Note: I found this especially interesting! Ronnie

It is thought that fish may miss critical migration cues in the barges that they would otherwise pick up during in-river migrations.

By Allison Lebeda, Joe DuPont, Lance Hebdon, and Jonathan Ebel. Idaho Fish & Game from The Fishing Wire Barging Juvenile Salmon and Steelhead through the Columbia and Snake Rivers does not work as well as natural migration. Juvenile salmon and steelhead born in Idaho waters must swim hundreds of miles and navigate a network of eight dams before they can reach the Pacific Ocean. Migrating through the mainstem hydrosystem can be one of the more daunting obstacles these young fish must face. These fish, which we commonly refer to as “smolts” can pass through a dam in one of three ways. First, they can be swept through the turbines, where the water forces large blades to rotate at high speeds. Second, a series of screens can guide smolts away from the turbines where they will be routed through channels and pipes around the dam. We call this the juvenile bypass system. Third, they can be carried over one of the dam’s spillways where they will plunge over a hundred feet into turbulent waters below. Thanks to recent changes in the operations of the dams, most smolts pass over the spillway. The diagram above depicts the three passage routes that smolts can use to pass dams on the Columbia and Snake rivers. NOAA Fisheries In the late 1970s, poor adult returns of salmon and steelhead prompted the U.S. Army Corps of Engineers (from hereafter referred to as “the Corps”) to develop a fourth method of passing large numbers of juvenile fish past the Snake and Columbia River dams: barging. Initially, two barges were available to transport juvenile fish, but gradually more barges were added, and by 1981, the barging program had the ability to barge large numbers of fish on a daily basis. Today, between 15 and 22 million smolts are collected from the juvenile bypass systems at Lower Granite, Little Goose, and Lower Monumental dams and placed in one of eight available barges. Barging typically occurs from late April through July, and transports smolts through the hydropower system until they are eventually released below Bonneville Dam. Collection and transportation, known as the Juvenile Transport Program, is a considerable collaborative effort by the Corps with private, federal, and state agencies. Each barging trip lasts two days and covers nearly 300 river miles, but is ultimately faster than the migration for fish that must pass through the dams on their own power.   At first glance, barging juvenile salmon and steelhead through the hydropower system seems the obvious solution to increase adult returns. Immediate survival of barged juveniles is nearly 98% compared to the 40-60% survival rate often experienced by smolts that must make the full journey past the dams in-river. Barging was the dominant method of passing smolts through the hydrosystem from 1981 through 2006 when 60-100% of smolts passing the dams were put on barges. However, with increased spill over the dams, the addition of surface spillway weirs, and upgrades to existing juvenile bypass systems, the relative benefits of barging have declined in recent years. The proportion of smolts put on barges now ranges from 10-50% of the run as a result of increased spill over the dams and the consequent decrease in fish entering the juvenile bypass systems. Despite high survival of barged smolts to the release site downstream of Bonneville Dam, transported fish often return at lower rates as adults than fish that migrated down the Snake and Columbia rivers on their own. One explanation for this is multiple species of smolts are often confined in crowded conditions when being barged, which can increase stress and allow diseases to spread more easily between fish. Additionally, returning adults that were barged as smolts tend to migrate upstream slower, fall back over the dams more often, and stray more than fish that were not barged. It is thought that fish may miss critical migration cues in the barges that they would otherwise pick up during in-river migrations. Ongoing research using smolts tagged upstream of the hydrosystem and tagged at Lower Granite Dam has helped modify the barging program to improve survival of barged fish. Of fish that enter a juvenile bypass system, those that are subsequently transported tend to return as adults at higher rates than fish that are bypassed and returned to the river. This is important because millions of smolts migrate past these dams this way each year. But, it is not as simple as one may think. The relative benefits barging provides to smolts varies by the timing of their migration, what species they are, their size, and whether they are a hatchery or wild fish.  For example, endangered Snake River Sockeye Salmon do not benefit from barging in most situations. This may be because they are smaller, can be easily descaled through abrasion, and prefer uncrowded open-water habitats found in lakes. Meanwhile, steelhead benefit from barging in many situations potentially because they are larger, more resilient, and prefer faster flowing habitats not found in reservoirs. Both these species migrate at the same time and are transported together. Unfortunately, there is no current way to separate the two species after they have entered the juvenile bypass systems and transport-destined raceways. For smolts migrating later in the season, those that are barged tend to do better than those that aren’t. This is likely because later in the year, migration conditions tend to worsen for smolts as flows decrease and water clarity and temperature increase. These conditions increase their stress levels and increase predation on them. When you consider all these things, it certainly adds complexity on evaluating whether a smolt should be barged or not. For now, managers have taken a spread-the-risk approach using barging in concert with improving in-river migration conditions.  In summary, although barging can increase the number of smolts that reach the ocean, transported fish often return at lower rates as adults than fish that migrate in-river.  Under certain conditions, barging juvenile salmon and steelhead can lead to higher survival and higher return rates as adults. Migration timing, fish size, river conditions, and fish species are just some of the variables that play a role in whether barging can be beneficial or not. Researchers with the multitude of cooperating agencies continue to learn from and modify the Juvenile Transport Program to best increase adult returns. Barging juveniles through the complex network of dams is not the sole solution to salmon and steelhead restoration, but it is one of multiple tools managers have that can aid in increasing juvenile survival and adult returns in some situations.

