimates.
Graph: Washington Department of Fish and Wildlife

Although that big number is encouraging, there is a need to protect other at-risk stocks in the region, said Kyle Adicks, intergovernmental salmon manager for Fish and Wildlife.
“All of our forecasting indicates a strong coho return to the Columbia, but a lot can change between now and when the fish start to arrive, including out in the ocean,” Adicks said in a news release. “We’ll be keeping a close eye throughout this year’s salmon-season-setting process on stocks of low abundance.”
Fishing along the Washington Coast is expected to be a mixed bag, with some stocks up and others down. Poor returns anticipated for the Queets and other coastal rivers could limit fishing off the coast, despite the large numbers of coho returning to the Columbia River.
Graph: Washington Department of Fish and Wildlife

All these forecasts are based on computer modeling that factors in many variables, from the number of juvenile salmon that leave the streams to the number of adult salmon returning in the previous cycle to the number of “jacks” that return a year before they are due. Also considered are ocean conditions, such as temperature, which have a major influence on the movement of salmon and their food supply.
Higher surface temperatures in the ocean off the West Coast in recent years are believed to be a major factor in the decline of salmon, which tend to do better in cooler waters. Global warming can affect salmon through every life stage, from the stream where they hatch out of gravel to the Pacific Ocean where they grow and mature.
Making things worse is a recurring patch of warm ocean water nicknamed “the blob” by Washington State Climatologist Nick Bond. Sometimes stretching from California to Alaska, the highest temperatures since 1982 were recorded during a period from 2014 to 2016. (See map at top of this page.) Last year, the blob’s reappearance brought temperatures nearly as high.
Lower-than-average sea surface temperatures have prevailed near the equator during February, portending better conditions for salmon in the Northwest. Map: NOAA’s Climate Prediction Center

Since then, ocean temperatures have declined to more normal conditions, which should benefit salmon, according to Marisa Litz, research scientist for Fish and Wildlife who spoke during Friday’s meeting. Other good news is the current mountain snowpack of between 95 and 150 percent of normal, which should help provide adequate flows of cool water during the critical spring period for young salmon, she said.
The Pacific Ocean currently remains in a cooler phase called La Niňa, which has resulted in below-normal ocean temperatures from the west-central Pacific Ocean to our region along the coast, according to a report released yesterday by NOAA’s Climate Prediction Center (PDF 3.3 mb).
“In the last week, negative anomalies strengthened across most of the equatorial Pacific Ocean,” the report says, providing additional atmospheric evidence of La Niña conditions.
The federal forecasters say there is a 60-percent chance that our current ocean conditions will transition by June to neutral — that is more average conditions midway between the cooler La Niña and the warmer El Niño. These more normal conditions are likely to persist into fall, according to most models.
These cooler ocean temperatures should help with the growth and survival of salmon that return to Puget Sound in the next couple years, although many other factors also play a role in the lives of salmon.
The latest salmon forecasts, a list of upcoming public meetings, and other information, can be seen on the North of Falcon webpage on the Department of Fish and Wildlife’s website.

New sewage-treatment permit would be a step to curbing nitrogen in Puget Sound

In an effort to stem the flow of excess nitrogen into Puget Sound, Washington Department of Ecology has proposed a new type of permit for some 60 sewage-treatment plants operating throughout the region.
The flexible permit, called the Puget Sound Nutrient General Permit, aims to hold nitrogen releases close to or below their current levels at most of the treatment plants while offering plant operators options for how to meet those goals. It’s a temporary solution, because the long-term goal is to make significant cuts in the total amount of nitrogen going into Puget Sound.

