Archive for August, 2019

Aug 8 2019

California Wetfish Producers Association Files to Intervene in Oceana Anchovy Lawsuit

August 8, 2019 — The following was released by the California Wetfish Producers Association:

The California Wetfish Producers Association (CWPA) has filed to intervene in a lawsuit filed by environmental group Oceana over California’s northern anchovy fishery. The filing will allow CWPA to participate in the lawsuit to protect the interests of California fishermen and processors who would face significant economic harm if the lawsuit were successful.

The lawsuit alleges that the National Marine Fisheries Service (NMFS) must set stricter limits on the northern anchovy catch. As the result of a recent Oceana lawsuit, where the Court required NMFS to revise its catch rule, the catch limit is currently set at 23,573 metric tons, which, according to NMFS estimates, is only 25 percent of the stock’s overfishing level.

Not only are additional restrictions on the anchovy harvest unnecessary, but greater cuts would result in significant job loss and economic hardship for California’s wetfish industry and coastal communities.

“If [Oceana] prevails in this case, there could be a drastic reduction from current harvest levels,” said CWPA in its filing. “Such a reduction in harvest opportunity will seriously and irreparably harm CWPA members and the wetfish industry.”

Anchovy fishing off the California coast


This would affect not just California wetfish fishermen, who rely on anchovy when other species, like squid or mackerel, are unavailable, but also the processors, distributors, and seaside businesses who rely on a consistent catch. If lower catch limits are approved, the jobs of at least 400 CWPA members alone will be at risk, as well as many thousands more in related industries.

“Fishermen up and down the California coast are facing threats to their livelihoods from this frivolous and unnecessary lawsuit,” said Diane Pleschner-Steele, executive director of CWPA. “We are asking to be involved in this lawsuit to ensure that the Court also considers the needs and concerns of our members and California’s coastal communities. Our fishery management policy mandates balance between protecting the ocean and sustaining fishing communities ”

The sharply reduced catch limits that Oceana seeks are not scientifically justified. The basis for Oceana’s case is a single, flawed study that significantly underestimated the size of the anchovy population, in 2015, leading to the first Court decision, That study excluded  the abundance of anchovy in inshore areas, for example. Cooperative surveys that CWPA has conducted with the Southwest Fisheries Science Center and the California Department of Fish and Wildlife  have documented tens of thousands of tons of anchovies in these areas that have simply not been counted in stock assessments. . This finding contradicts the argument that the anchovy population was dangerously low, and that the already precautionary catch levels must be reduced further.

“The best available science does not support Oceana’s position,” said Ms. Pleschner-Steele. “ The Court needs to allow NMFS to set appropriate catch limits based on sound science.”

Aug 8 2019

FEELING SQUIDDISH | Local market squid fisheries impacted by warm blob in Pacific

California Market Squid regenerative their population every year.


By Kimberly Rivers

The squid landing docks at the Port of Hueneme are quiet. In recent years the summer months were busy with dozens of boats coming and going, offloading millions of pounds of California Market Squid into tanks for export to Asia for processing and then returning to be served up for fried calamari or other dishes.

The local squid fishery declined from 2014-16 in response to a warm water mass called “the blob.” The name was coined by Nicholas Bond, Alaska-based research scientist with the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) at the University of Washington. Blob, as expected, is a reference to the amorphous monster from the 1958 horror classic film.

Typically ocean temperatures 50 miles off the Southern California coast are “very much in step” with the ocean temperatures at the equator, said Clarissa Anderson, executive director of the Southern California Coastal Ocean Observing System (SCCOOS). The system she manages is part of a network of systems monitoring ocean conditions worldwide. “Then they diverge when the blob hit in 2014 and only come back together again for the big 2016 El Niño, then diverge again. This may be related to the perturbation caused by the blob temp anomaly that lasted so long.”

The blob was a “large anomalously warm” area of the Pacific Ocean, “spread over a broad area, resulting in major ecosystem impacts,” said Anderson.

Anderson and Bond monitor different sensor systems in their regions and look for anomalies in the oceans. She said the blob mostly impacted the area for about two years and prevented mixing of water, caused the drought, wildfires,” and decimated the Dungeness crab industry along the Pacific Coast.

When asked whether we are seeing a blob 2.0, causing a decline in the squid fishery in the area, she said people may be “quick to call it that in homage to the past blob,” but she is not certain it’s a new blob, but might be that the blob never really left.

“We don’t have a threshold for when to call it a blob,” said Anderson. “I don’t know if we are having an actual true marine heat wave.”

Warm water prevents the normal upwelling of cool water from deeper water that contains important nutrients and food sources for species that live at shallower depths. “We have seen a lot of upwelling in the spring,” she said, noting that much of the ocean is looking like “business as usual” but with a “warmer background level of water.”

That warmer background water could reveal a trend, part of what is needed to identify a true anomaly, which would indicate something serious occurring. To confirm that, Anderson said data must be “compared to a background baseline,” and an increase in temperature is only significant when it “deviates from a background norm.” Reviewing temperatures each day is not enough; current day temps must be run against past data over time to identify a true change or trend showing temperature increase.  

After reviewing the most recent days’ data, Anderson said that there appears to be “anomalously warm water off the Central Coast.” She emphasized the data set covered “the climatology period 2007 to the present.” It does show a red blob-shaped area about 250 kilometers off the Central Coast that is four degrees higher than the normal range of temperatures.

In 2010, well before the blob arrived, squid season in the Ventura area brought in 126 million pounds of squid valued at $33.7 million. By 2016, total poundage dropped by a third to 34 million pounds valued at $16.8 million.

2018 data shows a continued declining trend totaling 27.6 million pounds valued at $13.6 million. Ventura Harbor and Port Hueneme landings for squid in 2018 were valued at $6.7 million and $6.8 million respectively, less than half of the 2010 value. Data and values are according to records held by the California Department of Fish and Wildlife.

