LAR_RST_Protocol_Updated.pdf

AMERICAN RIVER

ROTARY SCREW TRAP PROTOCOL

October 2018

AMERICAN RIVER ROTARY SCREW TRAP PROTOCOL

INTRODUCTION

SAFETY

COMPLETING DATA SHEETS

TRAP STATUS, ENVIRONMENTAL DATA, AND FISH CATCH DATA COLLECTION

Trap Status and Environmental Data

Cleaning the Trap

Fish Catch Data Collection

Setting Up and Maintaining Buckets, Insulated Coolers, and Live Cars

Collecting Fish

Random-Sampling Protocol

Processing Fish

Anesthetizing Fish

Collection of Fin Clips

Field Quality Check

Trap Maintenance

MARK/RECAPTURE TRIALS

COMPUTER DATA ENTRY AND MANAGEMENT

Data Entry

QA/QC Procedure

APPENDIX A: Field Data Sheets

Trap Visit Data Sheet

Unmarked Chinook Salmon Data Sheet

Unmarked Steelhead Data Sheet

Spring-run and Winter-run Chinook Salmon Fin Clip Data Sheet

Photonically Marked Chinook Salmon Data Sheet

Recaptured Chinook Salmon Data Sheet

Adipose Fin Clipped Salmonid Data Sheet

Other Species Data Sheet

Marked Data Sheet

Marked Chinook Salmon Data Sheet

APPENDIX B: Chinook Salmon and Steelhead Life Stages

APPENDIX C: Trap Visit Data Sheet Terminology

APPENDIX D: Equipment Lists

Catch Visit Equipment List

Bismark Brown Equipment List

Anesthetizing Equipment List

Elastomer Dye Equipment List

APPENDIX E: Fish Species List for the American River

APPENDIX F: Key to Juvenile Chinook Salmon and Steelhead

APPENDIX G: Process for Staining Chinook Salmon With Bismark Brown Dye

APPENDIX H: Process for Marking Chinook Salmon with Photonic Dye

APPENDIX I: QA/QC Procedure for Datasheets

APPENDIX J: Operational Procedure for Night Operations

INTRODUCTION

Monitoring data can provide the foundation for successful management programs if data are collected in a systematic, consistent, and comprehensive manner. The monitoring of the abundance/production of juvenile salmonids on the lower American River is important because large sums of funding are spent restoring aquatic habitat in an effort to increase the number of juvenile Chinook salmon (Oncorhynchus tshawytscha) and steelhead (Oncorhynchus mykiss) in that watershed. Rotary screw traps (RSTs) are one of the most important tools for monitoring juvenile salmonids. When data acquired with these tools is collected in conjunction with other monitoring data, there is a substantially improved ability to track the status of those salmonids and assess their response to past management activities. That data in turn can be used to adaptively manage future restoration projects so that they are more successful.

The objective of this document is to ensure that RST data from the American River in

California’s Central Valley is collected in a safe, systematic, consistent, and comprehensive manner. To address this objective, this protocol provides detailed descriptions for operating and maintaining RSTs, collecting and processing fish, collecting environmental data, conducting trap efficiency tests, and entering data into a RST “platform” developed by the U.S. Fish and Wildlife

Service’s Comprehensive Assessment and Monitoring Program (CAMP).

The American River RSTs are located 0.25 miles downstream of the Watt Avenue Bridge in

Sacramento County, California. Between two and three RSTs will be operated each year, and those traps could consist of different combinations of 5 and 8 foot RSTs. Under ideal conditions, it is expected that one 5 foot RST will be operated in the South Channel of the American River, and two 8 foot RSTs will be operated in the North Channel. In descending order of abundance, the following salmonids could be captured in the American River RSTs: fall-run Chinook salmon, steelhead/rainbow trout, spring-run Chinook salmon, winter-run Chinook salmon, and late-fall-run Chinook salmon.

The CAMP has developed a general protocol for conducting RST activities. That document can be found at https://www.fws.gov/cno/fisheries/CAMP/Documents-

Reports/Documents/2008_draft_CAMP_Rotary_Screw_Trap_Protocol.pdf. The general guidance in that document should serve as a companion to the more detailed guidance in this document.

Employees who are engaged in servicing the RSTs on the American River are responsible for having a firm understanding of all the information covered within this protocol.

https://www.fws.gov/cno/fisheries/CAMP/Documents-Reports/Documents/2008_draft_CAMP_Rotary_Screw_Trap_Protocol.pdf https://www.fws.gov/cno/fisheries/CAMP/Documents-Reports/Documents/2008_draft_CAMP_Rotary_Screw_Trap_Protocol.pdf

SAFETY

Safety should always be the field biologist’s primary concern. Never perform a task if it cannot be performed safely. A minimum of two crew members are required to service RSTs at any given time. At least one biologist must have a working cell phone when in the field.

RST activities occur in an environment where field biologists can be seriously injured by rotating mechanical parts, crushed between a boat and a trap, or drown if they do not wear personal protective gear. The American River is a large river in a major metropolitan area. As such, RST operations have the potential to seriously injure members of the public who use the river for recreational purposes if those individuals become caught in the trap. The proximity of the

American River RST site to the city of Sacramento also creates the potential that field biologists servicing the traps could be exposed to discarded hypodermic needles or pathogens that may be present in the river. These situations, in combination, therefore demand that field biologists servicing the American River RSTs pay attention to, and implement, measures that are designed to ensure their safety and the safety of the public.