Graphic: Washington Department of Ecology

Nitrogen, as we’ve discussed many times, is a major problem for Puget Sound. This so-called nutrient feeds the growth of plankton, which die and decay, consuming oxygen during the process. Low oxygen levels are a serious problem for fish and many other marine creatures, particularly in southern Hood Canal as well as several bays in South Puget Sound.
Sewage treatment plants have been found to be a significant source of nitrogen, thanks to findings from an elaborate computer simulation called the Salish Sea Model. The model, now housed at the Puget Sound Institute, describes the effects of nitrogen throughout Puget Sound based on the amount and location of nitrogen inputs, the size and shape of the waterway and currents created by tides and rivers. For a description of the problem, check out the overview in the Encyclopedia of Puget Sound, which also features a variety of focused articles addressing the issue.
The Salish Sea Model has revealed that nitrogen from sewage-treatment plants can create much more than localized water-quality problems. For example, large amounts of nitrogen from treatment plants in Seattle and Tacoma can be pushed by currents into South Puget Sound. There, the resulting low-oxygen levels create adverse effects in the inlets and shallow bays, which look like crooked fingers on a map.
One goal of the modeling effort is to calculate how much nitrogen can go into different parts of Puget Sound without triggering water-quality violations. Once these amounts of nitrogen are determined, actual limits can be calculated and theoretically imposed on the effluent coming out of each treatment plant. But those findings are not expected before 2023. See Puget Sound Nutrient Reduction Project.
The nutrient general permit for sewage-treatment plants would be separate from existing wastewater permits for each plant. While perhaps not as enforceable as strict numerical limits, the proposed “action levels” for each treatment plant in the general permit could be a first step in turning things around, according to members of an advisory committee helping to draft the new permit.
“We needed to get some kind of backstop,” said Mindy Roberts of Washington Environmental Council and a member of the advisory committee. “This permit has a kind of reasonable bound to it. Having said that, we are 20 years into this kind of assessment.”
It is obvious that something must be done, she said, because the Puget Sound ecosystem is already suffering from excess nitrogen. See the advisory committee’s 12-page summary of discussions (PDF 372 kb).
What to do about nitrogen pollution seems to have a lot of people tied in knots. Operators of many sewage-treatment plants are saying they need to see more scientific data before they commit to making upgrades to their plants. Total costs could amount to billions of dollars for the region.
In December, the city of Tacoma and four other sewer utilities filed a lawsuit in Thurston County Superior Court. They allege that the Department of Ecology effectively changed the state’s water-quality standards for dissolved oxygen through the use of computer modeling but without going through required rule-making procedures. The case is a first volley in what could be ongoing legal challenges to proposed controls on nitrogen. Other parties to the case are Birch Bay Water and Sewer District, Kitsap County, Southwest Suburban Sewer District, and Alderwood Water and Wastewater District.
Meanwhile, the environmental group Northwest Environmental Advocates is continuing to pursue its lawsuit, now on appeal. The lawsuit is designed to force the Department of Ecology to require upgrades to sewage-treatment plants that don’t already reduce nitrogen through tertiary treatment. Under a 1945 state law, state regulators must demand “the use of all known, available and reasonable (technology) … to prevent and control the pollution of the waters of the state of Washington.” This is the so-called AKART law.
Thurston County Superior Court rejected the arguments of NWEA. The ruling supported Ecology’s argument that a broad requirement for expensive treatment technology would not be “reasonable” under the law. Check out the appeal briefs by NWEA (PDF 1.1 mb) and by Ecology (PDF 2.3 mb). See also the first Water Ways post I wrote on this issue, Jan. 31, 2019.
As proposed in a “conceptual” draft (PDF 708 kb), the nutrient general permit would apply to the majority of sewage-treatment plants in the Puget Sound region and would go into effect for all at the same time. Ecology proposes to exclude 26 treatment plants that discharge into rivers, nine privately owned plants, all facilities on federal and tribal lands, and industrial operations. These various exclusions could be covered with nitrogen controls through other types of permitting.
The general permit establishes two action levels. The baseline level is roughly equivalent to the treatment plant’s current annual release of nitrogen. A second level, 5 percent higher than the baseline, allows for additional growth for plants where Ecology has already approved higher design capacities.
The draft permit calls for an “optimization framework,” in which treatment plant operators must implement low-cost measures to reduce nitrogen and then measure the outcomes. Operators would be allowed to customize their actions to suit their own plants, but they would need to share their successes and failures with Ecology and other operators. These low-cost actions, called Tier 1, could include adjustments to flow rates, aeration patterns and treatment cycles.
Tier-2 actions would be triggered when the baseline level of nitrogen is exceeded at the end of an operational year. Actions could include the purchase of new equipment, changes in piping configurations and the addition of one or more chemicals to reduce nitrogen.
Tier-3 actions would be triggered when a facility exceeds the higher (+5%) action level. These actions, which would be approved by Ecology in advance, could include more extensive operational changes, treatment process upgrades, and planning for advanced treatment such that design and construction would start as soon as formal effluent limits are established.
“We’re not proposing to require major infrastructure investments in the first five-year permit,” said Ecology spokeswoman Colleen Keltz in a blog post. “Depending on the current capabilities of each (treatment plant) and their community’s plans for growth and development, they will have a reasonable amount of time to plan appropriate upgrades or other improvements while remaining in compliance with their permits.”
Some 14 plants already remove nitrogen to some degree, with their nitrogen concentrations averaging below 10 milligrams per liter. Under the proposed permit, those 14 would not be subject to Tier 1 or Tier 2 actions but would still be expected to undergo low-cost optimization.
The general permit also calls for expanded monitoring of nitrogen and other constituents of sewage, as well as extensive planning and scientific studies at both facility and regional levels. The ultimate goal, according to Ecology, is to figure out the most effective ways to reduce nitrogen to improve water quality in Puget Sound and meet state standards for dissolved oxygen.
The comment period for the informal draft permit runs until March 15. (See comment form.) After that, the draft will be revised and resubmitted as a formal document with public hearings, written comments and official responses.
Meanwhile, the advisory committee continues to discuss the permit and related issues. For documents and meeting schedules, go to the committee’s EZ View page.
As discussions continue, Gov. Jay Inslee has submitted a $9-million funding request to implement the general permit as part of his overall budget to the Legislature. The money would be used to help the affected treatment plants develop plans and finance small nitrogen-reduction projects.
Related efforts:

Ecology’s story map on nitrogen. Click on the image to launch the page.
Maps generated from the Salish Sea Model showing surface layer transport in the Northwest Straits (left) and sea surface salinity (right). Images: Pacific Northwest National Laboratory

PSI launches Salish Sea Modeling Center

The Puget Sound Institute is launching a new program that will use supercomputers to advance ecosystem recovery of the Salish Sea. The Salish Sea Modeling Center will allow scientists from around the region to access sophisticated computer models to predict changes in the ecosystem. Work at the center will tackle vexing environmental problems such as the changing chemistry of the Salish Sea and other mysteries puzzling scientists. The center is supported by the Environmental Protection Agency and other regional water quality partners.
If you want to understand where fish or killer whales go, or how toxic chemicals move through the ecosystem, it helps to know how the water moves. The ebb and flow of currents is fundamental to scientific efforts to protect and restore the Salish Sea.
Researchers have known for many years that they could create physical models to simulate the movements of these currents. In the 1950s, engineers created scale replicas out of concrete that used saltwater and colored dye to track the motion of processes like tidal flows and circulation. These scale models were a standard for oceanographers for more than 30 years.
Now, computer models can replace circulating dye and water pumps with just about any conceivable data. They can reveal how water temperature changes, how fast Arctic melting will raise the tideline along the shore, or when global carbon emissions will eventually turn the Salish Sea acidic. They can anticipate herring spawns or answer policy questions about where and how to clean up toxic chemicals.

A map image showing the range of the Salish Sea Model. Photo courtesy of Pacific Northwest National Laboratory.
A map image showing the range of the Salish Sea Model. The range extends beyond the boundaries of the Salish Sea to include influences from coastal hydrodynamics. Image courtesy of Pacific Northwest National Laboratory.

