Have you ever reeled in a fish and seen a strange tag sticking off it? Chances are, that fish was part of a mark-recapture study. Capture-mark-recapture techniques (called “mark-recapture” for short) are used by fisheries biologists and managers to answer the question, “How many fish are there?” One of the biggest challenges in fisheries management is estimating the size of fish populations, but this information (also called abundance) is important for conservation and managing sustainable fisheries. In some cases, it is relatively easy to know a population’s size. For example, fish hatcheries know almost exactly how many adults they bring in for their broodstock, and they usually have a pretty good idea how many offspring are produced. By using a fish counting device like the Vaki Riverwatcher, biologists can know the almost exact number of adult salmon returning to a stream to spawn. But most of the time, it is much more difficult to know just how many fish of a certain species are in a body of water. When the exact number cannot be determined, we use statistics to come up with an estimate of population size.

Mark-recapture techniques have a long history in wildlife and fisheries biology because they can be used to estimate population size as well as population survival and growth. As the name of the technique implies, individuals of a population are captured using a sampling method and marked in some manner, such as with a tag. These marked individuals are then released back into the wild in hopes of being recaptured or re-sighted one day. Information on the number of marked recaptures and unmarked captures can be used to estimate population size, as shown in the diagram below.

Imagine that we want to determine how many bass are in a local fishing pond using a mark-recapture study. We treat the pond as a “closed system,” meaning no fish are entering (also no births) or leaving the pond (and no deaths) during the study. The simplest method to estimate how many fish are in the pond is called the Peterson method (also known as the Lincoln-Peterson index). To do this, we catch as many bass as we can in one trip, which is our sampling. Before releasing the fish back in the pond, we mark them in some way (with an external tag, fin clip, dye, PIT tag, etc.). Then, when we come back on the next trip, we catch fish again and count how many marked and unmarked bass are in our new sample. The proportion of marked bass recaptured out of the total number marked can be used to expand the number of unmarked bass caught on the second trip to a total population abundance.

This sounds simple enough, but things get more complicated in “open systems,” where fish can move freely in and out of the sampling area, and when a study spans multiple years, so individuals are born into the population or are harvested. This is the case with our ongoing study to estimate the population size of striped bass in the San Joaquin River using fyke traps and mark-recapture methods. The bass that we capture in our fyke traps are marked externally with numbered disc or spaghetti tags, and also tagged internally with PIT tags. However, striped bass are very mobile and not confined to just the San Joaquin River. Also, as a popular sport fish, they are subject to being harvested. So, to get an accurate estimate of population size, we need to account for movement and fishing pressure, and that is where anglers can be part of the recapture process too! If you call to report one of our tagged fish, you will be helping to improve knowledge on striped bass harvest and movement in and out of the San Joaquin Basin. Check out this video to learn more about our striped bass mark-recapture study.

Sometimes cutting off salmon heads is all in a day’s work. But it’s not a macabre fetish – we’re after valuable information about the fish’s life stored in its ear bones, or otoliths, which record rings like trees. The salmon have already died naturally after spawning, so we are taking this data opportunistically – which sometimes it means ending up with a freezer full of fish heads. This photo recently won our staff Photo of the Month contest for its unique perspective. Are you ready to saw?

While salmon have a high intrinsic value for ecological and cultural reasons, it is also possible to assign them a dollar amount – although not always easy. Each year, the National Marine Fisheries Service (NMFS) releases estimates of the economic impacts from commercial and recreational fisheries of two years prior. As you might expect, every year we hone in on the report’s data from salmon fishing in California. We are generally surprised by the overall lack of information on the economics of California’s commercial and recreational salmon fisheries. To help address this gap, for the last few years we have used the NMFS report (which provides estimates of economic impact) along with data from the Pacific Fishery Management Council (which provides estimates of the number of fish harvested) to calculate the economic impact of an individual salmon in California. Crunching the numbers for 2015 reveals that while the economic impact of each individual salmon was much higher than in previous years, the total economic impact of the fishery was a fraction of previous years due to reduced fishing opportunities and a fish population hit by drought.

Figure 1. Total economic impact of the commercial and recreational salmon fishery in California.

The majority of salmon caught in the 2015 fishery were born in the middle of a historic drought that drastically reduced the survival of juvenile salmon. As a result, the economic impact of the 2015 fishery was substantially lower than in previous years. The 2015 commercial and recreational salmon fishery in California had a total combined economic impact of approximately $121 million in terms of income, sales, gross regional product, and ripple effects to the economy, which was less than half of the 2013-2014 average ($276 million). Most of this was generated from the commercial salmon industry, which had an overall economic impact of approximately $88 million dollars for the state in 2015 in terms of sales, income, and value added to the economy (e.g., fees/licenses, boat maintenance, fuel, bait/tackle, and other associated goods and services used by commercial anglers). The economic impact of the commercial fishery was much less than in previous years (2013-2014 average of $188 million), reflecting a reduced catch that likely resulted from poor recruitment and juvenile survival during the drought. The 2015 commercial fishery harvested a total of 110,507 salmon, with total landings of 1.3 million pounds and revenues of $8.1 million (NMFS 2017, PFMC 2016). Commercial fishermen received an average ex-vessel price of $6.02 per pound at the dock, which is the highest ex-vessel price in recent years, and nearly $1.50 more than the 2006-2014 average (PFMC 2016).

Figure 2. Per-fish economic impact of a salmon caught in California in 2015.

Recreational angling had an economic impact of approximately $33 million in 2015, which was substantially lower than in previous years (Figure 1). The impact of the 2015 recreational fishery was less than half of the 2014 value, and less than a third of the 2013 value, which was a direct result of limited fishing opportunities and a reduced harvest in 2015. Recreational fishers harvested only 37,480 salmon from the ocean and 17,715 salmon from the state’s rivers, for a total recreational harvest of 55,195 salmon (PFMC 2016). To compare the relative value of commercial and recreational fishing industries on a per-fish basis, we calculated an estimate of economic impact for each fish caught in the state, which is based on metrics developed in 2001 by a state economist with the U.S. Department of Agriculture’s Natural Resource Conservation Service (Ransom 2001). Based on this estimate, the economic impact was $1,236 for each salmon caught recreationally in river, $295 for each recreationally caught ocean salmon, and $214 for each commercially caught ocean salmon (Figure 2). While the estimated value of a commercial fish is substantially higher than our estimates in previous years (which ranged from $138-151), it is still much lower than the value of a recreationally caught fish due to the necessarily higher efficiency of commercial fishing: one day of commercial fishing yields many more fish than one day of recreational fishing.

Any discussion of the economics of salmon in California should also consider the overwhelming contribution of the hatchery fish to the state’s salmon population, which carries a price tag of nearly $9 million per year in the Central Valley. Despite several warnings, very little is done to differentiate between wild and hatchery fish in California, resulting in challenges to promote natural spawning of wild fish in the state’s rivers while also producing hatchery fish for harvest. A relatively simple solution, the mass marking of all hatchery fish, would facilitate several key recovery activities (e.g., population assessments, broodstock management, limiting strays, and mark-selective fisheries) that could allow for increased harvest in addition to increased populations of naturally spawning salmon. These efforts ought to be implemented as part of a more holistic approach to salmonid management, in which hatcheries are not focused solely on releasing large numbers of fish, but instead are also considered alongside habitat quantity and quality, and juvenile survival. Ensuring long-term increases in economic benefits while supporting abundant wild salmon is an attainable goal in California, but will require some new approaches.

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

For the last few years, we’ve been conducting a study in the San Joaquin River for which we deploy multiple fyke traps in the spring and early summer to catch, tag, and release striped bass, black bass, and catfish species. One of the objectives of the study is to estimate the population abundance of these target species in the San Joaquin River, much like the California Department of Fish and Wildlife has been doing for striped bass in the Sacramento River since 1969. In order to calculate accurate population estimates, it is essential to tag and release as many fish as possible to improve the probability of recapturing a significant number of those tagged fish. There are several ways to increase the odds of capturing and recapturing the target species, such as using more fyke traps, sampling for a longer time, or increasing the efficiency of the trapping method (design a better trap). But one of our biggest hurdles is permitting constraints: we are only allowed to handle the targeted species when water temperature remains below a predetermined threshold. This temperature constraint is for the welfare of the fish to reduce stress and risk of mortality.

To help improve our study estimates, we have been trying to increase the number of fish that are tagged with Passive Integrated Transponders (PIT tags) by piggybacking on other projects that capture our species of interest. One of our electrofishing projects in the South Delta as well as electrofishing and fyke trapping efforts conducted by the U.S. Bureau of Reclamation as part of the San Joaquin River Restoration Program have all been tagging our species of interest when they are encountered. We currently have multiple methods of recapturing tagged individuals, which include catching them in our own fyke traps, detecting them with PIT tag antennas in the weirs on the Stanislaus and Tuolumne rivers, recapture by other research projects, and reporting of tag recaptures by anglers.