“The good news is that squid are pretty resilient,” said Diane Pleschner-Steele, executive director of California Wetfish Producers Association. The species does prefer cooler water, but is showing an ability to move and find food. “And squid are very cyclical . . . We can’t afford to lose our squid fisheries . . . and a number of species are going to be hit hard by ocean acidification and climate change.”

In terms of how warm water will impact market squid, “It depends where the food goes,” Pleschner-Steele said. “Squid are pretty voracious predators. When we have typical cooler upwelled water that is more nutrient rich, we have more squid.”

Squid will devour krill in the deeper offshore areas. As they move closer to shore to spawn, they become “cannibalistic” and eat each other. This may contribute to the resiliency as the ocean ecosystem changes.

Pleshchner-Steele also pointed to the normal cyclical nature of squid populations, saying “Ventura got used to having squid in the summer time.” The strong El Niña in the Pacific created an abnormal situation between 2010 and 2013, and a “decadal squid boom for southern California” led to the seemingly major shifts.  “My guess is to see a return to normal pattern.”

She referred to a research project of the California Department of Fish and Wildlife, completed in February, that “saw a bump in the para-larvae numbers” of market squid. She said that is a signal that there is likely to be an uptick in squid number in about nine to 10 months. “Ventura will just have to wait until fall.”

Original post:

Aug 6 2019

NOAA Releases 2018 Status of Stocks With New Emphasis on Environmental Impacts

The words “overfishing” and “overfished” are still used to describe seafood species with too high of a catch rate or too low of a population, but for the first time NOAA’s “Status of the Stocks 2018”, released last Friday, attributes impacts from global warming as causing changes in the sustainability status of fish stocks. It may be time to find new adjectives.

The bottom line for the report is the list, titled “Overfishing and Overfished Stocks As of December 31, 2018.” The good news in the 2018 report is that seven stocks came off the Overfishing List. But zero came off the Overfished List, five stocks were added to the Overfising List and eight stocks were added to the Overfished List.

The operative terms were defined by Alan Risenhoover, director of NOAA’s Office of Sustainable Fisheries, noted in Friday’s press conference.

“ ‘Overfishing’ is the rate of harvest, or the number of fish removed per year: one percent, ten percent, etc.,” Risenhoover said. “ ‘Overfished’ means that over time, overfishing creates a non-sustainable stock status for those species. It refers to overall population size.”

But it was environmental conditions that were listed as significant reasons for adding species to the lists, not what the fleets were doing.

“The total number of stocks listed as overfished increased, due to a number of factors including those outside the control of domestic fisheries management,” the report noted.

“The eight stocks added to the 2018 overfished list illustrate numerous challenges inherent in fisheries management,” the report author wrote.

“Environmental change, habitat degradation, and international fishing contributed to the status of the eight new overfished stocks. For example, relatively warm water conditions may be impacting the growth and reproduction of the cold-water Saint Matthew Island blue king crab. This stock has never been subject to overfishing and directed fishing for this crab has been prohibited since 2016.

“Warm ocean conditions, including the warm “Blob” in the northeast Pacific Ocean, reduced the number of spawning coho salmon returning to their natal rivers, and both Chinook and coho salmon have been impacted by habitat degradation caused by drought and lack of sufficient water for spawning,” the report noted.

“During the past 5 years, several of the fisheries for these salmon stocks have been declared fishery disasters under the MSA by the Secretary of Commerce due to factors beyond the control of fishery managers.”

NOAA partners with regional councils to manage the nation’s fisheries stocks, and works closely with other international bodies to manage stocks that are highly migratory and harvested globally. All management bodies use similar scientific principles to maintain sustainable populations, but very few include impacts of global warming or environmental changes, although almost all managers are aware of those impacts.

Managing fisheries on an ecosystem basis, rather than each species or species stock alone, was put into place by most U.S. management agencies in recent years. In Alaska, the effort to expand that to include weather systems, Arctic ice conditions, and stock migrations are underway.

Part of the problem is keeping up with rapidly changing warming ocean temperatures, especially in the north Atlantic and north Pacific. The nation’s most abundant fishing grounds in the Bering Sea are being impacted harder and sooner than many other productive areas because of the recent lack of sea ice and Arctic warming.

There are no models of how fisheries stocks react to these fundamental environmental shifts because the shifts have not happened on the current scale. Managers are aware of migration changes that may help some species and hurt others, depending on food availability, predators, and environmental conditions.

It is the biggest challenge NOAA Fisheries has faced perhaps in its history — how to manage stocks in a rapidly changing ocean.

For 2018, 43 fish stocks are on the Overfished List, with 28 on the Overfishing List. New England has the most Overfished species, with 15; the North Pacific has the least with 2 (St. Matthew Island and the Pribilof Island blue king crab stocks.)

After 9 years in a rebuilding plan with strict management, including a prohibition on landings, Gulf of Maine smooth skate was declared rebuilt in 2018.

“The renewed fishing opportunity and market for barndoor skate wings, following its rebuilt status, may lay the market foundation for a smooth skate fishery in the future,” the report noted.

Photo Credit: NOAA Fisheries

Peggy Parker

Original post: — reposted with permission.

Aug 6 2019

Research cruise off California finds life lacking in parts of the ocean

The California Cooperative Oceanic Fisheries Investigation captures a trove of data about what the ocean is like now, and how it compares to conditions decades ago

Scripps CalCOFI scientists and technicians deploy the Conductivity Temperature Depth sensor rosette over the side of the research vessel, Bold Horizon. (Natalya Gallo)

In parts of the California Current this summer, the ocean was clear, azure, and almost empty.

The high water clarity, and low biological productivity, were some of the defining features that struck scientists returning from a cruise with the California Cooperative Oceanic Fisheries Investigation (CalCOFI) program, a 70-year study of West Coast waters.

Although the lack of life sounds ominous, scientists said it’s neither good, nor bad, but an interesting observation that will add to their knowledge of the California Current.

“I have never seen the water so blue in my life,” said Dave Griffith, a fisheries biologist with the National Oceanic and Atmospheric Administration. “It was beautiful. It looked like Lake Tahoe out there. You don’t have upwelling, which is what brings the nutrients up to the surface.”