Providing the region’s policy leaders and scientists with these powerful tools is the goal of the Salish Sea Modeling Center, a new enterprise from the University of Washington Puget Sound Institute. The center will initially focus on expanding the capabilities of the Salish Sea Model, an advanced computer simulator developed over the past decade. The Salish Sea Model accurately describes how water, sediments, and nutrients enter and cycle through the Salish Sea, and is widely used by resource and regulatory agencies in the region. The model was developed by Dr. Tarang Khangaonkar and his team at the U.S. Department of Energy’s Pacific Northwest National Laboratory (PNNL). The work was done in collaboration with the Washington State Department of Ecology with grant support from the Environmental Protection Agency. Khangaonkar, who is both a principal program manager at PNNL and an affiliate professor at the University of Washington Tacoma, will serve as director of the Salish Sea Modeling Center. Support for the new center is provided by the Environmental Protection Agency’s National Estuary Program and other regional water quality partners.
“This is perhaps the first model of the entire Salish Sea that was built specifically for supporting ecosystem restoration and water quality management,” according to Khangaonkar, who says the massive, cross-border ecosystem posed significant challenges for developers during the early efforts. The Salish Sea’s 4600 miles of winding shoreline and its deep, underwater canyons, sills, and numerous islands were far too complex for conventional and commercially available models used in coastal applications at the time. “Computational challenges are particularly hard for our fjord-like estuary with its complex features,” says Khangaonkar. “In addition, the model must take into account runoff from 161 different watersheds, and wastewater load from nearly 100 outfalls from an ever-growing population along the shoreline.”
To capture these complexities, the model runs on a modified supercomputer consisting of up to 384 processors working in parallel (“like many desktop computers all working together,” Khangaonkar says). The result is a predictive tool that is already being applied to critical policy questions in the region. In recent years, the Washington State Department of Ecology began using the model to understand how nutrients from wastewater might be diminishing Puget Sound’s water quality. That work led to ongoing discussions about the future of the region’s wastewater treatment plants, and the model has been at the center of policy debates that could affect hundreds of millions of dollars in treatment plant retrofits.
But the model has quickly become a framework for probing many other scientific questions. Its open source software is designed to be used by anyone, and scientists from many different disciplines are now plugging in their data.
“Work at the center will focus on the use of the model to take on other issues of regional importance,” says Dr. Joel Baker, director of the Puget Sound Institute. “It allows a really well-designed and well-built model to be more widely used. We can now bring critical questions from policymakers back to the scientific community and ask, ‘Can you model this?’”
Puget Sound's orcas are among the species experiencing contamination from PCBs.
Puget Sound’s orcas are among the species experiencing contamination from PCBs.

One such question concerns the fate of toxic PCBs in Puget Sound. Scientists have noted that levels of PCBs have remained relatively constant in parts of the food web, despite efforts to remove them from sediments on the seafloor. Some theorize that legacy PCBs are entering Puget Sound through stormwater and are being cycled through the estuary without settling to the bottom. Puget Sound Institute scientists and their collaborators at the Washington Department of Fish and Wildlife are using simulations of the Salish Sea Model to better understand how important contaminants are moving throughout the Salish Sea.
“If it turns out this is true, just cleaning up the sediments may not fix the problem,” says Puget Sound Institute research scientist Andy James, one of the principal investigators on the project. Knowing how toxic contaminants move through the system could help policymakers identify the best places to focus their cleanup efforts, potentially reducing the amounts of harmful chemicals in fish that humans eat such as salmon.
Other mysteries currently being addressed by the model include the short-term effects of ocean warming on giant Pacific octopus populations, predictions of sea level rise impacts on estuary restoration, and the potential ways that eelgrass might offset ocean acidification.
In addition to its work with the Salish Sea Model, the center will also work with other organizations to combine information from computer simulations such as NOAA’s Atlantis food web model, EPA’s VELMA watershed model, or the University of Washington’s LiveOcean model which addresses water flow into the Salish Sea through the California Current.

Warm-water ‘blobs’ significantly diminish salmon, other fish populations, study says

It’s no secret that salmon and other Northwest fish populations are expected to shrink as a result of a warming Pacific Ocean. But a new study suggests that the resulting decline in commercial fishing by 2050 could be twice as great as previously estimated by climate scientists.
The higher estimates of population declines were calculated by researchers at the University of British Columbia, who took into account occasional “marine heat waves” that can play havoc with the ecosystem. A recent example is the warm-water event known as the “blob,” which included ocean temperatures up to 7 degrees above average (Fahrenheit) during a two-year period beginning in 2014.

Current sea surface temperature anomalies (variations from average) for the Pacific Coast off North and South America. The temperature scale is different from the maps above.
Map: NOAA Coral Reef Watch, April 23, 2020

