Category Archives: Hatcheries

Hatchery Reform – Part 2

Posted on by

Previously… Part 1: Central Valley Salmon and Steelhead Hatchery Program Reform

Environmental Factors Affecting Smoltification and Early Marine Survival of Anadromous Salmonids. 1980. GARY A. WEDEMEYER, RICHARD L. SAUNDERS, and W. CRAIG CLARKE1.

“There is reason to suspect that in many cases apparently healthy hatchery fish, though large and silvery, are not actually functional smolts and their limited contribution to the fishery, even when stocked into the same rivers from which their parents were taken, results from their being unprepared to go to sea. This failure to produce good quality smolts probably arises from an incomplete understanding of exactly what constitutes a smolt, as well as from a lack of understanding of the environmental influences that affect the parr-smolt transformation and which may lead, as a long term consequence, to reduced ocean survival.”

This paper is over thirty years old (1980), yet it still rings true. It is most certainly a complicated subject that is an on-going concern in hatchery science and management. There remains room for improvement if funding is available for hatchery program upgrades.

“In the absence of complicating factors such as altered river and estuarine ecology, smolt releases should be timed to coincide as nearly as possible with the historical seaward migration of naturally produced fish in the recipient stream, if genetic strains are similar. At headwater production sites, much earlier release may be called for… The desired result is that hatchery reared smolts which are genetically similar to wild smolts enter the sea at or near the same time.”

It has been apparent for many decades that Central Valley Fall Run and Spring Run Chinook have a classic “ocean-type” life-history pattern, wherein young spawned in the fall head to the ocean early in their first year rather than as yearlings. Even within the ocean-type, Central Valley Fall Run have two types: one has fry rearing in the estuary (Bay-Delta) and the other in rivers. Of these two types, Valley hatcheries have chosen to manage for the latter. Hatcheries pump out smolts by the millions in April and May, on top of a smaller number of “wild” river-smolts. I believe the “river-smolt” type has been the minority contributor at least since all the dams were built. There simply is not enough river habitat, and what there is has been severely degraded by dams, water management, and physical habitat damage (e.g., levees and land use). The majority contributor is the Bay-Delta or “estuary-smolt” type. Fry that move to the estuary in December-January grow quickly and enter the ocean as smolts in March, a month or more before the river-type. This is a huge advantage for the estuary-type. The hatchery programs could focus more effort on this type by out-planting fry to the estuary or lower river floodplains immediately above the estuary (e.g., Yolo Bypass). Experimental out-planting of hatchery fry to rice fields in the Yolo Bypass has proven promising2. There are also many natural habitats in the lower river floodplains and Bay-Delta that could accommodate out-planting.

This post is part of a 4 part series on hatchery reform, check back into the California Fisheries Blog over the next week for Parts 3 and 4.

Central Valley Salmon and Steelhead Hatchery Program Reform

Posted on by

Dr. Peter Moyle of the University of California, Davis commented last year commented on California salmon and steelhead hatchery reform at the California Fish and Game Commission’s Workshop on Strategic Improvement in California’s Anadromous Hatcheries, held in Sacramento on February 4, 20141.

Dr. Moyle remarked that hatcheries fail to meet their primary dual purposes of sustaining commercial and sport fisheries and assisting in recovery of wild (naturally spawning) salmon and steelhead. Hatchery strategies have led to the complete dominance (90%) of hatchery salmon and steelhead in most rivers, which will ultimately lead to “periodic shut-downs of the fisheries and extinction of most runs, even those supported by hatcheries.” He concluded that a much more radical reshaping of hatchery policy is needed.

He recommends two types of hatcheries: conservation hatcheries that focus on recovery of wild populations, and production hatcheries that focus on sustaining commercial and sport fisheries. He suggests abandoning wild salmon and steelhead management in favor of production hatcheries for some runs (e.g., Fall Run Chinook salmon).

Only the federal Sacramento River hatcheries near Redding operate in the recommended manner. The federal Livingston Stone Hatchery is a model conservation hatchery for endangered Winter Run Chinook Salmon. The Coleman National Fish Hatchery on Battle Creek is a production hatchery for Fall Run, Late Fall Run, and Spring Run Chinook, as well as steelhead. Only wild Late Fall Run, Spring Run, and Winter Run Chinook and steelhead are allowed to pass Coleman’s diversion dam to spawn in upper Battle Creek. Upper Battle Creek thus serves as a wild fish conservation hatchery.