A joint venture of Scripps Institution of Oceanography, the National Oceanic and Atmospheric Administration, and the California Department of Fish and Wildlife, CalCOFI was launched in 1949 as a way to understand the collapse of the once prolific sardine industry in California.

It soon expanded to become an exhaustive catalogue of fisheries, marine ecosystems and water chemistry. Its quarterly research cruises capture a trove of data about what the ocean is like now, and how it compares to conditions decades ago.

The ocean serves as a vast factory for manufacturing life, with plankton nourishing crustaceans and small fish, which in turn support marine mammals, seabirds, sharks and tuna. This summer, that production system seemed to be on pause, researchers said.

“Productivity conditions were very low, we weren’t capturing high biomass in any of our nets,” said Natalya Gallo, a postdoctoral researcher with the program, who volunteered on the cruise. “Marine mammal observations were low. That makes sense, because you have more animals when you have more food.”

Without the churning of nutrients from the ocean floor, the system stalls and ocean productivity — the amount of life produced at all those levels — declines.

That’s normal in the summer, when warmer water slows up-welling of nutrients from the sea floor, but researchers said ocean productivity seemed lower than usual, even for the season.

NOAA scientists and Scripps scientists work together to bring the Manta net back onboard, following a 15-minute sampling period of the ocean surface. Manta net samples often contained gelatinous organisms, copepods, and fish eggs and larvae.   (Natalya D. Gallo)

NOAA fisheries scientist, Dave Griffith, prepares to attach the Pairovet, a vertically sampling net, to the winch wire before its deployment. The Pairovet net is primarily used to sample anchovy eggs.   (Natalya D. Gallo)

NOAA fisheries scientist, Dave Griffith, holds a newly preserved zooplankton sample up to the light to get a better look at the amphipods and euphausiids in the sample.   (Natalya Gallo)

Chief scientist, Dan Schuller, prepares the Conductivity Temperature Depth sensor rosette for deployment as the crew leaves San Diego Bay and heads towards the first sampling station of CalCOFI Cruise BH1907.   (Natalya Gallo)


The ability to observe, measure and compare ocean chemistry and biology from year to year is the chief benefit of CalCOFI, which scientists said is the longest running set of marine data in the world.

“There was very little biomass at all, at all tropic levels, from (plankton) all the way up to marine mammals,” said CalCOFI Director Brice Siemons. “That is an observation, and we can put that in perspective in our time series, and compare it to all of the last 70 years.”

That’s why the 70-year time series of the California Current is so valuable, they said. The ability to maintain a running tally of ocean measurements allows researchers to sort out whether an event, such as this summer’s biological scarcity, is a short-time curiosity, or a long-time trend.

Over a 16-day cruise of the Southern California Bight and California Current, researchers took samples of water chemistry, plankton, fish eggs, marine mammal and seabird sightings, and other variables, at 70 research stations in a grid off the coast. Scientists with Scripps, in charge of oceanographic testing, lowered a device fitted with metal cannisters that measures water temperature and chemical properties at depth.

NOAA researchers study fisheries by sampling fish eggs and larvae, using four different types of nets. This time, it was slim pickings, particularly in the sea beyond the California Current — the open waters that scientists refer to as an “ocean desert.”

“This was exceptional,” Griffith said. “We weren’t seeing many eggs in the water, which is not uncommon, but there were areas where we were not seeing anything. It was pretty sparse.”

It’s unclear why the samples were so scanty as the ocean’s physical conditions didn’t seem out of the norm, said Dan Schuller, chief scientist for the cruise.

“There was nothing crazy anomalous in any of the parameters we were looking at,” he said. “Physical parameters — temperature, salinity, oxygen, chlorophyll — were pretty standard for a Southern California trip.”

Researchers said they’ll have to test their observations of low productivity against the data they get from analyzing their samples in the lab. It may turn out that there was more abundance of life than it appeared at first glance. And even if the ocean was less productive this summer, that could be part of cycles of boom and bust in marine populations.

Warm waters in recent years have suppressed some fish populations, but also led to favorable conditions for other species popular with fishermen.

“Fishes, especially near-shore commercial fishes — kelp bass, rock bass, the marine species that everybody likes to catch — they can’t particularly pick up and leave,” Siemens said.

Other migratory fish, such as yellowfin and bluefin tuna, are drawn to the balmy, near-shore waters, to the delight of San Diego fishermen.

“Somewhat counter-intuitively, when the water’s warm, and production is low, you get some of the best commercial fisheries, which is really good for our economy,” he said.

Although their biological samples were low overall, scientists did find creatures, including small crustaceans called copapods, as well as euphausiids, or krill, a shrimp-like crustacean. They pulled up chaetognaths, a transparent predatory worm that “should probably be featured in the next “Aliens” movie,” Gallo said.

They also found pyrosomes, a bizarre, colonial organism made up of many small tunicate worms, stitched into a translucent tube that can grow to an imposing 60 feet in length. Gallo said CalCOFI researchers found many smaller ones in their bongo nets — circular nylon nets shaped, as their name suggests, like bongo drums. The apparent abundance of these otherworldly creatures is exactly the sort of thing that CalCOFI data can put in perspective.

“Talking to some of the NOAA fisheries scientists, they said that pyrosomes used to be quite rate, and they didn’t see many,” Gallo said. “So that’s one of the things we can do with our data, and compare to (data from) the 1950s.”

Despite high waves, strong winds, storms and seasickness, the cruises are indelible experiences for the scientists on board. For Gallo, the chance to help write a chapter in a one of the most enduring stories of marine science was a professional milestone.

“I was out at sea with NOAA scientists who have been doing CalCOFI cruises since before I was born,” she said. “It’s almost three whole (generations of scientific) careers that have been dedicated to this time series that gives us this phenomenal understanding of the dynamics of the ecosystem off the West Coast, and how it has changed in the past, and how it may change in the future with climate change.”

For Griffith, a veteran of the CalCOFI cruises, the hard work and long hours are the price of perpetual wonder.

