FISHBIO: Fisheries research, monitoring, and conservation

March 25, 2013

After many dreary years of low salmon escapement in the Sacramento basin, the 2012 Sacramento Index (SI), or adult population estimate, of 618,258 Chinook proved to be the best year in California since 2005. Commercial and recreational ocean harvests south of Cape Falcon, Oregon, were each more than triple the previous season, with 180,700 and 91,200 Chinook salmon captured, respectively. The news of the first success of the river harvest in years likely spread like wildfire, and river harvests totaled 62,200 in the Sacramento—the best year since 2005. Meanwhile, natural and hatchery escapement were estimated to be 162,900 and 121,000, respectively. Last year, the stock was classified as overfished based on a 3-year geometric mean spawning escapement of 85,195. But no longer: in 2012 the 3-year geometric mean spawning escapement reached 161,471, well above the threshold of 122,000 needed for the Sacramento River Fall Chinook to be declared rebuilt.

In recent years, the Pacific Fisheries Management Council (PFMC) estimates have at times been far greater than the actual SI contribution to the Central Valley, requiring modifications to the estimates in 2012. Currently, estimates are made using a regression that relates the previous year’s jack (early maturing males) escapement to the following year’s total escapement. Essentially, the method predicts that if there are a lot of jacks in the basin this year, then next year will be a good year for salmon. In 2011, the total Chinook salmon jack escapement was greater than any year on record (85,719), and the current regression would have estimated a total of more than two million Chinook salmon returning in 2012! In an effort to come up with a more realistic forecast, PFMC used the data from only recent years (2009-2011) to come up with a modified regression that decreased the 2012 SI forecast to 819,400 Chinook salmon. The modified forecast still overestimated by 25%, but was more accurate than predictions in 16 of the last 20 years (Figure 1). However, in 2013 PFMC reverted to using the original regression (data from 1990-forward) to estimate the SI forecast in 2013 (834,208). Using the modified regression for the 2013 forecast, the estimate would only be around 260,000 Chinook salmon, which may have resulted in a California salmon fishing ban once again.

All this fluctuation proves the limitation and inaccuracy of using jack abundance alone to predict future salmon runs. Many factors affect salmon survival, and we currently have the technology to summarize these factors and create improved models that can accurately forecast the population. On the Columbia River, a team of scientists from NOAA and Oregon State University recently tested 31 different variables to determine which factors were good indicators for predicting adult spring run Chinook salmon (see The salmon hunger games). Chinook jacks were just one of many factors included in the salmon forecast, and were not even the most significant. The two most important categories of predictors were 1) large-scale oceanic and atmospheric variables, which evaluated the Pacific Decadal Oscillation and the Oceanic El Niño Index, and 2) growth and feeding variables, which evaluated food availability and timing, as well as salmon size (Burke et al.). While it is obviously difficult to predict the future, modifying the PFMC’s current forecasting method could avoid the pitfalls of relying too heavily on one variable, and also increase the forecast time to up to two years. Both of these factors could drastically improve our ability to manage salmon in the future.

Figure 1: Comparison of the actual adult salmon population to the PFMC forecast.

Figure 2. PFMC regression curves used to forecast 2012 SRFC (red) and 2013 SRFC (black).

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

Tags: Chinook salmon forecast, salmon forecasting, salmon population

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Fish Report, Research, Salmon, Salmon Abundance

The Salmon Hunger Games

February 4, 2013

Each year, salmon managers for the Columbia River try to peer into the future and foretell the number of adult spring Chinook that will return to spawn. They use this crucial prediction to divvy up salmon harvest quotas among commercial, recreational, and tribal fishers. Now, scientists have found a way to improve the fish forecast: harnessing the predictive power of ocean conditions. Once juvenile salmon leave their freshwater streams and enter the ocean, the culling that occurs in the first brutal months largely sets the number of fish that grow up and return to spawn in two or three years (Beamish and Mahnken 2001, Wells et al. 2008). The ocean is a complex and shifting arena where many poorly understood factors can make or break a teenage salmon’s shot at survival. In a paper published in the journal PLOS One last month, scientists from the National Marine Fisheries Service and Oregon State University identified key ocean factors, such as the abundance of prey and major ocean trends, that can better predict the number of fish that will live to make a river homecoming.

