Tag Archives: chinook

Connecting the Fraser salmon virus dots

Are the Fraser chinook that southern resident killer whales love to eat already infected by the Infectious Salmon Anemia virus (ISAV) just detected in 2 Fraser sockeye smolts?  Could this virus — not salmon leukemia — be what caused the the mortality-related genomic signature in Fraser sockeye reported earlier this year?

Remember that DFO scientist Miller-Saunders told Scientific American last spring that “there is some indication that the signature may be in Chinook and coho” salmon, too.  To what data was she referring, I wonder?  Was it derived from out-migrating smolts or returning adults, wild or hatchery fish?  Was she referring to Fraser Chinook and coho, or some other stocks?

In contemplating how ISAV may affect the Northeast Pacific ecosystem, the Final Recovery Plan for U.S. Atlantic Salmon (Gulf of Maine DSP, 2005) is truly frightening reading.  The section on ISAV (appended below) suggests: that the virus can kill 3-50% of each production cycle and can infect non-Atlantic salmon (coho salmon in Chilean pens), as well as non-salmonids like rainbow trout (cultured) and gadids (potentially our pollack and cod species!); that rainbow and brown trout can be asymptomatic vectors; and that wild Atlantic salmon have been infected.  The plan also notes that “sea lice have been shown to retain the ISA virus after feeding on infected salmon.”  That’s pretty troubling when juxtaposed with recent research on lice infestation of wild B.C. salmon

The outlook for the Salish Sea ecosystem (and particularly it’s endangered salmon stocks) looks even dimmer after perusing an article about experimental infection of herring with ISAV.  The take home message (from the abstract): “It is concluded that the ISA virus is able to propagate in herring and that the herring may be an asymptomatic carrier of the virus.”

It’s going to be fascinating (and probably depressing) to see whether a pandemic develops.  If it does, the long-term outlook for southern resident killer whales may be bleak, especially if DFO fails to act at least as quickly and rigorously with the salmon farming industry as the U.S. agencies did when attempting to control the initial outbreaks in Maine.

Excerpt from the Final Recovery Plan for U.S. Atlantic Salmon (Gulf of Maine DSP, 2005) starting on page 1-60 —

ISA is a contagious and untreatable viral disease that affects a fish’s kidneys and circulatory system with a variable mortality rate from 3% to more than 50% in one production cycle (USDA APHIS 2001). Atlantic salmon infected with clinical ISA are anemic, typically lethargic, swim near the surface and fail to swim upright. Experimental studies have demonstrated that the virus is transmissible through mucous, feces and blood of infected/diseased fishes (Nylund et al., 1994). This results in cultured fishes being particularly susceptible to exposure to ISAV by infected cagemates. Studies in Norway indicate that penned salmon populations held within five kilometers (km) of each other or the discharge of slaughter wastes are at greatest risk of contracting ISA (Jarp and Karlsen, 1997). There is no evidence that the virus spreads vertically (from parents to offspring) although poor disinfection of fertilized eggs may allow for external transfer of the virus. Poor culture practices in fish hatcheries and net-pens in an Atlantic salmon watershed could increase the risk of a wild population’s exposure to disease.

ISA is the most significant known disease threat to the DPS. The threat of ISA to the recovery of the DPS is both direct, through infection of wild fish, and indirect by compromising hatchery supplementation of the DPS. The infection of emigrating smolts or adults passing near infected net-pens may cause mortality. This risk is greatest in those rivers whose approaches are nearest the highest concentration of net-pens, specifically the Dennys, East Machias and Machias. Other DPS river populations may also be at risk if they migrate through areas where aquaculture facilities are concentrated.

ISA has the potential to compromise CBNFH and the GLNFH if ISA-infected fish are inadvertently brought into one of these facilities. For example, an ISA-infected salmon brought into CBNFH for broodstock purposes could potentially infect other fish at the facility. In fact in 2001, a Penobscot sea run salmon brought to CBNFH for use as broodstock initially tested positive for ISA. Subsequent tests were negative and no additional fish were found to be infected. Outbreaks of ISA in freshwater hatcheries have not been reported from major salmon producing countries that have experienced ISA outbreaks. Still the potential for juveniles that have never entered salt water to be carriers of the virus is currently unknown.

ISA has already had an impact on Atlantic salmon recovery efforts. An adult stocking experiment (see page 4-69) was not fully optimized due to ISA concerns. These concerns resulted in more than 50% of the net-pen reared broodstock being destroyed. This decision was made because fish health experts felt the close proximity of these fish to fish infected with the ISA virus (ISAV) in commercial aquaculture pens was a substantial risk to wild populations. This concern was later affirmed by the outbreak of ISA in marine pens in the Cobscook Bay region (see page 1-82).

ISA was first reported in Norway in 1984 (Thorud and Djupvik 1988). In more recent years, cases of the disease have been reported from eastern Canada (Mullins et al. 1998), Scotland (Rodger et al. 1998), the Faroe Islands (OIE 2000), and in Cobscook Bay, Maine (Bouchard et al. 2001). The virus has also been associated with disease in cultured coho salmon in Chile (Kibenge et al. 2001) and very recently has been detected in cultured rainbow trout in Ireland.

