Author Archives: Tom Cannon

Fishbio confuses yet again – this time it’s California Salmon Hatchery Programs

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The new internet “journalism” and “science” forums bring out fisheries issues for debate in an open forum in a timely manner. No longer do we have to wait for the peer-reviewed reports and papers to come out two or more years after the fact. I subscribe to all that I can find – blogs, newsletters, and websites. Two of my favorite blogs on California Central Valley issues are Fishbio’s Fish Report1 and UC Davis’s California Water Blog.2 For news and information nothing beats Mavens Notebook.3

A recent Fishbio post focuses on the problems with hatcheries.4 As in most posts (even mine), there is room for debate.

Their post begins with a discussion of the increasing reliance on hatcheries after 150 years of development in California. It fast-forwards to the present dependence on hatcheries for sport and commercial fisheries. It relates the recent recommendations of the California Hatchery Scientific Review Group:

  1. Define hatchery production goals in terms of the number of salmon that survive to age 3 in the ocean just prior to harvest, instead of setting goals based on the number of juvenile salmon released;
  2. Cease transporting and releasing juvenile salmon outside their river basin of origin;
  3. Improve monitoring and evaluation of hatchery operations; and
  4. Improve coordination of operations among hatcheries (CAHSRG 2012).

The Fishbio post then takes us subtly off-course with: “As a result of technological improvements and, possibly, human preferences to spawn the largest and fastest growing fish, salmon are growing to larger sizes faster in the hatchery environment, which has resulted in a new life-history type (springtime releases of “advanced smolts”). These large, young fish did not exist earlier in the time series, but they now dominate the type of fish released from state-operated hatcheries.”

While the state hatcheries do raise some “advanced” smolts for release into the Bay in late spring for the commercial fishermen, these fish are “advanced” only in the sense they are reared longer in the hatchery to a larger smolt size with greater chance of contributing to the commercial fishery along the coast after release in the Bay. The vast majority of the 30 million smolts raised in Central Valley hatcheries are “normal-sized” 3-inch April-May smolts, which in many cases are actually smaller and later ocean-entry than the wild salmon that enter the estuary as December-February fry-fingerlings and enter the ocean as smolts in March-April a month before their hatchery counterparts.

The post ends with a critique of hatchery practices: “Another marked change in hatchery practices occurred around year 2000, when fish began to be stocked at similar sizes in similar locations at similar times of year…. With long overdue, detailed hatchery information now freely available, more informed stewardship of California’s iconic salmon population is now possible.”

The fact is that stocking has become more diversified than ever. Millions are released at the hatcheries and in the mainstem rivers below hatcheries, often coincident with storm flows and good Delta conditions. Millions are released over the spring months directly into the Bay. The “advanced” smolts are usually released in June. In wet years, more are released in rivers, and in drought years, more are released in the Bay. Winter, Spring, Fall, and Late-Fall Run smolts are released at different times and places. Each hatchery has its own schedule to maximize use of the common resources (e.g., personnel, trucks, pens, ramps, etc.). Hatchery programs are now more “informed” and better managed and coordinated than ever before, and making concerted efforts to continue to improve.

Without the hatchery efforts in the past decade of drought, there would be few salmon left for sport and commercial fisheries. One of the greatest challenges for California fisheries management in the next decade is to continue to improve hatchery practices while also restoring wild salmon runs, so that the wild fish are not only kept from extinction but also contribute substantially to sport and commercial fisheries.

Sturgeon Science Symposium Puts Onus on Sport Fishing

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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

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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

Why Smelt Spawn in the Yolo Bypass

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In most years a concentration of spawning and rearing Delta Smelt is found in the Cache Slough Complex of the north Delta. The Cache Slough Complex consists of Cache Slough, Liberty Island and adjacent sloughs, and the Sacramento Deepwater Ship Channel. Upstream-migrating adult smelt ride the flood tide in winter seeking freshwater spawning habitat with warmer, more productive, stable conditions to spawn and rear their young. The Cache Slough Complex is such a place. Recent flood tide conditions at the junction of the Cache Slough help show how the smelt migration is accomplished (Figures 1 and 2). Flood tides carry the smelt upstream in the main Sacramento channel past Rio Vista to the mouth of Cache Slough, where the tide and fish turn left up the slough on toward the lower Yolo Bypass. The Bypass is a large area with a large tidal exchange and minimal freshwater inflow and outflow most years. In contrast, Steamboat and Miners sloughs and the lower Sacramento River channel above Cache Slough have strong freshwater flows and limited areas of tidal exchange, resulting in no upstream-directed flood tide flow. Their downstream-directed flood tide flows enter the Cache Slough flood tide, turning right and going upstream. These circumstances likely enhance smelt migration toward the Cache Complex and hinder migration up the Sacramento and its two branches that carry the main river inflow to the Delta.

Map of Floodtide flows in Jan 2016

Figure 1. Floodtide flows (cfs) on 1/24/16 in the lower Sacramento River near Rio Vista upstream to Cache Slough Complex. Red arrows are upstream flow rates. Blue arrows are downstream flows during the flood tide in Miner (top) and Steamboat (middle) sloughs, and Sacramento River (bottom). Light blue dots are CDEC gaging stations.