To determine which of the ocean’s biological and physical conditions most influence Columbia River spring-run salmon survival, the researchers gathered up 31 datasets, or indicators, and divided them into five basic categories. These included large-scale ocean and atmosphere factors; smaller-scale local or regional factors; fish growth and feeding; predation and disease; and measures of cohort abundance. They tossed everything into a statistical model that could analyze multiple sets of data at once, and calibrated the model using the numbers of returned salmon from 2000-2009. While no single variable distinguished itself as the best crystal ball to foretell salmon returns, some groups of indicators stood out as more important. Eating and bulking up are key in this fish-eat-fish world. Leading indicators included the abundance of planktonic salmon prey, such as copepods and fish larvae, as well as measures of salmon diet and growth. The scientists concluded that switching from feeding on plankton to fish soon after they enter the ocean, between May and June, plays a large role in deciding which juvenile salmon will clear the hurdle to adulthood.

Big-picture processes, such as large-scale patterns of ocean temperature, also heavily contributed to predictions of salmon survival, more so than local or regional measurements of temperature and salinity from Oregon and Washington. This may reflect the influence of widespread ocean conditions on salmon prey. The scientists’ model proved quite accurate in its predictions: it came only six fish shy of nailing the 2011 adult spring-run Chinook returns to the Columbia River (which numbered just over 221,000 fish), and its prediction of 179,000 salmon in 2012 came far closer than other estimates to the actual number of 203,000. The study authors note that factoring in many of the complex relationships that govern a salmon’s ocean experience improves on the forecasts currently used to inform salmon management decisions, which typically rely on just one or two indicators. Their technique could prove a valuable tool for setting salmon quotas, and helps us better understand the conditions that give young salmon favorable chances to beat the odds.

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

Tags: Chinook salmon forecast, Columbia River basin, Columbia River salmon, salmon, spring-run chinook salmon

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Fish Report, Salmon Abundance

Cautious optimism

October 1, 2012

While leaf peepers in New England eagerly await the fall of golden and red tinted leaves, West Coast fishery biologists and anglers are looking forward to a “fall” of a different kind. As the temperatures drop and the leaves change, the fall-run Chinook salmon begin the long journey back to their natal stream for spawning. Anglers are gearing up for prime inland salmon fishing and biologists have begun setting up fish counting systems in Central Valley rivers. Both are optimistic for what is anticipated to be a promising season for Central Valley salmon inland fishing and escapement (i.e., the fish that ‘escape’ the fishery and make it to the spawning grounds). The ocean fishing effort data reflect the increased enthusiasm among salmon anglers this year. As of August 31, recreational anglers off the coast of California are estimated to have made a total of 130,682 fishing trips, up from last year’s total of 91,098. The ocean salmon season is coming to an end and the harvest numbers show substantial improvement since 2005, indicating that folks in the Central Valley may have reason for excitement.

Figure 1. California ocean salmon harvest for commercial and recreational fishing. Data from 2001-2011 pulled from Table I-4 of the Review of 2011 Ocean Salmon Fisheries and 2012 data from the September Supplemental Information Report 4. Note: * Preliminary estimates.

The Pacific Fishery Management Council (PFMC) forecasted an overall Sacramento River fall-run Chinook (SRFC) salmon abundance of 819,400 adults this year. The California ocean harvest number are just component of the complicated sum used to estimate the Sacramento Index (SI) of SRFC abundance (i.e., the sum of recreational and commercial harvest attributed to SRFC, and SRFC escapement). Given the preliminary California ocean harvest was already 284,110 salmon as of August 31 (172,914 and 111,196 for commercial and recreational, respectively; Figure 1), everyone is hopeful that despite recent overestimates, the 2012 forecast was not overly optimistic. This preliminary harvest for California has already surpassed the overall annual SI for the past five years (41,100-257,900 salmon), indicating that the Sacramento population is continuing its climb back from the bottom. Unfortunately, catch numbers themselves are not a useful indicator of the actual SI abundance for a few reasons. The percent of SRFC salmon harvested in the ocean has fluctuated between 20% and 80% over the past ten years. Also, the total California harvest is a combination of Klamath River fall Chinook, SRFC and other Central Valley runs, thus an estimate of SRFC-specific harvest must be calculated. So, to know where the Sacramento River salmon stand in 2012 we’ll have to sit tight till next February when the official numbers are announced by PFMC.

