Using Otoliths As A Fish Identification Tool

Otoliths are a calcareous structure within the inner ear of fish. The word calcareous simply means a structure made primarily of calcium; thus otoliths are a hard, bony structure. These structures are sensitive to changes in acceleration and gravity. They play an important role in allowing the fish to detect changes in horizontal movement and acceleration.

The shapes of fish otoliths vary highly among different species but not within species. Layers that are mineral-rich and mineral-deficient are deposited in alternating succession around the original center of the otoliths, creating bands that resemble rings on a tree. The bands show up as dark and light areas when viewed under a light. The rates of deposition vary during different times of the year. During the summer months, warmer water and rapid growth cause the otoliths depositional rates to be more rapid than during winter months. By examining the otolith, we can tell how many seasonal changes a fish has experienced during its life, allowing us to determine the fish's age. This is an important tool that is used not only to determine age, but to also identify different stocks.

Water chillers at Quilcene NFH

Manipulating the rearing temperature at hatcheries allows otolith bands to be formed. One technique is to expose the fish to cold temperatures; this causes dark bands to form on the otoliths. This process is repeated for a specific number of times and timed intervals. Since the formation of these bands is controlled by hatchery personnel, a unique pattern of rings is formed that is not seen in wild stocks. This technique is a cost-effective way to accurately differentiate between hatchery and wild fish, as well as allowing the identification of hatchery release groups.

Kokanee egg trays at Quilcene NFH

Hatchery personnel from Issaquah State Fish Hatchery and Quilcene National Fish Hatchery will use this technique to mark Lake Sammamish kokanee salmon. When these fish return as adults, these otolith marks will allow the biologists to identify where the fish originated.

Measuring Tag Retention and Fin Clip Quality

Each year, our office coded-wire tags (CWT) and mass marks (adipose fin clip) over 2 million juvenile fish from the federal hatcheries on the Olympic Peninsula. The CWT is a tool that is used to assess overall success of hatchery practices. The tags are also used to estimate survival and assess run size and timing. Mass marks allow us to distinguish hatchery fish from wild populations. This is a key component in allowing fishing to occur for hatchery-raised fish in areas where they coexist with wild stocks.

Before these fish are released, a quality check must be performed to ensure successful retention of tags and proper clipping of fins. This is accomplished by examining groups of fish 1 month after being marked and tagged. The fish are individually passed over a detector to determine if a tag is present and then fish that received a clip are visually examined for the quality of the clip. This data is then recorded and used to calculate the success of our tagging and marking. Once examination is complete, the fish are returned to the raceways where they are cared for by the hatchery staff.

Following are three short videos demonstrating this process:

Coho Salmon Are Back in the Upper Big Quilcene River

Quilcene National Fish Hatchery, situated on the picturesque Big Quilcene River, has been raising coho salmon for many decades. During this time, most returning coho adults have been intercepted at the hatchery and used for human consumption and raising more fish. In recent years, a few adult coho have been allowed to pass upstream of the hatchery.

These practices are changing, however.  Managers have recognized that passing fish upstream of the hatchery has many benefits: River habitat can be used for natural production of coho salmon; coho eggs, juveniles, and decomposing carcasses in the river have many food web and ecosystem benefits; and people just plain like to see salmon spawning naturally in our rivers and streams!  In 2008 and 2009, hatchery managers allowed 200 adult coho to move upriver. During this time, USFWS biologists performed spawner and carcass surveys to evaluate how successful these fish were at spawning. We also performed snorkel surveys and installed a screw trap to evaluate rearing success of the juveniles.  


USFWS biologist checks the screw trap for fish

A screw trap (see picture) has a rotating cone that captures fish moving downstream. Fish are held in a live box at the back of the trap where they wait to be removed, identified, and measured by a biologist. Although it might look a little scary, these traps are actually very gentle on the fish.