“The ocean is a very powerful thing,” he said. “It’s a very resilient source. It’s just a curiosity. We’ll see something different next year. We see fish populations explode and then collapse, but they never go away…. It’s fascinating to watch.”

Scripps CalCOFI scientists and technicians deploy the Conductivity Temperature Depth sensor rosette over the side of the research vessel, Bold Horizon. (Natalya Gallo)

At the nearshore station off San Pedro, NOAA fisheries scientist Amy Hays (left), prepares to recover the Bongo net while Scripps CalCOFI researchers take water samples from the Conductivity Temperature Depth sensor. (Natalya Gallo)

During transit between stations, NOAA fisheries scientists collect fish eggs and larvae and count and identify them to examine fish spawning patterns across the CalCOFI grid.

Angela Klemmedson, research associate for the Scripps CalCOFI group, runs at test to measure the oxygen concentration in discrete water samples collected with the CTD rosette.

Original post:

Aug 6 2019

A world in a bottle of water

Revolutionary techniques using traces of environmental DNA are analyzing entire ecosystems “from microbes to whales”


Hilary Starks couldn’t wait to get her first three samples of the day. She was standing expectantly on the deck of the 117-foot research vessel Western Flyer in 2015, searching the waters of California’s Monterey Bay below. The winch on deck started moving as pulleys and wires slowly lifted what she was waiting for: a five-foot submersible carrying large plastic bottles full of seawater.

Starks, then a lab technician at Stanford University, knew that there were myriad bits of genetic information floating in the one-liter bottles, hidden to human eyes. And modern DNA-deciphering machines would later reveal secrets about the ecosystem the Western Flyer was sailing over.

Monterey Bay is home to hundreds of species of marine animals, but scientists are still far from knowing exactly how many of each there are, or how they move and interact with each other. Now researchers are analyzing the tiny traces of DNA that animals leave behind in the environment, to study their numbers and locations in a noninvasive way.

During the Schmidt Ocean Institute’s “Voyage to the White Shark Café” expedition last year, boatswain Mick Utley assists in the deployment of the CTD rosette, an instrument used to collect water samples and other oceanographic measurements from different depths of the ocean. CREDIT: SOI / MONIKA NARANJO


Modern gene-sequencing technologies have advanced so much that the analysis of such environmental DNA, or eDNA, from small samples of water or soil could revolutionize the way scientists understand ecology and conservation in ecosystems all over the world. “It’s really remarkable that in the twenty-first century we’re still not able to say exactly what lives in the ocean,” says Barbara Block, a marine scientist at Stanford who has been monitoring fish in the Pacific and Atlantic for decades. But today, just a liter of ocean water, housing millions of genetic sequences, can tell many tales about the ecological history of a place.

As ocean acidification and climate change become the new reality, scientists wonder what will happen to the distribution and well-being of plants and animals. “Monitoring communities and ecosystems is going to be much easier done by DNA methods,” says Elizabeth Andruszkiewicz Allan, an environmental engineer at Woods Hole Oceanographic Institution in Massachusetts who analyzed Stark’s samples while at Stanford. “You take one water sample and look for everything from microbes to whales.”

Just as we constantly shed DNA-containing dead cells, creatures in the oceans — from bacteria up to hulking blue whales — leave invisible environmental signs of their presence. Today’s sequencing tools are so powerful that researchers can now detect these minute traces of DNA spread out in the environment and, with refined computational methods, figure out what creatures they came from.

Finding the obvious and the elusive

To use eDNA to track species, scientists first multiply, then read, the segments found in a sample. Then they match them to known DNA sequences from species of interest.

In a study in 2012, for example, Philip Francis Thomsen, then at the Natural History Museum of Denmark and now at the University of Aarhus, and his colleagues collected seawater from sites around the Baltic Sea. They detected eDNA from harbor porpoises and long-finned pilot whales, the latter a species rarely seen in the Baltic — showing that the technology had the potential to “find” elusive species.


And last year, researchers in Alaska tracked the abundance of spawning salmon in a small stream by analyzing salmon DNA in the water, finding that it’s possible to use eDNA to estimate the abundance of a single species at a specific place even in flowing waters.

Sometimes, scientists use a version of the technique known as metabarcoding to assess DNA from whole groups of organisms, providing a broader snapshot of the biodiversity in a spot in the ocean. This has three key advantages compared to traditional ways of surveying biodiversity: It’s highly sensitive, it’s cheaper, and it’s noninvasive.

“So often, you have to kill whatever you’re interested in to collect it,” says Starks, who uses eDNA sequencing at her job at the consulting company Cramer Fish Sciences. “It’s nice to be able to not have to do that.”

Diving in

Use of eDNA analysis in the ocean got its start in the late 1980s, when scientists began looking at DNA in microbial blooms. Now scientists all over the world are studying all kinds of creatures and ecosystems to learn about the complexities of marine communities.

Thomsen, for instance, has used eDNA to study whale sharks in the Arabian Gulf and fish ecology deep off the coast of Greenland. Scientists in Southern California have detected white sharks with eDNA. Researchers in Alaska have studied the harbor porpoise, elusive in those waters. Australian scientists recently were able to detect signals from all of life’s major groups in that nation’s Coral Bay using eDNA methodology.

“I think it will have a big impact on our understanding of not only the dynamics of communities, but also the presence and absence of species,” says Melania Cristescu, an ecological genomicist at McGill University in Canada, whose work focuses on eDNA in freshwater environments. “That is what excites me.”

Thanks to the advance of genetic sequencing technologies, environmental DNA research, particularly in the ocean, has boomed in the last decades. Shown are scientific publications studying or referencing environmental DNA, per a major publisher’s database. 


Researchers in Monterey Bay started studying the eDNA of the animals that live in the area six years back, when Ryan Kelly, then a researcher at Stanford’s Center for Ocean Solutions, set out to compare eDNA sampling to traditional biodiversity surveys. Kelly wondered whether analyzing eDNA would be an accurate as well as a faster and easier method than having divers physically count animals underwater.