After a few years of extraordinarily low numbers, we may be approaching the light at the end of the tunnel. If the news is, in fact, as good as it sounds, we could be looking at the first sign of an industry on the rebound and the communities that have been affected by the California salmon collapse may feel some reprieve. However, the salmon harvest numbers are still far from the peak values seen in the early 2000s and the combination of events that lead to the collapse of Central Valley salmon in the first place is still under debate, so we aren’t out of the woods yet.

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

Tags: Chinook salmon harvest

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Salmon Abundance

Opening day

July 23, 2012

Due to drastically low Chinook salmon abundance, the California ocean and in-river salmon fisheries completely closed during 2008 and 2009, to allow the salmon population time to recover. Following the two-year closure, the salmon fishery re-opened with a severely curtailed season in 2010 followed by a more robust fishing season in 2011. This year marks the first year of “normal” recreational and commercial salmon fishing since California’s fall-run Chinook salmon crash.

The Central Valley recreational salmon fishing season officially began on July 16 on the Sacramento, Feather, American and Mokelumne rivers, and several areas will remain open well into December. The Mokelumne River will be open to salmon fishing for the first time in four years. However, the San Joaquin River and tributaries will remain closed to salmon fishing during 2012 to allow more time for abundance levels to increase. From all of the buzz, it’s clear that Central Valley anglers are enthusiastic about the predicted good salmon runs this season.

The return to a “normal” fishing season was prompted by the strong abundance projections (i.e., 819,400) for Sacramento River fall-run Chinook (SRFC) salmon this year. While the California Fish and Game Commission sets the instream fishing seasons, their decision is based on the abundance forecasts made by the Pacific Fishery Management Council (PFMC). The abundance forecast, or Sacramento Index (SI), includes the number of SRFC projected to contribute to escapement (that is, the number of adults returning to freshwater to spawn) and the number available for commercial and recreational harvest. These values were predicted to be 455,800 returning adult spawners and 363,600 harvested salmon, respectively in 2012. You may recall from a previous post, the abundance forecast for this year was based on a very limited data set. Now that the 2012 salmon fishing season is underway, we will have to wait until all numbers are in at the end of the season to see how close the PFMC was to the actual 2012 SI using a more conservative approach for forecasting the abundance estimate.

In the meantime, reports from commercial and recreational ocean fishing indicate a great salmon season is underway, with most boats obtaining their limits. In fact, according to recent news reports, so many salmon have been caught that the price of fresh Chinook dropped considerably and commercial fishermen went on a five day strike in Half Moon Bay, where processors were only paying $2.75 a pound, but fish were selling at the market for up to $20 a pound. The strike was short-lived and the commercial fishing boats are back to fishing after processors agreed to pay $3.50 per pound. Although salmon prices are still retailing for near $20 per pound, some supermarkets may lower their prices if salmon fishing remains excellent. Unfortunately for those Californians in the Central Valley looking to reel in their own Chinook, opening day for in-river fishing was a bust; however, it is still early and fall-run Chinook salmon won’t be ascending most rivers until August.

Tags: California salmon fishery

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Salmon Abundance

Jumping jack – part 1

July 2, 2012

Chinook salmon (Oncorhynchus tshawytscha) exhibit many interesting life history traits. Some of the traits are well known to many of us in California’s Central Valley. For example, they are anadromous (adults migrate from the ocean to spawn within rivers, typically to the river where they were born), they are semelparous (spawn once, then die), and they display diversity in freshwater return run-timings (e.g., fall-, late-fall, winter-, and spring-run). Another interesting trait is their ability to reach spawning maturity at different ages. In Central Valley rivers, returning salmon can range in age from 2 to 5 years, with the most common ages being 3 and 4 year-old adults. In a given year, a portion of the returning salmon will be 2 year-olds, termed “grilse”, having only spent one year in the ocean before maturing. Grilse are overwhelmingly made up of males or “jacks” (female grilse are referred to as “jills”). Grilse are not unique to Chinook salmon, they are found in other salmonid species such as coho and Atlantic salmon.