Graph of Tidal flows and stages Cache Slough and Sacramento Jan 2016

Figure 2. upstream of Cache Slough 1/24-1/26 2016. Blue denotes net positive downstream flows in Sacramento River continue on flood tides. Red denotes upstream directed currents in Cache Slough during flood tides. Gage locations for SOI and RYI are in Figure 1.

The Cache Slough Complex including the lower Yolo Bypass and Deep Water Ship Channel is a great place for smelt, salmon, and other native fishes in winter and spring especially in wet years like this. With freshwater inputs modest from Putah Creek, Cache Creek, and the Colusa Basin Drain, and a vast acreage of marshes, sloughs, and shallow bays with long water residence times and tidal sloshing, the whole place becomes “green soup” perfect for growing young smelt. With lots of municipal, urban, and ag runoff and drains, the area is nutrient rich, warmer, and more productive, growing plentiful plankton for smelt food, unlike the river and Delta in winter-spring.

In very wet years, all of that wonderful green soup is blown into the Delta and eastern Bay by floods pouring through the Bypass and out the mouth of Cache Slough. In wet and normal years much of the productivity and smelt reaches or extends into the Delta (e.g., 2011, the last good year for smelt). The Delta and Bay significantly benefit from these inputs.

But in the dry and critical years, especially multiyear droughts, things are not so good for the Cache Slough Complex. In winter, the tides still carry the adult smelt and juvenile salmon up into the Yolo Bypass, but with virtually no freshwater inflows. However, with continuing ag and municipal (e.g., North Bay Aqueduct) demands and most of the discharges, the place becomes a hot stew by late spring. Negative daily average net flows from all the local demands on water virtually trap young smelt in the Complex, as they are unable to ride natural net downstream flows to their spring-summer nursery in the west Delta and eastern Suisun Bay. With summer water temperature approaching 75-80°F, most of the smelt die from the heat or predation by abundant warm-water predatory fish.

The large acreages of planned habitat restoration in the Complex will increase its tidal influx, but do little about these dry year problems (or make them worse). The solutions have been known for a long time:

  1. Get the North Bay Aqueduct intake out of the Complex with a pipe to the Sacramento River.
  2. Divert more Sacramento River water into the upper Yolo Bypass at the Fremont Weir to add to minimum flows in the 40 miles of the Bypass.
  3. Fix the stuck-closed gate at the head of the Deepwater Ship Channel on the Sacramento River to allow more freshwater inflow into the Complex.
  4. Stop the use of tide gates for irrigating lands within and adjacent to the Complex.
  5. Improve the water quality of all discharges into the Bypass.

The key to fixing all the Bay-Delta ecosystem’s problems including saving salmon and smelt from extinction lies in managing hydrology and water use in dry years and multiyear droughts. The solutions, especially the five mentioned above, are really not that hard to implement.

Longfin Smelt Population Status Update – Disaggregating Forces helps determine Reasons for the Decline of Longfin Smelt

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Last summer I opined on the loss of the Longfin Smelt from the Bay-Delta estuary1. A recent paper in the Transactions of the American Fishery Society looks to “disaggregating forces”… “By disaggregating the life-stage-specific constraints on population dynamics, our results can help to inform a future ESA listing decision for Longfin Smelt and can assist in development of the accompanying recovery plan if the population is listed”.2

What the authors of the study did was to separate the population into life stages or age groups to view the population dynamics to determine at which stage or age the apparent cause of the decline may be occurring. With a two-year life cycle, there are basically two life stages. Young Longfin are produced and rear in their first year in the upper estuary (Delta and eastern Bay). The second year they continue rearing in the Bay and nearby ocean until reaching maturity and returning to the upper estuary to spawn. The review came to the following conclusions:

  1. It corroborated past studies in finding that production of young is related to freshwater inflow to the estuary.
  2. The production of young determines the subsequent abundance of age two adults.
  3. The production of young is also related to the previous number of adult age-2 spawners.
  4. The survival from age 1 to age 2 (young recruits to adult spawners) is related to Bay and Ocean conditions, and may be declining in recent decades.

While the first three “forces” were anticipated, the fourth indicates a decline in the production capacity of the lower estuary and ocean. The ocean has been a factor in recent decades decline and improvements in salmon, so why not Longfin? Seems logical. A decline in Bay productivity for whatever reason is more ominous. Could this be related to effects on the Bay from higher Delta exports over the last several decades, recent multiyear droughts, or the combination of both? Has the productivity of the Bay been compromised? “[T]he mechanisms affecting juvenile survival are more likely to operate in mesohaline or marine environments than in freshwater or low-salinity-zone waters.”

The facts remain that the population of Longfin Smelt in the San Francisco Bay-Delta estuary has crashed. The numbers recorded in recent index years is especially low (see footnote #1).

Bay-Delta trawl survey results for this recent December just published compared to past survey years (Figures 1 and 2) support my earlier conclusion – “they are gone”. The slow population death spiral from low young production, to poor spawner production, to poor young production, has reached its course, as also suggested by Hobbs and Moyle3.

Maps displaying trawl results

Figure 1. December catch of Longfin Smelt in Bay Otter Trawl Survey, 2011-20154.

Map of Trawl Results

Figure 2. December catch of Longfin Smelt in Bay Midwater Trawl Survey, 2011-2015.