The ISA virus has been known to cause disease in cultured fishes, principally in Atlantic salmon, although other species may act as carriers of the virus without signs of the disease. Species other than Atlantic salmon can become infected with ISAV and must be considered in the epizootiology of outbreaks and management of ISA. In laboratory studies, brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) have been shown to be asymptomatic carriers of the ISA virus that can transmit the virus to salmon by co-habitation (Nylund and Jakobsen 1995; Nylund et al. 1995; Nylund et al. 1997). Escaped or caged rainbow trout may pose a threat to wild Atlantic salmon by serving as a reservoir of ISAV.

Recent studies in the United States and Canada indicate non-salmonids (i.e., gadids) can become infected with ISAV. Whether these species act as reservoirs in wild populations remains to be determined. Assays of non-salmonid fishes taken from pens containing ISA-diseased cultured Atlantic salmon resulted in isolation of virus from tissues of asymptomatic cod (MacLean et al. 2003).

Results of recent studies conducted in Scotland and Canada indicate that ISAV exists at a low level in wild salmonids. ISAV has been found in Atlantic salmon aquaculture escapees (Olivier 2002; Raynard et al. 2001). There has been one case of wild salmon exhibiting ISA in Canada, but these wild fish were confined in a trapping facility with infected salmon of aquaculture origin.

At the time of the listing of the DPS as endangered in December 2000 (65 FR 69459), some U.S. net-pen sites in Cobscook Bay, the location of Maine’s greatest concentration of salmon aquaculture pens, were within five km of Canada’s ISA positive sites, raising concerns about the potential for this disease to infect U.S. aquaculture and wild salmon stocks. Subsequent to the listing of the Gulf of Maine DPS of Atlantic salmon as endangered, the disease spread to U.S. aquaculture sites within Cobscook Bay. The first known case of ISA in Maine occurred in Cobscook Bay at a salmon aquaculture net-pen site. The infection probably occurred in 2000 and was confirmed in February 2001. By September 2001, 50% of the net-pen sites in Cobscook Bay were ISAV-infected or diseased.

In January 2002, in an effort to control a catastrophic outbreak of ISA in Cobscook Bay, the Maine Department of Marine Resources (DMR), with the assistance of the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (USDA/APHIS), ordered the destruction of an estimated 1.5 million cultured salmon in the Bay. The industry was required to remove all fish from the Bay and a fallowing period, between sixty and ninety days, was imposed for the entire Bay in an attempt to eradicate the disease. The industry was also required to remove, clean and disinfect all the associated net-pens, barges and equipment at all the farms. The January 2002 order followed the voluntary removal by the aquaculture industry of nearly one million ISA- infected or exposed fish. In March 2002, ISA was also detected in an aquaculture facility in Passamaquoddy Bay. In response, the DMR issued an eradication order for the approximately 140,000 fish at the site.
In response to the ISA outbreak in Cobscook Bay, Maine DMR implemented new fish health regulations. The new DMR rules include mandatory surveillance and reporting of all test results for ISAV in salmon culture facilities. Sites with confirmed presence of ISAV are automatically subject to a remedial action plan developed by the DMR in cooperation with the salmon growing industry. Under the new regulations, the movement of vessels and equipment is also restricted. Prior to the rule changes, surveillance was not mandatory and reporting was only required when a case of the disease was confirmed.

The new rules require monthly sampling for all active finfish facilities in Cobscook Bay and quarterly testing for aquaculture facilities elsewhere in Maine. Reporting of results is mandatory and reports are provided to DMR. The DMR can require monthly testing for finfish facilities outside of Cobscook Bay if a positive case of ISAV is detected. The new rules expand DMR’s authority to take action at not only infected facilities, but also those exposed to ISAV. The rules require DMR to consult with all relevant state and federal entities with expertise in ISA control to keep ISA from spreading and prevent further outbreaks.

In response to the ISA outbreaks, the Maine DMR, with assistance of the USDA/APHIS also implemented an ISA control and indemnity program for farm-raised salmon in the U.S. The funds provided by the USDA were used to help the State of Maine with epidemiology and surveillance, and to indemnify the industry for their losses due to ISA. Under the DMR rule, all salmon growers in Maine must participate in the program. The goal of this program is to control and contain the disease through rapid detection and depopulation of salmon that have been infected with or exposed to the ISA virus.

In Spring 2002, Maine DMR authorized the restocking of Cobscook Bay. The Bay had lain fallow since January 2002. This authorization followed USDA approval of the cleaning and disinfection of equipment and the fallowing period. Subsequent to approval, the aquaculture industry stocked 1.9 million smolts on seven farms in Cobscook Bay. The number of smolts stocked was 30% lower than the amount historically stocked in this area (DMR 2002). New husbandry standards have also been put in place as part of the ISA control program. These new standards are administered by DMR.

The ISA control program initially divided Cobscook Bay into two management areas, a southern and a northern zone. The southern zone was stocked in even years beginning in Spring 2002. The northern zone was stocked only in odd years, beginning in Spring 2003. Recently, USDA and Maine DMR have determined that the entire Cobscook Bay would be managed as a single area. DMR estimated that by there would be approximately 25% fewer fish in Cobscook Bay compared to previous levels. In addition, several conditions are required for each lot of smolts that are introduced into net-pens from freshwater hatcheries. All aquaculture facilities in Cobscook Bay are only permitted to raise a single-year class of fish. A minimum thirty-day fallowing period between production cycles is required. No more than 10% of the fish at a site may be carried over between production cycles and then only upon approval by DMR. This approval requires that no ISA is detected at the site during the production cycle, that general fish health is satisfactory, that fish are removed by September 1, and that there be a biweekly surveillance of the site by a fish health professional. Movement of fish between farms in the same zone requires a permit and verification that ISAV has not been detected at either site in the four weeks prior to movement. There will be no moving of fish between zones. In addition, farms, aquaculture vessels and processing plants are subject to routine third-party biosecurity audits. Despite these measures, additional cases of ISAV were detected at aquaculture sites in Cobscook Bay beginning in June 2003 and continuing in 2004.