William Cheung, who led the new study, told me that previous estimates of declines in fish populations assumed that the waters would warm at a steady rate as a result of climate change. But the impacts are much greater, he said, when one considers the occasional shocks to the system caused by rapid warming. Climate-change models predict at least four additional “blobs” before the end of the century, although nobody can predict when exactly they will occur.
Cold-water fish subjected to warm water face a disruption in their normal body functions, reducing the size of the fish and increasing the risk of death. Warm water also can reduce the overall production in the food web, making it more difficult for fish to find suitable prey.
For the fishing industry, marine heat waves are not unlike a sudden pandemic such as COVID-19, William said. Fishing crews can adjust to normal fluctuations in fish populations, just as health-care providers adjust to flu seasons, but sudden and stronger disruptions can lead to more serious consequences.
“Last year, management agencies closed the Alaska Pacific cod fisheries (for 2020), because they had a suspicion that the blob was returning,” said Cheung, a professor at the UBC Institute for the Oceans and Fisheries. “There was concern that the already low Pacific cod population could be hit by a heat wave that could drive the fish stocks to very low levels.”
The 2019 “return of the blob” was not as long-lasting as the 2014-16 event, but waters off the coast are still warmer than normal.
The new study, published online in the journal “Scientific Reports,” combined climate and fish models to estimate the impacts of future “blobs” from Alaska to the Gulf of California. Findings suggest that the total biomass of fish will decline, and fish will move around to establish new distribution patterns. That will decrease the amount of fish available for harvest as well as changing the location where the fish can be caught.
William Cheung

While many studies have talked about fish stocks moving around in response to changing ocean temperatures, William said biomass decreases could be a more consistent indicator for assessing the impacts of marine heat waves on various species.
During a heat wave, the average biomass of sockeye salmon in the ocean off Alaska and British Columbia is expected to decline by more than 10 percent — in addition to a biomass decrease of 10 to 20 percent by 2050 under long-term climate projections.
Of 22 fisheries included in the study, only Alaskan Pollock in the Eastern Bering Sea is expected to increase significantly in biomass during marine heat waves. Pacific sardine and Japanese mackerel may show little change.
Because sardines do better in warmer waters, long-term models tend to project increases in sardine biomass along the West Coast over time, while anchovies, which prefer cooler waters, are projected to decrease. At the same time, such models predict that both species will expand their ranges northward, producing greater numbers in the Gulf of Alaska.
But the story is different when marine heat waves are added into the picture, according to the new study. Rapid warming can push temperatures to the limit for both sardines and anchovies, decreasing their total biomass in the Gulf of Alaska as well as along the West Coast.
The study found that the fish most impacted by a combination of long-term climate change and future “blobs” were pelagic (open water) species, followed by salmon and then bottom fish. Among the five species of Pacific salmon, the biomass of sockeye salmon is expected to decrease the most — 40 percent by 2100 throughout the study area. Coho are next on the list of affected salmon.
Pacific cod, sablefish and Pacific Ocean perch were the bottom fish projected to sustain the most losses throughout the area.
Worldwide, the frequency of marine heat waves has doubled since 1982, and climate models predict they will become more frequent and last longer in the coming years.
William noted that the study was based on a climate model that uses a high rate of greenhouse gas emissions (RCP 8.5). While recent temperatures seem to be following that high-emissions trend, emission reductions would have benefits for almost all fish populations. Still, any improvements in ocean-temperature trends will lag behind improvements in atmospheric conditions because of the heat-retention properties of water.
“Our results underscore the need for a reduction of anthropogenic greenhouse gas emissions – the fundamental driver of ocean
warming — to limit challenges from marine heat waves on fish stocks and fisheries,” William said.
The fact that marine heat waves can develop rapidly demands that scientists become better at short-term predictions, he said. Meanwhile, fisheries managers are challenged to develop plans that can respond quickly to changing conditions by reducing fishing seasons or moving fishing areas.
William plans further analysis of “blobs” across the globe, with a goal of developing projections of worldwide fishery impacts. That could lead to an economic analysis of future financial repercussions expected to result from sudden warming events in many locations.
NOAA stories for further reading:

Virus related to measles could push Puget Sound orcas to extinction, study says

Researchers studying the killer whales that frequent Puget Sound are growing increasingly concerned that a dangerous virus or other disease-causing organism could spread through the population and hasten extinction of these critically endangered southern resident orcas.
Without dramatic changes to their environment, extinction is already considered the likely future for the southern residents, as they continue to face shortages of food, high levels of chemical contamination and stress from the noise around them. Their numbers have declined from 98 animals in 1995 to 72 today.