The state hatcheries on the Feather, American, Mokelumne, and Merced rivers operate as production hatcheries, mitigating for the blockage of these major Central Valley salmon tributaries by dams. These hatcheries focus on Fall Run Chinook and steelhead, although the Feather River Fish Hatchery also supports Spring Run Chinook.

Only undammed Sacramento Valley tributaries Deer, Mill, Big Chico, Antelope, and Butte creeks support reliable native runs of wild Spring Run Chinook. Native-wild Spring Run are sustainable in these streams because habitats are accessible at higher elevations where over-summering habitat with deep, cool-water holding pools exists.

One way to improve production of wild fish is to develop conservation hatcheries that combine trap-and-haul programs with over-summering habitats above the dams, as recommended in the Central Valley Salmon Recovery Plan2. This would require a capture-sorting effort, as is presently done at Coleman Hatchery on Battle Creek. Wild fish would be trucked above the dams. Juvenile fish produced above the dams would be trapped and trucked downstream for release below the dams. Conservation hatchery components could be established initially at the four state hatcheries to get the program started with appropriate “wild” genetic stocks.

Wild populations of Winter Run and Spring Run could be established above Shasta Reservoir on the Sacramento River. Spring Run could be established on some combination of the upper Feather, Yuba, American, Mokelumne, Tuolumne and Merced rivers. Wild steelhead could be established above the dams in any of these rivers.

Meanwhile, production hatcheries of salmon and steelhead could continue below the dams. Marking production fish would allow separation of wild and hatchery fish, as well as mark-selective fishery harvest to preserve wild fish until such time wild stocks are sustainable. Trucking/barging of production smolts to Bay would reduce predation and competition with wild fish while increasing populations of production fish for harvest.

Dr. Moyle also recommended establishing wild salmon sanctuaries, as is currently being established on upper Battle Creek. The areas above the dams are good candidates for such sanctuaries. Undammed Valley Spring Run rivers are also good candidates. Isolated tailwaters on the lower Yuba, Mokelumne, and San Joaquin rivers may also be candidates.

More on hatchery reform options can be found at: http://cahatcheryreview.com/summary-conclusions/.

Debate on Salmon Trucking Heating Up

Posted on by

A recent FISHBIO blog post1 reported on the CalNev American Fisheries Society annual meeting, where AFS members considered the subject of “off-site” release of hatchery salmon smolts. The general perception is that releases away from hatcheries and the natal river leads to high stray rates, with some estimates of stray rates as high as 90%. The blog post discusses the problems caused by straying to non-natal rivers. The blog post states a concern that the practice of off-site releases will lead to reduced population fitness and genetic diversity, and that reproductive success will be half of wild-origin fish:

“Such losses in biocomplexity are dangerous because of the many threats salmon face in the highly altered Central Valley, and the potential inability of this species to persist if faced with a major environmental disaster, which the current drought in California may foreshadow. Yet despite recommendations from the California Hatchery Scientific Review Group, who warned about increases in straying rates due to off-site releases as early as 2010, managers from across the state have responded to drought conditions by trucking salmon from hatcheries to release sites in the Delta and Bay.”

While FISHBIO’s concerns about straying and genetics are well-founded, it is a little late for the Central Valley Fall Run Chinook. Studies have shown that populations across the Valley are homogeneous, with little or no genetic diversity, and consist mainly of hatchery fish and some natural offspring of hatchery fish. There really are no viable “wild” Fall Run Chinook populations left in the Central Valley. Even runs on rivers with no hatcheries (e.g. Yuba and Cosumnes rivers) are made up almost entirely of hatchery strays.

In making the decision to truck hatchery smolts to the Bay-Delta, Federal and State fisheries managers have recognized the harsh reality that having some salmon is better than having none. No one wants to go back to the bleak escapement years of 2007 to 2009, when less than 100,000 adult salmon per year returned to the Central Valley (compare with 870,000 in 2000 and 200,000-400,000 fish per year since 2009). Recent improvements were in large part due to the smolt trucking program in which 50-80% of Central Valley hatchery smolts were trucked to the Delta or Bay.