The DMR’s bay management program was developed following an evaluation of other bay management and ISA control programs in Canada, Ireland, Scotland and Norway. These nations have developed control programs intended to prevent further outbreaks of the disease. The DMR plans to codify bay management husbandry standards in a rule and establish other bay management areas where finfish leases are located. Successful sea lice management and control is a necessary component of bay area management as sea lice have been shown to retain the ISA virus after feeding on infected salmon (Nylund et al. 1993).

During routine surveillance of all salmon culture sites in Maine, an apparently new strain of ISAV was detected in November 2003 at a site approximately 50 miles from Cobscook Bay. This was the first detection of ISAV at any site in Maine other than Cobscook Bay. The new strain did not cause disease in the cultured salmon and did not grow in the laboratory on various cell lines typically used in ISA isolation. Gene sequencing of this organism indicates it is more closely related to a Norwegian strain than the New Brunswick strain that has caused the mortalities in Cobscook Bay. Subsequently, this new strain has also been found in Cobscook Bay sites. Efforts are underway to sequence archived samples to determine the significance of the virus in the Cobscook Bay system.

One potential mode of disease transmission is through biological sampling conducted by various state and federal agencies in DPS rivers. The development and implementation of disinfection and biosecurity protocols reduces the risk of a pathogen being moved from one location to another (G. Russell Danner, IF&W fish pathologist, personal communication 2004). Disinfection and biosecurity protocols, where not already in place, should be developed and implemented for all research and sampling activities taking place in rivers within the DPS (see page 4-63).

Updates from NOAA on Elwha science

Yesterday Sarah Morely of NOAA/NWFSC Watershed Program, Fish Ecology Division gave a 40-minute synopsis of the “Elwha River Dam Removal – Past, Present, Future.”  My notes are appended and the NOAA site has an abstract with recommended references (also appended in case the link breaks).

A small (fall) Elwha chinook (dated Oct 4, 2010)

The most interesting aspect of the talk from the perspective of the southern resident killer whales is that no one in the audience, including Mike Ford, offered a clear articulation of the strategy for recovering the Elwha’s chinook salmon — and particularly the possibly extinct spring chinook of 50-kg fame.  Given their strong preference for big chinook (Hanson et al., 2010), the southern residents would presumably benefit most from the fast recovery of the biggest Elwha chinook, but Sarah only indicated that her impression was that the return of salmon to the Elwha was going to more “natural” than managed.  With large salmon and a combined species population potential of ~400,000 fish, we ought to be very clear as a community about the chinook recovery strategy!

That led one audience member to wonder whether the spring run is really extinct and, if so, how long it might take the fall chinook population to naturally fill the spring niche.  He asked whether 25 years might be a good guess for natural recovery of the spring chinook runs if adults are not moved above Glines Canyon dam to facilitate their re-colonization of the upper Elwha and tributaries (as is currently being done at Condit Dam on the White Salmon), but Sarah didn’t volunteer a confirmation or an alternative estimate.  The audience member’s suggestion of possible extinction is echoed on the National Park Service’s web page on the historic range of Elwha chinook:

Very few, if any, spring-run Chinook remain in the Elwha.

This made me realize that I (or some other southern resident stewards) need to dig into the EIS and figure out if the spring chinook are being managed in an optimal way from the perspective of the salmon-eating killer whales.  If they are not, then perhaps we should all make it a priority to change the situation.

In sleuthing around for details on the Elwha chinook runs, I did start to answer a different long-standing question: “Why were the Elwha chinook so big?”  I had heard 2 compelling hypotheses: (1) velocity and vertical barriers are more substantial on the Elwha than on comparable (Olympic) rivers and selected for fish powerful enough to surmount them; and, (2) stream bed gravel size in the Elwha is much larger than on comparable (Olympic) rivers and only bigger salmon could dig in it to build their redds.

The second is refuted by Sarah’s response to a question I asked her after her talk: How does the sediment size distribution in the upper Quinalt compare with that in the upper Elwha?  She said the upper (east?) fork of the Quinalt was chosen as a comparison site because the river bed sediment size distribution is similar to that in the upper Elwha.  Yet the Quinalt does not host gigantic chinook…  But perhaps it has bigger velocity and vertical barriers than the Elwha?