Southern resident killer whales frequently come into “respiratory contact” with each other, as shown in this sequence of successive surfacing. First J42 (named Echo) is on the surface (i). As she submerges, J16 (named Slick) comes up closely on the far side (ii and iii).
Credit: Michael Weiss, journal Biological Conservation and Center for Whale Research

New research suggests that extinction could come sooner if the whales were to become infected with a novel pathogen, such as cetacean morbillivirus, which has killed thousands of Atlantic bottlenose dolphins on the U.S. East Coast but has not been seen in the Pacific Northwest.
“Given its fragile state, it is unlikely that this population would recover from the sudden increase in mortality that would result from a majority of the population becoming infected with CeMV,” states the new report.
Michael Weiss, a researcher with the Center for Whale Research and lead investigator on the study, said the prospect of CeMV in the southern residents can be compared in some ways to the recent outbreak in humans from the novel coronavirus: Just as humans lack immunity to the new coronavirus, the orcas have no history of exposure to CeMV, thus they are vulnerable to the worst effects of the organism.
“When I think of risks to the southern residents, I think the main risk is not getting enough food to remain nutritionally healthy,” said Weiss, a doctoral candidate at the University of Exeter in England. “But an outbreak of cetacean morbillivirus would be a nuclear meltdown. It has a low probability of happening, but the results would be absolutely catastrophic.”
Southern residents eat fish, primarily Chinook salmon — another species at risk of extinction. The lack of food, chemical contamination and stress can be thought of as contributing to the disease process among the whales. A high rate of inbreeding in this population also can affect their immunity.
“The misconception is that these animals are starving to death,” said Joe Gaydos, a veterinarian with the SeaDoc Society. “You need to look at the bigger picture of what these animals are dying from” — and the causes are varied.
In the realm of infectious disease, an orca may not be able to fight off an infection if it is already weak from lack of food, Gaydos said. If the infection persists, the animal could have a hard time catching fish to eat; it could become disinterested in food; or it might even be unable to adequately process the food that it does eat.
Toxic chemicals, particularly the polychlorinated biphenyls found in killer whales, can reduce an animal’s immunity, as can stress from noise or other causes. A whale in a weakened condition is more likely to succumb to any number of problems, including disease, congenital problems or trauma, such as being struck by a boat.
Strong social bonds among the southern resident killer whales can increase the opportunity for disease transmission, according to the new study published in the journal Biological Conservation. While CeMV is not the only organism that could threaten the population, Weiss said, the disease is frequently discussed as a significant threat.
Cetacean morbillivirus exists within a family of viruses that cause human measles, canine distemper and related diseases among cats and ruminants, such as goats, sheep and camels. The disease caused by the virus is highly contagious and can be spread through airborne droplets from the breath of an infected animal. Based on studies of other populations, CeMV is likely to kill 70-80 percent of the orcas that become infected, the new report says.
The study examined how infection could spread from one whale to another. In the wild, several orcas often surface together, exhaling plumes of mist that can be inhaled by a nearby whale. In the study, the frequency of close contact actually observed by whale researchers was factored into a new model, which can be used to predict how any infection could spread through the population from a single individual.
The initial infection could come from another species. Southern residents have been known to interact with harbor porpoises, humpback whales and Pacific white-sided dolphins — all thought to be susceptible to CeMV, making them potential sources for an outbreak.
Killer whales travel in family groups, led by an elder female and her descendants. Groups of these so-called matrilines make up socially related pods — specifically J, K and L pods among the southern residents. The new study showed that this modular organization could help reduce the spread of infection — but only minimally compared to groups of animals that interact in a more uniform pattern.
Using a variety of assumptions, the new model showed that occasionally the disease would fail to spread much beyond the initially infected individual, but in most cases about 90 percent of the orcas would come down with the disease and about 70 percent of those would die.
A vaccine to protect against cetacean morbillivirus has been tested, but not deployed, in bottlenose dolphins. If a vaccine were to be developed for the killer whales — and there are many challenges — one would need to vaccinate at least 42 of the 72 southern residents to substantially reduce the risk of a major outbreak, according to the analysis.
“The logistical challenges of vaccinating and monitoring individuals at sea and the potential stress these activities may cause the animals likely make the prospect of wide-scale vaccinations impractical, as well as potentially unethical,” the report concludes.
Other stories about disease in Puget Sound species include the three-part series “The Orca Docs: Can medical interventions help?” See also the entire section on disease in the Encyclopedia of Puget Sound.
Note: The word “novel” was removed from the headline, since CeMV is not new to some parts of the world.

