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.

On a recent trip to Southeast Asia a FISHBIO biologist examined a small fish captured in a net in the Cambodian dai (bagnet) fishery. Fish have evolved different jaw structures to maximize their effectiveness at capturing their preferred food type(s). The shape and location of a fish’s mouth can help fish biologists identify a species and its general diet. For instance, this fish from the Tonle Sap River has an impressive protrusible jaw, an indication that its diet likely consists of mobile prey such as zooplankton or other smaller fish. The protrusibility of the mouth can be an important indicator of food type, since it can determine the type of prey consumed and the method of prey capture. When its jaws and mouth are fully protruded, the mouth cavity is enlarged and adept to quickly suck in prey. Other species with protrusible mouths that are abundant in the United States include largemouth and striped bass, two well known predatory gamefish.

Check back over the next few weeks for more posts on our adventures and the interesting fish we captured in the Mekong Basin…

While most of us favor the comforts of home, our projects often dictate otherwise. Far from home, and exhausted after a long day of working on a fish counting weir, we crawled into tent cots to get a couple of hours of shuteye. When it comes to the quasi-nomadic lifestyle of a fish biologist these are pretty good accommodations.

Rotary screw traps are used extensively to monitor downstream migrating juvenile salmonids (See: The Count is on). Rotary screw traps utilize a rotating cone powered by river flow to funnel fish into an underwater live-well. The total number of rotations that the trap cone makes in a sampling period (usually 24-hours) is a measure of sampling effort, and the average rate of rotation is also an important factor. If a traps stops during a sampling period, these two pieces of information make it is possible to estimate how long the trap fished before being interrupted by debris.

For the past 20years rotary screw trap operators have relied on mechanical counters to record the total number of rotations in a sampling period but these have been problematic. Mechanical counters rely on an arm attached to the rotating cone to strike a lever on the counter to trip the rotary counter. The mechanical counters on the market today are manufactured with plastic components and lightweight springs that make them susceptible to failure when exposed to the harsh conditions at rotary screw traps during monitoring seasons that extend for several months annually.

We have  developed a prototype digital counter that works similar to a bicycle speedometer. This counter uses a small magnet attached to the rotating cone and records a revolution each time the magnet passes the receiver of the electronic counter. The receiver is wired to the water resistant counter which allows the counter to be mounted in a secure location away from any moving parts. We are currently operating this prototype simultaneously with mechanical counters on several of our traps to evaluate the accuracy and reliability, and so far the results look promising.

From a river’s headwaters to its confluence, physical variables impact the fish assemblages that may be present. Fish biologists and aquatic ecologists often identify these physical variables by classifying river segments, such as the bedrock canyon (photo above), into Channel Habitat Types (CHT). Geomorphological characteristics like gradient, channel confinement, stream size, and substrate define the channel habitat types. By assessing CHT fish biologists may determine quality and quantity of available habitat for a species of interest. For example salmonids are usually associated with higher gradient streams than warm water fish species in North America. Also, rainbow trout and steelhead are associated with relatively steeper, swifter habitats than juvenile Chinook salmon (Montgomery et al. 1999). Similar channel types are expected to respond to natural or human-caused changes in a similar manner, so by understanding these responses we can best preserve and restore habitat for desired species.

Adding a little humor to an otherwise routine task, this crewmember shows off his dance moves after cleaning algae from the viewing window of a fish counting weir. Using high tech electronic fish counting systems, like the Vaki Riverwatcher, to record fish passage provides highly accurate results; but like most things in life (here comes the cliché), you only get out what you put into it. Field technicians regularly visit our fish counting weirs to clean the camera lens, lights and glass that monitor the fish passage chute (or in this case the dance floor).

The Sacramento-San Joaquin Delta is a complex system to navigate and structures like the Delta Cross Channel (DCC) gates can turn a navigable waterway into an unexpected dead end. The DCC was constructed in 1951 to divert water from the mainstem of the Sacramento River into the Mokelumne River and through the interior Delta. The United States Bureau of Reclamation (USBR) built the DCC as a response to saltwater intrusion into the Delta, which occurs when water is exported from the South Delta. The gates can be opened and closed depending on water quality, flood protection, and fish protection requirements.

There are many structures in the Delta and Suisun Marsh designed to control salinity and water quality levels. Salinity intrusion is a major concern for agricultural and municipal water users that draw water from the Delta. Water managers use the 2 practical salinity unit isohaline, better known as “X2”, for tracking the direction and magnitude of fluctuations in salinity. The X2 is tracked as the distance upstream from the Golden Gate and is maintained by releasing water from upstream reservoirs and adjusting export rates. The position of the X2 is legally established through the 2008 biological opinion (OCAP) and subsequent court decisions.

