Life Cycle of the Coho Salmon in California

California is a pretty amazing place for many reasons, and one is that we have a lot of different species and subspecies of salmon! The Sacramento River, for example, is the only major river in the world that has four distinct subspecies, or runs, of Chinook Salmon!

Salmon are such amazing creatures! They are so important to the ecosystems in which they live, and they have been so important to human societies for so long that they get a lot of attention, and rightly so. And, when their populations are not doing well, ecosystems and human societies feel the impacts.

Two adult Coho Salmon migrating up a river. Photo: U.S. Fish and Wildlife Service.

Coho Salmon (Oncorhynchus kisutch), sometimes called Silver Salmon, are one of the species found in California. They are a species that live in the ocean for most of their lives, but then migrate up rivers and streams along the north and central coast of California to breed and lay their eggs in gravel beds in the upper watersheds. In addition to being found in California, Coho Salmon are also found breeding in rivers and streams along the Pacific coast of North America all the way to Alaska, and the Pacific coast in northeastern Russia as far south as northern Japan.

When they do this epic migration, how long it takes, where they lay eggs, how long those eggs take to hatch, what the young salmon need to survive and for how long, when the young salmon migrate down river and into the ocean, and how long they live there before returning to the river of their birth are all important aspects of Coho Salmon biology that need to be understood if restoration efforts are to be successful.

The grant program I manage funds salmon recovery projects, so I am writing this blog post in part to help myself understand the life cycle of the Coho Salmon so that I can make the best decisions I can when deciding what projects to fund. So, with no further adieu…

The Coho Salmon life cycle in California:

In January, adult female Coho Salmon will lay between 1,500 and 3,000 eggs each in a gravel nest, called a redd, in a stream in the upper watershed of a river system. After mating and laying eggs, the adult Coho die (more on this later).

Many of the eggs are eaten by other aquatic animals, but generally between 200 and 300 hatch. This takes between 50 and 70 days depending on water temperature.

A stream in the upper Navarro River watershed in California where young Coho Salmon spend a bit over a year feeding and growing. Photo: A Birding Naturalist.

Once they hatch, these young Coho Salmon spend approximately a year living in shallow areas of streams where they can hide amounts rocks and large woody debris and prey on smaller fish and aquatic insects.

After about 14 months living and growing in these shallow streams, the 50 to 100 surviving young salmon, that are now called smolts, begin to migrate down stream in spring. Their color changes. They loose the bars and spots that helped them to camouflage in the upper watershed streams and turn onto a bright silver color. Internal changes also occur with their gills and kidneys transitioning to be able to survive in salt water.

Once they reach the ocean in summer, the smolts spend about a year-and-a-half feeding and growing into adult salmon. Adult Coho commonly grow to about 18 lbs in weigh and 24 to 30 inches in length.

Beginning in December, the now three year old Coho Salmon begin their migration back up the rivers and streams. This first involves a transition period to allow their gills and kidneys to transition back to tolerating freshwater. The adult Coho also start to become more and more red in color as they migrate up the rivers. Once the adults are accustomed to freshwater, they begin swimming upstream, guided by scent and triggered by stream flow volumes, back to the upper watershed streams where they hatched.

Then in January, the one to four adults that have survived all the way to this point from all those eggs that were originally laid find a partner, mate, the females lay between 1,500 and 3,000 eggs each in a gravel nest, called a redd, and then the adults die. Unlike some other salmon species, Coho Salmon breed one time and then die. No adult Coho preform a return migration to the sea.

While the completion of the life-cycle of a Coho Salmon with the laying of eggs and death is the end of the individual salmon’s life, it is just the beginning of the lives of many other organisms and has effects that ripple out across the ecosystem. The dead adult salmon are important food sources for aquatic animals (such as crayfish, caddisflies, and rainbow trout) and terrestrial animals (such as bear, river otters, raccoons, and eagles). The decomposing adult salmon bring nutrients from the ocean in the form of their own tissues, and deposit those nutrients in mountain streams and rivers. In this way, they serve as an important source of nutrients, basically fertilizing the soils of the forests of the upper watersheds.