Crew members are required to wear their personal flotation devices at all times when they are on a boat or a trap.

Proper communication is essential when operating a motor vessel. When piloting a boat, the boat captain should make sure their intentions are clear to boat passengers. The captain should give clear warnings before they are about to engage or disengage the throttle, or make a turn.

This will give boat passengers proper time to sit down and become stable. The small boat used on this project can be very unstable especially when standing or kneeling, and may be easy to fall off of when an unexpected move is made.

Great care should always be taken when working on a RST. Be cautious to always keep hands, loose clothing, and other items away from the cone, shaft and other moving parts during trap operations. Be cautious when moving around on a trap because numerous hazards exist, e.g., the winch, cleats, cables, frayed cable, etc. Familiarize yourself with these hazards and use caution when moving about. Never move across the number one crossbeam (in front of the trapping cone) when the trap is fishing. If traps have been modified by installing catwalks in the front of the trap, biologists should use caution when they are on the catwalk and avoid the potential that they could accidentally end up inside the trap cone.

Always be aware of other crewmember locations and activities on the trap. Keep alert for boat traffic and boat wakes, and during high flow conditions watch for large debris that may collide with the RST or boat.

When pulling the boat up to a trap, all crew members should give this part of the operation their full attention. Do not place any part of your body in between the boat and a trap during an approach or while moored to a trap; together, the boat and trap can crush and cause severe injury to your body. If available, put the boat fenders over the side before pulling alongside a trap. The boat operator should drive the boat slowly when approaching a trap. The boat operator should carefully maneuver the boat alongside the trap pontoon so a crew member can step, not jump, from the boat to the pontoon. Once someone is safely on the trap and the boat has been secured to the trap, the boat operator can shut down the boat motor. The crew should make sure that the fenders are adjusted properly to prevent the boat and trap from rubbing together and that the boat is securely tied to the trap. The boat should never be operated directly in front of the trap; if the boat loses power, the current will push the boat into a trap cone and possibly damage and/or sink the boat. Assume the jet boat can lose the ability to propel itself when debris gets caught into the intake of the jet pump, and plan accordingly.

Transferring gear or persons between the boat and trap should occur with the full knowledge of all crew members. One person should be on the boat and another on the dock/trap and gear should be transferred from crew member to crew member. When stepping on or off the boat, be aware that the boat will shift. Furthermore, be very careful when stepping on or off the trap or walking on the trap. The pontoons and live-box lid may be slippery any time they are wet or biologist’s boots/shoes are wet, but they can be especially slippery due to frost or ice in the winter or algal growth in the spring and summer.

Check the winch cable and mooring cables for fraying. Use caution when handling cables to avoid punctures to hands from frayed cable. Check the following for damage: cone mesh, quick links, cleats, and eye bolts. If damage is found, notify the entire field crew of the damage and take steps to promptly repair that damage. When raising or lowering the trap cone or live-box door, all crew members should know each other’s whereabouts on or off the trap and everyone should be aware this procedure is taking place. One person should observe the trap cone while another person is raising or lowering the cone. Remember that it can be difficult to see the front of the cone when operating the winch. Crew members should look to make sure trap components are functioning properly, there are no obstructions in the pulleys and the #2 beam, collars are secure, debris has not accumulated on the trap components, winch cables are not damaged, etc. The person initiating a procedure should make it known by saying aloud that the trap cone or live-box door is about to be moved, and all others should acknowledge they are aware of what is about to take place. When the trap cone is being lowered, keep toes clear of the cone to prevent them from being crushed between the #2 crossbeam and the pontoon. Always secure the live-box door if it is in an open position to preclude the potential of being hit by the live-box door.

The crew should observe weather and river conditions prior to their day in the field. Utilize the guidance plots on the Department of Water Resources CDEC website to see if a forecasted increase of river rise and flow may occur when out in the field. On days when the river may rise, the crew must go to the field with waders and vest PFD’s. Such days tend to coincide with heavier and larger debris that may get caught on or in the traps.

COMPLETING DATA SHEETS

Properly completing data sheets is critical to project success; this aspect applies to every data sheet used during the American River RST project. Data sheets should be clear, legible, and contain all information needed to accurately interpret data at a later date, i.e., a data recorder should ask themselves if someone could accurately and completely infer what data were collected five years after the form was filled out. If there is more than one data sheet for a particular site, make sure they are labeled appropriately (e.g., site name, page 1 of 2, etc.). Make all information clear enough so someone not familiar with the field activities can interpret the data accurately (i.e., use standard abbreviations, no omitted data). There should never be any empty spaces for relevant data on a data sheet. If data are not taken, draw a line through the appropriate box and write a short explanation in the “Notes” section of the Trap Visit data sheet.

Additional comments regarding any variations in procedure, notable field conditions or other pertinent information should be recorded on the Trap Visit data sheet, e.g., any river conditions affecting trap operation or changes in a trap’s deployed position should be noted.