The first hypothesis is addressed in Brenkman et al., 2008 (special issue of Northwest Science).  They describe the velocity and vertical barriers on the Elwha:

The 7.9 km of main stem habitat currently available to anadromous salmonids in the Elwha River will increase to 71 km following dam removal. Possible seasonal velocity barriers exist in three main stem Elwha River canyons during periods of high river flows (Figure 2)—Rica (rkm 26.1 to rkm 27.3), Grand (rkm 31.1 to rkm 35.3), and Carlson Canyons (rkm 53.0 to rkm 54.5). Rica Canyon consists of bedrock, large boulders, and high-velocity water with several cascades and falls up to 1.8 m in height. The upstream portion of Grand Canyon contains several cascades and low waterfalls, and the lower 2.4 km of Grand Canyon contains approximately 15 cascades and falls. Carlson Canyon has a single waterfall that is 2 m in height (Washington Department of Fisheries 1971).
Seasonal velocity barriers in the Elwha River occur where the river channel is constrained by steep canyon walls and boulder- and bedrock- dominated substratum. Canyon reaches have channel gradients that are up to two times steeper (2% in Rica, Grand, and Carlson Canyons) than the average gradient for the entire 69 km of the main stem river (1%). High-flow events resulting from early winter storms and spring runoff create high-velocity cataracts that may constitute seasonal migration barriers to salmonids moving upstream. In contrast to these steep canyons, other sections of the Elwha River are much more gradual, with gradients of 0.3% from the mouth to Elwha Dam, 0.8% from Elwha Dam to Glines Canyon Dam, and 1.4% from Glines Canyon Dam to the headwaters of the main stem.

While salmon are generally capable of jumping 1.8-2m barriers, their ability to do so is limited by the pool size (particularly depth), relative position of the pool and the hydraulic jump, and degree of aeration in the pool.  I’ve yet to find these details, but if they don’t exist, I know what I’m doing on my next hike up the Elwha drainage!

MY NOTES ON THE TALK:

Sept 16 was beginning of deconstruction of dams. Deconstruction will take another 2-3 days. Salmon recovery is expected to take decades.

Background:

Global distribution of dams and reservoirs is extensive in termparate regions. Global Water System Project Database, 2011 (McGill University)

Poff & Hart, 2002, Bioscience: increased dam removal over last 30 (now 40?) years is due to replacement generally being more expensive than removal, BUT most removed dams have been small.

Imminent NW removals – Elwha, White Salmon, Sandy River, Marmot Dam on Little Sandy River, Rogue, Calapooia (Umpqua), Kalamat

Lower Elwha (190? 1913) and Glines dams (1932? 1927) reduced sediment, river movement, woody debris, as well as salmon populations. They will be removed concurrently in controlled increments over 2-3 years (to minimize impacts of sediment to fish as well as benthic organisms.

Link to web cam of sediment plume? (Bureau of Reclamation is managing erosion of 18 M m^3 of sediment, 50% fine, 30% coarse, suspended sediment concentrations of >10,000 ppm)

Monitoring efforts and objectives

Objectives: 1) Establish baselines (advanced) and 2) evaluate response to dam removal (just getting started)

Research areas: Former reservoirs, Nearshore (consortium of Fresh/Kagley/+), River ecosystem

Nearshore (slides from Kurt, but also USGS+ collaborators)

  • Monthly sampling (Mar-Sep) since 2006; 37m beach seine plus environmental data
  • Community composition doesn’t change much between years, but is a little different between their reference areas and the area expected to be impacted by sediments.

River ecosystem (Floodplain dynamics, aquatic foodwebs, fish recolonization [enumeration, distribution, predicted movements, genetic work])

Floodplain dynamics Pess, Beechie, LEKT, USGS, USFWS

  • Channel age, connectivity, distribution
  • Riparian vegetation diversity
  • Kloehn et al 2008, Influence of dams on river-floodplain dynamics in the Elwha River, Washington. Northwest Science 82.
  • Trout dominate surface water channels; Coho dominate in groundwater channels.
  • George snorkels to measure residual pool depth, pebble counts and spawnable area and fine sediment sampling.
  • 14 monitoring sites (7 below Elwha, 7 above Elwha; 2 mainstem, 2 tributaries, 10 floodplain)

Aquatic Foodwebs

  • Morley, Coe, LEKT, USGS
  • Nutrient Limitation, primary production, benthic invertebrate, marine derived nutrient transfer
  • Morley et al. 2008. Benthic invertebrate and periphyton in the Elwha River basin: current conditions and predicted response to dam removal. Northwest Science 82.
  • Duda et al., 2010. Isotope patterns.
  • River is nutrient limited in non-winter months by nitrogen and secondarily phosphorous
  • Elwha Fish Weir (species, sex, length, Tags (CWT, ?), scales, fin clip
  • Blue View (Keith Denton and 1 other) is helping with enumerating Coho when fish weir is non-functional in high flow periods.
  • Genetics of O. mykiss (resident rainbow and steelhead): see 3 gene pools or distinct populations: 3 native, 1 non-native (lower, resident, Trout Lake); no hatchery influence upstream of dams.
  • McMillan looking at resident rainbows vs anadromous steelhead metrics.
  • Kinsey Frick: Spawning movements of adult salmonids during dam removal. Catching fish in weir, tagging with radio tags, and releasing above
  • 20 chinook released above dam; relocated 3-4 that had found spawning habitat in lower Elwha while some returned to spawn below the dam. Plans to tag more chinook as well as other salmonids.

On-line resources

11:45 — QUESTION AND ANSWER SESSION:

  • Do you have plans to monitor hatchery stock status and impacts? At recent symposium, Norm Dicks mentioned that Chambers Creek (non-native steelhead) may be an issue, plus it is also focus of current law suit.
  • There used to be spring and fall chinook. The spring were the big ones and likely are extinct. Will spring chinook be brought in or are fall chinook expected to fill in that gap?
  • Me: How will chinook recovery be managed? Why was this approach taken, while more direct facilitation was done on White Salmon?
  • The Condit removal is supposed to take 3-5 days; why should the Elwha take so much longer?
Big Elwha salmon

Big Elwha salmon (from LEKT?)