Virus related to measles could push Puget Sound orcas to extinction, study says

Researchers studying the killer whales that frequent Puget Sound are growing increasingly concerned that a dangerous virus or other disease-causing organism could spread through the population and hasten extinction of these critically endangered southern resident orcas.
Without dramatic changes to their environment, extinction is already considered the likely future for the southern residents, as they continue to face shortages of food, high levels of chemical contamination and stress from the noise around them. Their numbers have declined from 98 animals in 1995 to 72 today.

Southern resident killer whales frequently come into “respiratory contact” with each other, as shown in this sequence of successive surfacing. First J42 (named Echo) is on the surface (i). As she submerges, J16 (named Slick) comes up closely on the far side (ii and iii).
Credit: Michael Weiss, journal Biological Conservation and Center for Whale Research

New research suggests that extinction could come sooner if the whales were to become infected with a novel pathogen, such as cetacean morbillivirus, which has killed thousands of Atlantic bottlenose dolphins on the U.S. East Coast but has not been seen in the Pacific Northwest.
“Given its fragile state, it is unlikely that this population would recover from the sudden increase in mortality that would result from a majority of the population becoming infected with CeMV,” states the new report.
Michael Weiss, a researcher with the Center for Whale Research and lead investigator on the study, said the prospect of CeMV in the southern residents can be compared in some ways to the recent outbreak in humans from the novel coronavirus: Just as humans lack immunity to the new coronavirus, the orcas have no history of exposure to CeMV, thus they are vulnerable to the worst effects of the organism.
“When I think of risks to the southern residents, I think the main risk is not getting enough food to remain nutritionally healthy,” said Weiss, a doctoral candidate at the University of Exeter in England. “But an outbreak of cetacean morbillivirus would be a nuclear meltdown. It has a low probability of happening, but the results would be absolutely catastrophic.”
Southern residents eat fish, primarily Chinook salmon — another species at risk of extinction. The lack of food, chemical contamination and stress can be thought of as contributing to the disease process among the whales. A high rate of inbreeding in this population also can affect their immunity.
“The misconception is that these animals are starving to death,” said Joe Gaydos, a veterinarian with the SeaDoc Society. “You need to look at the bigger picture of what these animals are dying from” — and the causes are varied.
In the realm of infectious disease, an orca may not be able to fight off an infection if it is already weak from lack of food, Gaydos said. If the infection persists, the animal could have a hard time catching fish to eat; it could become disinterested in food; or it might even be unable to adequately process the food that it does eat.
Toxic chemicals, particularly the polychlorinated biphenyls found in killer whales, can reduce an animal’s immunity, as can stress from noise or other causes. A whale in a weakened condition is more likely to succumb to any number of problems, including disease, congenital problems or trauma, such as being struck by a boat.
Strong social bonds among the southern resident killer whales can increase the opportunity for disease transmission, according to the new study published in the journal Biological Conservation. While CeMV is not the only organism that could threaten the population, Weiss said, the disease is frequently discussed as a significant threat.
Cetacean morbillivirus exists within a family of viruses that cause human measles, canine distemper and related diseases among cats and ruminants, such as goats, sheep and camels. The disease caused by the virus is highly contagious and can be spread through airborne droplets from the breath of an infected animal. Based on studies of other populations, CeMV is likely to kill 70-80 percent of the orcas that become infected, the new report says.
The study examined how infection could spread from one whale to another. In the wild, several orcas often surface together, exhaling plumes of mist that can be inhaled by a nearby whale. In the study, the frequency of close contact actually observed by whale researchers was factored into a new model, which can be used to predict how any infection could spread through the population from a single individual.
The initial infection could come from another species. Southern residents have been known to interact with harbor porpoises, humpback whales and Pacific white-sided dolphins — all thought to be susceptible to CeMV, making them potential sources for an outbreak.
Killer whales travel in family groups, led by an elder female and her descendants. Groups of these so-called matrilines make up socially related pods — specifically J, K and L pods among the southern residents. The new study showed that this modular organization could help reduce the spread of infection — but only minimally compared to groups of animals that interact in a more uniform pattern.
Using a variety of assumptions, the new model showed that occasionally the disease would fail to spread much beyond the initially infected individual, but in most cases about 90 percent of the orcas would come down with the disease and about 70 percent of those would die.
A vaccine to protect against cetacean morbillivirus has been tested, but not deployed, in bottlenose dolphins. If a vaccine were to be developed for the killer whales — and there are many challenges — one would need to vaccinate at least 42 of the 72 southern residents to substantially reduce the risk of a major outbreak, according to the analysis.
“The logistical challenges of vaccinating and monitoring individuals at sea and the potential stress these activities may cause the animals likely make the prospect of wide-scale vaccinations impractical, as well as potentially unethical,” the report concludes.
Other stories about disease in Puget Sound species include the three-part series “The Orca Docs: Can medical interventions help?” See also the entire section on disease in the Encyclopedia of Puget Sound.
Note: The word “novel” was removed from the headline, since CeMV is not new to some parts of the world.