Use the following conventions when filling out data sheets:

1. A data sheet will be filled out every time a trap is set and every time a trap is checked.

Use a pencil, and your best and clearest non-cursive handwriting.

2. Corrections can be made by erasing a mistake if the sheet is dry, or putting a line through the mistake and clearly writing correct information nearby.

3. Completely fill out each portion of a data sheet. If a section of the data sheet is left blank, draw a line through it and explain why it wasn’t filled out in the “Notes” section of the data sheet.

4. NEVER ESTIMATE DATA, i.e., record measured values only. If a value cannot be measured, put a line in the box where that value would be recorded and provide an explanation in the “Notes” section of the data sheet.

5. Zeros and lines are not interchangeable. Zeros should be used if the value was measured and found to be zero, or if zero fish were captured. Lines should only be used if the measurement was not taken or the section was left blank.

6. If there were logistical or operational conditions that occurred and resulted in an atypical sampling period, completely and clearly explain what the conditions were in the “Notes” section on the data sheet. Keep explanations professional and organized for clarity. (Ex:

if the trap was stopped on arrival, explain in the “notes” section what appeared to have stopped it.)

7. If a site was sampled and no salmonids were caught, fill in all of the relevant fields on the data sheet with trap check and environmental data, and mark the boxes for salmonid catch with zeros. If no fish of any species were caught, put a note on the data sheet explicitly stating no fish were caught. The occurrence of situations with no catch data is critical because it is used in the calculations of juvenile salmon production estimates.

8. For all fish species, the lengths of dead fish should be recorded separately from live fish on the data sheet, and the appropriate mortality status noted.

9. Plus counted fish need to be clearly labeled as “Live unmeasured” or “Morts unmeasured.” Those numbers should then be totaled on the Trap Visit data sheet.

10. The presence and number of marked juvenile Chinook salmon that are captured (or recaptured) should be recorded on the Trap Visit data sheet in the special section reserved for those fish. If more than one kind of mark is observed in the fish captured on a given day, take care to segregate the data from fish with each kind of mark.

TRAP STATUS, ENVIRONMENTAL DATA, AND FISH CATCH DATA COLLECTION

The procedures described below are presented in the sequential order that would be implemented in the field. This work flow has been designed to make field activities as simple, efficient, and complete as possible.

When traps are deployed in a “cone-down” position and are actively fishing, they will be checked at least once every 24 hours, and more frequently on days when there are high river discharge levels, heavy debris loads, or the capture of thousands of salmon that could adversely affect the health of fish sequestered in RST live-boxes. On days when traps will not be checked within a 24-hour period, trap cones will be raised out of the water and placed in a “cone-up” position to preclude fish capture.

Trap Status and Environmental Data

When the field crew initially arrives at the trap, they should inspect the trap for any signs of trespass or damage before they exit the boat and step on the RST. If no signs of trespass or damage are found, the crew can board the trap and collect and record data on the Trap Visit data sheet that characterizes the operational status of the trap and environmental parameters at the time of the trap visit. A separate data sheet should be prepared for each trap cone. The following data should be recorded on each Trap Visit data sheet prior to processing the trap livewells:

Date

Trap ID

Visit type ID

Trap functioning ID

Cone intakes status

Before cleaning cone revolutions per minute (RPM)

After cleaning RPM (taken after the trap cleaning process detailed below)

Water velocity

River depth

Staff gauge and time

Water temperature

Water dissolved oxygen

Water sample taken indication

Weather (including air temperature)

If the trap is stopped upon arrival, record the total number of revolutions on the counter and explain the circumstances in the “Notes” section of the Trap Visit data sheet.

Refer to Appendix C for instructions on how to collect and record data pertaining to the trap status and environmental parameters.

Cleaning the Trap

Before all the fish have been removed from a RST during a day time check, the trap should be cleaned so it can operate as efficiently as possible.

After cone intake status has been assessed, the cone intakes should be cleared of debris. Extreme caution should be exercised when attempting to remove small or loose debris from a rotating cone or shaft. If debris cannot be removed while keeping hands well clear of the rotating intakes, lock the cone in a non-rotating configuration before attempting to remove the debris. Always inform all present crew members before stopping the rotation of a cone.

Check for and remove any large debris from the front of the trap, stopping the cone if necessary.

Remove any large debris caught inside the trap by stopping the trap, and opening a cone door to access the inside of the cone. Never, under any circumstance, crawl or climb inside the RST cone while the trap is on the river.

Clean the rear live-box screen with a scrub brush and rinse the debris off as best as possible.

Under no circumstances should the live-box screen be removed unless sampling has been terminated. If the live-box screen needs to be removed, all fish and debris should be removed first and a new time should be recorded for the Visit Time 2 field on the data sheet. Sweep silt/debris out of the live-box, rinse debris off the trap deck, and check/clean pontoons for algae growth.

If a trap cone needs to be raised or lowered for cleaning purposes (or if the trap needs to be moved on or off the river), always be cautious when using the winch crank. When raising the cone, keep a hand on the winch crank handle at all times and make sure the latch is caught in the gear securely. Latches tend to wear and if not secure, the winch handle may spin quickly and cause injury. Make no attempt to stop a winch handle that is unsecure and spinning quickly. If the trap cone needs to be lowered, one person will lower the trap cone, while another guides the

A frame. Be sure both individuals are aware of the other person’s actions and coordinate their respective activities. The person on the winch should announce that the trapping cone is coming down while the other person should watch for problems as the trap cone lowers.