Colorado’s Whirling Disease Resistant Rainbows

From The Fishing Wire Some good news for a change to end this week . . . . By Joe Lewandowski After more than 20 years of study, frustration, experimentation and dogged persistence by CPW’s aquatic researchers, the tide has turned in the fight against Whirling-disease.Biologists boat electrofishing on the Gunnison River. Photo by © Bill Vogrin/CPW. Whirling Disease first impacted Colorado’s rainbow trout in the mid-1990s and eliminated many wild populations of this popular sport fish. The aquatic tragedy sparked a decades-long effort by Colorado Parks and Wildlife research scientists to find a remedy and re-establish populations. About Whirling Disease Myxobolus cerebralis, a metazoan parasite, can cause a serious affliction in some species of trout and salmon known as whirling disease. The water-borne parasite may not directly kill trout, but severely infected young trout often develop debilitating deformities of the skull and spinal column or display the erratic tail-chasing behavior from which the disease gets its name. To learn more, please visit the CPW website. Since 2003, the researchers have been crossing a strain of rainbow trout resistant to the disease with other strains of rainbows in the hope of developing a trout that would fend off whirling disease. Now, after more than 20 years of study, frustration, experimentation and dogged persistence by CPW’s aquatic researchers, the tide has turned in the fight against the dreaded disease. Whirling-disease resistant rainbows are now thriving in the wild and the agency is collecting their spawn, enabling hatcheries to propagate millions of fish that will be distributed to rivers and streams throughout the state. I CPW is stocking fish resistant to the disease throughout the state. Photo by © Joe Lewandowski/CPW. “Thanks to advance genetic testing, we know these fish are maintaining their resistance to whirling disease,” said George Schisler, CPW’s aquatic research chief. “Now they are surviving, reproducing and contributing to future generations of Gunnison River rainbows. ”This long success story started on an August day in 1994 when former CPW researcher Barry Nehring, while walking the riverbank in the Gunnison Gorge, noticed small fish swimming helplessly in circles. He knew immediately that the fish were infected with a microscopic spore that damages the cartilage of young fish and prevents them from swimming and developing normally. Whirling disease had arrived in the wild. George Schisler with Hofers trout.The disease was accidentally introduced to Colorado in the late 1980s when infected fish were imported to state and private hatcheries. After those fish were stocked in 40 locations, the spore spread and within a decade infected many rivers throughout the state. The disease kills young fish, so eventually, natural reproduction by wild rainbows ended across much of Colorado. In search of a remedy, CPW scientists and biologists from wildlife agencies throughout the West started researching the disease in the late 1990s. At a national conference in Denver in 2002, a researcher from Europe who studied whirling disease gave a presentation about a strain of disease-resistant rainbow trout he’d found at a hatchery in Germany. Schisler, working with the University of California-Davis, imported eggs and then tested the hatched fingerlings, known as Hofers – named after the German hatchery. He found they were 100 times more resistant to the disease than the various CPW rainbow strains. He also learned that because these fish had been raised in a hatchery for decades, they showed no inkling of the flight response needed to elude predators in the wild. So researchers started crossing them with wild strains, such as the Harrison Lake and Colorado River rainbow to produce fish that exhibit wild behavior and maintain resistance to whirling disease. Those fish were stocked in rivers around the state and some natural reproduction started. Biologists working in the East Portal Section of the Gunnison River gorge began documenting wild reproduction of rainbow trout in that location in the mid-2000s. These fish demonstrated strong resistance to whirling disease, but also had instincts to survive in the wild. Through advanced genetic analysis, Schisler and his research partner, Eric Fetherman, determined that a DNA marker unique to the stocked Hofer-crosses appeared to have been incorporated into this population, resulting in observed resistance to the disease. The researchers and agency aquatic biologists determined that developing a brood stock using the Gunnison River trout would be the best way to repopulate Colorado’s rivers with wild rainbows. Since 2014, more than 500,000 eggs have been collected from these fish to stock into whirling disease positive rivers and to create hatchery brood stocks.The trout now has its own moniker: The Gunnison River Rainbow. Photo by © Joe Lewandowski/CPW.CPW’s Glenwood Springs hatchery is propogating both the pure Gunnison River Rainbows and crosses of those fish and other strains of whirling disease-resistant rainbows.  This summer more than 1.3 million of fingerling disease-resistant rainbows will be stocked in rivers and streams throughout the state. The ultimate goal of the stocking effort is to restore natural reproduction in the wild, eliminating the need to stock rainbows in the future.However, re-establishing the rainbows continues to be a long-term project. After rainbows vanished, brown trout took over Colorado’s big rivers. They prey on the small rainbows that are stocked or hatch and compete for food and habitat with adult rainbows. Biologists say it will take many years for rainbows to become firmly established. Research scientists don’t declare victory easily, but Fetherman noted that the research project in the East Portal is officially closed. Populations across the state will continue to be monitored because the tiny worms that produce the spores causing whirling disease will likely always exist in Colorado’s rivers.“I feel like we’ve done some good work and these fish are ready to be stocked statewide,” Fetherman said. For more information on CPW’s aquatic programs, please visit the Colorado Parks and Wildlife website.Written by Joe Lewandowski. Lewandowski is a public information officer for the Colorado Parks and Wildlife southwest region.