Questions I didn’t ask:

  1. What is evidence of 100 lb chinook? Have all sources of evidence been pursued? (Middens? Interviews? Historic photographs? Written accounts? Inference from tree ring growth rate and/or isotope ratios?)  What is the source and story of the photo in your title slide (shown at right and credited to LEKT = Lower Elwha Klallum Tribe)?
  2. Are sediment size distributions similar in Quinalt to in the Elwha? Are such distributions governing invertebrate community structure?
  3. Why is recovery expected to take decades? (Urgency is lent by the SRKW’s need and preference for chinook.)

Follow research to do:

  • Frick re plans for upper Glines?
  • Is “out-planting” mentioned in the EIS?
  • Ask Eric Anderson how long fall chinook would take to fill niche of spring chinook.
  • Surely there are studies of how fast adaptation occurs from other removals or mitigation efforts?
  • How much sediment is behind Condit?

Clipping from the NWFSC talk announcement web site:

Elwha River Dam Removal: Past, Present, and Future

Date and Time: October 06, 2011, 11:00-12:00 Pacific Time Zone [Check U.S. Time clock for your local time]
Location: NOAA Northwest Fisheries Science Center (NWFSC) (2725 Montlake Boulevard East, Seattle, WA 98112; Map to NWFSC), Room: Auditorium.
Speaker(s): Sarah Morley (Research Ecologist, Watershed Program, Fish Ecology Division, NOAA NWFSC)
Speaker’s Email: sarah.morley@noaa.gov
OneNOAA Seminar Sponsor: NOAA NWFSC Monster Seminar JAM
Abstract: The removal of the Elwha River dams on the Olympic Peninsula of Washington State is a unique opportunity to examine ecosystem recovery on a watershed scale, and has spurred collaborative research efforts among divergent groups. For the past century, the two dams have blocked the upstream movement of anadromous fish to over 90% of the watershed, and restricted the downstream movement of sediment, wood, and other organic materials to the lower river and estuary. Populations of all five Pacific salmon species and steelhead in the Elwha are critically low, habitat complexity decreased in the middle and lower river, and downstream coastal habitats are sediment starved. Simultaneous deconstruction of the two dams began in September 2011 and will take three years to complete. During and after that time, researchers are examining dam removal effects in three geographic regions: the soon-to-be former reservoirs, across the river floodplain, and in the nearshore environment. Short-term (< 3 years post dam removal) monitoring is focused on the projected downstream transport of approximately four million cubic meters of fine sediments accumulated in the reservoir deltas, associated peaks in river and estuary turbidity levels, and re-vegetation of the reservoir themselves. Longer-term effects of dam removal (> 5 years) to be evaluated are the delivery of gravels and cobbles to the lower river and nearshore, the re-establishment of a natural wood delivery regime, the re-colonization of the upper watershed by anadromous fish, and the associated effects on aquatic and riparian foodwebs. This talk will provide an overview of the Elwha restoration project, but particularly highlight the research of NWFSC researchers examining river floodplain dynamics, salmon re-colonization, and aquatic foodwebs. The removal of the Elwha Dams has been long awaited by the Lower Elwha Klallam Tribe and others and will provide ongoing learning opportunities for future dam removal efforts across the United States and elsewhere.
About the Speaker: Sarah Morley is a field ecologist whose research focuses on biological assessment-using biota to evaluate the condition of a place and better identify the causes of degradation. Within this broad framework, she has conducted research on the effects of urbanization on the health of Puget Sound streams and evaluated the effectiveness of restoration actions on streams and rivers across the Pacific Northwest. Recent projects include examining the effects of shoreline armoring on the biota of the Duwamish River estuary, the effectiveness of green stormwater management strategies in improving urban stream health, and aquatic foodweb effects of dam removal on the Elwha River. Sarah holds a B.S. in Environmental Science from U.C. Berkeley and an M.S. in Aquatic and Fisheries Sciences from the University of Washington. She has been a member of the Watershed Program at the Northwest Fisheries Science Center since 2000. http://www.nwfsc.noaa.gov/research/staff/display_staffprofile.cfm?staffid=649

Salient Publications

  • Duda, J. J., H. Coe, S. A. Morley, K. Kloehn. 2011. Establishing Spatial Trends in Water Chemistry and Stable Isotopes (d15N and d13C) in the Elwha River Prior to Dam Removal: A Foodweb Perspective. River Research and Applications. doi:10.1002/rra.1413
  • Kloehn, K.K., T.J. Beechie, S.A. Morley, H.J. Coe, and J.J. Duda. 2008. Influence of dams on river-floodplain dynamics in the Elwha River, Washington. Northwest Science 82: 224-235.
  • Morley, S.A., J.J. Duda, H.J. Coe, K.K. Kloehn, and M.L. McHenry. 2008. Benthic Invertebrates and Periphyton in the Elwha River Basin: Current Conditions and Predicted Response to Dam Removal. Northwest Science 82:179-196.
  • Morley, S. A., P. S. Garcia, T. R. Bennett, P. Roni. 2005. Juvenile salmonid (Oncorhynchus spp.) use of constructed and natural side channels in Pacific Northwest Rivers. Canadian Journal of Fisheries and Aquatic Sciences, 62:2811-2821.
  • Pess, G. R., S. A. Morley, J. L. Hall, R. K. Timm. 2005. Monitoring floodplain restoration. Pages 127-166 in Roni, P. (Ed.) Methods for monitoring stream and watershed restoration. American Fisheries Society, Bethesda, Maryland.