Coho Salmon are amazing animals with an amazing life story. I am very happy to be doing work that will help to provide the habitats and water they need to allow them to continue it to the next chapter.

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The Fish Friendly Farming Project

I have been working at the Delta Conservancy for a little over a year, now. In that time, one of the major projects I have been working on is our Proposition 1 Grant Program. Proposition 1 was a water bond passed by voters in 2014. Among many other things, it allocated $50 million dollars for the Delta Conservancy to give out to fund projects that would restore habitat, improve water quality, and/or support sustainable agriculture within the legal boundary of the Sacramento-San Joaquin Delta. A large part of my role here has been to help our Program Manager and higher ranking staff to form the competitive process by which organizations could submit proposals for projects, the process of reviewing and ranking those proposals to determine which will be funded, and then the management of the specific grant awards to successful projects.

In 2015, just before I began working here, the Delta Conservancy received its first round of project proposals (there will be subsequent rounds in the fall of 2016, 2017, 2018, and 2019). I was very involved in reviewing those proposals and scoring them to determine which would go on to be awarded funding. We have now gone through the entire process of reviewing the proposals, recommending the most qualified proposals to our board of directors for approval, and then writing the actual grant agreements which is pretty exciting because it now means we are able to move forward with giving funds to get projects accomplished.

I thought it might be interesting to introduce you to those projects as they get underway. I am going to be the grant manager for four of the projects from our 2015 batch of proposals. The first to begin was the Lower Marsh and Sand Creek Watershed Riparian Restoration Planning Project that I wrote about here. Our second grant funded project was just signed, and it will help create a fish friendly farming certification program for growers in the Delta, and it is the one I will focus on in this post.

Fish Friendly Farming (FFF) the title given to a whole process by which growers in a region can agree to use techniques called Beneficial Management Practices (BMPs) when growing their crops. By voluntarily conforming to these BMPs, growers are using land and water resources that minimize harmful effects on fish and wildlife, and maximize conservation strategies.

Different BMPs need to be created for different geographic regions because those different regions have a huge range of factors, many or most of which may vary. What types of crops are grown in a region? What types of soils are those crops growing in? How much water is available, and of what type (groundwater versus surface water, for example)? What species of fish and wildlife are found in a region? What types of habitats occur in a region? All of these and more mean that BMPs need to be very carefully applied so that they remain consistent and useful. This link contains information and a video on the Fish Friendly Farming program that has been developed for the wine country of Napa and Sonoma counties in California.

Fall-run Chinook Salmon

One area in which BMPs have not been well developed is the Sacramento-San Joaquin Delta, and developing this BMPs is exactly what the first goal of this project will be. A second will be to publish and distribute the Delta specific BMPs in a handbook that can be used by growers. A third goal will be to enroll Delta growers in the voluntary process so that they can become certified Fish Friendly Farms. This project will be conducted by a non-profit organization called the California Land Stewardship Institute (CLSI). The CLSI will work with growers, other agricultural specialists, ecologists, and conservation biologists to create BMPs for the major crop types in commonly grown in the Delta. This project has a budget of $89,450 awarded from the Proposition 1 Grant Fund by the Sacramento-San Joaquin Delta Conservancy.

In the three years that this certification development project will take, it is going to be very interesting to see what practices are identified as the most effective at protecting wildlife while still maintaining the economic output of the agricultural products. I will keep you posted on these developments and also on the other grants I will be managing as they come online.

As of this writing, we are about to receive our second round of full proposals which will then require review and scoring. I am looking forward to seeing what projects are proposed and which are successful and will be funded by the Delta Conservancy.

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Getting Water to the Desert is Complicated

California has a weird dichotomy (ok, it has many weird dichotomies, but I am only going to focus on one right now), and that is most of the people who live in this state are in the southern half, but most of the water falls in the northern half. So, what are we to do? Since people need water to survive, there are really only two options. Option one, bring the people to the water. Option two, bring the water to the people. Obviously, we as a society, have chosen option two.

