Longfin Smelt – January 2017 Larval Survey

Posted on February 2, 2017 by Tom Cannon

In a recent post on the status of the state-listed longfin smelt, I remarked on the dire straits of the population in the San Francisco Bay Estuary. I noted that the first measure of a population collapse would be the lack of population response in wet year 2017 as determined by the larval longfin smelt catch in the January 2017 Smelt Larval Survey. The January 2017 survey results are now in and indicate very low catch (15) relative to the first eight years of the survey. Additional larval surveys in February and March and the spring 20-mm Survey will likely confirm these results. The low larval count reflects the lack of adult spawners in the population. Most of the winter 2017 spawners came from the winter 2015 brood. The question remains whether the population can rebound under such low recruitment of juveniles into the population and whether juvenile survival (recruit per spawner) can increase under 2017’s favorable wet year conditions.

Catch of longfin smelt in January Smelt Larval Survey 2009 to 2017. Data Source: http://www.dfg.ca.gov/delta/data/sls/CPUE_Map.asp .

More on Delta Smelt Tidal Surfing

Posted on January 26, 2017 by Tom Cannon and Chris Shutes

The last post about risk to Delta smelt was on January 9. Adult smelt migrate into the Delta from the Bay in winter to spawn. They take advantage of the flood tide to move upstream. However, with flood flows as high as 100,000 cfs entering the north Delta from the Sacramento River, the Yolo Bypass, and Georgiana Slough in mid- to late January 2017, there are no flood tides to ride into the north Delta spawning areas.

The only option for the adult smelt is thus to ride the incoming tide up the San Joaquin River into the central and south Delta (Figure 1). South Delta export pumping is currently at 14,000 cfs, near maximum capacity, using four rarely used auxiliary pumps. This pumping increases the pull of the incoming tide, reducing the effect of the inflow from the San Joaquin, Calaveras, Mokelumne, and Cosumnes rivers. While Delta inflow from these rivers is relatively high (Figures 2-5), it does not offset the influence of the incoming tide as does the inflow from the Sacramento.

Net tidal flows in lower Old and Middle Rivers (OMR flows) remain at the allowed limit of -5000 cfs, consistent with the smelt Biological Opinion. Several adult Delta smelt were salvaged at the export facilities in mid-January. ¹ This scenario is considered a “high risk” to Delta smelt by the Smelt Working Group, because of the continuing risk that the pumps will draw or attract adult smelt into the central Delta and subsequently into the south Delta.

Under lower San Joaquin River flows, the maximum allowed export pumping is 11,400 cfs. High San Joaquin River inflow allows exports of 14,000 cfs that do not generate OMR flows more negative than -5000 cfs. The theoretical benefit of high San Joaquin River flows is that it should keep flow into the central and south Delta moving westward. But a large portion of that inflow is diverted south into the Head of Old River toward the pumping plants (Figure 6).

Figure 1. Approximate flood tide flow in cubic feet per second in mid to late January 2016. Blue arrows represent high Sacramento River, San Joaquin River and Mokelumne River flows (during flood tides). Red arrows depict negative flows of incoming tides. Note the south Delta incoming tide of -20,000 cfs would be less if not for the 14,000 cfs export rate at the south Delta pumping plants.

Figure 1. Approximate flood tide flow in cubic feet per second in mid to late January 2017. Blue arrows represent high Sacramento River, San Joaquin River and Mokelumne River flows (during flood tides). Red arrows depict negative flows of incoming tides. Note the south Delta incoming tide of -20,000 cfs would be less if not for the 14,000 cfs export rate at the south Delta pumping plants.

Figure 2. San Joaquin River flow at Mossdale at the head of the Delta upstream of Stockton and the Head of Old River. Note that on Jan 6 when flow reached about 6,000 cfs, the tidal signal dissipated when flow overcame the tidal forces.

Figure 3: Flow from the Calaveras River, upstream of the Delta. The Calaveras enters the Delta at Stockton.

Figure 4. Release from Camanche Dam to the Mokelumne River. CDEC does not show flow values for the Mokelumne at gages further downstream. The Mokelumne enters the Delta near Jersey Point.

Figure 5. Cosumnes River flow well upstream of the Delta. Much of the high flow peaks enters the river’s connected floodplain, roughly between Lodi and Elk Grove, and does not flow immediately to the Delta. Flows in the Cosumnes enter the Mokelumne before passing into the Delta

Figure 6. Flow entering the entrance to Old River from the San Joaquin River near Stockton.

https://www.usbr.gov/mp/cvo/vungvari/dsmeltsplitdly.pdf Note: website has changed to this new site. ↩

More on Splittail Status

Posted on January 23, 2017 by Tom Cannon

Recently, I summarized survey information from the Bay-Delta on Sacramento splittail that depicted a potentially grim picture of the future of this special status species. In that post, I did not include trawl survey info from Suisun Marsh Fish Study collected annually by UC Davis (Figure 1), which indicates a core population of adult splittail still present in Suisun Marsh. Other core populations exist in San Pablo Bay (Petaluma and Napa Rivers). Peter Moyle and Teejay O’Rear (UC Davis, personal communications) believe the Marsh core population is sufficiently strong and resistant to extinction.