This year, we tested a novel idea to further increase our fish recaptures: we modified a fyke trap so that it does not actually trap fish, but allows the fish that enter to pass through and continue on their way while passing through a PIT antenna. We are referring to this modified piece of equipment as a passive fyke. A fyke trap usually has two cones, or fykes, that constrain the fish to pass through smaller circular openings until they become trapped in the upstream end of the trap, and are unable to find the opening through which they entered. To modify this trap, we removed one of the cones so that fish only have to pass through a single three-foot-diameter circular opening containing an integrated PIT tag antenna (shown in the photo below). The outer wire mesh on the upstream side of the trap was removed to allow fish to freely exit the trap. We have also included underwater cameras to record fish that pass through the fyke and integrated PIT tag antenna.

Because no fish are handled by people with this device, we can continue to sample later into the summer as water temperatures increase and we are not allowed to trap and handle individuals. The hope is that PIT tagged fish will pass though the antenna on the passive fyke and get recorded by a shore-based recorder. The cameras will also allow us to determine the number of untagged fish passing through the passive fyke. This system requires weekly battery replacement and data downloads, and is expected to significantly improve our odds of collecting additional recapture data. It shows that with some creativity, even fish trapping can be automated.

Have you ever reeled in a fish and seen a strange tag sticking off it? Chances are, that fish was part of a mark-recapture study. Capture-mark-recapture techniques (called “mark-recapture” for short) are used by fisheries biologists and managers to answer the question, “How many fish are there?” One of the biggest challenges in fisheries management is estimating the size of fish populations, but this information (also called abundance) is important for conservation and managing sustainable fisheries. In some cases, it is relatively easy to know a population’s size. For example, fish hatcheries know almost exactly how many adults they bring in for their broodstock, and they usually have a pretty good idea how many offspring are produced. By using a fish counting device like the Vaki Riverwatcher, biologists can know the almost exact number of adult salmon returning to a stream to spawn. But most of the time, it is much more difficult to know just how many fish of a certain species are in a body of water. When the exact number cannot be determined, we use statistics to come up with an estimate of population size.

Mark-recapture techniques have a long history in wildlife and fisheries biology because they can be used to estimate population size as well as population survival and growth. As the name of the technique implies, individuals of a population are captured using a sampling method and marked in some manner, such as with a tag. These marked individuals are then released back into the wild in hopes of being recaptured or re-sighted one day. Information on the number of marked recaptures and unmarked captures can be used to estimate population size, as shown in the diagram below.

Imagine that we want to determine how many bass are in a local fishing pond using a mark-recapture study. We treat the pond as a “closed system,” meaning no fish are entering (also no births) or leaving the pond (and no deaths) during the study. The simplest method to estimate how many fish are in the pond is called the Peterson method (also known as the Lincoln-Peterson index). To do this, we catch as many bass as we can in one trip, which is our sampling. Before releasing the fish back in the pond, we mark them in some way (with an external tag, fin clip, dye, PIT tag, etc.). Then, when we come back on the next trip, we catch fish again and count how many marked and unmarked bass are in our new sample. The proportion of marked bass recaptured out of the total number marked can be used to expand the number of unmarked bass caught on the second trip to a total population abundance.

This sounds simple enough, but things get more complicated in “open systems,” where fish can move freely in and out of the sampling area, and when a study spans multiple years, so individuals are born into the population or are harvested. This is the case with our ongoing study to estimate the population size of striped bass in the San Joaquin River using fyke traps and mark-recapture methods. The bass that we capture in our fyke traps are marked externally with numbered disc or spaghetti tags, and also tagged internally with PIT tags. However, striped bass are very mobile and not confined to just the San Joaquin River. Also, as a popular sport fish, they are subject to being harvested. So, to get an accurate estimate of population size, we need to account for movement and fishing pressure, and that is where anglers can be part of the recapture process too! If you call to report one of our tagged fish, you will be helping to improve knowledge on striped bass harvest and movement in and out of the San Joaquin Basin. Check out this video to learn more about our striped bass mark-recapture study.

Fall is in full swing, and so is the fall-run Chinook salmon migration in the Central Valley.  As is our fall tradition, we’ve installed fish counting weirs on the Stanislaus and Tuolumne rivers as part of our annual salmon monitoring. These fence-like structures direct fish through a single opening into a Riverwatcher scanner, which gives us a count, measurement, and video clip of every single passing fish. This set up provides a highly accurate way to monitor the salmon migration in real time on both of these tributaries to the San Joaquin River. As of Tuesday, November 5, our weirs had documented 1,406 salmon on the Stanislaus River and 1,054 salmon on the Tuolumne River. While the numbers are a bit lower than last year (when we had 3,289 and 2,316 salmon on each river, respectively, at this time), there should still be fish spawning activity to witness at the upcoming Stanislaus River Salmon Festival this Saturday, November 9, from 10 am–3pm at the Knights Ferry Recreation Area.

If you stand on the bridge at Knights Ferry and observe salmon in the river down below, those fish have migrated more than 180 river miles from the Golden Bridge – and that’s after migrating many more miles in the ocean! It’s a truly incredible feat worth celebrating. These long-distance swimmers play an important role in delivering nutrients from the ocean to the rivers where they come to spawn. In fact, much of the nitrogen in trees and other plants growing along streams in some areas can be traced back to the ocean and was delivered by spawning salmon. We recently shared this story of salmon migration with many schools near our Oakdale office as part of their annual Ag Days, and also with dozens of students from Manteca as part of a recent AgVenture outreach event.

Our team is gearing up for another big presence at this year’s Stanislaus Salmon Festival as part of another fall tradition. We’ll have revamped our “Salmon Cam” so you can watch salmon on their redds from different angles, and will have some fun new games at our booth. Come learn how salmon “smell” their way home to their spawning locations, or how we use microchips to do mark-recapture studies on fish! We’ll also be bringing out one of the inflatable catarafts used for our electrofishing studies on the Stanislaus River. Visitors will be able to climb inside to see what if feels like to sit at the oars. The 11th annual Salmon Festival is sure to be a fun and engaging event for the whole family, complete with more than 35 different exhibitors staffing interactive booths, fly fishing demonstrations, carcass surveys, musical performances, and plenty of food, crafts, and calendars of student salmon artwork available for purchase. Please stop by our booth to say hello!

With a new mark-recapture project getting underway in the San Joaquin River, we recently held a training at our Oakdale office to make sure all of our field crew have their fish tagging skills up to speed. We tag fish for a variety of reasons at FISHBIO. Sometimes we mark juvenile salmon with temporary dye to test the efficiency of our rotary screw traps. Sometimes we use sophisticated tags, such as acoustic tags, to track the movement of a fish. And sometimes we want to apply a simple but lasting tag with a unique number to help us identify a fish if we recapture it in the future. The recent training focused on applying colorful external t-bar and disc tags, as well as internal Passive Integrated Transponder (PIT) tags that will be used as part of our mark-recapture study to estimate the fish population sizes in the San Joaquin River.

The training was a good refresher, since we also use PIT tags to monitor steelhead on one of our study rivers. PIT tags are like the microchips implanted in cats or dogs, and can be used to assign each fish a unique code.  The tags do not have an internal battery, so they never expire, and are read using radio frequency to excite the tags at an antenna or hand-held reader. We tag rainbow trout (Oncorhynchus mykiss) to see whether they stay in fresh water or go out to the ocean and return a few years later. To apply the tags, we make a small incision in the abdomen of the fish behind the pectoral fins and slide the tag into the open cavity. After a small amount of glue is applied to quickly seal up the incision, the fish is back in the water within seconds to continue its journey. With a few rounds of practice in our Fish Lab under their belts, our crews are ready to be efficient and effective fish taggers.

Juvenile salmon outmigration season is underway! As the young fish make their way through the rivers and out towards the ocean, we monitor their population with the help of rotary screw traps. Today’s Film Friday selection shows you how we mark some of the fish we capture with photonic dye. The number of marked fish that we recapture helps us calculate how efficient the trap is. Working together, we were able to mark 2,500 fish in a single day!

The Vaki Riverwatcher (www.riverwatcher.is) is used to monitor fish movements in more than 300 rivers in countries all over the world, including Canada, China, the Czech Republic, Germany, Iceland, Ireland, Poland, Portugal, Scandinavia, South Korea, Spain, Switzerland, the United Kingdom and the United States. This robust distribution leads to many users with questions about the device. As the North American distributor for Vaki, FISHBIO often receives questions from current and prospective Riverwatcher users, which inspired us to produce some videos to help answer the most frequently asked questions. The 10 most frequently asked questions and their answers are provided in the video series “FAQs – The Vaki Riverwatcher.”