So there are a lot of people in the desert who are not going to move and who need water (remember this point). So be it, we can figure out a solution to this problem. California took a page from the Romans, and in 1963 began building an aqueduct to bring water from the northern half of the state to the southern half. Once it was completed, the series of canals, pipes, pumps and reservoirs stretched over 400 miles from Clifton Court Forebay in the California Delta near the city of Tracy to (at its farthest point) Castaic Lake in western Los Angeles County.

To collect all that water and then get it to move all that distance, including over some significant mountains, requires some significant pumps. These things are huge and take a huge amount of energy to run. They are so large that when turned on, they can alter the flows of rivers. When the pumps are off, the Sacramento and San Joaquin Rivers flow together in the delta and then pass through the Carquinez Straights into the bay and eventually into the Pacific Ocean. When the pumps are turned on, much of the flows of those rivers change course the are drawn to the pumps, and not out to the bay. This leads to a bunch of problems.

One is that with less fresh water flowing into the delta, salt water from the bay spreads farther inland. This can alter growing conditions for crops and water quality for many cities. The altered flows also affect many fish species. Chinook Salmon and Green Sturgeon and Delta Smelt and Steelhead are all species of fish that are protected by the California Endangered Species Act, the Federal Endangered Species Act, or both! Some species of these fish use water currents to guide their migrations out to sea and then back up the rivers. If the currents lead them to the sea and then back up to the rivers then everything works fine. However, if the currents lead them to the pumps everything is not fine. As I’m sure you might guess, fish that get pulled into those giant pumps do not survive.

Since they are listed species, we the people of California need to work to protect these fish so that they do not get killed off. Ok, we can figure out a solution to this problem. The California Department of Water Resources (DWR) has built fish screens to stop fish from being drawn into the pumps. However, what happens is that get pulled close to the pumps, and then just mill around right in front of the screen. What do we do with all these fish? They have to go somewhere, or else there will just be more and more and more of them which will not be good for the fish. Ok, we can figure this one out too. DWR built a system of pipes and tanks so that the fish could swim down the pipe and be collected in the tanks. Then the tanks are loaded onto trucks and driven away to the a release site in the delta. Before I move on, I should say that a lot of study, engineering, and biology has gone into the design of those pipes and tanks to insure that the fish are not injured as they move through them. However, this process has now led to more problems. Many predatory fish, many of them Stripped Bass, have figured out that lots of fish come out of those release sites. Underwater cameras have shown that the fish actually hear the trucks coming and gather at the base of the release pipe to eat the fish as they come down. So while we thought we were saving the fish from death by getting them away from the pumps, we were actually just sending them to their death down the mouths of predators. Well, we think we can figure out a solution to this problem as well by establishing more release sites and mixing up the schedule of when different release sites are used. This should make it so that the predators do not have established sites for a meal and so do not gather in such numbers which should mean that the fish DWR release actually survive and swim away. However, this strategy is still being developed and judging from the long list of problems so far, there is no guarantee that it will not lead to even more of them that we cannot yet foresee.

And remember, all of this is so that we can bring water to people living in the desert.

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Chinook Salmon of the California Delta

As part of my current job with the California Department of Water Resources, I assist in collecting data for a study that is monitoring predators in the Clifton Court Forebay (CCF). The CCF is where water is collected and then pumped into the California Aqueduct for transport to southern California. One of the challenges to providing water to southern California is that there are several threatened or endangered species that live in the delta. Fish that get sucked into the pumps of the aqueduct do not survive, so keeping state and federally list species out of the system is important. The study I have been working on the past four months is examining threats to the listed species. One component of that study is to catch predatory fish such as Stripped Bass (Morone saxatilis), Largemouth Bass (Micropterus salmoides), and several species of Catfish (Ictalurus spp. or Ameiurus spp.). Once captured, these fish are tagged with little transmitters that send out signals that can be detected by underwater microphones, called hydrophones, that are setup throughout the area. By tracking when and where these predatory fish go, we hope to be able to figure out a way to reduce the number that come into CCF and eat the listed species.