After all debris has been removed from the cone intakes, the inside of the cone and the front of the cone, the cone exteriors should be scrubbed to remove built up algae. Cones can also be lightly tapped with a broom end to remove leaf litter and other small debris.

After the trap has been cleaned and is rotating in the water, the rotation rate of the cone should be assessed again and the RPMs are recorded in the, “After Cleaning RPM” field on the Trap Visit data sheet.

Fish Catch Data Collection

Weather and river conditions will dictate the order of the trap cleaning and fish processing activities. When the weather is cool and the potential that temperatures could be a stress factor for fish is minimal, trap maintenance activities should occur first, and then fish processing. This approach maximizes the amount of sampling to the fullest extent possible. If the weather is warm or fish could be adversely affected if they are held for a substantial period of time, the fish should be processed first, and then trap maintenance activities should occur. The text below assumes that trap maintenance activities will occur first since weather and river conditions will most commonly be benign.

If at all possible, the trap cone should not be raised before the fish are removed from the live-box. Raising the trap cone creates a gap through which fish can escape, so it is best to keep the trap cone in the fully down position until the live-box has been cleared.

Setting Up and Maintaining Buckets, Insulated Coolers, and Live Cars

Prepare to remove fish from the live-box by filling buckets with river water. Live cars or insulated coolers will also be prepared for fish sequestration if more than 500 fish are observed in the live-boxes when they are first checked. When fish are being held in buckets, place the buckets in the shade and place lids on top of the buckets when they are unattended.

Use the dissolved oxygen (DO) meter to periodically check the water temperature and dissolved oxygen levels in the containers used to sequester fish. Make sure the difference in water temperatures and dissolved oxygen levels between the buckets/coolers and river does not exceed a 2° Celsius or 7–10 milligrams/liter difference, respectively. Add fresh river water to the buckets and coolers if they become too warm or experience depleted dissolved oxygen levels. If necessary, use an aerator to help maintain DO levels that are equal to, or greater than, the river water. Frozen water bottles may be added to containers used to hold fish on warmer days to help maintain cool water temperatures.

Collecting Fish

Before clearing the trap live-box, set up a work station. Fill a large 18 gallon tote halfway with fresh water, and set up buckets filled with water within easy reach. Begin the process of clearing the trap live-box by scooping larger debris out of the live-box with a pitchfork, making sure to search that debris for fish. If fish are found with the large debris, remove the fish and place them in a bucket with fresh water. After the larger debris is removed, use the pitchfork to scoop debris from the surface of the live-box, shaking the pitchfork lightly to dislodge any fish trapped within the debris. Place the pitchforks of debris into the 18 gallon tote until the tote contains only as much debris as can be completely submerged by gently tamping down. Then, grab about a quart of debris from the tub at a time, and place on a flat surface such as a large fish measuring board.

Debris can then be spread out and sorted through to find any fish. Carefully sort through the debris using a stick, salad tongs, or other probe, DO NOT use your hands; hypodermic needles or other sharp objects could be present.

When debris is on the sorting surface, removed from the water, it is important to sort the fish out as quickly as possible. Carefully find and remove all fish, remembering that some will be very small. Place fish in buckets filled with water according to the conventions listed below.

After any fish have been sorted out, place the debris remaining on the sorting surface into a five gallon bucket, making sure to pack down the debris to get an accurate amount. When the five gallon bucket is full, discard the debris behind the trap, and keep tally of the number of buckets that have been filled to quantify the total amount of debris in the livewell. Collect man-made trash and dispose of it properly.

When a majority of debris has been removed from the live-box using the pitchfork, replace the water in the 18-gallon tub. Then, use a large net to scoop smaller debris and fish out of the live-box. Scoop no more than 1/2 a net of fish/debris at a time, and gently empty the nets to place the contents in the fresh 18-gallon tub of water.

When removing fish from the live-box, be careful not to smash fish between the rim of the dip net and the wall of the live-box. The live-box corners are typically where fish get killed. If feasible, chase fish out of the live-box corners before attempting to scoop them with the net.

Fish should be placed in separate buckets as follows:

a) All steelhead, late-fall-, spring-, and winter-run Chinook salmon.

b) Marked fall-run Chinook salmon.

c) Unmarked fall-run Chinook salmon.

d) Non-salmonid species, including larger piscivorous fish that could potentially feed on smaller fish as fish are held and processed.

Field biologists who have received adequate training should be able to recognize juvenile steelhead based on morphological features; Appendix F provides reference material that can be used to disseminate between steelhead and Chinook salmon. The presence of marked fall-run

Chinook salmon can be assessed by looking for fish with a colored mark or Bismark brown dye; it is especially important to examine every salmon to see if they have these marks since their detection will drastically affect the ability to develop salmon production estimates.

The presence of non-fall-run Chinook salmon can be ascertained by referring to the length-at-date charts developed by Fisher and Greene, i.e., salmon that have a fork length that is outside the length range for a given sample day could therefore be spring-, winter-, or late-fall-run

Chinook salmon.

