Spring Run Salmon Restoration in San Joaquin River – Some Questions

Pilot study release of Feather River hatchery smolts at the Golden Gate. (DFW photo)

Pilot study release of Feather River hatchery smolts at the Golden Gate. (DFW photo)

50,000 Spring Run Chinook smolts from the Feather River Hatchery will soon be released into the San Joaquin River near Merced, as was the case in 2014 and 2015. The action is part of the effort to restore Spring Run to the lower San Joaquin below Friant Dam near Fresno. The smolts each have a coded-wire tag in their nose and an adipose fin clip so their survival can be monitored.

So how have the first two releases fared? Were any collected in Delta surveys, at south Delta pump salvage facilities, in Chipps Island trawls, ocean fisheries, spawning surveys? Data available now from these surveys should be providing early indications of success rates for comparison with other restoration programs. After all, it is an adaptive management program.

Given that the last three years have been dry years especially in the San Joaquin, I do not hold out much hope for the survival of these three years of smolt releases. I hope I am wrong, but information is lacking on the first two releases. Did any make it down the river to the South Delta pumps? Did any make it to the Bay (Chipps Island trawls)?

If not, then some adjustments should be made this year.

  1. Hatchery trucks from Fresno could travel further downstream to the Delta or Bay.
  2. Smolts could be barged from Merced or Stockton to the Golden Gate (see photo above).1

At a minimum, some early indicators would help us all see some progress for the program and deflect the naysayers who would write off the whole program.2

February Delta Smelt Update

The February trawl survey indices are in – there are a few Delta Smelt left (Figure 1).

The Smelt Working Group, created as prescribed in the Smelt Biological Opinion issued by the US Fish and Wildlife Service (in the Department of Interior), has stated following its meetings on February 15 and 22: “The fact that sporadic Delta Smelt catches have continued to occur at Prisoners Point under the lowest February SKT survey on record indicates that the risk of entrainment remains high and is incompatible with current pumping levels.” 1

After its February 22 meeting, the Working Group added: “Salvage: Four delta smelt on February18, geographic influence of the pumps extends to the lower San Joaquin River at the more negative end of this flow range, especially affecting the southern bank near Jersey Point. Recent salvage of adult Delta Smelt confirms that entrainment into the export facilities has occurred and likely is continuing…. The Working Group concluded that any salvage observed at either facility will be of high concern because Delta Smelt abundance is at a historic low, contributing to low detection probability of Delta Smelt in salvage under RPA compliant operations (BiOp page 338). One fish was detected in salvage sampling on January 21 and February 18, counting as eight salvaged Delta Smelt due to an expansion factor of four.”

Following these meetings, the US Bureau of Reclamation (also in the Department of Interior), which operates the federal export pumps in the South Delta, exported more than double the recommendation of the Smelt Working Group. Together the state and federal exports were nearly triple the recommended amount (<2000 cfs). This situation, where the state and federal experts in the Smelt Working Group were ignored by their managers, who instead maximized Delta exports in February, is a gross violation of the intent of the state and federal endangered species acts and species protections in the biological opinion. Graph of Kodiak Trawl Figure 1. Record low indices for Jan-Feb 2016 in Kodiak Trawl Survey2

Few Smelt Left are at High Risk

This third week of February 2016 the Smelt Working Group concluded “the risk of entrainment remains high and it is incompatible with current pumping levels”1. Basically as Delta inflows decline after the early winter stormwater recedes in early February and South Delta exports increase, the risk to Delta Smelt is high with the onset of spawning imminent. Despite the high risk assessment, state and federal managers have decided to raise exports to the maximum allowed under the Delta Smelt Biological Opinion, to 6,000 cfs, which is triple the 2000 limit suggested by the working group, and about a third of Delta inflow. The working group warns the managers that just because there are few smelt being seen in Delta surveys does not mean that the remnants of the populations are not at risk.

The working group is also concerned with what may soon occur once smelt do start spawning. As Longfin Smelt have begun spawning, I have summarized recent data to specifically look at that risk. Figure 1 shows the recent early February Smelt Larval Survey results along with annotations of net flows. Under 6000 cfs exports negative upstream net flows occurs throughout the central Delta (red arrows). The larval smelt in this area will transport to the south Delta over time. With spawning smelt in this area, their offspring will also likely move south to the pumping plants.