Fall-run Chinook Salmon

One of the listed species we are concerned with are Chinook Salmon (Oncorhynchus tshawytscha), and I got an up close and personal look at one just a few days ago. As the team I was a part of was fishing in CCF, I got a hit on the lure I was using. It felt like a brick had been dropped on my line as the fish swam away from me and the boat. As I worked to real the fish in, everyone on the boat was getting curious to see what species I had hooked, just how big it was going to end up being. When I had finally pulled the fish to the surface, we were all really surprised to see that it was a Chinook! We are not supposed to catch salmon, and generally they do not attack the lures we use, additionally salmon at this time of year are not really eating but are instead focused on finding a mate and spawning. So this really was a surprise! When we got it on board to get the hook out of its mouth we quickly measured it (61 cm), weighted it (6.55 lbs), and got it back in the water so that it could go on its way.

Getting to see this fish, the largest fish I have ever caught, to hold it and then to watch it return to the water got me thinking a lot about Chinook Salmon. I am starting a new job on Monday which will focus on restoring many areas of the delta, and listed species will be a large part of those projects, so I figured that learning a bit more about salmon would be a good idea.

It turns out that there are four different runs of salmon that move through the California Delta. The different runs are defined according to when the different populations enter freshwater as they travel up from the Ocean and San Francisco Bay through the Delta and up the various rivers of California. The four runs are the Central Valley Fall-run, the Central Valley Late Fall-run, the Sacramento River Winter-run, and the Central Valley Spring-run. Each of these runs are considered to be evolutionarily significant units and so are monitored and managed for their specific needs.

Central Valley Fall-run Chinook, like the one I caught, are the most abundant of the four runs. They move through the area from July to December and spawn from early October through December. There is a fair bit of variability from stream to stream. Fall-run Chinook are an important economic factor due to the large numbers that are caught by both commercial and recreational fisheries in the ocean and by recreational anglers  once they reach freshwater. Even so, due to concerns about population size and the influence of hatchery-raised Chinook, this run is listed as a species of concern under the federal endangered species act.

Central Valley Late Fall-run Chinook migrate into the river systems from mid-October through December and spawn from January through mid-April. Again, due to concerns about population size and the influence of hatchery-raised Chinook, this run is listed as a species of concern under the federal endangered species act.

Sacramento River Winter-run Chinook pass through the Golden Gate from November through May and then move into the Sacramento River from December all the way through early August. They then swim up the mainstem of the Sacramento River to spawn from mid-April through August. These salmon used to go farther up the Sacramento River watershed and spawn in the McCloud River, the Pit River, and the Little Sacramento River. However, the construction of several dams have not blocked access to these historical spawning grounds. Despite these dams, the population of Sacramento River Winter-run Chinook was able to maintain a fairly healthy level until the 1970s when they began to decline. By the early 1990s only about 200 spawning salmon were observed. In 1989 this run was listed as endangered under the California Endangered Species Act and they were then listed as endangered under the federal Endangered Species Act in 1994.

Central Valley Spring-run Chinook begin moving up the Sacramento River from March through September. They generally the find areas of cold water to wait out the summer and then spawn from mid-August through October. This run used to be the largest in central California however, only small remnant populations are left in small creeks that make up some of the tributaries of the Sacramento River. Some Spring-run Chinook still occur in the mainstem of the Sacramento and Feather Rivers, but they sometimes hybridize with Fall-run Chinook. The reduced spawning areas, small population size, and hybridization threat lead the Central Valley Spring-run Chinook to be listed as threatened under both the federal and California Endangered Species Acts in 1999.

So, there you have them, the four Chinook Salmon runs of the California Delta. There are many other runs in other parts of the state, all with their own unique stories and histories. It will be interesting to see how I will be interacting with these runs in the habitat restoration work I will be doing. I will keep you informed!