The Riverwatcher is an infrared fish counter that utilizes an underwater camera and lights to provide a robust record of fish passages, and records information in a database that is organized for efficient and accurate data summary and reporting. As many fish biologists know, scanning endless hours of video surveillance from video monitoring studies or scouring a particular spot in the river for hours in all weather conditions is not only a daunting task, it is also very labor intensive, which increases project costs. Installing an automated fish counter like the Riverwatcher can significantly reduce the time and effort needed monitor fish passage events.

One of the most frequently asked questions we receive is, “Does the Riverwatcher automatically identify species?” Although the Riverwatcher does not automatically identify species, biologists find that one of the advantages of using the Riverwatcher is that it takes considerably less time to manually identify species when utilizing the intuitive Winari database software.  Riverwatcher users around the world have reported the ability to process 24 hours of data (or about 500 passages) in 15 minutes, which results in budget savings that can be used for other studies to answer questions that are generated after analyzing multiple years of Riverwatcher monitoring data collection.

Another frequently asked questions is, “How does the Riverwatcher detect fish?” The Riverwatcher uses infrared light to detect fish. In order to accomplish this, fish are directed between two scanner plates that consist of one infrared light transmitting plate and one infrared light receiving plate. As the fish passes between the scanner plates, the transmittance of infrared light between the two plates is interrupted, thereby triggering the Riverwatcher system to record the event as a passage. Subsequently, the system records more detailed information from the passage event.

Many people also ask, “Does the Riverwatcher work in turbid water?” Yes, this is one of the biggest advantages of the Riverwatcher: you can still detect and identify fish passages during high turbidity events. The scanner plates transmit light to detect fish passages, so as long as the light can be transmitted through the turbid water from one scanner plate to the other, you can efficiently count fish.

Check out the video series to learn the answers to more frequently asked questions. We hope that you find these videos helpful – and if you still have unanswered questions, or want more information relevant to your specific monitoring challenges, don’t hesitate to contact us. We always enjoy answering people’s questions because we usually learn from the discussion too!

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

If uncoiled and stretched to its full length, the DNA contained in a single human cell would be about two meters long, and the total length of all the DNA in a human body would span twice the diameter of the solar system! This astonishing abundance of genetic material means that living organisms are constantly shedding a massive library of genetic data into their environment in the form of sloughed off cells as they go about their lives, thereby providing a molecular trail of breadcrumbs for scientists to follow. This DNA that exists outside of an organism is known as environmental DNA, or eDNA, and a rapidly growing field of science is focused on the detection and analysis of these molecules. Environmental DNA represents a particularly powerful tool in aquatic habitats, where taking a water sample can help detect fish species that are rare or difficult to sample with traditional methods, determine which fish species are spawning in a given area, detect nearby terrestrial animals, and much more. To overcome the challenges of detecting and analyzing eDNA, scientists are developing, standardized approaches, such as a new eDNA sampling backpack, that allow for more accurate and precise results.

Similar to other innovations in fish sampling technologies, such as early prototypes for electrofishing systems, scientists working with eDNA have been exploring various methods using modified tools that were built for other purposes. For example, some protocols have required taking large volumes of water back to the lab for processing, whereas others have required filtering water in the field using home-made or repurposed filtration systems. Although these experiments have yielded insightful information, the lack of standardization among a variety of approaches and equipment makes it difficult to compare the efficiencies and results of various studies. In an attempt to address this issue, Smith-Root, Inc. has created a purpose-built eDNA sampling system. The ANDeTM Sampling Backpack is modeled on their backpack electrofishing systems, and a recent publication describes the process through which it was developed (Thomas et al 2018).

This intelligent pump system can regulate water filtration based on input from multiple sensors, allowing the user to control important variables that may affect eDNA detection, such as pressure, filtration rate, sample volume, and filter size. As part of their development process, the Smith-Root biologists evaluated each of these variables and provided recommendations on how to achieve the best retention of eDNA on the filters. FISHBIO recently tested out  the ANDeTM system as part of  habitat surveys in southern California streams in an attempt to detect federally endangered Southern California Coast steelhead (Oncorhynchus mykiss). Using traditional seining, snorkeling, or electrofishing approaches in these streams would require crews to sample many sites in difficult-to-access areas and would inevitably disturb these endangered fish. Instead, collecting water samples for eDNA analysis at just a few key locations over the course of several months will allow FISHBIO biologists to non-invasively and efficiently determine if and when O. mykiss are present in the system. This new tool promises to be a valuable asset in FISHBIO’s arsenal of fisheries sampling equipment and will allow for a novel approach to the study and monitoring of important fish species.

With the fall salmon migration now underway, we will soon be conducting surveys to understand which habitats are best suited for salmon spawning. Read how we get a lay of the land in today’s Flashback Friday.

Characterizing habitat types is an important component of environmental science, and many of our projects require understanding a study site’s geography (see On Point, It’s a Wrap!). To collect this information, we often conduct stream cross sections. We first divide the river into a number of sections that represent the length of the study site, then take depth and velocity measurements at equal distances across the width of the stream in each section. Cross sections allow us to piece together a habitat map based on data collected at different points that represent the habitat as a whole.

The technician seen here is taking velocity measurements while out on a redd survey (see Hunt for Redds in October).  We take cross sections during redd surveys to get a more detailed look at the environment in which salmon prefer to make their nests. For example, eggs may be less successful at hatching in areas where water velocity is too slow because of poor oxygen exchange and the accumulation of metabolic waste around the eggs (Chapman 1988). On the other hand, adult Chinook salmon are not expected to spawn where the water velocity is too high because the effort needed to fight the current may sap their available energy reserves (Brett 1965).  The data collected from a cross section can then be applied to activities like habitat restoration and help create more suitable habitat to meet the needs of both spawning and rearing salmon.

With salmon spawning season in full swing, our fisheries technicians and biologists are hard at work both in the office and out in the field collecting and analyzing data. Whether it’s installing or maintaining portable resistance board weirs and rotary screw traps, reviewing the live footage of fish passages, or conducting redd surveys, the spawning and migration seasons are busy times for us at FISHBIO. We conduct redd surveys on approximately 450 miles of river annually to document trout and salmon redds, or nests. Moreover, the work we do requires a unique set of skill and experience. Not only can it be hard for the inexperienced eye to spot a redd at all, it can be especially difficult to distinguish rainbow trout redds from salmon redds, which are sometimes found in the same stream at the same time.

A Chinook salmon redd

So, how do we do it? During redd surveys, a biologist and technician raft downstream to locate where nests have been made in the gravel of the river bed and to collect environmental data. This information helps biologists accurately estimate the number of salmon and steelhead migrating to the rivers, also known as escapement, and to better manage flows for fish survival. The information can also be useful for mapping habitat (Groves et al. 2013) and estimating population sizes in a cost-effective way. Biologists have used redd surveys to estimate Chinook salmon escapement for decades, and we have been conducting redd surveys at FISHBIO for almost 15 years, so there are some well-known characteristics that scientists use to help determine whether a redd was built by a chinook salmon or a rainbow trout.

These clues include the location of the redd in the stream and its substrate; salmon prefer to lay eggs mid-stream and in larger gravel, whereas trout prefer to build near banks in smaller gravel (Giovannetti et al. 2013). The size of the redd is another clue, as salmon typically lay larger sized redds than trout (Reynolds et al. 1990). The presence of a fish can help identify who laid the eggs, since a salmon will stay near their redd to guard it from predators. Finally, timing is another indicator: Chinook salmon typically spawn from November to January, and trout from January to March. Our technicians memorize these signs so they can perfect the art of being “wildlife detectives” while identifying redds. However, nature doesn’t conform to rules, so even after doing our best to study up, we find the varied conditions encountered in field rarely fit a text-book example. But with guidance from our senior biologists and several seasons of experience, our entry-level technicians soon become specialists in the art of biology themselves.

Drone shot of salmon redd on the Stanislaus River

Over the years we have spent a lot of effort helping fish to spawn on both sides of the Pacific Ocean, yet occasionally a project comes along that requires us to do exactly the opposite. We recently completed one such project to prevent the spawning of Chinook salmon in the Sacramento River. While this may seem a bit odd, considering recent efforts to bolster salmon populations in the basin, we were tasked with preventing spawning in a small area of the river in order to facilitate the construction of a new bridge at Jelly’s Ferry near Red Bluff, California. The bridge, originally constructed in 1949, has begun to deteriorate in recent years and is currently closed to traffic. Prior to construction of the new bridge, we were charged with placing an anti-spawning mat along the river substrate in a particularly favorable-looking area of gravel downstream of the bridge, in order to ensure that potential spawning activity by Chinook salmon did not interfere with construction activities.