So far, results have been encouraging. In the spring of 2010, we estimated that 1,000 to 2,500 outmigrating smolts resulted from the 2008 spawners. Not bad for a system recognized as having minimal spawning and rearing habitat! We will be continuing our studies next spring to see what results from the adults passed in 2009. Sadly, for various reasons, no adults were passed upstream this year. Nonetheless, passing coho upstream to spawn naturally is something we plan on doing every year as standard practice.


Andrew measures, weighs, and marks the fish captured in the screw trap



Measuring Survival of Salmon Produced at Federal Hatcheries

We are often interested in determining if salmon grown and released at a U.S. Fish and Wildlife Service hatchery survive in the ocean better than salmon from other hatcheries. Likewise, we need to determine how many hatchery fish are caught in commercial, tribal, and recreational fisheries that occur in the Pacific Ocean and Puget Sound. In order to do this, we sample the fall Chinook, winter steelhead and coho salmon when they return to Makah, Quilcene and Quinault National Fish Hatcheries to detect how many contain a tag made from a small piece of wire.


Dissecting salmon snout

These tags are inserted into the noses of thousands of baby salmon each year before we release them from the hatcheries. Each tag has a 6-digit number that identifies each group of fish that we are responsible for monitoring. When the fish are released from the hatchery, we enter the tag number into a database along with information about where and when these fish are released. When the fish return to the hatchery 2 to 6 years later, the adult fish are put through a metal detector to check for a tag. If a tag is present, the fish is measured and the head is taken back to our lab. 

Back at the lab, we dissect the tag from the salmon’s snout and read the number with a microscope. The tag numbers are then entered into the same database along with other biological information we collect. State and tribal agencies similarly enter the tag numbers they detect in adult salmon caught in fisheries taking place in the Pacific Ocean and Puget Sound. At the end of the year, we summarize information in this database to evaluate the success of each U.S. Fish and Wildlife Service hatchery and its ability to produce enough fish for the many anglers who rely, in part, on hatchery fish for tribal culture, commercial interest, and recreation.

Here are two short videos showing how we process the salmon heads to recover the tags:

Lake Sammamish Kokanee Salmon Supplementation Program

Our office, along with King County and the Washington State Department of Fish and Wildlife (WDFW), has been working to restore the Lake Sammamish kokanee salmon population. This population once numbered in the thousands, but recent adult returns have been less than 100 fish. Currently, kokanee primarily spawn in three small tributaries: Laughing Jacobs Creek, Ebright Creek, and Lewis Creek.


Ebright Creek

One major component of the recovery effort is a supplementation program to improve survival rates from the egg stage to the fry stage. Adult kokanee will be spawned at the Issaquah State Fish Hatchery (SFH). Half of the eggs will be incubated at Issaquah SFH and half will be taken to Quilcene National Fish Hatchery where they will be reared to the “eyed-egg” stage of their life. After all eggs have reached the eyed-egg stage, they will be placed in experimental rearing systems at Issaquah SFH.  Each experimental rearing system will use water taken from their natal stream to provide adequate imprinting. Shortly after the kokanee fry have emerged from their eggs, WDFW and King County staff will then plant the kokanee fry back into their natal creek.

We began this year’s supplementation effort last week. King County and WDFW field crews looked for fish in the three spawning creeks. During the first week, crews captured 6 males and 1 female in Ebright Creek.  The female was successfully spawned with 2 of the males; the other males were saved for later spawning.  This week (week 2), an additional 6 females and 8 males were collected from Ebright Creek and 1 female and 2 males from Laughing Jacobs Creek; all fish were successfully spawned. Over the next 2 months, the crews will be collecting adults once or twice each week.