He knew that DNA degrades fast in the ocean, so he first wanted to test just how reliable and sensitive eDNA technology could be. To that end, he started his work in a controlled setting at the Monterey Bay Aquarium, where the 4.5-million-liter Open Sea Tank hosts 12 species of animals, including Pacific sardines, mackerel and sea turtles.

“Here we have a known community — we can see the fish in the tank,” Kelly remembers thinking. “If we take a liter of water out of this, can we see the genetics of the DNA of the fish that are in there?”

His team collected water samples from the tank and tested the eDNA. Not only did the team detect the eDNA of most of the bony fish groups resident in the tank, but the method also pinpointed the DNA from the food species fed to those animals.

Beyond what divers can see

Kelly next wanted to look at eDNA in the ocean. He worried that eDNA in seawater could be carried long distances by currents and that samples might therefore not represent the actual biodiversity of a site. So in 2013, he and his team put this concern to the test in the well-studied waters off Pacific Grove, a city northwest of Monterey. Alongside the eDNA work, divers also recorded the vertebrate species they saw at the sample sites, including rockfish, wrasses, surfperch and seals.

The divers spotted 12 types of fishes and marine mammals; the eDNA technique detected 11 of these. But the genetic analysis also revealed 18 additional fishes, mammals and birds that the visual surveys missed even though the animals are known to live there. Kelly’s team also found that eDNA analysis could distinguish between habitats as close as 60 meters apart. Following this work, marine biologist Collin Closek, also at the Center for Ocean Solutions, similarly found that eDNA from untested Monterey Bay water samples matched visual observations of anchovies and humpback whales recorded at the same time.


A harbor porpoise (Phocoena phocoena) photographed in the Bay of Fundy, Canada, in September 2012. Harbor porpoises can be hard to track, so researchers use eDNA to study their population and genetics.


In other words, “eDNA doesn’t just move everywhere; it doesn’t just swash around the ocean,” says Kelly, now at the University of Washington. “It stays in one place. And that was really important to know.”

Searching farther and deeper

But researchers so far had only explored the waters near shore. That’s why, in September of 2015, Starks set out on the Western Flyer  to discover what underwater secrets eDNA could reveal much farther out, in the open ocean.

As the bottle-laden submersible came up from deep waters, Starks poured the seawater samples through tiny plastic filters to capture all the floating genetic material. Then she placed the filters in a –80°C shipboard freezer so that the DNA would stay intact until Andruszkiewicz Allan could analyze it in the lab. For two days, the Western Flyer  roamed the ocean while a sleep-deprived Starks worked around the clock to pull 63 more samples up from all over Monterey Bay.

The lab analysis revealed eDNA from 72 fish and mammal species, including sharks, herring, lanternfish and sunfish. Some were deep-living denizens that scientists hadn’t previously known inhabited Monterey Bay, such as long-bodied wrymouths, also known as ghostfish.

Researchers in the area aim to learn still more from eDNA. Scientists at the Monterey Bay Aquarium Research Institute have used submersible robots to automate the collection of water samples from the bay. Andruszkiewicz Allan is working on a project to model how eDNA moves in the ocean so that one could know where and when an animal shed the genetic material originally.

During a 2018 expedition, Elizabeth Andruszkiewicz Allan filters seawater samples to extract and detect environmental DNA from vertebrates that have visited the waters of the White Shark Café, an area in the Pacific Ocean between California and Hawaii where white sharks gather in the winter and spring.


Stanford’s Block, who has been tagging white sharks along the Pacific coast for years, is using eDNA to estimate their abundance — and, in the lab, trying to develop a test to detect the sex and reproductive status of bluefin tuna in the bay. “I think it’s important to have a new technology other than a fishnet to assess who’s there,” she says.

Enhanced fish-finding

Environmental DNA could also help monitor fish populations every year. Various species of salmon used to swim in the Monterey Bay region, says Closek, but they’re rare now, and scientists would like to know where they are and if they’re returning. Use of eDNA could track those species and determine if they are coming back to locations they historically inhabited.

Researchers are also eager to learn more about whales. Humpbacks were aggressively hunted in the Pacific during the 1800s and early 1900s and their population, once 15,000 strong, dropped to 1,200 by 1966. Since receiving federal protection a half-century ago, their numbers have been rising, reaching at least 18,000 in recent years. “Our understanding of where those whales are located can be further improved by being able to have these eDNA locations,” says Closek.

Scientists also hope that these studies can inform policy decisions through detection of hard-to-distinguish and endangered species in a location, or invasive species that threaten native wildlife. The US Fish and Wildlife Service has used eDNA since 2013 to monitor for two invasive Asian carp species in and around the Great Lakes, for example. “eDNA provides the here-and-now view of the living world that policy decisions demand,” wrote eleven researchers, including Kelly and Thomsen, in a 2014 paper in Science.

Not so fast

Environmental DNA methods have their drawbacks. Every step from sample collection to results can go wrong: “You have to be very clean,” Cristescu says. Very few labs, she adds, have the cleanliness standards needed for eDNA work, so the chances of “finding” species that are not actually present is high. And despite the sensitivity, it’s also possible to miss species that are there if the amount of eDNA is too scant or too degraded, or if a key step in the technique is not performed correctly.

Environmental DNA also cannot yet reveal information on the sex or age of individuals of a species, so the technology will probably not replace traditional surveys any time soon. But it can certainly complement them. “This is just a different net” for catching animals, Kelly says.

“It’s a new frontier of how we’re seeing the world in a really different way,” he says. “Who wouldn’t want to look into a glass of seawater and see starfish, and orcas, and everything in between?”

Editor’s note: The text was amended on August 5, 2019 to add Philip Francis Thomsen’s current affiliation with the University of Aarhus.

Aug 1 2019

A Deep Dive into the San Diego Fishing Industry

A little market, some big boats, and a $2 billion project are poised to revive San Diego’s commercial fishing industry

“The beginning was tough—they didn’t trust us,” says Yehudi “Gaf” Gaffen, CEO of Protea Waterfront Development, referring to San Diego’s fishermen and women. “For decades they’ve been discriminated against and business has been taken away from them. People take advantage of them.”