The anti-spawning mat consisted of chain-link fence that covered an area of nearly 3,500 square feet along the river bottom. The mat was secured to the substrate using earth anchors and steel pins, which had to be pounded into the substrate using a hydraulic jack hammer. Once secured in place, steel cable was woven between the different sections of fencing for added strength. Securing the mat was made all the more complicated by the high flows that we experienced in 2019, which necessitated the use of scuba gear to install the mat in depths of water greater than six feet in some areas. Of course, all of this reinforcement was necessary to keep in the mat in place during times of the year when flows in the Sacramento can reach as high as 119,000 cfs, as they did on April 1, 1974. Although flows didn’t reach nearly as high as in 2019, the anti-spawning mat performed admirably and didn’t budge an inch over the 6 months that it was in the river.

This effort, counterintuitively, may have prevented harm to an endangered fish species (winter-run Chinook salmon) that has seen its population decline precipitously. A myriad of factors, including dangerously high water temperatures during the drought, have resulted in runs of less than a 1,000 fish (both natural and hatchery spawners) in recent years. Although the bridge is located downstream of the majority of winter-run spawning habitat in the river, any redds dug in the area could have been affected by siltation, construction debris, load noises, and contaminants associated with construction activities. Hopefully, this mat will encourage spawning in more suitable habitat upstream (including new habitat in Battle Creek) during construction activities, and we will all get to enjoy the access and recreation opportunities afforded by the new bridge.

We’ll go to great lengths to rescue fish, even when it takes us to unexpected places. When we got a call from the Modesto Irrigation District to remove stranded fish from the Tuolumne River’s north bank tunnel, we knew it would be interesting. The main canal tunnel near the town of La Grange is a 16-ft. diameter concrete pipe that is more than a mile long. Both ends of the pipe travel at a downward angle and meet at a low spot, 1,200 feet from the west entrance. The tunnel, which was undergoing routine maintenance, was mostly drained of water, but some fish were stranded in a pool eight feet deep at the low spot of the canal.

On the day of the rescue, we went over the salvage plan and safety procedures with the help of MID. Then we watched as a utility terrain vehicle (UTV) carrying our 12-ft. jon boat descended into the pipe. We felt like it was never going to reach the water.  Every sound was amplified by the echo of the tunnel, even when the UTV was just a small blinking light a quarter of a mile away. When it returned from dropping off the boat, we loaded the rest of our gear into vehicle, but this time we followed it into the tunnel. Once we reached the water, we loaded the jon boat with three large ice chests, outfitted with aerators, along with seine nets and scoop nets. We rowed across to the other side of the pool, dropping a seine net in the middle where it was shallow enough to stand. We then worked our way up into the tunnel and corralled the fish into increasingly shallow water.

Working in the dark with only the light from our headlamps, we could feel the fish bumping into us as we shuffled our feet along the curved walls of the tunnel. When we got to a point where we could easily scoop up the fish, we caught and transferred them into the ice chests, and ferried chests full of fish back to the UTV. Once we emerged out of the tunnel back into daylight, we transferred the fish into a 350-gallon holding tank in the back of the FISHBIO truck. After repeating this process throughout the day, we rescued a total of 997 rainbow trout, six sculpin, three bluegill, and a green sunfish, which we released into their new home in the Modesto Reservoir. It’s not every day you get to carry a thousand fish out of the dark!

Raw water, also known as natural water, is water that comes directly from the environment and has not been subjected to any treatment to make it suitable for human consumption. According to local and state laws, when a new surface water treatment plant is to be built, numerous tests are required at the potential location to analyze and quantify various impurities present in the water. FISHBIO has recently been collecting raw water samples for such laboratory analyses. Water samples are collected from the river and kept on ice to maintain a consistent temperature during transportation to the lab. Lab tests include general water characteristics, microbiological parameters, nitrogen compounds, and many others. These tests will continue to run over the course of two years to get continuous measurements throughout changing river conditions over different seasons. For example, storm events may cause higher levels of turbidity, nitrogen, and microbial contamination, which are important to document.

Water samples are collected every two weeks as consistently as possible, always focusing on the same stretch of the river in moving water away from the bank – which can prove challenging as the water level rises and drops throughout the year. Each sampling event begins with basic water measurements, including temperature, dissolved oxygen, pH, conductivity, and turbidity. To collect the water, we use an extendable pole with a steel cable running through it to control the cap of an attached jar. The telescopic pole makes it possible to collect water samples from fast flowing water, undisturbed by the bank of the river. Once the jar is in the river, the collector pulls the cable, which opens the cap and allows water to flow in. The cable is then released, closing the cap and trapping water in the jar. After the pole is removed from the river, the jar is pulled off and the collectors pour the raw water into specific containers for testing.  Once transported to the lab, scientists can analyze the characteristics of the water and determine if it is a suitable source for a drinking water treatment facility.

If the water passes all of the tests, a facility can be built to treat the water for human consumption.  Once at a treatment facility, the water is pumped through a network of pipes for purification.  During preliminary treatment, screens and bars remove the large debris.  The water then flows to primary disinfection, where the results of the water sampling tests come into play.  Depending on the biochemical makeup of the water, certain chemicals will be added to control the water’s odor and taste.  After being treated with chemicals, the water will filter gravity through a media filter, which is comprised of activated carbon and sand. The filtered water can then go to holding tanks until it is distributed to the respective water supply.  A lot goes into ensuring raw water is safe for people to drink, including the  collection of consistent and accurate samples for preliminary testing.

For the last few years, we’ve been conducting a study in the San Joaquin River for which we deploy multiple fyke traps in the spring and early summer to catch, tag, and release striped bass, black bass, and catfish species. One of the objectives of the study is to estimate the population abundance of these target species in the San Joaquin River, much like the California Department of Fish and Wildlife has been doing for striped bass in the Sacramento River since 1969. In order to calculate accurate population estimates, it is essential to tag and release as many fish as possible to improve the probability of recapturing a significant number of those tagged fish. There are several ways to increase the odds of capturing and recapturing the target species, such as using more fyke traps, sampling for a longer time, or increasing the efficiency of the trapping method (design a better trap). But one of our biggest hurdles is permitting constraints: we are only allowed to handle the targeted species when water temperature remains below a predetermined threshold. This temperature constraint is for the welfare of the fish to reduce stress and risk of mortality.

To help improve our study estimates, we have been trying to increase the number of fish that are tagged with Passive Integrated Transponders (PIT tags) by piggybacking on other projects that capture our species of interest. One of our electrofishing projects in the South Delta as well as electrofishing and fyke trapping efforts conducted by the U.S. Bureau of Reclamation as part of the San Joaquin River Restoration Program have all been tagging our species of interest when they are encountered. We currently have multiple methods of recapturing tagged individuals, which include catching them in our own fyke traps, detecting them with PIT tag antennas in the weirs on the Stanislaus and Tuolumne rivers, recapture by other research projects, and reporting of tag recaptures by anglers.

This year, we tested a novel idea to further increase our fish recaptures: we modified a fyke trap so that it does not actually trap fish, but allows the fish that enter to pass through and continue on their way while passing through a PIT antenna. We are referring to this modified piece of equipment as a passive fyke. A fyke trap usually has two cones, or fykes, that constrain the fish to pass through smaller circular openings until they become trapped in the upstream end of the trap, and are unable to find the opening through which they entered. To modify this trap, we removed one of the cones so that fish only have to pass through a single three-foot-diameter circular opening containing an integrated PIT tag antenna (shown in the photo below). The outer wire mesh on the upstream side of the trap was removed to allow fish to freely exit the trap. We have also included underwater cameras to record fish that pass through the fyke and integrated PIT tag antenna.

Because no fish are handled by people with this device, we can continue to sample later into the summer as water temperatures increase and we are not allowed to trap and handle individuals. The hope is that PIT tagged fish will pass though the antenna on the passive fyke and get recorded by a shore-based recorder. The cameras will also allow us to determine the number of untagged fish passing through the passive fyke. This system requires weekly battery replacement and data downloads, and is expected to significantly improve our odds of collecting additional recapture data. It shows that with some creativity, even fish trapping can be automated.

Over the years we have spent a lot of effort helping fish to spawn on both sides of the Pacific Ocean, yet occasionally a project comes along that requires us to do exactly the opposite. We recently completed one such project to prevent the spawning of Chinook salmon in the Sacramento River. While this may seem a bit odd, considering recent efforts to bolster salmon populations in the basin, we were tasked with preventing spawning in a small area of the river in order to facilitate the construction of a new bridge at Jelly’s Ferry near Red Bluff, California. The bridge, originally constructed in 1949, has begun to deteriorate in recent years and is currently closed to traffic. Prior to construction of the new bridge, we were charged with placing an anti-spawning mat along the river substrate in a particularly favorable-looking area of gravel downstream of the bridge, in order to ensure that potential spawning activity by Chinook salmon did not interfere with construction activities.