With most of the larval Longfin in Suisun Bay because of the earlier storm flows, the risk to the population is low. Yet, these are a state endangered species with these export operations causing a measurable take. With Delta Smelt yet to spawn, they are more likely to be found further upstream because of lower Delta inflows, thus putting their larvae at greater risk than Longfin, especially given ripe adults are present in the central Delta.

One final note, with these operations and declining Delta inflow, the low salinity zone where smelt larvae concentrate will be drawn ever eastward from eastern Suisun Bay into the central Delta. This pattern will increase the risks to smelt. The upstream edge of the low salinity zone is moving upstream in the lower San Joaquin channel with the higher exports as seen at Antioch (Figure 2) and False River (Figure 3).

February Longfin Smelt densities from Larval Smelt Survey

Figure 1. Early February Longfin Smelt densities from Larval Smelt Survey2 with added annotations of net flow in the Central Delta zone of influence (red circle) of the South Delta exports. Blue circle shows catch at Jersey Pt station (809). Red arrows depict net negative flows on the order of 400-5000 cfs3. (Note these early February Longfin larvae densities are by far the lowest observed in the eight years of surveys.)

Feb Salinity (EC) at Antioch

Figure 2. Salinity (EC) at Antioch in the San Joaquin channel of the west Delta during February 2016. (Source: CDEC)

Salinity (EC) in False River

Figure 3. Salinity (EC) in False River in the central Delta during February 2016. (Source: CDEC)

Sturgeon Science Symposium Puts Onus on Sport Fishing

Life History of Southern DPS Green Sturgeon

The Problem – Sturgeon are Declining

A day-long symposium on March 3, 2015, Sturgeon in the Sacramento–San Joaquin
Watershed: New Insights to Support Conservation and Management,1 put the onus on sport fishermen to save Central Valley sturgeon. Contributors suggested that to maintain a healthy population of white sturgeon, mortality of adult females has to be eliminated, sport fishing harvest of adults should be halted, and sport fishing should be confined to no more than catch-and-release, with no fishing during the spawning season.

The stated reason for such constraints is that there is a 15- to 20-year period until first spawning, and that thereafter sturgeon often spawn only once every five years. “[I]t is essential not to lose the enormous re-population potential of each spawning female.”

The contributors also noted that strong year classes of sturgeon only occur in wet years when young survival is high. The 2006 year class was the last year class to contribute strongly to the adult population. Essentially what they are saying is that survival of young is so poor and intermittent that recruitment into the adult population is too low to allow any sport fishing harvest.

Of note, there was no mention whether the number of adults spawners has been or is now a limiting factor in the number of recruits produced in the very wet years. Such a state would indeed be a great concern. If the number of eggs laid in very wet years with the present adult population was insufficient to saturate the existing spawning and rearing habitat with young, then the population would be on an accelerated path to extinction. However, if the number of eggs laid is sufficient to saturate the habitat and recruitment (survival of young) is only a function of habitat conditions, then the reason for poor recruitment is not over-fishing but poor or degraded habitat. The intermediate condition where both factors are important is possible if not likely. How the fishery should be managed would also be different in the three conditions.

Also important are any changes in the trajectory of the habitat conditions. If habitat is being gradually degraded by man’s direct effects or climate change, that too can drive the population downward by reducing the production capacity of habitat or increasing the natural mortality of sturgeon. Sport fishing harvest has to be sensitive to such changes, if only to being falsely blamed for any decline or accepting a need to change even to the point of mitigating for the other effects.

Approach to Recovery

Based on the symposium and its summary paper it appears that the onus has been put on sport fishing as the cause as well as the solution to declining sturgeon populations. There was little mention about the effect of habitat conditions (other than the historical imposition of dams). There was mention of stranding and rescue of sturgeon in the Valley bypasses. “An individual-based model indicated that in the absence of rescue, the current population of green sturgeon in the river would have declined by 33% over 50 years (Thomas et al. 2013).” This anecdote was offered more as evidence that harvest should be curtailed as opposed to being a major factor in the decline that should be fixed. The fact is that large numbers of adult sturgeon get “lost” or become stranded or die in the Yolo and Sutter bypasses and in the Colusa Basin Drain each year, especially in wet years when their eggs are most needed.