Historically, the number of jacks returning in any given year has provided a general indication of the number of 3 and 4-year old Chinook expected to return in upcoming years. Thus, the Pacific Fishery Management Council uses this information to predict the annual Sacramento River fall-run Chinook (SRFC) abundance (i.e., Sacramento Index) for establishing ocean harvest quotas. However, beginning in 2009, the relationship between the number of jacks and expected returns of 3 and 4-year olds has shifted for SRFC, leading to over-predictions of abundance in recent forecasts (PFMC 2012). The number of SRFC jacks returning in 2011 was the largest on record resulting in jacks representing almost 50% of SRFC abundance, which is the highest percentage of jacks seen in the past few decades (Figure 1).

Figure 1. Data gathered from PFMC Review of 2011 Ocean Salmon Fisheries show the percentage of Chinook salmon jacks each year.

In periods of increasing abundance of SRFC, the jacks will make up a larger portion of the SI than during the year before. The 2011 increase in jacks as a percentage of returning spawners can be partially, but not entirely explained by increasing overall abundance of SRFC (Figure 1). Other factors that may have contributed to this increase include their parental history and rearing environment, which can affect growth rates and age-at-maturation. In spawning experiments, younger returning males occurred from parental pairings of jacks mated with Age 4+ females compared to pairings of Age 4+ males with Age 4+ females (Hankin et al. 1993). This result may be due to the coupled influences of parental history on growth rates and subsequent growth rate influences on maturity rates. In research comparing growth rates of different parental pairings (Berijikian et al. 2011), the growth rates of offspring sired by jacks were consistently higher than those sired by older males. While this result may seem counterintuitive, it is consistent with many published studies. Individuals with higher growth rates, within a cohort of Chinook salmon (all offspring from a single year), are more likely to mature sooner (at younger ages) compared with individuals with lower growth rates (Ishida et al. 1998; Scheuerell 2005).

Biologists are working to understand the driving force behind these fluctuations in jack abundance, but whether the dramatic increase in percentage of jacks in 2011 is just a reflection of the increasing overall SRFC abundance, an effect of the proportion of jacks successfully mating, or is influenced by another environmental or biological factor, the unusually high percentage has our attention.

Tags: Jacks, salmon

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Salmon Abundance

Salmon economics

April 30, 2012

As word spreads of the abundance of Chinook salmon being caught off the coast of California, anglers are eager to make their way to the sea in hopes that they are as fortunate. The extended fishing season and forecast of an unprecedented salmon rebound have only added to the excitement, which is predicted to bring greater profits to coastal communities. Rumors have been floating around that anglers are limiting out and are back at the docks by 9 am and salmon fever is now full-bore. This is a great sign for the communities that have fallen on hard times due to low salmon abundances and the restrictions placed on sport fishing over the last few years.

The Pacific Fishery Management Council (PFMC) pre-season report predicted that most areas along the West Coast around recreational fishing communities would see an increase in the amount of tourist traffic and money this year compared to recent years. In 2011, folks along the West Coast made an estimated total of 211,200 angler trips and that number is projected to increase by 123,300 trips in 2012. Furthermore, the additional activity is estimated to be valued at almost $10 million more than the 2011 estimate of $17 million. In a down economy, this is great news for the California charter fishing industry, which took a hit after the 2007 season and the collapse of the Sacramento River Fall Chinook (SRFC) salmon fishery. However, the fishing frenzy caused by the increase in abundance could have negative effects on the recovery of the salmon. PFMC stated in the Review of 2011 Ocean Salmon Fisheries that SRFC are currently overfished based on the fact that the three-year geometric mean for escapement is below 91,500 fish. In times when abundance is still recovering and there is a lot of excitement around the fishing community it is important that we remain cautious about the future of Chinook salmon.

This year, the salmon fishing season is long and there will likely be a lot of fish captured during the next few months. Depending on your location the recreational fishing season started as early as April 7 and is expected to go through early November, while the commercial fishing season will begin May 1 and end September 30. Catch totals for recreational and commercial fishing are projected to be around 215,000 and 555,000, respectively, along the West Coast with almost half of the catch occurring south of Horse Mountain (Fort Bragg). Due to the overestimate of salmon abundance in recent years the catch of SRFC has actually been lower than predicted (23% lower in 2011) in years past, but if the fish continue to bite then there will be a lot of salmon harvested.