The anti-spawning mat consisted of chain-link fence that covered an area of nearly 3,500 square feet along the river bottom. The mat was secured to the substrate using earth anchors and steel pins, which had to be pounded into the substrate using a hydraulic jack hammer. Once secured in place, steel cable was woven between the different sections of fencing for added strength. Securing the mat was made all the more complicated by the high flows that we experienced in 2019, which necessitated the use of scuba gear to install the mat in depths of water greater than six feet in some areas. Of course, all of this reinforcement was necessary to keep in the mat in place during times of the year when flows in the Sacramento can reach as high as 119,000 cfs, as they did on April 1, 1974. Although flows didn’t reach nearly as high as in 2019, the anti-spawning mat performed admirably and didn’t budge an inch over the 6 months that it was in the river.

This effort, counterintuitively, may have prevented harm to an endangered fish species (winter-run Chinook salmon) that has seen its population decline precipitously. A myriad of factors, including dangerously high water temperatures during the drought, have resulted in runs of less than a 1,000 fish (both natural and hatchery spawners) in recent years. Although the bridge is located downstream of the majority of winter-run spawning habitat in the river, any redds dug in the area could have been affected by siltation, construction debris, load noises, and contaminants associated with construction activities. Hopefully, this mat will encourage spawning in more suitable habitat upstream (including new habitat in Battle Creek) during construction activities, and we will all get to enjoy the access and recreation opportunities afforded by the new bridge.

Today’s Film Friday walks through the steps needed to assemble our custom-designed mount for an ARIS or DIDSON sonar camera.

Madisyn Pyorre on an Alaskan salmon boat

I come from a small coastal town in northern California, where someone in every family usually is a commercial fisher, or knows somebody who is. I was introduced to ocean sport fishing at a young age by my grandfather, and later had the opportunity to work in Alaska on a family friend’s commercial fishing boat. As someone who has enjoyed both catching and eating seafood for my entire life, I pondered the source of my store-bought fish, and I wondered if the seafood prepared for me at local restaurants was really as ‘sustainable’ as it was marketed to be.

My name is Madisyn Pyorre. Currently, I am completing a science communication internship at FISHBIO while I finish up my Environmental Studies B.A. at UC Santa Cruz. Before transferring to UCSC, I had the opportunity to take on an independent research study at Cabrillo College that was a project of my own design, and a chance to address some of my personal questions about fisheries sustainability. I crafted a survey of nine free-response questions that were designed to inspire honest and realistic feedback from local fishermen on topics such as the fishing methods they used and associated bycatch (or unintended species caught), the meaning of sustainability, and their opinions on the status of commercial fishing in Monterey Bay. Next, I contacted five artisanal fishermen from a diverse set of backgrounds, who fish out of one or more of the three harbors in the bay. These included Skylar Campbell, commercial fisherman of Monterey Harbor; Ian Cole, founder of Ocean to Table; Hans Haveman, owner of H&H Fresh Fish; Alan Lovewell, founder of Real Good Fish; and David Toriumi, commercial fisherman of Santa Cruz Small Craft Harbor. After conversations that sometimes lasted up to three hours, I played the role of a detective to sort through each response, and decided that sustainability was indeed a main goal of our local commercial fishermen.

Skylar Campbell’s boat in Monterey Harbor

The first few questions of my survey were a chance for me to learn about the fishers’  personal motivations for pursuing a commercial fishing career. Some were enamored with fishing at a young age and turned their love for fishing into lifelong careers, while others were academics interested in the seafood supply chain, or businessmen who wanted to start their own local seafood brands and empower other fishers through community-supported fisheries (CSFs). When I asked for a personal definition of the term sustainability, I received responses ranging from the simple, like “being able to harvest seafood forever” (Toriumi), to the complex , like “not extracting more than the ecosystem can replenish so as to not compromise future generations, and not damage the ecosystem and habitat during the extraction” (Lovewell). Not only did the fishermen prove proficient in defining sustainability, but they also practiced it– the most common fishing method used was the traditional and basic technology known as hook-and-line fishing. This requires only a fishing pole and human muscle power, has little to no impact on the seafloor habitats, and results in extremely low bycatch rates.

For a long time, I had the perception that most, if not all, commercial fishermen overstep legal fishing guidelines. However, when I asked fishermen about the frequency of breaking or bending the rules with the goal of increasing catch, they reported that there seems to be a “very little amount of people cheating the system” (Haveman), which I was pleased to hear. On the topic of current fishing regulations and restrictions, the fishermen had interesting thoughts to share, admitting that, while regulation is “necessary for sustainable harvesting,” (Toriumi) it can feel as though there is no compromise when it comes to protecting fishers’ livelihoods, such as in the event of emergency fishery closures. I was correct in my assumption that fishermen had a “natural distrust” (Cole) for regulatory agencies, but was intrigued by the fishermen’s ideas about how to dissolve this barrier between fisherman and regulator. When I asked about ways to make positive change in the future of the commercial fishing industry, the group offered solutions involving public education and restoration of the commercial fisherman’s image. “Educating the public on fisheries,” and shifting the public focus to support local fishers can help to “rebuild fisheries” (Campbell). Other proposed solutions include “increasing communication between fisheries researchers and the actual stakeholders” (Havemen).

Madisyn Pyorre halibut fishing in Alaska

While my sample size of five interviews is not large enough to make broad assumptions about the entire commercial fishing industry, conversing with these local fishermen gave me a unique glimpse behind the scenes of the artisanal fishing sector. If there is anything I learned throughout this study, it is that fishermen should be credited for their wealth of knowledge about ocean conditions, and should be considered a unique resource when it comes to fisheries research. Through my conversations with these fishermen, an unexpected theme emerged: that the source of many controversies in the commercial fishing industry were less an issue of sustainability, and more an issue of discordance between fishermen and their regulatory counterparts. I found value in the fishermen’s thoughts on this supposed barrier, and I am eager to explore this topic further. I believe that the sustainability of commercial fishing requires a sustainable relationship between fishermen and regulating entities – as the saying goes, it takes two to tango. (A full description of my findings can be downloaded here.)

This story was written by Madisyn Pyorre for an internship with FISHBIO through the UC Santa Cruz Environmental Studies Department.

Fall is in full swing, and so is the fall-run Chinook salmon migration in the Central Valley.  As is our fall tradition, we’ve installed fish counting weirs on the Stanislaus and Tuolumne rivers as part of our annual salmon monitoring. These fence-like structures direct fish through a single opening into a Riverwatcher scanner, which gives us a count, measurement, and video clip of every single passing fish. This set up provides a highly accurate way to monitor the salmon migration in real time on both of these tributaries to the San Joaquin River. As of Tuesday, November 5, our weirs had documented 1,406 salmon on the Stanislaus River and 1,054 salmon on the Tuolumne River. While the numbers are a bit lower than last year (when we had 3,289 and 2,316 salmon on each river, respectively, at this time), there should still be fish spawning activity to witness at the upcoming Stanislaus River Salmon Festival this Saturday, November 9, from 10 am–3pm at the Knights Ferry Recreation Area.

If you stand on the bridge at Knights Ferry and observe salmon in the river down below, those fish have migrated more than 180 river miles from the Golden Bridge – and that’s after migrating many more miles in the ocean! It’s a truly incredible feat worth celebrating. These long-distance swimmers play an important role in delivering nutrients from the ocean to the rivers where they come to spawn. In fact, much of the nitrogen in trees and other plants growing along streams in some areas can be traced back to the ocean and was delivered by spawning salmon. We recently shared this story of salmon migration with many schools near our Oakdale office as part of their annual Ag Days, and also with dozens of students from Manteca as part of a recent AgVenture outreach event.

Our team is gearing up for another big presence at this year’s Stanislaus Salmon Festival as part of another fall tradition. We’ll have revamped our “Salmon Cam” so you can watch salmon on their redds from different angles, and will have some fun new games at our booth. Come learn how salmon “smell” their way home to their spawning locations, or how we use microchips to do mark-recapture studies on fish! We’ll also be bringing out one of the inflatable catarafts used for our electrofishing studies on the Stanislaus River. Visitors will be able to climb inside to see what if feels like to sit at the oars. The 11th annual Salmon Festival is sure to be a fun and engaging event for the whole family, complete with more than 35 different exhibitors staffing interactive booths, fly fishing demonstrations, carcass surveys, musical performances, and plenty of food, crafts, and calendars of student salmon artwork available for purchase. Please stop by our booth to say hello!

In just a few days, staff from all three of our California offices will be converging on Reno, Nevada, for the American Fisheries Society annual meeting from September 29–October 3. Given the combined meeting with The Wildlife Society and the impressive array of fisheries talks from across the country (and around the world!), it is sure to be a head-spinning whirlwind of a week. FISHBIO staff will be presenting on every day of the conference, with a total of eight talks in all. Here’s a sneak peek at our presentation lineup so you can mark your calendars in preparation for the big event!

