2024 Volume 2

Diet DNA: What Are Green Crabs Eating?

It’s a beautiful, blue-sky day in Willapa Bay. The sunlight dances on Stackpole slough as a light breeze ruffles the surface of the water. We can still hear some birdsong from the woods along the shoreline. And I’m stuck in thick, gloopy mud up to my waist, trying not to sink any further as I helplessly wait for Crab Team program lead, Emily Grason, to dig me out. 

I’ve worked in some of the muckiest reaches of the Chesapeake Bay, and nearly lost several boots to the mudflats of Puget Sound. But I have never become so stuck in the mud that I needed someone else to pull me out. Putting aside the embarrassment of doing so in front of Emily Grason, expert navigator of Crab Team’s muddiest trapping sites, I did feel like I had finally experienced a right of passage for any coastal scientist.

And, thankfully, my muddy misstep proved to be a small hiccup in an otherwise successful trip. The 178 European green crabs we trapped on that September day would join 186 others, collected earlier that summer, to help us answer the question: What are green crabs eating in Willapa Bay?

The Hypothesis 

Broad and adaptable eating habits help species like European green crab thrive outside of their native range. Studying the diets of green crabs where they are invasive can help us predict their impact on local ecosystems – including impacts to species that we eat, and which provide water filtration, and other benefits and services. Green crab populations in Willapa Bay have risen dramatically in recent years, with large numbers of green crabs observed on local shellfish beds. As a result, shellfish growers and resource managers are concerned that green crab predation on Manila clam (Ruditapes philippinarum) may be causing reductions in local harvest. 

These observations led us to make the following predictions: (1) European green crabs trapped on actively farmed Manila clam beds will frequently have Manila clam in their stomachs; and (2) more green crabs trapped on clam beds will have Manila clam in their stomach contents than green crabs trapped on clam beds, at slough sites without aquaculture.

The Investigation: Using DNA to Find Out What Crabs Eat 

A common method for studying the diet of aquatic species is to remove their stomach contents and visually identify food items. Depending on how recently a fish has eaten, their last meal can be pretty easy to figure out (you can even do it yourself using these stomach photos taken by NOAA Fisheries researchers!).

But as Crab Team co-lead Sean McDonald puts it, crabs are “self-contained blenders.” In addition to shredding their prey with their formidable claws, and mouthparts, crabs have a unique structure in their stomach, known as a gastric mill or ‘stomach teeth,’ that further grinds down whatever they just ate. If stomach-teeth sound like something out of a horror movie, they can be a nightmare — for scientists. When we open up a crab stomach, it looks a lot like a grainy smoothie. This makes it extremely difficult to identify food items, especially if we want to know that a shell fragment came from a Manila clam instead of a Pacific oyster, or any other bivalve.

Advances in genetic technology have made it possible to identify stomach contents without actually seeing intact food items. DNA-based diet analysis simultaneously identifies a range of food items in a crab’s stomach using the genetic material (DNA) that those items have left behind. This process, known as DNA metabarcoding, uses a short DNA sequence (a “barcode”) in much the same way a grocery store uses barcodes on cereal boxes; by “scanning” the DNA barcode with a DNA sequencing machine, and matching that barcode to an online database, we can match the DNA to the species that left it behind. 

Sounds pretty straightforward, right? Here’s the catch — the stomach is a very difficult place to get DNA from. It’s full of acids and digestive enzymes, which interfere with the chemical reactions we need to prepare DNA for the sequencing machine. And the physical and chemical breakdown of food items during digestion also breaks down DNA in the stomach, leaving behind low quality, too-short DNA fragments that we can’t analyze. Add in the fact that this technique has been applied to European green crab only once before*, under slightly different conditions, and we had to get a little creative. 

To preserve the DNA in each crab’s stomach, Crab Team and partners hauled heavy packs of dry ice onto the Willapa Bay mudflats, freezing the trapped green crabs as quickly as possible. We carefully drew each crab’s stomach contents out through its mouth with a pipette – essentially, pumping the crab’s stomach – to avoid contaminating crab stomach samples with outside DNA. Finally, we used specialized lab protocols, which we optimized for our samples, to isolate food item DNA from interfering stomach acids and enzymes. Each of these methods were developed with the help of Argentinian and Canadian green crab researchers, and members of the UW-based Kelly Lab.

This all yielded small amounts of DNA, invisible to the naked eye, in a tube smaller than a pinkie finger. At this point, there still isn’t enough DNA for the sequencing machine; we need to make more of it using a “copy-and-paste” process called PCR, or polymerase chain reaction (yes, the same PCR for diagnosing COVID-19). After we’ve made enough copies of DNA, we can scan it with the sequencing machine and match the resulting data to an online database, which tells us which food items that DNA came from.