Klamath River dam removal proposed

Things are really looking up for the salmon-eating killer whales of the west coast.  For the third time this fall, progress in removing dams on west coast salmon rivers has been made.  First there was press regarding the beginning of the removal of the Elwha dams.  Then news came of preparations for dam removals on the White Salmon (including this Yakima Herald story about trucking fall chinook above the dams).

Now coverage is emerging about the draft EIS/EIR regarding removal of 4 hydroelectric dams on the Kalamath River in California.  The document was made available on September 21 and is open for public comment for 60 days (until November 21).  Copco No. 1 (pictured in the AP photo below) is one of the dams that may be demolished.

Recent press, including a 9/27 piece in India Country Today Media Network and a 9/22 story in SFGate, contain potentially good news for endangered southern resident killer whales which spend some of their winter months hunting in along the west coast in the migratory path of adult Kalamath salmon.  If things don’t get bogged down at the Federal level, the proposed plan may be approved by the Secretary of the Interior as soon as March, 2012.

The India Country states:

Over the past century, the number of salmon in the run has dwindled from millions of fish to less than 100,000 in most years.

And when the dams are gone, fisheries are expected to double in size.

Notable quotes from SF Gate:

Dismantling the four hydroelectric dams on the Klamath River would open up 420 miles of habitat for migrating salmon…

The long-awaited environmental report on what would be the biggest dam-removal project in California history predicted an 81.4 percent increase in the number of chinook salmon and similar increases for steelhead trout and coho salmon.

The dams – Iron Gate, Copco 1, Copco 2 and J.C. Boyle – have blocked salmon migration along the California-Oregon border since the first one was built in 1909 and have been blamed for much of the historic decline of chinook and coho salmon and steelhead trout in the Klamath.

The ultimate goal is to restore what has historically been the third-largest source of salmon in the lower 48 states, behind the Columbia and Sacramento rivers.

 

 

 

Big fall chinook run expected on Columbia

Today’s Weekender Report from WDFW suggests SRKWs could have some good eating off the mouth of the Columbia this fall.  Does anyone have a read on how the Fraser chinook runs are faring this summer?  Why don’t killer whale conservationists have an easy way of monitoring the abundance of northwest salmon?

Anglers are reeling in chinook salmon off the coast, pulling up pots full of crab in Puget Sound, and casting for trout in alpine lakes on both sides of the Cascades.  Summer fisheries are in full swing, and anglers can look forward to even more great fishing opportunities in the days ahead.

A prime example is the Buoy 10 salmon fishery, which runs Aug. 1-28 at the mouth of the Columbia River. A big run of 776,300 fall chinook is expected to return to the big river this year, and fishery managers predict that anglers will catch approximately 11,000 of them between Buoy 10 and Rocky Point, 16 miles upriver.

“Buoy 10 is a very popular fishery, drawing tens of thousands of anglers every year,” said Joe Hymer, a fish biologist for the Washington Department of Fish and Wildlife (WDFW).  “Fishing tends to start out slow, then accelerates quickly through the month of August.”

Glimpses into the Columbia spring chinook fishery

In our on-going efforts to monitor Pacific salmon dynamics and interpret them from the perspective of southern resident killer whales, today brings news of a 6-hour commercial net fishery opening on the lower Columbia River.  It’s amazing that it’s even worth going out in a boat when the catch is limited to the first six hatchery-origin chinook!  I guess one can infer there about 200 boats in the fleet, based on the limit and the predicted total catch of about 1200 chinook (70% from upper Columbia and Snake Rivers).

From the southern residents’ perspective, interesting questions are how many fish are expected and when are they arriving (especially compared to past years).  The columbian.com article ends with this:

The forecast is for an upper Columbia run of 198,000. Through Sunday, a total of 262 spring chinook have been counted at Bonneville Dam.

The source of these data was revealed by a recreational fisher’s guide to catching spring chinook on the lower Columbia as the Fish Passage Center (FPC) which is in the business of counting fish in the ladders of the many Columbia River dams.  The guide also gave a big-picture description of the overall spring run timing as “about 6 weeks in late March through April” and provides a nice summary of how the fishery follows the fish up the various tributaries of the Columbia, starting with the Willamette (because OR releases hatchery fish there a couple weeks before WA).

It would be interesting to juxtapose the timing and locations of all available winter/spring orca sightings outside of Puget Sound from past years with the time series of spring Columbia (and Fraser?) fish passage.  For starters, here is a link to Columbia adult fish passage data, some of which are summarized in the following graph that shows the spring chinook run is just beginning on the Columbia.  And here I was thinking that commercial and recreational openings would not occur until some substantial portion of the run had made it to the spawning grounds!

Now is the time of year when the NWFSC crew would typically be preparing for their spring cruise to search for southern residents on the outer coast of WA, including off the Columbia where they have observed SRKWs feeding on chinook from the upper Columbia and Snake .  Unfortunately, NOAA funding and/or ship logistics have ruled out such a cruise this year.

Salmon & orcas in Patagonia catalog

The new Patagonia catalog (out yesterday) has a full page spread by Steven Hawley entitled “The Idaho Tide.”  It eloquently connects the wolves of Idaho’s Frank Church Wilderness with Snake River salmon and the southern residents, and it includes a great paragraph (below) with a quote-worthy line by Ken Balcomb:

“I think any reasonable biologist will tell you the only way to take advantage of [the intact salmon habitat left on the Snake River] is to tear out the dams.” — Ken Balcomb, Center for Whale Research

The full text of the piece is appended (and archived as a PDF). Inspired readers can take action here (too bad such a link wasn’t provided in the catalog!)…

Thanks to Dan Drais of Save Our Wild Salmon for the heads up on this one.  Watch for Hawley’s new book next year, “Recovering the Lost River” (the Columbia).