Monday, September 30

At 9:20 am, biologist Dana Lee will be giving the talk, “Use of low-cost autonomous, underwater camera systems to advance understanding of fish habitat usage and behavior.” This presentation will discuss several versions of automated cameras that FISHBIO has developed to passively monitor fishes in floodplains and fish passage structures. This talk is in the session “Using Applied Technology in Fisheries Monitoring and Research,” held in the Reno-Sparks Convention Center, A18. Read the abstract in the session lineup.

On Monday, FISHBIO staff are also helping to organize and moderate the session “Migratory Freshwater Fishes: Global Status Update and Swimway Initiative.” We are co-organizing this session with our colleagues at the University of Nevada, Reno, from the Wonders of the Mekong Project, as well as the World Fish Migration Day Foundation. This day-long symposium will include talks highlighting the global status of migratory fishes and managing their migration routes (or swimways), and end with a panel discussion of future steps towards filling knowledge gaps and achieving sustainability. The session will be held from 8:00 am–5:20 pm in the Reno-Sparks Convention Center, A3. See the session lineup.

• As part of this session at 2:10 pm, biologist Tyler Pilger will be giving the talk “Caught between a rock and a hard place: monitoring Chinook salmon in California’s Central Valley.” This presentation will provide an example of a robust migratory fish life-cycle monitoring program that has been developed for fall-run Chinook on the Stanislaus River to inform the management of these iconic Pacific salmon. Read the abstract in the session lineup.

Tuesday, October 1

We will be giving two presentations in the symposium “Channels for Change in the Mekong: Integrating Multiple Disciplines for New Frontiers in Managing the Mekong River Basin,” being held from 8:40 am–5:00 pm in the Atlantis Hotel Grand Ballroom 3. This symposium is organized by the Wonders of the Mekong project, and will discuss interdisciplinary approaches for understanding environmental stressors and informing management in the Mekong Basin.  See the session lineup.

• At 8:40 am, Scientific Collaborations Director Shaara Ainsley will be kicking off the symposium with the talk “Continuing the conversation on Mekong River management at the annual AFS Conference.” This presentation will show how the session builds on two previous Mekong-related symposia held at AFS in 2015 and 2017, including discussions of development, fisheries stressors, and solutions. Read the abstract in the session lineup.

• At 3:20 pm, Communications Director Erin Loury will be giving the talk, “Communicating the Wonders of the Mekong to build support for conservation.” This presentation will describe how the Wonders of the Mekong project is using engaging online content, printed communications materials, and unique personal stories to reach both urban and rural audiences in Cambodia, as a way to celebrate the country’s rich natural and cultural heritage related to the Mekong River. Read the abstract in the session lineup.

At 1:10 pm, Erin will also be giving the talk “Lights, Camera, Science! Using video to communicate scientific studies.” This presentation will discuss how to plan, produce, and share a video to communicate a scientific paper, based on the example of FISHBIO’s publication and video about juvenile salmon outmigration on the Stanislaus River. Topics will include using the Message Box tool, filming interviews and B-roll, and sharing videos on social media. This talk is in the session “Beyond the Publication: Science Communication Strategies to Increase the Impact of Your Research,” held in the Atlantis Hotel, Grand Ballroom 4. Read the abstract in the session lineup.

Wednesday, October 2

At 10:30 am, Erin Loury will be giving the talk, “Engaging Communities, Protecting Freshwaters: Lessons from Fish Conservation Zones in Laos.” This presentation will discuss successes and challenges from FISHBIO’s experience establishing and monitoring community co-managed freshwater protected areas (known as Fish Conservation Zones or FCZs) in Laos, including developing a guidebook for assessing FCZ effectiveness. This talk is in the session “It Takes a Village: Success Stories in Community-Based Conservation,” held in the Reno-Sparks Convention Center, A1. Read the abstract in the session lineup.

Thursday, October 3

At 3:40 pm, biologist Michael Hellmair will be giving the talk “Early-season reproductive failure of Chinook salmon: limited behavioral plasticity in warming rivers?” This talk is in the session Climate Change Across the Salmon Life Cycle. Atlantis Hotel, Grand Ballroom 1. This presentation uses temperature and juvenile salmon data on the Stanislaus River to demonstrate diminished reproductive success of Chinook salmon during the recent California drought, and reveals a shrinking window for suitable juvenile emigration conditions based on long-term air temperature trends. Read the abstract in the session lineup.

At 4:40 pm, Scientific Director Matt Peterson will be giving the talk “Project update on establishing a nonnative predator research and pilot fish removal program on the Stanislaus River, California.” This presentation will discuss current results from the Stanislaus Native Fish Plan, an ongoing collaborative scientific effort to assess the impact of non-native predator removal on juvenile salmon survival. This talk is in the session “Invasive Fishes: Ecology and Management,” held in the Atlantis Hotel, Grand Ballroom 3. Read the abstract in the session lineup.

With this jam-packed schedule, it’s sure to be a busy week from beginning to end. Our videographer Dee Thao will also be filming the AFS conference to produce a video (check out our video from AFS 2015 in Portland), so be sure to give her camera a wave. And if you see any of our staff coming and going throughout the conference, we hope you’ll say hello!

Our latest video marks the culmination of a multi-year effort working with communities in Laos to establish Fish Conservation Zones (FCZs) in the Mekong River. Since 2014, FISHBIO has received a series of grants from the Critical Ecosystem Partnership Fund to help villages set up these community co-managed freshwater protected areas that can allow fish populations to recover from overfishing. In particular, the FCZs focus on important habitat for the critically endangered Jullien’s Golden Carp (Probarbus jullieni). In total, a network of seven FCZs has been created among nine communities in northern Laos. These are the first FCZs of to be established in the mainstem Mekong River in this part of the country.

Community members play a large role in the FCZ management process, from deciding where the protected areas should be located, determining the rules and penalties, and patrolling the protected areas to enforce the regulations. FISHBIO has helped develop and strengthen FCZ management by facilitating official government approval of the regulations, hosting FCZ establishment ceremonies, and conducting outreach with the community. Buddhist monk blessing ceremonies and fish releases have been performed and spirit houses have been installed at the FCZ sites to integrate protected area management with Lao cultural beliefs. Throughout the course of the project, FISHBIO hosted two exchange visits to bring the communities together and learn from each other’s experience, and also conducted fish surveys to evaluate the performance of the FCZs. In this video, several community members share their hope for the FCZs to benefit both fish and people into the future.

Since 2014, FISHBIO has helped to establish seven Fish Conservation Zones (FCZs) at nine villages in northern Lao PDR with funding from the Critical Ecosystem Partnership Fund (CEPF). FCZs are no-fishing areas managed by the community to protect critical fish breeding and nursery habitats, while also limiting the overharvest of target species such as Probarbus fish in the Mekong River. The success of any FCZ depends upon the local community respecting the fishery regulations, continued effort of patrolling and enforcement, regular community meetings to address any conflicts or concerns, and long-term support from the government (district and village level organizations) in decision-making. Essentially, building support from stakeholders involved in fishery management is critical to achieving the overarching goal of creating FCZs. One way to build this support is by creating a network between project villages and strengthening it with a communication platform that allows experience sharing and exchange of ideas for enhanced FCZ management.

FISHBIO previously organized a study tour in March 2018 that brought together seven communities from Sanakham, Kenthao, Xayabouri, and Nan districts Vientiane, Xayabouri, and Luang Prabang provinces for learning from one another. After the addition of three new FCZs in 2019 (Sa Kai 1 – Tha ban; Sa Kai 2 – Khone kham, and Ang Noi) in Sangthong District, Vientiane Capital, it was time for another networking opportunity, especially to allow the new FCZ villages to learn from the others through face-to-face interaction and FCZ tours.

From February 25–28, 2020, FISHBIO organized its second study tour and exchange visit as a component of the CEPF project Strengthening Community Co-Management of a Mekong River Fish Conservation Zones Network. This was an opportunity to bolster the existing network between communities with FCZs, and also train community members in conflict management strategies around fisheries regulations and compliance. On February 26, a meeting was organized to inaugurate the study tour with welcome remarks from the Nan District Vice Governor Mrs. Hongkham. A total of 50 people attended the meeting at the auditorium of Nan District Education Office in Luang Prabang Province. The participants were a mixture of people from the FCZ villages (30 people), Department of Livestock and Fisheries sub-district, district, and provincial-level staff and the District Vice Governor (17 people), and FISHBIO Lao staff (3 people). FISHBIO staff provided an an overview of the CEPF projects that supported the establishment of FCZs in 7 designated sites of the nine villages. After that, the representatives from seven participating communities (Ang Noi and Houayla villages were unable to attend) presented updates on their FCZs, their experiences of FCZ management, patrolling, enforcement and constraints, and recommendation for improved management in future.