Female kokanee salmon



Male kokanee salmon

Elwha River Weir

An adult fish trap, termed a resistance board weir, was installed in the Elwha River in September 2010 to begin counting adult salmon, trout, and char migrating upstream and downstream in the Elwha River. The weir is part of a multi-agency effort, which includes the Lower Elwha Klallam Tribe, National Oceanic and Atmospheric Administration (NOAA), Olympic National Park, U.S. Fish and Wildlife Service, U.S. Geological Survey, and Washington Department of Fish and Wildlife (WDFW), to monitor the influence of removing two Elwha River hydroelectric dams on salmon and steelhead returns to the Elwha River ecosystem. The goal of the project is to count migrating adult salmon and steelhead to determine if run sizes increase in the Elwha River following dam removal. A portion of the adult salmon captured at the weir will also be used as broodstock for hatchery production and conservation.  Hatcheries will be used for Chinook salmon, coho salmon, chum salmon, pink salmon, and steelhead as a safeguard to protect Elwha River salmon runs during dam removal, which is expected to result in short-term sediment concentrations that may kill adult salmon. In addition, information will be obtained from the weir to determine when different species of adult salmon enter the river, their age, and genetic makeup.

Adult trap (resistance board weir) in the Elwha River

At 195 feet across, the Elwha weir is thought to be the largest floating weir on the WestCcoast. The weir consists of 52 floating panels connected to a substrate rail. The substrate rail is comprised of 10-foot sections of 3-inch angle iron which are bolted together and secured to the streambed using rebar stakes. The floating panels block fish migration and direct the fish to one of four trap boxes; these boxes can be placed in different positions as needed. There are currently three upstream trap boxes---two on one side of the river and one on the opposite bank. There is also one downstream trap box. Now that the substrate rail is in place, the weir can be installed in approximately 2 days and removed in only a few hours.

The new Elwha weir fished for 30 days in 2010 and captured a total of 492 adult salmon and trout, representing eight different species, including Chinook, pink, chum, coho, and sockeye salmon, steelhead, cutthroat trout, and bull trout. Chinook salmon were captured in the greatest number---461 individuals. Pink salmon were the next most common species captured with 12 individuals.  Although the weir was pulled prior to the peak of the coho and chum salmon runs, both species were captured. In addition, summer-run and/or early returning winter-run steelhead were captured.  The capture of pink salmon surprised us, since pinks generally return to Puget Sound rivers only during odd years (2009, 2007, etc.). They have, however, become more common during even years over the last decade.
 

The weir fishing at 2,200 cfs

The weir is planned to fish a majority of the time during the summer and early fall, when Chinook and pink salmon are migrating into the Elwha River. However, it is expected to fish only part-time during late fall through spring when storms and/or snow melt result in high water in the river. The weir fished successfully during flows of 2,200 cubic feet per second (cfs) in late summer (500 cfs is the normal low flow during summer). This was encouraging, since the weir was predicted to be able to fish up to about 2,000 cfs. 

The weir is planned to be re-installed in early 2011 to direct adult steelhead to the river margins where they will be counted using SONAR. The trap boxes will be installed in late winter or early spring to trap adult steelhead. The weir will be removed again during the spring snow melt and then reinstalled with traps as flows begin to decrease in early summer.

This project was funded in part by funds provided to the cooperating agencies as part of their annual budget.  Additional funds were obtained through the President’s stimulus program (American Recovery and Reinvestment Act). The project is currently funded through September 30, 2012.

Here are some of the fish captured by the weir:



Chinook salmon

 

Coho salmon

Chum salmon



Pink salmon



Sockeye salmon



Bull trout



Cutthroat trout

 

Steelhead



My Life Aquatic - Part 4

My summer as a USFWS STEP employee proved to be an amazing experience! I was given the opportunity to work on multiple field and public outreach projects, job-shadow biologists and technicians, and gain important on-the-job experiences. In addition, this position enabled me to earn my final upper division sciences credits via independent study with The Evergreen State College. With my undergraduate degree in Environmental Science and Stream Ecology under my belt, as well as my newly updated resume, I am now in a great position to compete for future employment opportunities in conservation science.