Make sure fish are not over-crowded (i.e., < 50 smolts or < 100 fry per 5 gal bucket;

1,000individuals per standard-size cooler (18 gal)). If fish exhibit strange behavior, transfer them to another bucket/cooler to replenish oxygen and gently lower water temperatures. Fish that flare their gills or start to gather along the surface of the water are signs of reduced oxygen levels. With a large quantity of fish in the bucket, this can happen very quickly, especially when the weather is warm. Water in the 18-gallon tote should also be refreshed as necessary to ensure fish health.

At the moment the live-box is clear of fish and debris, two measurements must be taken and recorded immediately on the Trap Visit data sheet: (1) enter the time in the Visit Time 2 field and (2) record the Total Revolutions Since Last Trap Check on the counter. The Visit Time 2 field reflects the time that the trap was completely cleared of fish and debris for one day, and represents the start of the next sampling period that ends on the following day. The Visit Time 1 field should be filled out from the previous day’s Visit Time 2 field.

When finished, the total amount of debris captured in the trap should also be recorded in the

“Debris Volume” field on the Trap Visit data sheet, and the type of debris caught (aquatic or terrestrial) should be recorded under “Dominant Debris Type.”

Random-Sampling Protocol

During peak emigration periods, the RSTs capture more Chinook salmon than can be individually processed. On these occasions a sub-sampling protocol is used to randomly select

100 fish that are measured and weighed. A random sample is statistically representative of the non-sampled fish, therefore the information gathered from the sampled fish (FL measurements, run designation, etc.) can be generalized or expanded to describe the unmeasured fish. The following procedure pertains to the random selection of 100 Chinook salmon that are assessed for fork length, weight, and life stage. All Chinook salmon captured in excess of the measured

100 are referred to as “plus counts.” If less than 100 Chinook salmon are captured, every fish is assessed for fork length, and life stage, and >40 mm fish are measured for weight.

Typically, the first 120 or so Chinook salmon encountered will comprise the random sample.

However, these 120+ salmon should not be completely composed of salmon found while sorting through debris, as this may bias the random sample. Instead, the majority of the random sample should be obtained by using the net after most of the debris has already been cleared from the live well. Furthermore, the random sample should not contain spring- or winter-run Chinook salmon, since the “plus count” will not contain these runs. The protocol for the random sample is as follows:

1. As much debris as possible should be cleared out of live well to facilitate counting fish and to avoid crushing fish in debris when lifting out of the water with a net.

2. Refresh the water in the 18 gallon tub.

3. Using the large dip net, gently net out random groups of fish from the live box and place them into the tub of water.

4. From the tub, take a small dip net and randomly collect and count out at least 120

Chinook salmon and place them in an aerated holding bucket. These fish will be saved to weigh and measure. If estimating, it is better to err on the side of too many fish than not enough.

5. Fall-run Chinook salmon in excess of the random sample that remain in the tub or trap live well are not measured and weighed, but “plus counted” (i.e. enumerated and immediately released downstream of the traps.) However, each of the “plus count” salmon must still also be checked for marks and observed for length-at-date (LAD) run designation.

a. If a “plus count” salmon appears to be a spring-, or winter-run salmon by LAD criteria, it must be counted separately and assessed for fork length, life stage, and mark status, and a fin clip taken. Since Central Valley spring- and winter-run

Chinook salmon are federally listed as threatened or endangered taxa, the trapping activities must attempt to identify every spring- and winter-run Chinook salmon that is captured so that data can be reported to NMFS.

b. Late-fall run salmon are not listed as threatened or endangered, so LAD late fall-run Chinook salmon do not need to be separated out of the “plus count.” However if a “plus count” includes both LAD late fall- and fall-run Chinook salmon, this should be specifically noted on the datasheet.

Note: If a mark-recapture trap efficiency trial is scheduled to occur within the next 48 hours following capture, “plus counted” fish may be enumerated and retained for use in the trial, instead of released immediately.

Processing Fish

After the trap has been cleaned and fishing resumed, the collected fish should be processed in the following order:

1. Spring- and winter-run Chinook salmon (natural or hatchery)

2. All steelhead

3. Unmarked Chinook salmon random sample

4. Marked fall-run Chinook salmon

5. Non-salmonid species

The table below identifies how each group of fish should be processed. The data from those individuals should be recorded on their respective data sheets.

Sampling Strategy For Different Fish Species Collected During Rotary Screw Trap Operations

Spring and Winter-run

Chinook Salmon Steelhead

Unmarked Chinook

Salmon

(Random sample)

Marked Fall-run

Chinook Salmon Non-Salmonid Species

• Count • Count • Count • Count • Count

• Assess for mortality status and check for marks

• Assess for mortality status and check for marks

• Assess for mortality status and check for marks

• Assess for mortality status and check for marks

• Assess for mortality status and check for marks

• Measure up to 100 randomly-selected fish for fork length and assess for life stage

• Measure up to 100 randomly-selected fish for fork length and assess for life stage

• Measure up to 100 randomly-selected fish for fork length and assess for life stage

• Measure up to 100 randomly-selected fish for fork length and assess for life stage