The Reveal: What Are Green Crabs Eating in Willapa Bay?

Getting results from DNA research can feel like turning the last page of a really good mystery novel, or being a kid on Christmas morning. It’s hard to capture the excitement and awe of opening that data file and finally finding out what was in each crab stomach, each tiny sample of invisible DNA. Especially after all of the delays and challenges associated with conducting this research in the middle of a global pandemic, including supply chain disruptions that left us scrambling for lab materials. 

Another reason getting DNA data is like finishing a mystery novel – there is always a surprise reveal at the end. The big surprise in our data was that only one of the green crabs we studied showed evidence of consuming Manila clam, despite the fact that more than half of the crabs we analyzed were trapped directly on clam beds. This finding means it is unlikely that larger, male crabs consume a lot of Manila clams during the summer months, which was not what we had hypothesized. However, it does not rule out the possibility that green crabs rely more on Manila clam as food at other times of the year, or that smaller sized green crabs may consume smaller Manila clams.

Somewhat less of a surprise – green crabs had a wide diet, and we documented more than 50 unique items in the stomach contents of green crabs analyzed. What was at the top of the menu? Many of the green crabs we trapped had recently been munching on the native hairy shore crab Hemigrapsus oregonensis (12 crabs, or 18%), and the eastern soft-shell clam Mya arenaria (7 crabs). Negative impacts to these two species have been observed in other areas where green crabs are abundant (including California and Maine, respectively). Based on Crab Team trapping, we know that the native hairy shore crab is frequently found in the same places as green crabs, as is the sand shrimp Crangon franciscorum – which we found in the stomachs of 10 green crabs – and the Pacific staghorn sculpin, Leptocottus armatus – which we found in 7 green crabs. Interestingly, we also found that green crabs had recently consumed a variety of non-native species, including the invasive mud snail Batillaria attramentaria and several species of non-native amphipods.

For a more detailed accounting of these crabs’ stomach contents, check out the project summary or, if you’re a number cruncher, you can download the data table from our peer-reviewed paper.

Where Do We Go From Here?

Although our observations did not support our predictions, we did observe green crabs eating other ecologically important native species. For example, the sand shrimp C. franciscorum is an important food resource for Dungeness crab, sturgeon, and other fishes. Washington Sea Grant Crab Team and partners continue working hard to trap and remove green crabs throughout Willapa Bay. Crab Team researchers are also following up on the observations of hairy shore crab in quite a few of the crab stomachs. Former Crab Team postdoctoral fellow, Ben Rubinoff, conducted a field experiment and data explorations to see there is evidence that this predation could be leading to measurable impacts on the local populations of our hairy heroes (more to come!).

And for other researchers who want to keep exploring the possibility that green crabs are preying on Manila clams, we’ve extensively documented all of our methods and made our lab and analysis protocols publicly available online.

Green crab is particularly concerning as an invasive species due to its role as a flexible predator along marine shorelines. However, predicting the specific impacts of this predator in a new location can be really difficult at the early stages of invasion. It often takes time for populations of invasive predators to grow large enough to even cause a measurable impact in the populations of their prey species – much longer than we would want to wait to do something about it! These new methods offer managers a sensitive tool to get timely information on green crab diets, and enable us to be more forward looking at what changes might be coming to our shorelines if green crab populations continue to grow as they have over the last several years.

–Mary C. Fisher

Header image: Sunrise in Oysterville, WA Photo: Emily Grason

*While we try to link you directly to the research we reference, some of the studies cited in this article are not open access. If you have any questions about any of the works cited here, please feel free to reach out to crabteam@uw.edu.

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A Hum in the Night: The Peculiar Plainfin Midshipman in the Salish Sea

The plainfin midshipman (Porichthys notatus) has long been an enigma to shoreline residents and explorers. Most have never heard of the fish until they’ve heard the fish. That was certainly the experience of houseboat residents in Sausalito, California; for years they reported disturbing droning noises that lasted through the night, impacting their sleep and stirring up concerns about malfunctioning equipment. However, the true source of the hum wasn’t human-made; it was the unique vocalization of the male midshipman. Male midshipman fish produce a continuous humming sound during their summer breeding season, using specialized muscles around their swim bladders to amplify their call and attract females to their nests.

This unexpected revelation has led to local fascination with this “singing fish,” inspiring even a festival in Sausalito. Though also widespread in the Salish Sea portion of Washington’s coastline, midshipman vocalizations have not yet been implicated in local noise disturbances, but the fish plays an essential role in our local ecosystem and has attracted the attention of scientists and conservationists.