Since my STEP position with the Washington Fish & Wildlife Office Fisheries Division (USFWS), I have been exploring work opportunities in fisheries, forestry, and plants, as well as public education and outreach work. With more work experience, I plan to develop existing skills, gain new experience, and explore potential areas of focus for a master’s project. The sky is the limit as I have the flexibility to move to different places in order to achieve these goals. In addition to looking for employment, I have been making myself available as a volunteer to the USFWS and the local Stream Team. The Chehalis Watershed Festival, for example, was a great volunteer experience as it allowed me to give back to the USFWS and the community while further honing my outreach skills.

My long-term goal will be to pursue a Master’s of Science degree focused on ecological conservation and restoration. This degree will be the culmination of my training toward becoming a professional biologist. My STEP position was an important stage in this journey and I feel that from the knowledge and experiences gained, I am ready for my future educational and career pursuits.

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Hoh River Project - Field Work 2

Measuring habitat at Hoh II

We continued field work for the Hoh River habitat study in September. Habitat surveys were conducted to identify the distribution of habitat types within Hoh I (engineered logjam) and Hoh II (riprap) sites. Fish abundance, density, and diversity were assessed using seining and mark-recapture methods.

At each of the two sites, we captured and marked fish with Bismarck Brown on one night, then recaptured fish on the following night. Recapture rates for coho and Chinook salmon at Hoh I and Hoh II sites were 12% and 9%, respectively. From these numbers we will be able to make rough population estimates, as well as compare habitat use at the two sites. Additionally, we recaptured 46 previously PIT-tagged salmonids at Hoh I and 16 at Hoh II. We also tested the effectiveness of a fixed PIT tag reader for detecting previously PIT-tagged fish by placing it at the base of a logjam at Hoh I.

Prototype mobile PIT tag reader installation at Hoh I

It was a fun-filled but hectic week as we scrambled to get everything done before forecasted rain increased river discharge to a point that we couldn’t work, which would have washed away all of our sampling efforts. On the second night, we compressed two nights’ work into one by recapturing at Hoh I and also marking at Hoh II--working from 7:30pm to 5:00am.

Data entry, checking, and analysis will be completed from October through December. In January, we will return to the Hoh River to do another population assessment of the two sites.

Olympic Mudminnow – Western Washington Wetlands Survivor

Olympic mudminnow

The Olympic mudminnow is a small fish that only occurs in western Washington. Olympic mudminnow live in marshes and wetlands with a muddy bottom and abundant aquatic vegetation. Typically they do not occur where there are large, predatory fishes, such as largemouth bass. They eat fish larvae, eggs, and small invertebrates, and have a remarkable tolerance of low oxygen levels. The Olympic mudminnow may be an indicator species to monitor the potential impact of climate change on wetlands and fish in western Washington.

Western Washington wetland

The Washington Department of Fish and Wildlife (WDFW) conducted mudminnow surveys in past years and created a database of inhabited sites. Our office is currently working with WDFW to revisit several of these sites to see if these fish are still present. Upon capture of a mudminnow, we remove a small part of the caudal fin for genetic analysis to help us determine the relative uniqueness of each Olympic mudminnow population. This is our first year working with this unique species and we plan to collect more data at additional sites in upcoming years.

Pacific Lamprey - An Unusual Fish

Pacific lamprey being measured

With the decline of lamprey in many rivers of the Washington Coast work is being conducted by the U.S. Fish and Wildlife Service to better understand why.

One type of lamprey that is of special concern is the Pacific lamprey. Lampreys are an unusual fish that resembles an eel, even though they are not related. They are a very important food source to fish, birds and mammals. Pacific lampreys spend more than half of their life buried in sandy or muddy spots of the river. Like a salmon, when the timing is right, young lampreys will move from their home in the river to the waters of the Pacific Ocean. Adults will return to the rivers and move upstream to lay eggs after spending a couple of years at sea.