• Measure up to 50 randomly-selected fish for fork or total length and assess for life stage

(adult/juvenile)

• Weigh the first 25 with fork length ≥ 40 mm

• Weigh the first 25 with fork length ≥ 40 mm

• Weigh the first 25 with fork length ≥ 40 mm

• No weight taken • No weight taken

• take fin clip (upper lobe of caudal fin) from each fish

• take fin clip (upper lobe of the caudal fin) from two late fall-run per day as applicable

• If more than 50 of one run, “plus count” remainder

• If more than 100, “plus count” remainder

• If more than 100, “plus count” remainder

• If more than 100, “plus count” remainder

• If more than 50 of one species, “plus count” remainder

Following the above table, fish will be evaluated for species and salmon run type (if applicable), counted, checked for marks and mortality status, measured for fork length, assessed for life stage, weighed, and will be clipped for genetic run assessment (spring-, winter- and a selection of late fall-run Chinook salmon only). Fish that are measured for fork length, weighed and/or clipped for genetic analysis should be anesthetized prior to processing using the procedures described in the “Anesthetizing Fish” section below. When processing, hands, dip nets, and measuring boards should always be wetted before coming in contact with fish.

Fish species identification can be accomplished using various keys that include fish found in the

Central Valley; Appendix E provides a species list for fishes that are likely to be caught in the

American River based on previous RST work, and the appendix identifies three references that can be used to identify fish species in California’s Central Valley. If a fish is collected and biologists are not sure of the species identification of that individual, several close up pictures of the fish should be taken with a digital camera. Biologists should then refer to the species list and references in Appendix E in an effort to determine the species ID. If a fish cannot be identified to species, then the data sheet should reflect a more general taxonomic name for that individual.

This situation may be especially true for various groups that include lampreys, Cottids (sculpins), Centrarchids (bass and sunfish), Catastomids (suckers) and Cyprinids (minnows). Individuals pertaining to these groups should receive special scrutiny in an effort to make taxonomic assignments as accurate as possible.

For fish identified as Chinook salmon, a salmon run designation will be assigned using Fisher’s length-at-date table. For each specific date, the table will be used to determine a maximum and minimum fork length for each salmon run. Salmon measured to have fork lengths between the maximum and minimum range for a given day will be given an “at-capture” run designation accordingly. Salmonids such as Chinook salmon and steelhead should also be checked for hatchery produced marks (i.e. a clipped adipose fin) or marks that could have been applied as part of a trap efficiency test described in the “Mark/Recapture Trials” section below. Salmonid life stages will be assessed according to the morphological features described and illustrated in

Appendix B.

All fish lengths will be measured to the nearest 1.0 millimeter using a measuring board. For fish species with a forked tail, fork length will be measured laterally along the mid-line from the tip of the snout with closed mouth to the center of the fork in the tail. For species without a forked tail (i.e., lamprey, sculpins, mosquitofish, threespine sticklebacks and some bullheads), total length will be measured laterally along the mid-line from the tip of the snout with closed mouth to the posterior edge of the tail.

Fish weights will be measured to the nearest 0.1 gram using a scale. When weighing, fish should be placed into a weigh-boat filled with fresh water instead of placed directly onto the scale surface. This will minimize the time the fish is out of water, limit stress and reduce fish movement while weighing. When placing the fish into a tared weigh-boat, care should be taken to minimize the loss of water, as this will affect the accuracy of the weight.

If river temperatures exceed 21°C, enumerate and release all listed species; do not hold for processing. On a case by case basis, if temperatures are high, and even with frequent water changes, air bubblers and frozen water bottles, fish health is a concern, enumerate the fish and release them. Additionally, if individual fish appear to have diminished health (obvious wounds, extended trouble staying upright, etc.) minimize handling of these fish; enumerate and release them immediately.

All fish species should be released below the RSTs after they have been processed, unless the fish will be used for an efficiency trial or euthanized and retained for study purposes.

Anesthetizing Fish

Fish that are assessed for fork length, total length, and/or weight, should always be anesthetized prior to measuring. To anesthetize fish, a solution with Alka-Seltzer is used. In general, fish are immersed in a bath of Alka-Seltzer at a concentration of one tablet for each liter of water. The action of the anesthesia is readily reversed when fish are transferred to fresh water.

The effectiveness and effect of premixed solutions is related to a variety of factors including concentration, fish size, water temperature and stock solution age. Overexposure (in time or concentration) to the Alka-Seltzer solution will lead to death of fish. Biologists should always observe the gill activity of fish immersed in an anesthesia solution; fish with markedly reduced gill activity should be transferred immediately to fresh water for recovery.

Fish should be placed in the Alka-Seltzer solution in batches of ~25 individuals to avoid anesthetizing more fish than can be processed. Fish size and the crew member’s quickness in measuring fish are factors that should be considered when determining how many fish to anesthetize at once.

After fish have been measured they should immediately be placed in a 5 gallon bucket of fresh water for recovery. This bucket should contain 1 teaspoon of Poly Aqua to aid in recovery. Poly

Aqua will aid in the regeneration of their slime coat that may have been shed during capture and handling. Once fish have fully recovered, they can be released back in the river.