Tags: California salmon fishing

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Conferences and Events, Salmon Abundance

Salmonid restoration conference

April 9, 2012

The Annual Salmonid Restoration Conference kicked off it’s 30th anniversary last week in Davis, California, with a loud cheer from the audience as Chuck Bonham, the new Director of California Department of Fish and Game, led the crowd in a call-response during the audience participation segment of his unusually animated plenary speech. Not that plenary speeches are necessarily boring, but Bonham’s goal to get the crowd of laid back fisheries biologists from state and federal agencies, universities and consulting companies riled up was definitely uncommon. The annual conference of California’s salmonid biologists was well attended and session topics ranged from the “Genetic effects of hatcheries on Chinook salmon populations in the Central Valley” to “The role of coastal lagoons and ocean conditions on salmonid restoration”. At times the question and answer sessions would turn into heated debates, especially with regard to the effects of hatcheries on salmon populations, what one plenary speaker Jim Lichatowich called “the myth of hatcheries”. However, the debates remained civil and, as usual, the best discussions occurred over coffee in the courtyard.

Coincidentally, the conference followed on the heels of the Pacific Fishery Management Council’s decision last Thursday to approve California’s longest commercial salmon fishing season in years. Although there are indications that fall-run Central Valley Chinook salmon may be on the rebound, it is important to remember that the ESA listed fish stocks, such as the Sacramento River winter-run and the Central Valley spring-run Chinook, are still at critically low abundances. Conferences like these are important occasions for sharing ideas, sharing information and advancing the conversation on salmonid recovery. In the words of Chuck Bonham, “If all we’re doing is talking to ourselves, we ain’t getting closer to solving our problems.” Of course nothing is solved easily when it comes to California salmon and there is always more to learn.

Tags: Pacific Fishery Management Council, Salmon fishing season

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Salmon Abundance

Salmon boom or…?

March 12, 2012

News of a good California salmon fishing season is spreading like wildfire, but we are cautiously optimistic. The Pacific Fishery Management Council (PFMC) calculates the Sacramento River fall-run Chinook (SRFC) salmon abundance forecast to inform decisions regarding the commercial and recreational fishing in California, and they have overestimated the abundance in 6 of the last 7 years. We reported recently that the actual 2011 Sacramento Index (SI) of SRFC abundance was approximately 301,945 salmon or 41% of the preseason estimated SI of 729,900 salmon.

Why are the forecasts inaccurate? The PFMC forecast is calculated based on the number of jacks that returned to the spawning grounds during the previous fall. Chinook jacks are males within a year class that mature early and return at age 2. The abundance of jacks is believed to reflect the overall abundance of the cohort and thus, the abundance of the fish returning next year at age 3, which assumes that the proportion of salmon that return as jacks from any given year class remains relatively constant. However, the last three years we have seen a surprising increase in the number of jacks returning to Central Valley rivers. It is unclear whether this increase in jacks is a sign of more salmon, a sign of a shift in age-at-maturity, or an indication of both.

To adjust for the increased abundance of jacks, the PFMC has only included the 2009-2011 escapement data in the regression used to estimate the 2012 abundance of SRFC salmon. The resulting estimate (i.e., 820,000 salmon) is much less than the prediction would have been if they had been consistent with previous forecasts (i.e., 2.2 million salmon) and included in their model data from 1990-2011. Statisticians caution against extrapolating to predict a value well outside of the range of data, but essentially that is what was done to estimate the 2012 abundance. This is especially concerning given that the prediction is based on a regression with only three samples (three years of jack returns). We understand that despite this uncertainty PFMC must make an abundance prediction based on the available science, but it is important to see this prediction in context.

Based on PFMC’s own status determination criteria (SDC) the SRFC are considered overfished due to low returns in the past three years. While salmon abundance is likely to be greater in 2013 than in 2012, given the uncertainty of this year’s abundance forecast, in addition to the “overfished” status of the stock, we wonder whether the abundance is going to meet the expectations of the management council.

Tags: Forecast, salmon

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Salmon Abundance

PFMC fall-run Chinook predictions were optimistic

February 22, 2012

Each February, the Pacific Fishery Management Council (PFMC) releases their Pacific salmon abundance estimates from the previous year to compare with their preseason forecasts and to help develop management decisions for the upcoming season. Last year, the PFMC’s preseason forecast projected that the Sacramento Index (SI) for 2011 would be 729,900 Sacramento River Fall-run Chinook (SRFC), an incredible rebound from recent years of low abundance. The SI includes the number of SRFC expected to contribute to escapement (that is, the number of adults returning to freshwater to spawn) and the number available for commercial and recreational harvest, which, in 2011, was predicted to be 377,000 returning adult spawners and 352,900 harvested salmon, respectively.