Work on the Big Quilcene River has begun to see how well the lampreys are doing. To do this, lampreys are coaxed out from the river bottom using a mild electrical current that stuns them long enough to be captured. After a few measurements are taken on each lamprey, the fish are released unharmed at the same spot in the river where they were captured.

Looking for lamprey in the Big Quilcene River

Coho Have Returned!

Sorting coho salmon

It’s that time of year again when thousands of coho salmon return to Quilcene National Fish Hatchery after having spent the last year and a half feeding in the Pacific Ocean.

Our office coded-wire tagged a portion of these fish as juveniles in 2008 in order to measure their survival. We test the returning fish with magnetic detectors to identify those fish that still have tags. The tags are removed and read and the survival rate calculated. Quilcene coho survive at a fairly high rate, so after a day of sampling hundreds of fish for tags our arms are pretty worn out. This year we're especially tired---Hatchery Assistant Manager Dan Magneson said that these are the biggest fish he can recall in recent memory.

Please visit Quilcene National Fish Hatchery to see us in action or to enjoy a guided tour. Tours can be arranged by calling the hatchery at 360-765-3334.

Hoh River Project - Field Work 1

Field work for the Hoh River habitat study has started for 2010. We used beach seines, minnow traps, and hook-and-line methods to capture more than 1,700 fish at the two study sites (974 at the engineered logjam site - Site 1 - and 785 at the riprap site - Site 2). Most of the fish captured were juvenile salmon and trout; however, we also caught other types of fish. Our catch included Chinook salmon, coho salmon, cutthroat trout, rainbow trout (steelhead), Mountain whitefish, dace, and lamprey. A few crayfish were also captured.

We implanted PIT tags in 933 fish that were over 65 mm (2.55 inches) in length. The purpose of this tagging is to compare fish survival at the two sites over the next couple of months. We plan to return to the sites in September to conduct a habitat survey, perform a fish survey to look for the fish we just PIT tagged, and determine the total number of fish in both sites.

Ohop Creek Fish Rescue

About 100 years ago, farmers in the Ohop Valley dug a large ditch along the valley wall to contain Ohop Creek, a tributary to the Nisqually River, to develop grazing land for dairy cattle.

On August 11, approximately 30 people from the Nisqually Land Trust, Nisqually Tribe, Washington Department of Fish and Wildlife, U.S. Fish and Wildlife Service, Stream Stewards, Washington Conservation Corps and Mason County Conservation District gathered for a fish rescue operation at Ohop Creek near Eatonville, WA.

We restored 1.2 miles of Ohop Creek to its natural condition through a concerted effort from the agencies listed above.

We started collecting fish in the 1/3 of a mile of the ditch using electroshockers, dip nets and seines, then transferring the fish to a large holding tank. Once the fish were collected they were taken to the restored creek where the fish were identified, enumerated, measured and released. We found Coho fry, lamprey, dace, crawfish, sculpins, fresh water mussles, large scale sucker, and some non-native warmwater fish.

My Life Aquatic - Part 3

Since my last blog update I have had the pleasure of assisting with three different monitoring and research projects with the USFWS. I have worked with colleagues on the Duwamish Estuary, Issaquah Creek and the Hoh River. Participating in these projects as a STEP student has been a great opportunity for me to diversify my field experience.

My first field work opportunity with the USFWS was a habitat mapping event on the Duwamish Estuary, located in Seattle, Washington. This is a restoration monitoring project that focuses on two species of sedges - Lyngbye's sedge ( Carex lyngbyei) and Soft Stem Bulrush (Scirpus validus). I became familiar with the morphological features and life histories of these two sedges and it was my first experience collecting field data in an estuary.
The sampling events I assisted with at Issaquah Creek are part of the Water Resource Inventory Area (WRIA) 8 project. Under the Watershed Planning Act (WA State - ESHB 2514), WRIA 8 is monitored to ensure that the best possible management practices are implemented to protect Washington’s water resources. Our USFWS sampling crew teamed up with King County employees to conduct habitat surveys and fish population surveys via electroshocking. This was a great example of how different agencies can work together to practice fisheries conservation.
I am currently focusing on the sampling events on the Hoh River and they have proved to be amazing adventures! I have learned new skills such as beach and herd seining, minnow trapping and surgically inserting PIT tags into juvenile salmonids (trout, whitefish and salmon). Some of this work included night sampling which was a new and exciting experience. For more information on this project, be sure to visit the Hoh River Project page on this site.