Collection of Fin Clips

Fin clips will be collected from all juvenile salmon that key out to be spring- or winter-run

Chinook salmon according to the length-at-date criteria and from a selection of salmon that key out to be late fall-run by LAD criteria. These fin clips will ultimately be used to assess the salmon run of each clipped individual. The fin clips should be collected after the fish has been anesthetized, measured and weighed, by taking a small pair of surgical scissors and removing not more than ¼ of the upper lobe of the caudal fin. The fin clip should then be placed in a vial with

200 proof ethanol. The vial number should be recorded on the datasheet next to the data describing the clipped individual. The vial should then be stored in the office to avoid contamination or accidental use for additional clips.

Field Quality Check

The first step of data quality assurance/quality check (QA/QC) happens in the field. After all the data have been collected during a sampling visit, each data sheet should be reviewed before the biologists leave the trap site to make sure all information is complete, and any missing values are collected. Common errors include leaving blanks on the data sheet, illegible entries, clarity of plus counts, incorrect species or station codes, and unclear comments. The field quality check should occur before leaving the site so additional data can be collected if necessary. Do not leave data sheets in vehicles or in clipboards as they may get lost or damaged, and return the completed data sheets to the office the same day they are filled out.

Trap Maintenance

Before the field crew leaves the traps at the end of a sample period, they should inspect:

1. The live-box seal for any cracks and proper seating around the trap cone.

2. The trap cone shaft and bushings for cracks and abnormal or excessive wear.

3. The cone’s screen for any tears, separation from the cone frame, and the access doors for proper closure. Rivets that attach the screen to the frame often need replacing throughout the season.

4. The winch system, including the cable and pulley, for proper function.

5. The counter system for proper function.

6. The anchor points and cabling system for weaknesses/non-secure attachment.

7. That the collars are firmly attached and the collar bolt is tight. The collar should not spin independently of the axle.

MARK/RECAPTURE TRIALS

RSTs only capture a small fraction of the total number of fish migrating past a trap. To estimate the total number of fish migrating past the RSTs on the American River, it is necessary to conduct mark/recapture trials to quantify trap efficiency; i.e. the percentage of the total fish population sampled by the traps. These trials should, under ideal circumstances, be conducted in a manner that reduces sampling bias, and should be conducted as often as possible, or whenever there are substantial environmental changes that could affect the efficiency of the traps, such as a marked increase in stream discharge. Potential sources of bias that could affect the accuracy of the trap efficiency tests are as follows:

1. The behavior of the fish that are captured on a daily basis is different than that of the fish used in trap efficiency trials.

2. The trap efficiency test fish are not recognized as they are recaptured.

3. Predation of released fish

4. Schooling of released fish

5. The environmental factors during the efficiency test period change dramatically

The following describes the procedures that should be taken to avoid the aforementioned sources of bias for each trap efficiency test.

Under ideal circumstances, wild salmon should be used instead of hatchery salmon when conducting trap efficiency tests. Wild salmon that are caught with the RSTs should therefore be used to conduct trap efficiency tests whenever possible. With that sampling in mind, field staff should retain captured wild fish and sequester them in live cars that are held in the RST live-boxes until such time that a sufficient number of salmon have been collected to conduct a trap efficiency test. Based on historical trap efficiency results, field staff should strive to release at least 1,000 fish during a given efficiency test. Releasing a smaller number of fish has historically resulted in too few recaptures to make the trap efficiency test worthwhile.

To conduct the trap efficiency trials, fish are marked with a colored Visual Implant Elastomer

(VIE), photonic dye and/or a Bismark brown Y stain (BBY). Photonic dye and/or VIE is the preferred method of marking fish, as they are typically less stressful for the fish and may be less likely to affect predation. These tagging methods can be difficult to apply to fry and are therefore used on larger salmon, greater than 50 mm in fork length, as described in Appendix H: Process for Marking Chinook Salmon with Photonic Dye and the VIE Project Manual from Northwest

Marine Technology https://www.nmt.us/wp-content/uploads/2017/11/VIE-Project-Manual-Nov-

2017-1.pdf. Fish less than 50 mm in fork length must be dyed with the BBY whole body stain as described in Appendix G: Process for Staining Chinook Salmon with Bismark Brown Dye.

To create the ability to discriminate between different groups of marked salmon that were marked as part of a trap efficiency test, it is critical that the marking patterns be applied in a manner and combination where biologists can successfully discriminate between different groups of marked fish. Combinations of marking patterns that could cause confusion in proper identification, e.g., applying a green mark to the upper caudal fin one week and then applying a blue mark to the upper caudal fin the following week should also be avoided.

Complete the Marking Data Sheet and Marked Chinook Salmon Data Sheet and be sure to accurately quantify and record the number of salmon that were successfully dyed or stained.

Take a random sample of 100 of the successfully marked salmon and measure and record their fork lengths. Record any mortalities that occurred during the marking process.

Fish will then be transported to the release site at approximately one pound of fish per gallon of water; therefore the amount of coolers/aerated containers will vary depending on the size of the fish. The appropriate dosage of slime coat protectant should be added to each aerated cooler to ensure fish health. On warmer days, ice may need to be added to fish holding containers to keep the holding water from becoming too warm. The DO and water temperature in the transport containers should be noted and recorded before leaving the hatchery.

https://www.nmt.us/wp-content/uploads/2017/11/VIE-Project-Manual-Nov-2017-1.pdf https://www.nmt.us/wp-content/uploads/2017/11/VIE-Project-Manual-Nov-2017-1.pdf

Releases should occur as close to twilight/dusk to reduce the risk of predation on marked salmon.