During one of the sessions, we familiarized the participants with our virtual communication platforms: a WhatsApp group and two Facebook pages (FISHBIO Laos and Fish Conservation Zone Mekong Fish Network), where we share updates from our FCZ projects to build awareness about the conservation of Probarbus fish and other endangered aquatic animals. Our hope is that community members will use these platforms to communicate information and updates that would help improve FCZ management, and some are indeed already using it.

The conflict management portion of the workshop included a presentation from FISHBIO introducing conflict types and management styles learned from a previous training in Vientiane Capital. We then engaged in group exercises separated by village to perform activities such as conflict mapping. As part of the exercise, each group discussed the problems that arise while managing an FCZ, who addresses the issue, the direct and indirect impacts associated with conflicts, and follow-up action. People presented their results in pairs and also shared their practices of enforcement and conflict management in villages. Most said the FCZ management committee investigates the issue in consultation with government officials (sub-district office) and the village committee, and deals with violators according to the FCZ regulations. Villagers recommended collaborative action between villages and government staff (sub-district officials) for outreach activities, patrolling, and any follow-up action regarding violations and conflicts.

On February 27, participants traveled to Houaykhoulouang village to visit the oldest FCZ sites: Houaykhoualouang, Korkfak and Pakpui FCZs, established in 2014. These FCZs protect deep pool habitats that are important refuge habitats. We started our boat tour at Houaykhoualouang FCZ, sharing stories of the deep pools and objectives behind selecting the sites. We observed multiple no-fishing and FCZ regulations signs along the shore as we kept moving, and then we stopped by Pakpui FCZ for lunch on the sandy beach. Finally, we traveled back to the Houaykhoulouang village office for group discussion to gather more information about the governance style from all the participating villages using indicators from the FCZ assessment guidebook developed by FISHBIO: G1 Existence of an active management committee, G6 Clear enforcement procedures and level of patrolling effort, and G7 Level of compliance with FCZ regulations. Each village representative shared their FCZ organizational structure, decision-making body, range of issues discussed in the community meetings related to FCZs, general decision-making process, enforcement procedures, violations, record keeping, and challenges.

The participants reflected positively on their two-day experience at the end of the event, saying  they learned new insights from attending the study tour, especially the opportunity to travel beyond their villages and mingle with people from other FCZ villages. The exchange visit helped to familiarize those villages new to FCZ management with more experienced villages. The training also helped build common ground for all stakeholders to take collaborative action against illegal fishing and FCZ-related conflicts. We hope this was a valuable contribution to sustaining the long-term management of these community FCZs into the future.

This post was written by Biraj Shrestha, a master’s student at the University of California, Santa Cruz who is completing a capstone project with FISHBIO Laos as part of the Coastal Science and Policy Program.

When it comes to managing sustainable use of natural resources, conflicts can naturally arise. Such is the case of artisanal fisheries management in Laos where our Fish Conservation Zones (FCZs) have experienced some challenges regarding the enforcement of FCZ regulations. The restrictions on fishing at FCZ-designated stretches of the river and confiscation of the fishing gear have previously provoked some fishers to damage the boats of the enforcement team. Other patrolling teams are hesitant to enforce the regulations against people in power. We imagine others must face these challenging dynamics among the more than 1,300 FCZs throughout Laos.

To help provide skills and resources to settle such differences, FISHBIO decided to provide conflict management training to our staff and other fisheries practitioners in Laos, with the hope to then bring this training into local communities. We partnered with Dr. Jennifer Bond from Charles Sturt University, Australia, who traveled to Laos to lead a conflict management training with twelve officials representing Theun-Hinboun Power Company (THPC), Nam Theun 2 Hydropower Project, World Wildlife Fund (WWF), Department of Livestock and Fisheries (DLF), and FISHBIO staff from the U.S. and Laos. The training was conducted for two days on October 9 and 10 in the DLF office in Vientiane, Laos.

The purpose of the training was to make the trainees aware of the dynamics of conflict in natural resources management, with a focus on fisheries, and guide the participants in how to reach agreeable solutions working closely with communities. The conflict management process began with an introduction of conflict and its various types, and then group exercises such as conflict mapping, which was centered on the theme ‘fish conservation vs. food security,’ and used Venn diagrams of overlapping circles were used to represent potential interrelated conflicts, with the size of the circles represented the extent of the conflicts. As part of the conflict assessment process, participants learned how to fill out a stakeholder analysis matrix in detail so that various stakeholders related with the conflict could be identified. The stakeholder analysis table helped participants to fill out different fields for each stakeholder, such as perception and position of conflict, degree affected by and degree blamed for the conflict, influence over the conflict management process, and capacity required for the stakeholders to be involved in the conflict management process. Such assessments could be completed in communities using a number of methods such as individual interviews, focus group discussions, participatory activities like drawing a conflict tree, or through holding community meetings.

The training wrapped up with a briefing on conflict management options as joint decision-making (negotiation and mediation), third-party decision making (adjudication and arbitration) and separate action (retreat). Mr. Sinsamout Ounboundisane, Director of FISHBIO Laos facilitated the training by acting as a translator, and the trainees reflected their learnings at the end of the two days. We hope that familiarity with these skills will be help participants be better equipped to handle conflicts they may encounter as part of their work.

This post was written by Biraj Shrestha, a master’s student at the University of California, Santa Cruz who is completing a capstone project with FISHBIO Laos as part of the Coastal Science and Policy Program.

The endangered delta smelt (Hypomesus transpacificus) lies squarely in the middle of a heated debate over the current state of California’s Sacramento–San Joaquin Delta and how its waterways should be managed. Commonly referred to as an indicator species, or one whose abundance reflects a specific environmental condition, population levels of the delta smelt provide a relative status update to the overall health of the Delta ecosystem. In recent years, it has become apparent that delta smelt, along with several other mid-water species known to commonly occur within the Delta, are being pushed to the edge as population levels precipitously decline. The results of the 2015 and 2016 spring kodiak trawls conducted by the California Department of Fish and Wildlife both showed a record decrease in the relative abundance of delta smelt, with only 13 adult delta smelt collected In 2016. In light of this serious situation, a symposium was presented by the Delta Science Program and the UC Davis Coastal and Marine Sciences Institute on March 29^th to discuss the challenges facing delta smelt and to help consider future actions to facilitate their recovery.

Figure 1. The CDFW’s Spring Kodiak Trawl Delta Smelt index, 2004-2016. (CDFW Tech. Memo. June 2, 2016).

The symposium featured a discussion from a diverse array of experts on pathways forward to assist delta smelt with recovery from what some consider the brink of extinction. To date, the conversation regarding how to better manage the Delta for the recovery of this key species has centered on the need to provide a greater amount of flow to the Delta. However, much of the symposium’s panel discussion reflected the sentiment that a more comprehensive approach to Delta management is required to reverse the current downward trend in smelt populations. Dr. Christina Swanson, the director of the National Resource Defense Council’s Science Center, noted that management should be encouraged to think on a broader scale with a more multi-species ecosystem approach. She argued that it is a mistake to ask what is the “one thing” that we can do to better manage the system. Several of the panel members agreed that taking a multifaceted approach may yield better results, with many members noting several environmental factors such as turbidity and habitat quality also need to be addressed.

A decades-long approach to management focused primarily on flow to the Delta has led to further population declines, showing little promise for being the “silver bullet” needed to return the Delta to healthy ecosystem. Recently, a delta smelt recovery action plan was drafted by the California Natural Resource Agency that highlights the multi-faceted approach discussed at the symposium. While modifications to current flow levels entering and leaving the Delta is still a featured component of the thirteen-point Delta Smelt Resiliency Strategy, several of the other discussed projects focus on contributing environmental factors such as turbidity, salinity, habitat restoration, and food availability. In order to address issues with reduced levels of turbidity, the strategy includes actions to remove invasive, submerged aquatic vegetation that have been known to trap sediment, and to add additional sediments to the low salinity zone. There are also plans to restore spawning habitat in Suisun Marsh and Cache Slough, and to look into the possibility of restoring the Franks Tract State Recreation Area.

This current iteration of a strategy to restore delta smelt populations is an encouraging sign of progress in the field. It is the type of collaborative, multi-faceted approach called for by the diverse group of speakers assembled by the March symposium. The strategy to use flow as a singular factor to address population declines has proven to be an antiquated one, as a wide array of studies (Sommer et al. 2007, Kimmerer et al. 2009, Mac Nally et al. 2010, Feyrer et al. 2007, Latour 2016) have shown several interconnected factors all influence the survival of many species in decline throughout the Delta. This plan should prove to be a more adaptive strategy to manage the smelt population, and could provide the framework for the management of other species down the road.

This post featured in our weekly e-newsletter, the Fish Report. You can subscribe to the Fish Report here.