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Hoh River Project - Overview

USFWS and Washington Department of Transportation (WSDOT) are working together to investigate the response of fish and stream habitat to alternative riverbank stabilization techniques. The WSDOT Hoh River project is located on the western side of the Olympic Peninsula where WSDOT is attempting to protect U.S. Highway 101 from eroding into the Hoh River as a result of river channel migration during flood events. WSDOT has installed engineered logjams consisting of large pieces of natural wood and tree rootwads along the river bank in the first site called Hoh I. River bank in the second site (Hoh II) is currently treated with large angular rock, often called riprap. This riprap, which has continuously failed to protect the bank, will be replaced with engineered logjams during the summer of 2011 or 2012.

Both approaches have been used to stabilize eroding banks, especially when infrastructure such as roads and houses is threatened. Several reports, however, suggest that the more commonly used method of stabilizing river banks, rock riprap, negatively impacts fish habitat complexity and aquatic communities including fish. Additionally, several reports suggest that wood is an important ecological component of aquatic systems, and fish and other aquatic life often occur in greater densities and diversity at locations associated with wood. As a result, large wood complexes, such as engineered logjams, are viewed as an alternative tool for bank stabilization and stream restoration. Therefore, bank stabilization with engineered logjams may provide the dual benefit of protecting infrastructure and conserving aquatic natural resources, such as fish populations, when compared to alternative stabilization techniques.

USFWS and WSDOT are conducting the Hoh River study to compare fish habitat diversity, fish density, growth, survival, movement, and species diversity in Hoh I and Hoh II. Fieldwork started in August 2009 with two study components. Fish survival in both Hoh I and Hoh II was estimated and compared between sites by capturing, tagging, and recapturing fish at a later date. A total of 495 fish were tagged with passive interrogated transponder (PIT) tags between the two sites. The second study component relied upon acoustic tagging technology to provide spatial information in order to identify how fish utilize the engineered logjams at the Hoh I site. In this second effort, USFWS technicians and biologists deployed a series of sound recorders called hydrophones on the river bottom. Twenty-nine fish were captured and surgically implanted with an acoustic tag. The hydrophones passively tracked the location and movement of the tagged fish over a couple of weeks. Preliminary results from Hoh River study indicate that engineered logjams are a valuable technique for bank stabilization projects and can provide favorable habitat for juvenile salmonids when compared to sites utilizing other bank stabilization methods.

In August 2010, we plan to PIT tag more fish at both sites. We are also preparing to collect habitat information in order to describe differences in the habitat quality and quantity from the perspective of fish in the study areas. Check back for postings of our upcoming fieldwork!

My Life Aquatic - Part 1

A Look At A U.S. Fish & Wildlife Service Seasonal Employee's Summer Through A Fish- Eye Lens


My name is Caprice Fasano and I am a stream ecology major at The Evergreen State College. When looking for summer opportunities this past spring, I had three goals in mind: professional field experience in fisheries conservation, college credits, and income. My search ended when I found out about the U.S. Fish & Wildlife Service (USFWS) STEP program. The STEP program stands for Student Temporary Employment Program and is designed to provide the opportunity for students to experience the advantages and challenges of working for the Federal Government. The conservation field work opportunities through the Fisheries Division of the Washington Fish & Wildlife Office (USFWS) were exactly what I was looking for, so I applied, went through an interview process and was eventually offered a fisheries technician position. This blog is an opportunity to share this exciting work experience with you.

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