Can we have our cake and eat it too? Are there measures we can undertake to improve diversity and reduce straying? Yes, there are many, but they come with costs and with no guarantees.

The hatcheries can be more selective in the genetic material (parents) they use in producing smolts. Hatchery managers can barge smolts to the Bay to reduce straying (during barging, the smolts are suspended from barges in net pens, and thus imprinted on their natal waters during their trip downstream). Hatcheries can mark all hatchery fish to clearly differentiate between wild fish and hatchery fish (generally, hatcheries currently mark only 25% of hatchery juveniles). The Fish and Game Commission could establish mark-selective sport fisheries that allow sport harvest only of hatchery fish. The fisheries agencies could develop Wild Fall Run sanctuaries on some tributaries.

Ultimately, long-standing aspects of Delta operations must change to allow more juvenile salmon to get out of the system and more adult salmon to find their way back to natal streams. Delta exports during the spring are particularly devastating to juvenile outmigrants from the San Joaquin tributaries, including the Mokelumne, because these juveniles are drawn to the south Delta pumps. Low Delta outflow, particularly during spring, magnifies the effects of exports. Opening the Delta Cross Channel during spring may actually improve survival of San Joaquin and Mokelumne juveniles, but only when combined with high Delta outflow. Closure of the Delta Cross Channel gates during the fall, either by design or through fortuitous operational decisions, has reduced straying of Mokelumne River salmon adults to the American River, allowing multiple small pulse flows from the Mokelumne in the fall to help improve adult returns.

Central Valley Hatchery Steelhead Program Misdirected

Posted on by

Approximately 1.3 million yearling Steelhead smolts are released each year in rivers below our three state and one federal Central Valley Steelhead hatcheries. The hatcheries include Coleman Hatchery (federal) on Battle Creek near Redding, Feather River Hatchery (state) near Oroville, Nimbus Hatchery (state) on American River near Folsom, and Mokelumne River Hatchery (state) near Lodi. The smolts are generally released as yearlings in February at about 4 to-the-pound and 6-10 inches in length. In some drought years (e.g., 2014), Nimbus Steelhead are also released to the American River as several-month-old fingerlings in June because hatchery source water from Lake Natoma is too warm to carry the fish through summer until the normal February release date.

The problem with releasing over a million hatchery Steelhead smolts into the rivers in the spring is that wild Spring-Run and Fall-Run Chinook salmon fry emerge or have recently-emerged from redds at this time. The one-inch salmon fry are ready-made prey for the hatchery Steelhead smolts. Figure 1 shows the partial stomach contents (six salmon fry) of a hatchery Steelhead smolt caught in early March in the lower American River.

Figure 1.

Figure 1. Partial stomach contents of an American River hatchery steelhead smolt (head at right) captured in early March 2015 near Sunrise Bridge. There were partial remains of twenty salmon fry in various stages of digestion in the stomach.

While many hatchery Steelhead likely migrate from the rivers towards the Bay-Delta soon after release, many also stay in the rivers. This is especially true in the American River, where they may be released early as fingerlings prior to summer and are thus likely to take up residence in the river. Many Feather hatchery smolts take up residence in the lower Yuba River. Smolts released in rivers also are more prone to becoming permanent river residents in drought years when there are fewer pulses of flow to stimulate emigration to the sea, especially in the Feather, American, and Mokelumne Rivers. Salmon fry may become prey of the hatchery Steelhead smolts for a few days to a month or more.

Releasing hatchery Steelhead into the lower rivers in such large numbers also impacts wild Steelhead that are present in much smaller numbers. The hatchery smolts compete with the wild smolts. Hatchery smolts attract large numbers of predatory birds and fish (e.g., Striped Bass). Hatchery smolts also feed on wild Steelhead fry that emerge from redds from April to June.

What can be done to help solve the problem?