Looking at Figure 1, the Suisun Marsh population survived the 1987-1992 drought, building in numbers with strong recruitment (ages 0 and 1) in the wet years of 1995-2000. Recruitment declined during the 2007-2009 drought, but there was strong recruitment in the wetter 2010 and 2011 water years. Recruitment declined in the 2012-2014 drought years, but remains substantially higher than at the end of the 1987-1992 drought. Teejay O’Rear states the population has remained strong through 2015 and 2016, with some recruitment in the wetter 2016, and likely strong recruitment in the spring of 2017, presuming it stays wet.

Figure 1. Catch-per-unit-effort of Sacramento splittail in Suisun Marsh 1980-2014 by age group. (Source: Teejay O’Rear, UC Davis)

Winter-Run Chinook Salmon Status – End of 2016

Posted on January 15, 2017 by Tom Cannon

The prognosis for winter-run Chinook salmon is not good following very poor survival of the 2014 and 2015 spawns in the Sacramento River below Shasta Dam. The run had been recovering after the 2007-2009 drought (Figure 1). However, year class production suffered in the 2012-2015 drought, culminating with the year class (spawn) failures in 2014 and 2015 (Figure 2) caused by egg stranding and high water temperatures. Run size and juvenile production/survival estimates for 2016 are as yet incomplete, but production of juveniles as estimated from Red Bluff rotary screw trap data indicates some improvement over 2014-2015.¹ The somewhat higher number of recruits produced in 2013 likely boosted the spawning run in 2016.

With water year 2017 starting out as a wet year with considerable flooding, conditions for the emigration of the 2016 year class should be optimal. If wet conditions persist, spawning and rearing this spring and summer for the 2017 year class should also be optimal. Planned release of 600,000 winter-run hatchery smolts in the coming weeks coincident to high Sacramento River flows also bodes well for the 2016 spawn and the future 2019 run. However, the prognosis for the 2017 and 2018 runs remains in doubt because of the above-mentioned 2014 and 2015 year class failures.

Additional insight into the future is possible by taking a closer look at the population’s spawner-recruit relationship that I prepared for the past four decades (Figure 3). Recruitment appears to be a function of both the number of spawners three years prior to any given year and environmental conditions between spawning and emigration in a given year. (Other factors such as ocean conditions may also add to variability in the data.) The recruits-per-spawner ratio is higher three years after wet years than three years after dry years. The runs in 2017 and 2018 are likely to be severely depressed because of extremely poor 2014 and 2015 recruitment, and may possibly be as low as those produced after the 1987-91 drought (only 100-200 wild spawners).

For further reading on winter-run status see:

Figure 1. Winter-run Chinook salmon escapement (run size) into upper Sacramento River near Redding, CA from 1974-2015. (Data Source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

Figure 2. Survival of winter-run year classes below Shasta Dam from 1996-2015. The water temperature standard for the Sacramento River near Red Bluff was weakened during 2012-2015 drought. The severely weakened water quality standard in 2014 and 2015 led to poor survival and virtual loss of two year classes. (Source: http://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/docs/nmfs_yip_03182016_ppt.pdf)

Figure 3. Winter-run Chinook spawners versus number of spawners three years later (recruits) for years 1974 through 2012. Selected wet year spawn dates shown in blue. Selected dry year spawn dates shown in red.
(Data source: http://www.dfg.ca.gov/fish/Resources/Chinook/CValleyAssessment.asp)

https://www.fws.gov/REDBLUFF/RBDD%20JSM%20Biweekly/2016/Biweekly20161202-20161216.pdf ↩

Splittail Status – End of 2016

Posted on January 13, 2017 by Tom Cannon

The prognosis for splittail was not good in 2015¹ after four years of drought and little recruitment since 2011. The below-normal water year in 2016, with its limited winter flooding, brought no apparent recovery in the Fall Midwater Trawl Index (Figure 1). Summer salvage (Figure 2) indicated that there was some production in 2016, although salvage was two orders of magnitude lower than the previous normal water year 2010 (Figure 3) and three orders of magnitude less than the previous wet water year 2011 (Figure 4).

If water year 2017 were to continue on its current trajectory and become a wet year with widespread flooding, conditions for splittail spawning and rearing this winter and spring would be optimal. A positive response in salvage, Fall Midwater Trawl Survey, and FWS Seine Survey would indicate some form of recovery in the population. However, a lack of response on the order of that which occurred in 2011 would be a signal that the population is in dire straits and at risk of recruitment failure and eventual extinction. In the absence of a 2011-magnitude response in the next wet year, the fisheries agencies should conduct a comprehensive review to evaluate whether to re-list² splittail under the federal and state endangered species acts.