Therefore, field staff should plan accordingly to ensure they can conduct all the necessary activities to release fish by sunset. There are two release distribution methods used depending on river flow. If the current river flow is below 1,500 cfs, fish will be transported to the release site via truck and set in the river in an appropriate amount of live cars to acclimate. Then wading across the width of the river, fish should be released in small net fulls (piecemeal) so that they don’t have an opportunity to “school” as they move downstream. If flows are above, 1,500 cfs, the same distribution method is used via boat rather than wading. If a boat is used to release fish and must travel downstream after a release, remain at the release site for ~15 minutes, then float or row downstream. Prior to release, record the number of dead or weak swimming fish and remove them from the live marked fish; these fish will not be released at the site rather released downstream and excluded from the trap efficiency trial.

It is important to note that fluctuating river flows will impair the accuracy of a trap efficiency trial. Therefore, releases should occur when discharges from Nimbus Dam are stabilized.

Additionally, for more accurate passage estimates, an effort should be made to conduct as many trap efficiency trials as possible at various river flows.

COMPUTER DATA ENTRY AND MANAGEMENT

Data sheets need to be delivered to the data manager or placed in the “Completed Datasheets” paper tray before the end of each work day.

Data Entry

Data will be stored and analyzed in the Comprehensive Assessment and Monitoring Program’s rotary screw trap platform (Platform). Data should be entered in the Platform as soon as possible after collection. Care should be taken to assure data are entered correctly.

QA/QC Procedure

Ensuring that field data is entered into the Platform accurately and completely is essential to data management.

First, data sheets will be checked as described in Appendix I to make sure the data sheets have been completely filled out and there are no errors before data are entered into the CAMP

Platform. Any corrections made during this process will be made in red ink. Datasheets that have been checked for quality assurance should be indicated by initials and date. Corrected data will be entered into the CAMP Platform by the data lead and then QA/QC’d by crew members to ensure that data has been entered correctly.

The verification process will check for entry errors by comparing data sheets with queries that produce hard copy reports of data entered into the Platform. If errors are found, they will be noted on the QA/QC Datasheet with the appropriate correction. To minimize the possibility that entered errors are overlooked, the QA/QC process of entered data should never be done alone. After data is checked, QA/QC data sheets will be signed with initials of the persons checking data and the date verified. The data lead will then correct entries in the CAMP

Platform.

The Platform and its associated QA/QC database have a number of tools that were developed to look for problems in the quality of the data and the data entry process. Staff that enters data into the Platform should refer to, and become familiar with, the user manuals that were prepared for the Platform and the QA/QC database; doing so will provide the ability to detect and then correct problems with the RST data.

Data entry error example: in the course of reviewing the measurements of the randomly selected juvenile salmon that were measured on day X, a salmon is found that is outside the typical size range for a fall-run Chinook salmon on day X based on the length-at-date criteria, the record for that salmon needs to be changed to reflect the appropriate salmon run according to the length-at-date criteria for the day that fish was captured. The person who finds this error should report it on the QA/QC data sheet with their initials, and date verified. Then return the QA/QC data sheet to the data crew lead so that the CAMP database can be updated accordingly.

An effort should be made to verify data on a weekly basis. The QA/QC routines in the platform should be executed and the reports associated with those QA/QC routines should be checked to look for missing data, out of sequence records, and biological attributes that are unusual or abnormal.

After the data has been verified by the crew, the data crew lead will use the QA/QC database provided by Connie Shannon to further check for any additional data entry errors that may have occurred during the data entry process.

APPENDIX A: Field Data Sheets

Trap Visit Data Sheet. Used to record environmental data, trap data, and summarize catch totals.

Unmarked Chinook Salmon Data Sheet. Used to record a random sample of 100 Chinook salmon.

Unmarked Steelhead Data Sheet. Used to record a random sample of 100 steelhead.

Spring-run and Winter-run Chinook Salmon Fin Clip Data Sheet. Used to record data on spring-run and winter-run Chinook salmon when fin clip samples are taken.

Photonically Marked Chinook Salmon Data Sheet. Used to record data on hatchery Chinook salmon that have been marked with photonic fluorescent dye used for a trap efficiency trial.

Recaptured Chinook Salmon Data Sheet. Used to record data on Chinook salmon after they’ve been recaptured from a trap efficiency trial.

Adipose Fin Clipped Salmonid Data Sheet. Used to record data on ad-clipped (hatchery origin) Chinook salmon or steelhead.

(Not Random)

Other Species Data Sheet. Used to record data on bycatch (species of fish other than our target taxa).

Marked Data Sheet. Used to record data during marking on

Marked Chinook Salmon Data Sheet. Chinook salmon after they’ve been marked for a trap efficiency trial.

APPENDIX B: Chinook Salmon and Steelhead Life Stages

Smolt Index Life Stage Criteria

1 Yolk-sac…