PSI is hiring a postdoc for a water quality modeling project

The Puget Sound Institute (PSI) is looking for an early-career research scientist or engineer to contribute to a collaborative project modeling the sources, movements, and fates of toxic chemicals in the Salish Sea.
In this position you will be responsible for aggregating, evaluating, and interpreting large monitoring data sets to support the development of a deterministic, hydrodynamic water quality model. You will also serve as the collaborative link between the modelers from the Pacific Northwest Laboratories, who developed the Salish Sea Mosel, and water quality scientists and engineers from PSI, Washington Department of Fish and Wildlife, and other stakeholders.
The successful candidate will have:

  • PhD in environmental chemistry/engineering, oceanography, or closely related field;
  • Demonstrated ability to quantitatively describe chemical transport at the ecosystem scale;
  • 3 months of job-related experience;
  • Experience working in estuarine environments (helpful but not required).

Position title: Postdoctoral research Scientist 2
Supervisor: C. Andrew James (jamesca@uw.edu)
Location: Center for Urban Waters, 326 East D. Street, tacoma
Schedule: Full time
To Apply: Visit UW Hires and search for Req# 175691
Priority Consideration Date: January 31, 2020

How herring learn from their elders

Young Pacific herring (Clupea pallasii) learn migration behavior by joining up with older fish, according to a new paper co-authored by Puget Sound Institute Lead Ecosystem Ecologist Tessa Francis. The paper, published this month in the ICES Journal of Marine Science, showed how this behavior leads to greater spatial variability in biomass, and that commercial fishing could disproportionately affect some herring populations.
Citation:
Alec D MacCall, Tessa B Francis, André E Punt, Margaret C Siple, Derek R Armitage, Jaclyn S Cleary, Sherri C Dressel, R Russ Jones, Harvey Kitka, Lynn C Lee, Phillip S Levin, Jim McIsaac, Daniel K Okamoto, Melissa Poe, Steve Reifenstuhl, Jörn O Schmidt, Andrew O Shelton, Jennifer J Silver, Thomas F Thornton, Rudi Voss, John Woodruff, Handling editor: Ken Andersen. (2018). A heuristic model of socially learned migration behaviour exhibits distinctive spatial and reproductive dynamics. ICES Journal of Marine Science. fsy091. https://doi.org/10.1093/icesjms/fsy091
View the abstract. 

How herring learn from their elders

Young Pacific herring (Clupea pallasii) learn migration behavior by joining up with older fish, according to a new paper co-authored by Puget Sound Institute Lead Ecosystem Ecologist Tessa Francis. The paper, published this month in the ICES Journal of Marine Science, showed how this behavior leads to greater spatial variability in biomass, and that commercial fishing could disproportionately affect some herring populations.
Citation:
Alec D MacCall, Tessa B Francis, André E Punt, Margaret C Siple, Derek R Armitage, Jaclyn S Cleary, Sherri C Dressel, R Russ Jones, Harvey Kitka, Lynn C Lee, Phillip S Levin, Jim McIsaac, Daniel K Okamoto, Melissa Poe, Steve Reifenstuhl, Jörn O Schmidt, Andrew O Shelton, Jennifer J Silver, Thomas F Thornton, Rudi Voss, John Woodruff, Handling editor: Ken Andersen. (2018). A heuristic model of socially learned migration behaviour exhibits distinctive spatial and reproductive dynamics. ICES Journal of Marine Science. fsy091. https://doi.org/10.1093/icesjms/fsy091
View the abstract.