Gaffen and his company have won the bid to redevelop the San Diego harbor. Their $2 billion “Seaport San Diego” plan will historically alter the future of the city’s waterfront—70 acres, to be almost exact. The fate of local fishers lies largely in his hands.

And a little fish market on a little dock may be the reason both Gaffen and the fishers themselves are so keenly aware of their vital importance.

Right: Seaport developer Yehudi “Gaf” Gaffen photographed at the docks.

The Glory Days

There’s a decent chance San Diego’s fishermen and women have stopped reading this story by now, because it starts with a quote from a developer. Fishers have historically viewed developers as their most feared predator. In a city like San Diego, the water’s edge is the gold vein, the bounty, the most valuable thing. And while many players are involved—the San Diego Unified Port District, the California Coastal Commission, the people of San Diego (who own the land)—the fight over it usually boils down to fishers versus developers. Boats versus hotels. Bait versus brunch.

Tuna Harbor—located at the end of G Street, sharing a parking lot with the Fish Market restaurant, the USS Midway, and the American Tuna Boat Association—is one of two remaining spots along San Diego Bay dedicated to commercial fishing (the other is Driscoll’s Wharf). Longtime San Diego fisherman David Haworth stands on the edge and points at things. To parking spots that read “Reserved for Commercial Fishermen.” To the swarm of pedestrians and tour buses clogging the lot. To an aging dock where lobster traps and nets are stacked like a working-class art installation. To the 100 or so boats, where men with reptilian skin tanned like news anchors repair, well, everything.

Customers wait in front of Tuna Harbor Dockside Market at 7 a.m., an hour before it opens.

“This is our Alamo,” he says, then laughs, acknowledging what happened at the Alamo.

San Diego was once known as the Tuna Capital of the World. At its peak in the early 1970s, the harbor was littered with gargantuan tuna boats, some with helicopters on the top deck for spotting fish. Every major cannery, including Bumble Bee, was based here. The industry employed over 4,000 people, the city’s third-largest employer behind the Navy and aerospace.


The Long Climb Back

Then fishing famously died, for many reasons. But mostly dolphins. During the gold rush for yellowfin and albacore tuna, nearly six million dolphins were killed, according to Sarah Mesnick, an ecologist in the Marine Mammal and Turtle Division of the Southwest Fisheries Science Center (SWFSC). Dolphins dying in nets was an international PR nightmare. Even suburban kids and moms thought bad thoughts about our fishing folk.

In response, the US passed the Marine Mammal Protection Act of 1972, severely limiting how American fishers could earn their living. In survival mode, boats fled San Diego and changed flags—to Mexican, Ecuadorian, Western Samoan, anything but American. Abroad, they found governments who didn’t care much about bycatch (dolphins, sea turtles, etc.), quotas designed to preserve the ocean’s stock, or labor rights. A lot of them still don’t. “We know, because we fish next to them every day,” Haworth says.

San Diego’s harbor gradually replaced commercial fishing spots with cruise ships, yachts, recreational fishing boats, floating museums. The decimation of the industry did have some positive outcomes, though: Over the past 50 years, the US has become a world leader in sustainable fishing.

“The dolphin mortality has dropped dramatically, from hundreds of thousands a year to under a thousand,” Mesnick says. Fishing’s not an exact science. If you drop a hook in the water, something’s going to bite it. But from a statistical standpoint, less than a thousand is basically zero.

Left: Peter Halmay, uni diver and president of the San Diego Fishermen’s Working Group

Bluefin tuna—once the poster child for overfishing—are rebounding far stronger than official projections. An expert who agreed to speak anonymously said the US could raise its bluefin quotas right now. But the political nature of the fish has led government agencies to be extremely conservative, which means a couple more years. San Diego’s rockfish were nearly fished out in the ’80s, when everyone in restaurants ordered the red snapper (the menu misnomer for rockfish). Mesnick says they’ve rebounded, and local fishers are reporting huge stocks.

American sustainability efforts were carried out by commercial fishers. And the price was paid by commercial fishers. The half dozen I spoke with agreed that the restrictions were necessary after centuries of unregulated overfishing. “But we were told ‘short-term pain for long-term gain,’” says Peter Halmay, a 78-year-old uni diver and president of the San Diego Fishermen’s Working Group. “We’ve been under very strict guidelines for the last 20 years. And the stocks came back way faster than people anticipated. There’s going to be a movement to open up these groundfish to pay back these fishermen for preserving it.”

The Import Problem

The current reward for commercial fishers’ sustainability efforts? Of the 7.1 billion pounds of seafood Americans eat annually, over 90 percent is imported. Theresa Talley, researcher at Scripps Institution of Oceanography, published a report that found only eight percent of San Diego’s 86 seafood markets consistently carried local fish. This is bad news in many, many ways.

“US fleets pay more for gas, pay higher NOAA fees, regulatory fees, workers’ comp fees… the list goes on,” says Paddy Glennon of Superior Seafood, a decades-long proponent of sustainable seafood. “They don’t have that in Mexico. In Mexico they can fish for sea bass 11 months out of the year. Our fishermen get a month and a half. I love our brethren across the border, but they’re playing by a whole different set of rules.”

“The thing that’s sad about America,” says Haworth: “Our negotiators are terrible. At one point we were allowed to catch 900 tons of bluefin. Then our negotiator came to us and said he agreed to reduce it to 600 tons—for two years. What kind of negotiating is that? Meanwhile Mexico got 6,000 tons and Japan got 15,000 tons. Our whole quota isn’t even one load for other countries.”

Countries outside the US—not just Mexico, but in Asia, Africa, everywhere—can undercut American fishers by charging a much lower price. “You go into any wholesaler and you’ll see 80 percent Mexican sea bass, 20 percent American,” Glennon says.