Stocking Young Atlantic Salmon Downstream Means Higher Survival Success
From NOAA Fisheries
from The Fishing Wire

When it comes to recovering endangered Atlantic salmon, it makes a difference where smolt stocking takes place along a river. A new model can help by evaluating estimated survival of smolts released at different stocking locations.

Stocking Green Lake National Fish Hatchery smolts in Maine’s Narraguagus River. Photo: NOAA Fisheries

Young Atlantic salmon smolt released at lower-river stocking sites on the Penobscot River are more likely to survive and enter the ocean than those released higher in the river system. They encounter fewer barriers such as man-made dams during their migration to the estuary, and their migration path is shorter. NOAA Fisheries scientists built a model that can help select release locations to improve survival of stocked smolt as they head for the ocean.

The 2018 Northeast Fisheries Science Center study, published in the Canadian Journal of Fisheries and Aquatic Sciences, highlights the continuing challenge to conserve this endangered species.

“This model is an important tool to support decision-making for the recovery of wild, self-sustaining Atlantic salmon populations,” said Justin Stevens, a fishery biologist at the Center’s Maine Field Station in Orono and lead author of the study. “Hatchery smolt stocking is a common strategy used in the program, and now we have a way to effectively evaluate its success.”

Using Historic Salmon Survival Rates to Improve Prospects for the Future

The researchers built a model to simulate historic survival of migrating Atlantic salmon smolt at different locations along the Penobscot River from 1970 through 2012, using existing studies of smolt survival. The model assessed the relative survival risks posed by three factors: dams, discharge into the river, and the length of the migration route.

By far, the number of dams encountered during downstream migration had the biggest effect on survival. The more dams the smolts encountered, the lower the survival rate.

A number of dams have been removed from the Penobscot River in the past few years. However, more than 100 man-made dams remain. Most are relative small and used for water storage or are remnants from 19th century industrial activities.

This study focused on 18 dams commissioned to generate hydroelectric power during the study period, for which hatchery records were also available. These dams are situated along primary salmon migration paths in the five sub-basins of the river.

Model Results Can Guide Management Decisions

“The information learned from this study can be used by state and federal managers to better inform future stocking practices and to work with the hydroelectric industry to minimize the impact of dams,” said Stevens.

This study provides a quantitative way to evaluate the effect of dams on smolt survival during downstream migration in the largest U.S. Atlantic salmon river.

The model calculates marine survival, from post-smolt to adult salmon. It accounts for losses during both freshwater and estuarine migration, and is an important new tool for making decisions about habitat improvement, fishery management, and Atlantic salmon recovery activities.

A Bit More About Endangered Atlantic Salmon

Atlantic salmon smolt migrate from freshwater river habitat downstream to the ocean. Many do not survive the journey past multiple dams or their time at sea.

If they do survive, as adults they need to migrate from their time in the ocean back to the river. Adults then swim upstream past dams to spawn and complete their life cycle. Making multiple trips during their lifetime further reduces the likelihood of repeat spawners, and that negatively affects population growth.