There was discussion of juvenile survival. “[L]ittle is known of the swimming capacities of larval sturgeons, though the risk of larval sturgeon entrainment is likely influenced by both the ontogeny of swimming capacity and the interactions of sturgeon with water diversions.
Green sturgeon were also much more likely to become impinged upon screens (than White Sturgeon). “Of the more than 3,300 water diversions located in the Sacramento–San Joaquin watershed, the majority (ca. 98%) are estimated to be unscreened. The number of green sturgeon entrained and killed by unscreened water diversions is unknown….. Therefore, efforts to increase the number of migrating green sturgeon that successfully reach estuarine and marine environments should focus on juvenile life history stages, and take into account the behavioral and physiological changes that accompany such a migration… Substantial recruitment depends on extremely high Delta outflows during winter and spring. The mechanisms underlying this relationship are the subject of on-going investigations, but are likely some combination of adult attraction to upstream spawning grounds, suitability of spawning substrate, and survival of age–0 fish during the migration downstream to the estuary. (Emphasis added)

Symposium Conclusions and Recommendation

There were three primary conclusions and associated recommendations from the symposium.

  1. Maintain a healthy population of white sturgeon by eliminating mortality of adult females. Sportfishing harvest of adults should be halted, or fishing at least confined to catch-and-release outside of the spawning season. Having survived the 15- to 20-year period until first spawning, and subsequently only spawning every 5 years, it is essential not to lose the enormous re-population potential of each spawning female. Loss of a single spawning female that will produce several hundred thousand eggs each time she spawns. Comment: There was no mention of reducing the stranding of sturgeon in the flood bypasses (Yolo and Sutter) despite stating the important contribution of 24 rescued in a limited effort in a 2010 overflow event. Hundreds, perhaps thousands, of adult sturgeon stray into the bypasses each year.2 Many are lost or unable to find suitable spawning habitat. That compares to the several hundred harvested each year by sport fishermen (see figure below) under strict harvest regulations, out of an adult population of 25,000-50,000.3

  2. Protect and restore critical key habitat in order to conserve and reestablish to conserve and reestablish sturgeon populations. Gravel beds are critical for successful spawning and egg survival. Deep holes are critical as energetic refuges for sturgeon holding in the river.Comment: No mention was made that many of these key spawning habitats are degraded in dry years by low flows and high water temperatures in the late spring spawning season. Demersal adhesive eggs and hatched young are subject to lethal water temperatures (>65oF) in dry years.4 Low flows also contribute to starvation, predation, and reduced downstream transport.
  3. Take a holistic approach to life history and habitat research and monitoring. This should include a robust program of conventional mark–recapture to determine population size, population year–class composition, and mortality rate—in addition to advanced telemetry and habitat mapping methods. This approach should also include continuous monitoring of dissolved oxygen, the most critical environmental factor for oxyphilic sturgeons: they are broadly tolerant of wide ranges in temperature, salinity, and flow that are all much less critical factors for their population success. Comment: Water temperature, flow, entrainment, and predation are the key factors of poor recruitment (survival) in non-wet years. These factors are far more important for sturgeon in the long run than the harvest of several hundred adult sturgeon each year from a population of 25-50 thousand adults.

Smelt Update – January 2016

The evidence is quite clear from all recent surveys that the Delta and Longfin Smelt populations have indeed crashed,1 and remnants remain vulnerable to Delta exports despite the wet winter to date. The latest survey is the January Kodiak Trawl survey that captured only 7 Delta Smelt (see Figure 1 below). Only 4 have been salvaged at south Delta pumps, compared to 56 last year in January.2 Adult Delta Smelt have been caught in Early Warning Surveys in the central Delta during the past month (Figure 2). The presence of Delta Smelt in south Delta salvage collections and in early warning surveys in the lower San Joaquin River channel in the central Delta indicate a high risk to the remaining population from Delta exports, according to the Smelt Working Group.3

Graph of January Survey Catch

Figure 1. Catch of Delta Smelt in January Kodiak Trawl Survey 2002-2016.4

Graph of Delta Catch

Figure 2. Catch of adult Delta Smelt in Early Warning Survey.5

Similarly, Longfin Smelt are at record low numbers (see latest post6), and larvae are now being collected in small numbers (again record low densities for January surveys) in Suisun Bay and the Delta (Figures 3 and 4). Their presence in the central Delta in the lower San Joaquin River channel indicates that a portion of the population spawned in the central Delta and remain vulnerable to South Delta Exports.

Map of Jan 2016 Catches

Figure 3. Catch density distribution of Longfin Smelt larvae in early January 2016 Smelt Larvae Survey. 7

Map of Jan 2016 Catches Longfin Smelt

Figure 4. Catch density distribution of Longfin Smelt larvae in mid-January 2016 Smelt Larvae Survey.8