Safina on orcas in LA Times

latimes.com

Save the salmon — and us

Above is a link a nice Op-Ed piece by Carl Safina.  Below is my response, submitted today to the L.A. Times.

In his 1/24/10 opinion “Save the salmon — and us,” Safina points out that new research says orcas prefer salmon.  But the in-press analysis of prey scraps by NOAA’s Brad Hanson is more specific: like humans, the southern resident killer whales’ first choice for a summertime meal is the biggest, fattiest, salmon around — the Fraser River chinook.  Along the west coast, the biggest chinook are associated with the biggest river systems (the Fraser in the summer; the Columbia and Sacramento in the winter) because it takes a big, strong fish to swim thousands of kilometers inland (e.g. to Idaho).  For the orcas’ sake, we need to prioritize chinook recovery in the biggest rivers.

To keep the orcas visiting the Salish Sea during the summer, we should all be more involved in conserving the chinook (and other salmon) runs of the Fraser river, along with recovering stocks in the rivers of western Washington.  We Americans should get more involved in the battle raging in British Columbia between Norwegian salmon farms and advocates of wild Fraser sockeye like Alexandra Morton.  Her proposed actions to protect sockeye smolts from diseased farm fish will also help baby chinook on their way to the open Pacific, and thereby ensure future meals for southern residents.  Activists can also help the orcas by bolstering conservation efforts in Washington State, like the recent delta restorations in the Skagit and Nisqually rivers, or the removal of Elwha river dams (now starting in 2011 thanks to stimulus funds).

To prevent extinction of orcas we must protect their winter food sources.  We need to call our legislators, most importantly the recalcitrant Senators from Washington, to initiate a new approach to salmon management in the Pacific Northwest.  The current plan for Columbia salmon is a Bush-era cop-out that parasitized new-NOAA-head Jane Lubchenco like a B.C. sea louse jumps a Fraser sockeye smolt.  To recover, the Columbia/Snake salmon need innovative, dramatic action — including dam removal — not the business-as-usual that led to salmon ecosystem collapses first in England and then along the Atlantic seaboard (read “King of Fish” by David Montgomery for historic perspective).  The best idea I’ve heard is to place a salmon specialist on the President’s Council on Environmental Quality to mandate and facilitate a new regional collaboration already called for by Congressional leaders from Oregon and Idaho. 

One year into the Obama administration is a good time to call for such high-level solutions.  We should demand full funding of the recovery plan and research to support it — both of which have been under-funded by ~70% since the southern residents were listed as endangered.  Oh, and the word “orca” should be in the next salmon treaty, too, because it appears that they are at the table from California to Alaska — whether human fishers like it or not.


Elwha dam removal timing

Good news for Elwha salmon from the March NPS newsletter. Might dam removal begin in 2011, instead of 2012? I’m trying to keep track of the timeline (and be sure it doesn’t slip backwards) here.
clipped from www.nps.gov
Work Progressing on Elwha Construction Projects; Ever Closer to Dam Removal

aerial view of large construction project underway
The Elwha Water Facilities (EWF) and the Port Angeles Water Treatment Plant (PAWTP; pictured) will protect the industrial and drinking water supply for Port Angeles-area users from the increased sediment load the river will carry during and after dam removal.
The PAWTP is scheduled for completion late this coming fall, while construction of the EWF is approximately one year ahead of schedule, with completion anticipated in February 2010.
blog it

Contaminants in SRKWs

Sandra O’Neill, Contaminants in salmon

We’ve heard that S and N residents are both eating mostly Chinook.  Why are the southern residents more contaminated than the northern residents?

Contaminants in fish are determined by:

  • where they live
  • what they eat
  • how long they are exposed
  • how fat they are

Chinook and Coho have elevated [PBDE] because they stay close to shore, while other salmon have undetectable levels.  For PCBs are more widely dispersed and present in all salmon, but are highest in Chinook.  Puget Sound fish are always much more contaminated than northern fish.

Along the west coast, [PCB] peaks at Puget Sound and are about the same at Skeena (north extreme) and Sacramento (south exptreme).  Within Puget Sound, the resident Chinook (blackmouth) are ~3x as contaminated as non-resident Chinook.

Prey quality is also decreasing along W coast.  Size is decreasing and kcal/fish is variable.  PS fish are smaller and have lower lipid concentration.  This means Puget Sound non/resident Chinook will give you ~7/16X PCBs compared to Skeena Chinook!

Peggy Krahn, persistent organic pollutants (POPs) threats to SRKWs

Fisheries and Oceans Canada collected 3 biopsy samples in 2004; NWFSC collected 18 samples in 2006-7.

Most SRKWs have [PCB] exceeding threshold for health effects.  Juveniles have much higher concentrations of many POPs (PBDEs, HCGs, and HCB) than adults in their pods.   This happened mostly by transfer from their mothers during lactation.  The levels are above the estimated threshhold for health effects.

The prevalence of DDT use in CA raises the ratio of DDTs/PCBs above 1.  K and L pods have this California signature while J pod doesn’t, which is nicely explained by the observation that J pod haven’t been observed south of Newport, OR.