That gives light to the ultimate cruel irony: Americans’ desire for sustainable, ethically caught seafood has resulted in Americans eating far more unsustainable, unethically caught seafood. An aphorism I heard over and over again during my research: Instead of asking why American seafood is so expensive, customers should be concerned about why imported seafood is so cheap.

Dave Rudy, owner of Catalina Offshore Seafood, says that US fisheries and management are the best in the world. “But consumers still look for low prices. We have to constantly remind them that low-priced fish is not the best thing for you, and supporting local fishermen is important.”

SWFSC’s Mesnick points to the dozen or so American fishers using drift gill nets to catch swordfish; they are often targeted by environmental nongovernmental organizations, or ENGOs. “These are the same fishermen who’ve been involved in fisheries management and research and reduction of bycatch,” she says. “They work with scientists to fish where they’re not hurting marine mammals and turtles. These are very advanced fishermen with very advanced gear. If you shut them down and still want to eat swordfish, you’re importing the swordfish from places who have none of that. So you’re hurting the species.”

San Diego fisherman Kelly Fukushima calls it “the transfer effect.” “Every time you punish a local fisherman, you increase the amount of bad habits you have to import,” he says. In our fight to save the turtles, we’re eating more turtles in imported seafood.

Or, as Glennon puts is: “That 59-cent can of tuna is not just tuna.”

“Another mall on the water would be a huge disgrace to the harbor.” —Yehudi “Gaf” Gaffen

Commercial fishers make their living by being out on the water, not by attending meetings or launching publicity campaigns. Meanwhile, the ENGO Oceana launched a video series casting a negative light on commercial fishing. The titles include “Lauren Conrad Wants to Save the Sea Turtles,” “January Jones Is Scared FOR Sharks,” and “Miranda Cosgrove Wants to Keep Dolphins Singing.”

A representative for Oceana told me they’re supportive of American fishermen and women, and they’re all after the same goal: sustainable seafood. But every fisherperson I talked to took issue with ENGO’s portrayal of them (so did the scientists). They argue that they’re not the problem, and haven’t been for some time. The problem lies with dubiously regulated fleets overseas. And videos using January Jones don’t seem intended for the market in, say, Samoa.

As one of the most sustainable sushi chefs in the country—Rob Ruiz of The Land & Water Co.—once told me: “One of the most endangered species in our waters is a fisherman.”

To change this and tell their real story, fishers needed a public place. And in California they found it at markets like Dory Fleet Fish Market in Newport Beach, and Tuna Harbor Dockside Market in San Diego.

Big Changes for the Bay

Protea Development’s $2 billion plan to make over the waterfront is expected to break ground in 2024. Called Seaport San Diego, the project envisions more public parks, open spaces, and new stores and restaurants where Seaport Village and the nearby Tuna Harbor Dockside Market currently stand on the marina.

According to the developer’s website, the plan includes 400,000 square feet of retail space, an aquarium, hotels, a veterans’ museum, and a 480-foot tower with an observation deck. Protea Development and the San Diego Fishermen’s Working Group signed a memo of understanding in late 2018 that Tuna Harbor will remain in the redevelopment plan, and that improvements will be made to the harbor to allow commercial fishing to thrive, such as a new processing plant and a bridge where visitors can watch fishing boats offload their catch.

The Little Market That Could

Every Saturday, a little pier near Seaport Village is lined with tables. Each table is teeming with one of the over 130 species caught by San Diego fishers. There’s urchin, black cod, mackerel, rock crab, spider crab, yellowtail, bonito, halibut, mahi-mahi, skipjack, wahoo, mongchong, opah, bluefin—you name it. A fisherman talks to a few customers, explaining what a sheepshead is, how to cook it. His wife stands nearby holding their newborn.

In 2014, San Diego fishers began efforts to sell their catch directly to consumers, just as farmers do at farmers’ markets. It required the passage of a bill (AB 226, aka “Pacific to Plate”), but Tuna Harbor Dockside Market finally opened for business in 2015 with a whimper: five fishers filling about a tenth of the pier outside Chesapeake Fishing Company.

“We just wanted to make sure the public had access to 100-percent sustainable, traceable fish,” says Fukushima.

“I thought we were gonna replace some of the middlemen,” says Halmay, one of Tuna Harbor’s founders. “Then I realized that wasn’t the goal. The goal was to simply show that fishing exists in San Diego.”

The market made fishing cool again. —Kelly Fukushima

Market attendance was slow, but they kept showing up each weekend rain or shine. Then San Diego’s Asian communities discovered it, particularly Filipinos (San Diego is home to the country’s second-largest Filipino population). In many Asian cultures, seafood is an almost-daily staple. Fresh seafood is not a delicacy inasmuch as a standard. Asian customers also supported the diversity of seafood found at the market.

“We have different species that different ethnic communities like,” says Halmay. “About 60 percent of our customers are Asian, and they know how to cook dogfish and mackerel. Your white La Jolla customer is buying the spot prawns.”

Just as monocultures like corn and soy have devastated farmlands, a country that eats only a few species of fish creates a dangerous imbalance in the oceans. In 2015, only 10 fish species made up 90 percent of American seafood sales (salmon and shrimp alone accounted for 55 percent). Overfishing a single species—tuna—led to the collapse of San Diego’s fishing fleet in the ’70s.

“Like a lot of things in life, being diverse and moderate is good,” explains Mesnick. “Tuna are top predators. You can’t just eat the lions of the sea. Eating through the food chain is good for your health and the sea.”

The next wave to discover Tuna Harbor were the chefs. JoJo Ruiz remembers being picked up by Paddy Glennon for his first trip to the market. They arrived before dawn and met all the fishers and their families. “It’s changed my entire cooking career and my life,” Ruiz says. “A lot of chefs say the same thing. If it wasn’t for the market, we’d still be using langoustines and turbot, stuff flown from all over the world.”