On February 9th, 2012, the PFMC released the 2011 escapement estimates that proved rather dismal with only 121,742 SRFC adults returning to the Sacramento River basin for spawning (0.3% below the minimum conservation objective of 122,000). Based on the PFMC’s newly adopted status determination criteria (SDC), SRFC are considered “overfished” whenever the 3-year geometric mean spawning escapement is less than the minimum stock threshold (MSST) of 91,500. As such, the PFMC report indicates that the SRFC should be considered overfished since the geometric mean of SRFC escapement in 2009, 2010, and 2011 was 85,195.

A low number of returning adults could be explained by high harvest rates. However, based on preliminary California coastal catch numbers (commercial and recreational at 69,783 and 49,020, respectively) and the preseason Central Valley inland estimate of 61,400 (inland catch not available at the time of the PFMC’s report), it appears that combined California coastal and inland harvest was relatively low at approximately 180,203 fish. As a result, the SI for 2011 was approximately 301,945 or 41% of the preseason estimated SI of 729,900.

Figure 1. Percent difference from preseason forecast vs. post-season abundance (PFMC 2012 and Preseason Report 1 2011).

So what happened to the other 59% (427,955) Chinook salmon that were predicted to be along the California coast and migrating through the Delta this last Fall? Based on the recent history of PFMC predictions, it is not surprising to see such a large difference between their preseason forecast and the actual SI estimate (Figure 1). Last March, FISHBIO noted that in 2010 the PFMC’s preseason forecast was over 1½ times the actual post-season value (PFMC 2011), and in 2009 the preseason forecast was over 3 times the actual post-season value (PFMC 2010a). Although PFMC’s 2011 SI prediction was 729,900, they indicated that actual abundance could be as low as 231,671 Chinook salmon due to a wide 95% confidence interval around the estimate. Despite the possibility that actual abundance can be substantially lower than predicted values, the PFMC uses their annual predictions as guidelines to set fishing rules and regulations. By not using more conservative estimates, management strategies may be implemented that are not as protective as they should be, particularly when actual abundance is substantially lower than the forecasted abundance (for example, 41% of the predicted SI in 2011).

Figure 2. Percent of the Sacramento River Fall-run Chinook salmon that are jacks (PFMC 2012, Table B-1 and B-2).

Figure 3. Regression used by PFMC to forecast the population of Sacramento River Fall-run Chinook salmon (Preseason Report 1 2011, Figure II-2).

The data indicate that the accuracy of PFMC’s predictions has been worse in recent years and at the same time, jacks (male salmon that mature early and return at age 2) are making up a larger portion of the run (Figure 2). The SI forecast is calculated based on the number of jacks that returned in the previous year; for example, the 2011 abundance forecast of 729,900 was made based on the presence of 27,483 jacks that migrated through the Sacramento River watershed in fall of 2010. If the PFMC continues to forecast the SI based on this method and uses the total number of jacks observed in 2011 (i.e., 88,167), then their prediction for the fall of 2012 will be greater than 2 million Chinook salmon (Figure 3). The PFMC has acknowledged that due to the way that predictions are calculated, “there is a potential for the SI forecast to be biased high in years when the strength of successive cohorts is increasing” (PFMC 2011). If the PFMC continues to make predictions in the same manner, they are likely to drastically over-estimate the number of Chinook salmon, and fishing regulations may jeopardize the future of the SRFC population.