Teresa Mongillo, predicted contaminant levels in SRKWs

Developed an IB Model which assumes that the Amount of prey consumed = PCB, PBDE in prey + milk – gestation -lactation

Currently there is no change in the [PCB] while [PBDE] is increasing exponentially.  Projections were made for different scenarios (variable rates of increase).   The model predicts that PCBs will begin to decline after 20+ years; PBDE levels will exceed current PCB levels in 2-40 years.

PCBs increase with age in males, but decreases with offspring in females.  In contrast, PBDEs don’t seem to increase but they cluster into groups that are living vs dead… this suggests a potential dose-related effect on calf survival. PCBs decrease with birth order (the first-born gets the biggest load).

Questions:

Rich Osborne: Are heavy metals in such low concentration that they are not of concern?  Peggy: Epidermis samples are reserved for stable isotopes and genetics, so there is a sample size limitation.  Sandra: Hg levels are slightly higher in Chinook and Coho.

Jeff Lorton:  Should we tell our passengers not to eat Chinook?  Should we catch/release Chinook across whole region?

Ken Balcomb: Has anyone initiated a study of POPs in local humans, e.g. sports and commercial fishers?  There is good analogous study from the Great Lakes.

Strong spring chinook run on the Columbia

Here we are in mid-February, a couple weeks into the blackmouth opening in the Salish Sea, and WDFW is opening up recreational fishing for spring (winter?) Chinook running in the Columbia [see today’s email announcement below].  This makes me wonder where the southern residents are at the moment and what the run timing looks like for California Rivers, coastal OR rivers, and the Fraser.  Why in the world isn’t a simple Gantt diagram for this famous phenomena!?

This is the first time I’ve gotten a sense of when the spring run gets going and it’s earlier than I expected.  Yesterday Sam Wasser showed us some plots that suggest that southern residents are about as well fed as they are all summer when they first show up in ~June.  That got me wondering whether Fred Felleman is right — that their main source of annual sustenance is the really big, oily spring Chinook destined for the highest parts of the biggest river systems (and fisher’s dinner tables, now).

WDFW NEWS RELEASE

February 12, 2009
Contact:  WDFW Region 5 Office, (360) 906-6708

Columbia River spring chinook season reflects projection of strong runs

OLYMPIA – Anglers will be able to fish for spring chinook salmon from the mouth of the Columbia River to Bonneville Dam through mid-April under initial seasons adopted Wednesday, Feb. 11, by fishery managers from Washington and Oregon.  Anticipating a strong run of spring chinook to the upper Columbia River and improved returns to the Willamette, the two states agreed to provide significantly more days of fishing – particularly below Hayden Island – than last year.

According to the pre-season forecast, nearly 300,000 upriver spring chinook are expected to enter the Columbia River this year, which would make this year’s return the third highest since 1977.  An additional 37,000 “springers” are also expected to return to the Willamette River, up from 27,000 last year.

“This is shaping up to be a very good year for spring chinook fishing in the Columbia River,” said Cindy LeFleur, Columbia River policy coordinator for the Washington Department of Fish and Wildlife (WDFW).  “The first fish have just begun to arrive, and we hope to see a lot more of them in the months ahead.”

Below Hayden Island, the new season provides 30 days of spring chinook fishing in March and April, compared to just 12 days last year.  During those two months, anglers also will have 39 days – up from 36 days last year – to catch and retain spring chinook from Hayden Island upriver to Bonneville Dam.

LeFleur noted that the fishery could extend beyond April, but that late-season regulations have not been set because of differences between the fish and wildlife commissions of Washington and Oregon over how to allocate the catch.

In March and April, Columbia River anglers will be able to fish for spring chinook salmon at the following locations and times:

* West power lines on Hayden Island downstream to Buoy 10:   Seven days per week from March 1-15.  Beginning March 16 through April 18, fishing will be limited to three days per week, Thursdays through Saturdays.
* West power lines on Hayden Island to Bonneville Dam:   Seven days per week from March 1-22.  Beginning March 23 through April 22, fishing will be limited to four days per week, Wednesday through Saturday.
* Tower Island power lines above Bonneville Dam to McNary Dam:   Seven days per week from March 16 through April 30.  The Washington and Oregon bank fishery will also be open from Bonneville Dam upstream to the Tower Island power lines.

Until March 1, the spring chinook fishing is open under regulations described in the 2008-09 Fishing in Washington rule pamphlet (good until April 30, 2009).  Anglers fishing for spring chinook salmon may also retain shad and hatchery steelhead, as outlined in the rule pamphlet.

In all areas, anglers are required to release any chinook salmon not clearly marked as a hatchery-reared fish, since a portion of the wild upriver spring chinook run is protected under the federal Endangered Species Act.  Unmarked steelhead must also be released.  Hatchery fish can be identified by a clipped adipose fin with a healed scar.

Under a new rule approved by the Washington commission, anglers fishing below McNary Dam may retain two hatchery-reared adult salmon or steelhead (or one of each) per day.  However, only one adult chinook salmon may be retained per day downstream from Bonneville Dam.

LeFleur noted that standing rules limit incidental mortality of wild spring chinook intercepted and released in all state fisheries – recreational and commercial – to 2.2 percent of the total run.   “It’s essential that anglers observe the rules requiring the release of wild salmon and steelhead,” LeFleur said.  “Our ability to continue these fisheries depends on it.”