The Suisun Marsh Salinity Control Gates (SMSCG) are large, radial arm floodgates similar to the DCC, which restrict the flow of high salinity water from Grizzly Bay into Montezuma Slough and maintain lower salinity in the brackish marsh. Additionally, the California Department of Water Resources (DWR) annually installs three agricultural barriers and one fish barrier in the South Delta. The agricultural barriers in Old River, Middle River and Grant Line are rock barriers designed to increase water height, circulation, and quality. The Head of Old River Barrier (HORB) is a fish barrier designed to improve operational flexibility of the State Water Project and help reduce fishery impacts by preventing migrating fish from entering Old River. Before heading out to explore the California Delta it’s best to do your homework and check on the status of the delta structures to prevent running into a dead end.

In his annual State of the State address, California Gov. Jerry Brown reiterated a desire to move forward with the Bay Delta Conservation Plan (BDCP) and have a proposal ready this summer outlining a project that is intended to restore the Delta ecosystem while still providing water to communities throughout the state (the co-equal goals of the BDCP). Of course, he is referring to the controversial peripheral canal project, which would divert water from the Sacramento River around the delta (or through, depending on the alternatives) and directly to the main aqueducts of California via the state and federal pumping stations.

The existing system draws water from the southwest section of the Delta, manipulating flow throughout the estuary. One study suggests that increasing exports likely increases the number of salmon from the Sacramento River that stray into the southern Delta and become entrained in the pumps (Newman and Brandes, 2009). Another study demonstrated that survival is lower for San Joaquin River salmon using the Old River route during outmigration (that leads towards the pumping stations), than for salmon migrating in the mainstem of the river (VAMP 2011). If the pumps entrain fish, they are salvaged and trucked to several release sites throughout the western Delta; however, not all entrained fish will survive the salvage process. The California Department of Fish and Game (CDFG) released the 2011 data showing that a record 11 million fish were salvaged while a record amount of water was drawn at the pumping stations. It is yet to be determined if the abundance of salvaged fish is a sign that the populations are rebounding or if the higher numbers are due to the record volume of pumped water, or most likely a combination of the two.

A total of $125 million has been spent since 2006 on the BDCP and Delta Habitat Conservation and Conveyance Plan (DHCCP) planning activities and another $115 million is expected to be spent through 2013. Estimates indicate that the peripheral canal could cost roughly $12 billion, but there is no way to truly know the price tag until a plan is drawn up and an environmental impact report is conducted.

One thing is certain, the Delta is a vulnerable ecosystem that is being pushed to its limits. If there is not a strategy to modify the way we utilize our resources or present ways that we can reduce the amount of resources used, then we will continue to struggle with prioritizing social matters and environmental concerns.

Yesterday, by unanimous decision, the California Fish and Game Commission rejected proposed changes to striped bass regulations. To reduce predation on native salmonids and Delta smelt, the California Department of Fish and Game (CDFG) proposed decreasing size restrictions and increasing bag limits of striped bass. The sport fishing regulation changes were intended to reduce the size and abundance of striped bass in the Delta and Central Valley tributaries, and were proposed as part of a settlement agreement to a lawsuit by the Coalition for a Sustainable Delta. No word yet on how this will impact the original lawsuit, but, we think it’s fair to say that this issue is far from over.

Last week we conducted electrofishing in New Bullards Bar Reservoir as part of a Federal Energy Regulatory Commission (FERC) relicensing assessment. FERC is the government agency that regulates and monitors hydroelectric projects and fisheries research is often required during relicensing of hydropower projects. The purpose of the study was to provide information concerning the distribution, occurrence, and condition of fishes in the reservoir. In this case, we conducted the electrofishing at night since it yielded a greater diversity of species and number of fish, and also reduced impacts of the project on recreational users. Another perk of conducting our sampling at night is that it left the day free for taking in the local sights.

New Bullards Bar Dam, which stands 645 ft. above the canyon floor, is touted as the 2nd tallest dam in California and the 5th tallest in the United States (Oroville Dam is the tallest at 770ft.). It is quite an impressive site to look over the side of the concrete monolith into the canyon that once held the full force of the North Fork Yuba River. Some water is release at the base of the dam to support the fishery below, but the majority of the water now travels 4.7 miles through an underground tunnel to the New Colgate Powerhouse. New Bullards Bar Dam was constructed by the Yuba County Water Agency as a flood control reservoir in response to the flood of 1955. The dam was completed in 1969 and provides 170,000 acre feet of flood control storage space. Unlike many similar dams, people are still allowed to travel across this structure and gain an appreciation for its massive scale.