  1. Hatchery Steelhead smolts should be trucked to the lower Sacramento River rather than being released in their natal rivers.
  2. The trucked hatchery smolts should be placed in barges, then barged from the Sacramento River to low salinity waters of the Bay to reduce the probability of their immediately returning to their natal rivers (and to maximize their survival to the ocean). Barging is necessary to minimize subsequent adult straying to non-natal rivers, a problem if smolts are trucked all the way to the Bay.
  3. Fingerlings should also not be released into natal rivers below the hatcheries. They too should be trucked then barged to the upper Bay.
  4. Pre-smolts could be released in early winter to natural floodplain habitats or even to specially designed flooded rice fields to grow to smolt size.

These actions, if taken, will both reduce predation on wild salmon and Steelhead fry and markedly increase survival of hatchery Steelhead to the Ocean and subsequent escapement of adult Steelhead to the rivers. Record low numbers of Steelhead returned to Central Valley rivers in winter 2015. More on this subject will come in later posts.

For more details on the Steelhead hatchery programs see the following website: http://cahatcheryreview.com/summary-conclusions/

Mark-Selective Chinook Fishery in Puget Sound

Posted on by

Puget Sound is a large inland marine water body in Washington State that supports runs of five Pacific salmon, steelhead, and multiple marine fish species. Chinook salmon are a very popular recreational and (in the past) commercial species in Puget Sound. To support the naturally spawning Chinook salmon runs, numerous hatcheries were built in throughout the Pacific coast area.

As a result of the Endangered Species Act, the Chinook salmon fisheries were very restricted or completely closed to protect wild (“naturally spawning”) fish. This included closure for all (both hatchery and wild) Chinook salmon.

Through various planning efforts by sports fishermen, Native American tribes, Washington Department of Fisheries and Wildlife (WDFW) and others, a mark-selective approach for providing some fishing opportunities for Chinook salmon was developed. The approach involved marking of hatchery fish by removal of the adipose fin (a small fin near the tail) to identify hatchery fish from wild ones. Once removed, the fin does not normally regrow, and therefore, if caught by a fisherman, the fish can be identified as a hatchery fish and retained (if it meets other restrictions such as size limit, season, etc.). Wild fish (with the adipose fin) can then be readily identified and released. In addition, a certain percentage of hatchery fish may have a small “coded-wire tag” inserted into their heads. This provides additional information about the fish such as which hatchery it was reared in. WDFW has also added rules that wild salmon cannot be brought aboard a vessel (i.e., inside the gunwale) to assist in releasing the wild fish unharmed.

Each year, the WDFW and Native American tribes (co-managers of the fisheries in Washington State) set quotas on the number of marked Chinook salmon that may be taken in Puget Sound (which is divided into several subareas to assist in management for various runs of Chinook salmon. For example, one subarea may be dominated by a run to a specific hatchery. Depending on the projections for adult returns to that hatchery, a quota for take is established and considered in the overall quota for that subarea).

The quotas for each subarea are monitored through dockside sampling. They are also supported by WDFW staff that fish for Chinook salmon with methods similar to those used by private and charter sport fishing groups. This “on the water” sampling provides key information about take, wild/hatchery fish ratios, and fishing effort. The information is used to support the overall development of quotas.

Seasons and quotas are set early in the year so that some planning by fishermen (e.g., vacations, days off, etc.) can be made. However, if the quota is reached early, the season may be closed early.

Overall, the mark-selective approach has re-opened fishing opportunities. These have been very popular with fishermen, as noted by the large groups that are currently observed on the water. This has also helped support economically important aspects such as charter fishing, tackle shops, boat sales, etc.

The WDFW has provided very detailed information about the mark-selective Chinook salmon fishery in Puget Sound (and elsewhere in Washington State) in multiple publications and press releases (see wdfw.wa.gov/publications). These publications provide information on the overall program, sampling techniques, quota development, and other pertinent aspects of the mark-selective approach.

Several issues have arisen about the approach, which are of interest. These include costs associated with marking millions of hatchery fish and monitoring programs, incomplete or non-marking of hatchery fish, mortality associated with capture and release of wild fish, and other aspects of the program. However, overall, this approach has helped to provide fishing opportunities that would not be possible under the no-take restrictions that were originally imposed by the Endangered Species Act.

Hatchery Chinook salmon

Hatchery Chinook salmon taken in a Puget Sound mark-selective fishery. Photo by the author.