Historically, Atlantic salmon in the United States ranged from the Housatonic River of Long Island Sound to the Aroostook River in eastern Maine. There were an estimated 500,000 adult fish in precolonial days.

Today, U.S. Atlantic salmon are limited to eastern Maine and the population numbers fewer than 2,000 adult fish. The Penobscot River supports the largest population, aided by a hatchery-smolt stocking program that produces about 75 percent of the annual adult returns.

This year has been designated as International Year of the Salmon. It is the kickoff for an international effort though 2022 to bring countries together to share knowledge, raise public awareness, and take action to conserve and recover both Pacific and Atlantic salmon.

The Mind-Boggling Journeys of One Atlantic Salmon
By John Holyoke
from The Fishing Wire

“Charlie” the Atlantic salmon (right) swims among other salmon in a pool of the Sandy River in western Maine. Charlie is a repeat spawner, and was captured twice at Waterville’s Lockwood Dam, exactly two years apart. Photo Casey Clarke/Maine Department of Marine Resources

Your morning commute to work might be hectic and harrowing, but before you start feeling sorry for yourself consider the journeys that Charlie — the name given to a soon-to-be-famous Atlantic salmon — has taken over the past few years.

Charlie recently was captured in a fish lift at the Lockwood Dam on the Kennebec River in Waterville. That on its own is not a surprise. The fact the adult salmon was actually what’s called a “repeat spawner” and had been captured at the same facility exactly two years (and thousands of miles) earlier was grounds for celebration.

“This is the only repeat spawner we have ever had [in the 13 years since the Lockwood facility has been operational],” said Paul Christman, a marine scientist for the Maine Department of Marine Resources.

Christman said that over the course of a year, all of Maine’s salmon rivers might see one repeat returnee, most of those counted on the state’s busiest salmon river, the Penobscot. This year, more than 1,000 salmon have returned to the Penobscot. Just 56 have been counted at Lockwood. Making Charlie particularly intriguing is the fact he’s either a naturally reared fish from eggs planted by fisheries personnel or a wild-spawned fish.

And the journeys that Charlie has made are mind-boggling, Christman said.

According to the U.S. Fish and Wildlife Service, young Atlantic salmon can travel more than 6,000 miles during their migration to and from the North Atlantic, where they will spend between one and three years before returning to their native rivers. That means Charlie might have 12,000 miles on his fins by now. He has surely earned a break, which he is currently taking.

Charlie was first caught on June 18, 2017, and had a radio tag and a “PIT” tag attached to him. The PIT tag allows scientists to identify him by a unique 16-digit number. The radio tag allowed them to track him until he regurgitated it at some point after he began his return to the Atlantic two years ago.

The crew’s radio tracked him to a pair of comfortable pools in the river where he spent the summer.

Then, after making his way back downriver (and over four hydroelectric dams), he headed back to sea where he flourished for two more years before swimming back to Lockwood Dam on the Kennebec.

An obliging crew then gave the salmon a ride back to the Sandy, and that’s where he remains, resting comfortably after his second grueling trip in two years.

“As of last Thursday, he was sitting in one of the pools that he sat in two years ago,” Christman said.

Christman said DMR personnel have snorkeled nearby and report that Charlie looks healthy — and big.

Jennifer Noll, another DMR fisheries scientist, reported that when Charlie was captured two years ago he was almost 29 inches long. Now, he measures nearly 34 inches from snout to tail.

Christman said many fish die in their natal rivers before even heading to sea once, and they face countless challenges while in the ocean. Upon their return to a river, they must overcome more obstacles and survive predators that would like to enjoy a salmon dinner.

The fact Charlie has made those grueling, life-threatening trips twice makes him a rare fish indeed.

“He has defied all the odds. He has actually survived an enormous amount of mortality,” Christman said. “He is at least two years older, three years older than all the other [salmon] in the Sandy River. This guy has seen it all and survived. It really is amazing.”

Christman thinks Charlie successfully spawned two years ago — spawning redds were found near where he was hanging out — and hopes he is able to do the same this year.

Passing along his genetics to future generations can’t hurt, after all.

“This guy really wins. I mean, he’s got it all,” Christman said. “It’s really amazing to see a fish that has been through it all and survived [all of those threats]. I just can’t fathom.”

“Charlie” the Atlantic salmon would have made his way up this part of the Kennebec River to reach the Lockwood Dam, both in 2017 and in 2019. A marvellous tale of a charismatic species making the Kennebec River a home for spawning. Photo Maranda Nemeth.