Endangered fishes of the genus Probarbus and many other aquatic animals are now protected in several deep pools and spawning habitats of the Mekong River. As part of FISHBIO’s project funded by the Critical Ecosystems Partnership Fund, we organized a ground-breaking ceremony to install signs at three new Fish Conservation Zones (FCZs) in Luangprabang Province of northern Lao PDR. The workshop was held in Pakpee, a village of the Kamou ethnic group in Nan District. A number of people gathered to mark this special day, including the Nan District Governor and representatives from other relevant sectors at the district level, such as agriculture and forestry, natural resources and environment, information and culture, soldiers, and police, as well as residents from neighboring villages on both sides of the river in Luangprabang and Xaiyabouri provinces.

During the workshop, the Nan District Governor officially put into effect the regulations of three FCZs belonging to the village. Then, FCZ signs were unveiled at each site to help people clearly understand the regulations for protecting fishes inside the FCZ boundaries, and how avoiding the use of harmful fishing gear can benefit future generations. Now that the signs are in place, more work is needed to educate villagers to understand the regulations, and to take active ownership of managing and protecting their local fisheries resources. After a year of conducting biodiversity surveys, village workshops, and government meetings, it is gratifying to see these FCZs officially launched. We are looking forward to following up with the community and training villagers to enforce the regulations of their new conservation zones.

Fish bones have plenty of stories to tell – particularly a special type of ear bone called an otolith that keeps a record of a fish’s entire life. A whole field of fish science revolves around the study of these little bones, which can reveal a fish’s age and movement. Our staff in Laos got their hands on a surprisingly large otolith while visiting a conservation hatchery in Thailand – but not without some struggle first! Fish have three pairs of otoliths located behind the brain, each with a different shape, that help the fish with hearing and balance. The largest pair, the sagittae, is most commonly studied because these otoliths are the easiest to find when dissecting a fish. The other otoliths are called the lapilli and the asterisci.

Similar to tree rings, fish otoliths lay down roughly one pair of translucent and opaque bands every year to make a ring. These show up as light and dark bands under a microscope, and counting them provides an estimate of the fish’s age. Additional studies are also needed to validate these ring counts – that is, to verify if one pair of bands actually does equal one year of age, or if the fish deposit bands more or less frequently (Beamish and McFarlane 1983). Records of a fish’s size in combination with its age help scientists determine how fast a fish species grows. Otoliths also provide a wealth of information in their microchemistry, or the concentrations of different trace elements and isotopes, which can reveal a fish’s migration patterns and different habitats it has used (Feyrer et al. 2007).

Our staff in Laos are currently studying Probarbus fishes, including Jullien’s golden carp (Probarbus jullieni), and wanted to to see how feasible it would be to extract otoliths from fish in marketplaces. (Although the fish are listed as endangered, they are still regularly sold and eaten in Laos and Thailand). We visited a hatchery that had a Probarbus fish head in their freezer, which the staff gamely let us use for practice. It was quite a workout to carve through the thick, frozen fish skull. After several minutes of futile sawing, it became clear the little knife we had would not do the trick. We know from our California work that retrieving salmon otoliths also requires some serious tools. Once our Lao biologist produced a machete, a few hacks was all it took for an otolith to fall right out.

Otoliths come in a diversity of sizes and shapes, but we were particularly surprised by the heft of the Probarbus otolith. Since ear bones are the smallest bones in the human body, it’s remarkable they attain a considerable size in fish. Then again, Probarbus can grow to be one of the largest freshwater fish in Southeast Asia, so maybe it’s not surprising their ear bones are large too. The maximum age for Probarbus jullieni is currently unknown or unpublished, as is the case for most Mekong fishes. Since we don’t know the length of the fish this otolith came from, we won’t be able to determine the fish’s growth rate. But we do know one thing for sure: Probarbus otolith recovery is enough to work up a sweat in the humid Thai air!

Sometimes river habitats need a helping hand to alleviate critical bottlenecks that reduce fish survival and limit the size of fish populations. Well-designed habitat restoration projects that draw on research to help fish can provide a significant boost to fish abundance and survival (Bonneville Power Administration 2014). Now, one such restoration project comes to life in our new video: Replenishing a River: Stanislaus River Honolulu Bar Restoration. The project, funded in large part by the Oakdale Irrigation District (OID), created vital habitat to improve the numbers of young salmon and steelhead rearing on the Stanislaus River in California’s Central Valley. The video chronicles the transformation of a two-and-a-half acre region of the river called Honolulu Bar, and discusses OID’s commitment to stewardship and giving back to the Stanislaus River.

The Honolulu Bar project represents a collaboration between Oakdale Irrigation District (OID), the U.S. Fish and Wildlife Service, CBEC, River Partners, and FISHBIO. We were able to draw on 20 years of Stanislaus River fisheries monitoring data funded by OID to design a habitat we were confident would meet the needs of fish. The ambitious project addressed many challenging features that made the site less than ideal for fish, due to decades of human alteration to the river. Honolulu Bar’s in-stream island lacked the slow-moving, shallow water floodplain habitat that young fish need to rear and grow. With the help of heavy machinery, we dug down the elevation of the island, allowing water to flood over it at a broad range of river flows. We then took the gravel removed from the island and selected rocks of a specific size to create better quality habitat for salmon to spawn.

Habitat restoration is no small feat: it requires years of monitoring and constant effort to repair and maintain a healthy restored habitat. Monitoring the performance of a restored area not only includes sampling for macroinvertebrates (see Focus on fish food) and assessing salmonid populations (see Who’s at home?), but propagating vegetation as well. Vegetation survival is important to the growth and survival of reintroduced native wildlife in turn, since native plant species help provide appropriate habitat for both riverine and terrestrial animals. The species reintroduced to the Honolulu Bar restoration site shown above are typically found in riparian habitats occurring throughout the Central Valley.

The FISHBIO technician seen here is broadcasting a mix of seeds native to Californian riparian habitats. This mix of western goldenrod, evening primrose, gumplant, and others will play an important role in establishing an effective ground cover to keep invasive species from overtaking the area. In addition to the scattered seeds, plugs of creeping rush and Santa Barbara sedge were planted intermittently throughout the floodplain. The seeds and cuttings lay the groundwork for an appropriate vegetation structure that provides food and cover for terrestrial species, and helps protect the floodplain from excess erosion and changes to its physical characteristics.

During the floodplain reconstruction, several types of common invasive plant species were removed (see On the (invasive species) battlefield). The Tree-of-Heaven (Ailanthus altissima) is an invasive commonly found near California waterways. It can change streambed ecology by forming dense thickets that crowd out native plants, alter physical habitat, and produce chemicals that prevent other plants from taking root nearby. Established trees can be incredibly difficult to remove, as they can reproduce by sending out shoots or re-sprouting from root fragments left in the soil. The Himalayan blackberry (Rubus discolor) is another common riparian intruder that is highly competitive and rapidly displaces native plant species. Blackberry thickets can become so dense that they block terrestrial animals’ access to the water, and the lack of light can severely inhibit the growth of ground cover species. These invasive plants, among others, display highly aggressive growth and reproduction rates. The most effective way to combat these common intruders is to prevent their introduction in the first place, such as avoiding their use in landscaping. When choosing ornamental species for your home garden, it’s worth noting that there are many beautiful plants native to California to choose from.

Do you like working outdoors? Want to help restore important fish habitat on the Stanislaus River? FISHBIO and River Partners are looking for volunteers to plant native trees at Honolulu Bar on Saturday, January 26, from 10 am to 1 pm. All the planting tools will be provided, along with drinks and snacks. We recommend bringing work gloves and rubber boots, since we’ll be wading across a shallow channel to get to the planting site. There will be waders or hipboots available for anyone who doesn’t have boots.

Volunteers will get to see the handiwork of our latest restoration project first hand. The lower Stanislaus River is crucial habitat for steelhead trout and fall-run Chinook salmon. But during the Gold Rush, dredges destroyed many of the large stretches of silt-free gravel that the fishes need to spawn and their eggs need to develop. Last year, we completed a project with the Oakdale Irrigation District, the U.S. Fish and Wildlife Service, CBEC, and River Partners to restore the floodplain at Honolulu Bar (see Restoration complete). We used some heavy machinery to level the steeply sloped banks of the island so water could flood over it, and hauled gravel to replenish spawning beds. We also cleared invasive vegetation that had taken over the site, such as tree-of-heaven and Himalayan blackberry (see On the invasive species battlefield). Now it’s time to replant native species that belong in this riparian habitat.

You can help us plant more than 100 cuttings of black willow, sandbar willow, and cottonwood trees. Native plants like these play many important roles in keeping river ecosystems healthy. They shade the water and keep it cool, stabilize the bank, filter sediments, and provide habitat for the insects that young salmonids eat. So plant a tree, help a salmon. We will be meeting at the Honolulu Bar Recreation Area in Stanislaus River Parks. For more information, please contact Jason Guignard at jasonguignard@fishbio.com.