Chef JoJo Ruiz at Hotel Del Coronado’s new Sere~a restaurant, demonstrating their whole-fish presentation. | Photo: Justin McChesney-Wachs

Ruiz, executive chef at Lionfish and the new Serea at Hotel del Coronado, credits the market for his being named a James Beard Smart Catch Leader for sustainable seafood. At Sere~a, he presents local fish whole to diners, lets them look their dinner in the eye and choose one, and then the kitchen fillets and cooks it for them. He swears not only by the ethics of sustainability and connecting people to their food source (“I want my son to have the same seafood I have”), but also by the taste.

“Fresh, local vermilion rock cod is 10 times better than frozen red Thai snapper used at most restaurants,” he says. “Local halibut as a crudo is better than Alaskan halibut. Have you seen the claws on spider crabs? They’re giant; big as my wrist.”

There’s a parallel between Tuna Harbor Dockside Market and San Diego’s famed Chino Farm. It was Chino delivering the produce for the early farm-to-table movement. Alice Waters and Wolfgang Puck were regulars. Now Tuna Harbor is fueling the boat-to-throat movement, with regular customers from some of San Diego’s top seafood spots—Juniper & Ivy, Ironside, Wrench & Rodent, The Land & Water Co., The Fishery, The French Gourmet, and Saiko Sushi.

“In my 20 years of commercial fishing, I’ve never seen such a big increase in the demand for local fish,” Fukushima says. “The market really revitalized the fishing industry. It’s attracted a lot of people to the waterfront and made fishing cool again. Fishing was seen as something only outcasts or criminals or people without real jobs do. At the market they see the fishermen, meet their families, see them working together.”

It’s that humanizing element—and the ability to be an “attraction,” with people coming down to watch boats unload fish, snapping pics for the Insta—that may have motivated Yehudi Gaffen to make commercial fishers a focal point of his redevelopment plan.

Left: Ironside Fish & Oyster Bar’s chef de cuisine, Mike Reidy

The Future Is Now

The seaport plan includes hotels, a veterans’ museum, restaurants, almost 400,000 square feet of retail, an aquarium, and a 480-foot “Spire” observation deck. If all goes well, they’ll break ground in early 2024. But the plans and discussions that will guide these tectonic shifts are happening right now. Waterfront businesses must speak up, or risk being left out.

“Another mall on the water would be a huge disgrace to the harbor,” Gaffen says. “Another Disneyland would do a disservice and have no place. There has to be authenticity of a waterfront project.”

When the port first asked for redevelopment proposals, Haworth says they warned the fishers. “They said, ‘Listen, guys, you better negotiate with the developer, because we don’t have any money for Tuna Harbor. If you want it revitalized you better make the deal.”

The initial discussions with Gaffen were heated. Fishermen and women are notoriously defensive of their territories, because their territory has been taken from them—once allotted nine acres on the harbor, they’re currently down to 3.9. So Halmay and a few others formed the San Diego Fishermen’s Working Group. They started showing up to seaport plan meetings and port meetings, having productive sessions with Gaffen and his son-in-law, an ex–Navy SEAL named Alex Buggy.

Nick Haworth and his father, David Haworth. David’s father, retired, is also a fisherman.

“Where there’s two fishermen there’s usually six opinions,” Gaffen laughs.

“Forming the fishermen’s group let us speak with one voice,” Halmay says. “We had to stop fighting fires and build a fire station first. The working group is that fire station.”

For instance, they sent Gaffen’s first proposal back with some curious markups. “The first few designs and drawings came back and they had them labeled HS1 and HS2,” he explains. “And I remember saying ‘What is that?’ It was Horseshit 1 and Horseshit 2. On a fisherman’s list of people they trust, we’re not on it.”

Gaffen and the seaport plan have to balance every interest, not just the fishing community’s—yachts want space in the harbor, people want parks, tour buses want parking, restau­rants have wants, hotels have wants. So many wants. Plus there’s the money issue. Unlike other governing agencies, the port doesn’t receive any public funding. They depend on money from leases, and commercial fishing has not been an eco­nomic boom for San Diego since the collapse. Not compared to, say, a luxury hotel. Not even close.

“If it wasn’t for the market, we’d still be using langoustines and turbot, stuff flown from all over the world.” ——JoJo Ruiz, Executive Chef, Sere~a and Lionfish

It was so fortuitously timed that Tuna Harbor Dockside Market has grown into a legitimate attraction. But even that was small potatoes until—seemingly out of nowhere—the big boats started showing up again.

“These tuna boats came in at just the right time,” Halmay says. “Just as Gaf was asking us, ‘How do we know you’re going to have this demand?’—here they came! I said, ‘Hey guys, here’s your demand!’”

The three big boats—carrying between 20,000 and 40,000 pounds of tuna—belong to Hawaiian Fresh Seafood, which just relocated to San Diego from Honolulu. Owner Frank Porcelli (a grad of Poway High) says he has plenty more boats he’s ready to bring in, many from the overcrowded Honolulu Harbor. But in order to accommodate this growth, San Diego desperately needs more infrastructure—slips, storage for traps and nets, ice machines, loading docks, cranes, and so on.

In September 2018, Gaffen and the Fishermen’s Working Group signed a memo of understanding. In it, Gaffen promises a list of items to “facilitate the revitalization of San Diego’s commercial fishing industry”—making improvements to Tuna Harbor, building a new processing plant, a bridge where visitors can watch fish be offloaded, and most importantly keeping yachts and recreational boats out of their “Alamo.”

Some are skeptical. The seaport plan to build a veterans’ museum and a processing plant on the G Street Mole (not to mention the new Manchester Group hotel across the street) will bring more traffic to what is already one of San Diego’s most congested parking lots. “They’re trying to stuff 10 pounds of [stuff] into a five-pound bag,” Fukushima says. Nearly all fishermen I talk to doubt whether Gaffen and the seaport plan can pull this off without grinding commercial fishing to a halt.

Gaffen and Buggy are confident they can. They’ll build a workable space for San Diego’s fishers—and help establish the city as the capital of sustainable seafood.

“It’s a differentiator and it’s authentic,” Gaffen says. “Com­mercial fishing is starting to come back. It’s a vital security need. If we can catch local, sustainable seafood for our community and restaurants—it’s a legacy I’d be really proud of.”

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