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DWR: My First Two Months

I have been working for the California Department of Water Resources for a couple of months now. It has been a really cool experience in many ways, and I thought that sharing some of those experiences would be fun. So, here are a bunch of photos from my first two months on the job. The job, in this case, is focused on a place called the Clifton Court Forebay in eastern Contra Costa County. This is one of the main points where water is collected and then pumped from the Forebay into the California Aqueduct for transport to southern California. One of the major problems with this pumping system is that it is so powerful it pulls lots of fish into the Forebay including several species of threatened or endangered species such as Chinook Salmon, Steelhead, and Green Sturgeon. In response to this puling in of high numbers of fish, high numbers of predators also concentrate around the Forebay. These predators include predatory fish such as Stripped Bass, Large-mouth Bass, and several species of catfish. Other predators are many species of piscivorous birds such as herons, egrets, pelicans, grebes, terns, etc. The main point of the project I am working on is to find ways of reducing the numbers of predators in and around the Forebay. To do this, we are trying to figure out how and where the predators most commonly access the Forebay. This includes frequent avian surveys around the Forebay and also tracking the movement of the predatory fish. This tracking is accomplished by capturing fish and preforming surgeries on them to implant PIT tags and/or acoustic tags in them. These tags emit sound at particular frequencies and in particular patterns. Each tag has a unique combination of frequency and pattern which allows each tag to be individually identifiable. Microphones are setup around the Forebay and in the canals that connect to the Forebay so that as fish swim around, their tags are picked up and their locations recorded. In this way, we can track fish movement to a pretty fine level of detail. Pretty cool!

So, with that background, here is what my job actually looks like (all photos are my own unless otherwise noted).

The front doors of my building.

This is the Resources Building in downtown Sac.

My little corner.

Sunrise over the yard where we keep our trucks and boats.

This is me with my first Stripped Bass. It is just a small one, but still big enough to tag! (Photo courtesy of Mike Cane).

A view of the edge of the Forebay.

Osprey.

Bald Eagle.

The portion of the Forebay that leads into the pumps.

Tule beds in a corner of the Forebay.

A view across the Forebay.

One of the canals that leads into the Forebay.

The east slope of Mount Diablo in the distance.

Can you see the bird?

There it is! This is a Snowy Plover that I found on the edge of the Forebay. I was pretty excited to find this federally threatened species, especially since this was decidedly outside its normal habitat and range.

Here is another photo of the same HY Snowy Plover.

A flock of Long-billed Curlews and WIllets hanging out on the edge of the Forebay.

Long-billed Curlew.

Long-billed Curlew in flight.

I found this Red-shouldered Hawk on the bank of the Sacramento River as I walked to work one morning. It is sitting on a California Groundsquirrel.

Piscivorous birds lined up on one of the wing walls in the Forebay.

There are obviously a lot of fish to be had.

Pied-billed Grebe nesting in the floating vegetation that grows in the Forebay.

Clark’s and Western Grebes nesting on the Forebay.

This large fly (about 2-3 cm long) landed on the truck. Any ideas as to an ID?

Another view of Mount Diablo.

Me conducting an avian survey (Photo courtesy of Michelle Tyson).

Caspian Tern, Snowy Egret, and California Gulls.

American White Pelicans feeding in the Forebay.

One American White Pelican swam quite close to us as we were counting.

Clark’s and Western Grebes nesting in a patch of floating vegetation.

A closer look at the Clark’s and Western Grebe nesting colony.

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The Ethogram: Creature Feature: Hagfish

Check out my post on The Ethogram (which is the Animal Behavior blog of U.C. Davis) on Hagfish at: http://theethogram.com/2015/01/26/creature-feature-hagfish/

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Salmon Return to the San Joaquin River!

A long fought legal battle.  A long sought agreement between many diverse parties.  A massive restoration effort.  And now an amazing success.  Chinook Salmon have returned to the San Joaquin River for the first time in almost 70 years!  Hopefully, they will spawn and so reestablish a breeding ground in what used to be their native range.  Read a more complete account at:

http://switchboard.nrdc.org/blogs/mschmitt/a_historic_day_salmon_return_t.html

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