Tags: fall-run Chinook, Sacramento Index (SI), west coast escapement

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Salmon Abundance, Services

Fall-run Chinook salmon hatchery abundance

December 7, 2011

As the year comes to a close, so does the 2011 fall-run Chinook salmon spawning season. Central Valley tributaries are experiencing an increase in the number of salmon migrating upstream from the Delta this season. The increase is a positive sign for the future of the salmon, but this is not the whole story. Last year we reported that we were observing higher than normal counts of adipose fin clipped (ad-clipped) salmon and this year, at least in the San Joaquin Basin, we are again seeing higher than usual ad-clipped fish. Due to the Constant Fractional Marking Program (CFM), we expected that the number of observations of ad-clipped salmon would rise, reflecting a higher proportion of ad-clipping at hatcheries. However, we were puzzled at first over this year’s numbers, until we read the 2010 CFM report. Unlike previous years, every salmon that was released from the Mokelumne River Hatchery in the spring of 2009 and 2010 was CWT and ad-clipped, and according to the CWT database the majority of the fish were released into the San Francisco Bay. According to the recent Hatchery and Stocking Program Environmental Impact Report/Environmental Impact Statement (2010) Mokelumne River fish that are released into the Bay show a high propensity for straying. The report describes an independent assessment of straying based on coded wire tagged hatchery fish released between 1987 and 2007, which found that among other tributaries, 15% of the bay released fish strayed to the Stanislaus River and 11% to the Tuolumne River. Coded wire tags collected over the past few months during DFG carcass surveys will be examined to determine the source of the stray hatchery fish in 2011 in the Stanislaus and Tuolumne.

Table 1. Ad-clipped Chinook salmon in the San Joaquin Basin.

San Joaquin River Basin
In the San Joaquin River basin, the Tuolumne River salmon run continues to climb well above the counts recorded in recent years. Passages are recorded by a Vaki Riverwatcher fish counter at the Tuolumne River weir (2,646 as of 12/4/11; Figure 1). The Stanislaus River weir installation was delayed this year due to high flows, but the weir was finally installed on November 8. As of December 4, a total of 682 salmon have been recorded, which is already greater than the entire run (n=408) in 2007 (Figure 2). On the Mokelumne River, passages to-date for 2011, as recorded by video monitoring (18,102 salmon as of 11/29/11), continue to steadily climb (Figure 3).

Figure 1. Daily cumulative Chinook passage at the Tuolumne River Weir, 2009-2011.

Figure 2. Daily cumulative Chinook passage at the Stanislaus River Weir, 2003-2011.

Figure 3. Daily cumulative Chinook passage at Woodbridge Dam on the Mokelumne River, 2009-2011.

Sacramento River Basin
The Battle Creek net passage count of fall-run Chinook has fluctuated since the last update but, due to salmon migrating upstream and down, has remained relatively stable at 24,892 (as of 11/21/11; Figure 4).

Figure 4. Daily cumulative Chinook salmon passage in Battle Creek, 2003-2011.

It has come to our attention that the data previously presented for the year-to-date fall-run Chinook passage on the Yuba River unintentionally misrepresented the passage data available from their website. Data from 2007-2009 was incomplete, and counts during all years may have included individuals from overlapping Chinook runs (i.e., spring, fall and late-fall runs). For more information regarding the Yuba River passage data, please see the annual reports available online at: www.yubaaccordrmt.com.

Russian River Basin
Passages within California’s own Russian River continue to rise. As of November 30, salmon counts at the Mirabel Rubber Dam are higher than they have been since 2006 (n=3,084; Figure 5).

Figure 5. Annual fall-run Chinook passage at Mirabel Rubber Dam on the Russian River, 2000-2011.

Columbia River Basin
Further north, at Bonneville Dam on the Columbia River, the fall-run Chinook season has come to an end for 2011. This year, 401,576 Chinook salmon (as of 11/15/11) have been recorded passing the dam, which is consistent with the average for the last ten years (Figure 6).

Figure 6. Annual fall-run salmon passage at Bonneville Dam on the Columbia River, 2000-2011.

Fall-run Chinook salmon counts are definitely moving in a positive direction in 2011, but the increase in marking efforts and observations have demonstrated that a troubling proportion of the run consists of fish that originated from a hatchery. Even low levels of hatchery straying can reduce genetic and life history diversity and jeopardize the viability of the populations (Lindley et al. 2007). The fact that so many salmon in the Central Valley are of hatchery origin is a sign that despite the recent gains, there should still be concern over the future of the Central Valley fall-run Chinook.

Tags: Fall-run Chinook salmon, hatchery abundance

Salmon forecast: a chance to reflect and improve

The Salmon Hunger Games

Cautious optimism

Opening day

Jumping jack – part 1

Salmon economics

Salmonid restoration conference

Salmon boom or…?

PFMC fall-run Chinook predictions were optimistic

Fall-run Chinook salmon hatchery abundance

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