In addition to the males’ nocturnal “songs”, the plainfin midshipman is known for their distinctive physical traits. Their flat, broad head and wide mouth sometimes confuse them for a sculpin. But rows of light-emitting photophores along their belly give them an almost otherworldly appearance. These bioluminescent organs resemble the buttons of a naval uniform, which inspired their name, and are only activated during courtship season. Interestingly, although they have the same photophore anatomy, midshipman in Puget Sound do not actually luminesce*, which could be explained if their diet does not include the necessary ingredients for the chemical reactions. It begs the question of whether they have to make up for this courtship deficit with better, or louder, singing.

How Do They Sing? Understanding the Midshipman’s Nocturnal Calls

The sounds that midshipman fish make are more than just quirky—they’re a critical part of their reproductive strategy. Dr. Joseph Sisneros at the University of Washington has led groundbreaking research into the mechanisms behind these fish calls. Sisneros and his collaborators, including Dr. Paul Forlano from Brooklyn College, have examined how midshipman males generate these hums to lure females into their nests during the summer breeding season. Males contract their sonic muscles, which are located around their swim bladders, at incredibly fast rates—up to 100 times per second! This turns the swim bladder into a resonating chamber, amplifying the hum that can be heard by humans both above and below the water.

Much like birds, frogs, and even humans, the plainfin midshipman has evolved to communicate through sound in social contexts, primarily for mating. Dr. Andrew Bass and colleagues have mapped the neural pathways that control sound production; the male midshipman brain is literally wired to make sound. Additionally, Dr. Sisneros has characterized how, during the summer breeding season, female midshipmen undergo hormonal changes that enhance their auditory system, making them particularly attuned to the male’s hum. That hum really is…

A Song to Get Them in the Mood

During the breeding season, male plainfin midshipman construct nests under rocks or in other concealed locations in the intertidal zone. These nests are essential for the reproduction of the species, as the males must not only attract females but also care for the eggs once they are laid. Large, healthy males build the highest quality nests, and it’s no coincidence that these males also produce the loudest calls.

Once a female responds to the male’s call and approaches his nest, she will deposit her eggs, which adhere to the nest’s ceiling or walls. The male then fertilizes the eggs and takes on the role of protector, guarding the nest from predators and occasionally fanning the eggs with his fins to ensure they receive adequate oxygenation. Males are known to fiercely defend their nests, and they remain in the nest to care for the developing eggs for several weeks.

Interestingly, not all males engage in humming. Research by Dr. Bass and his team have shown that plainfin midshipmen exhibit two distinct male morphs: the “Type I” males, which are larger, produce the humming sounds, and actively guard nests, and the “Type II” males, which are smaller, do not hum, and adopt a sneaker strategy. Type II males try to sneak into nests guarded by Type I males to fertilize the eggs in an opportunistic manner. This reproductive strategy is relatively rare in the animal kingdom but has been observed in other fish species as well.

A Resident of Washington’s Waters, including Crab Team Sites

Crab Team monitors have occasionally encountered plainfin midshipman during regular sampling surveys, both inside and beyond the traps. Although these fish aren’t the focus of Crab Team’s work, and they spend quite a bit of time as adults in relatively deep or open water, documenting them in traps still offers valuable insight into local biodiversity and use of habitats likely to be impacted by green crabs. From 2015 to 2023, only 10 midshipman fish were captured in WSG Crab Team monitoring, all of which are sites within the Salish Sea, i.e., none at coastal locations. It may be no coincidence that all 5 of the sites were lagoons, which provide the calm, shallow waters midshipmen prefer for nesting. The timing of these captures, from May through August, corresponded with the species’ breeding season, suggesting that the main way Crab Team documents this local species is related to breeding behavior. That said, a juvenile was recorded at Nick’s Lagoon in September 2024, further contributing to the emerging picture of their seasonal movements and life cycle and how they might overlap with green crabs.

Conservation Concerns: The Impact of Climate Change

While the midshipman’s haunting hum and occasional capture in crab traps might seem like amusing quirks, these fish, like many marine species, are not immune to the pressures of environmental change. One significant event that has highlighted their vulnerability was the Pacific Northwest’s unprecedented heatwave in June 2021. Temperatures reached as high as 115°F in some areas, devastating marine life along the coast. Beaches were littered with dead marine creatures, including clams, mussels, and even fish. 

Plainfin midshipman were among the casualties, specifically because their nests were exposed to extreme temperatures during low tides. Anecdotal reports from local residents and scientists described abandoned midshipman nests and dead fish along the shores, as the intense heat dried out intertidal zones where the fish were breeding. These conditions likely caused stress for nesting males, which, without cooler water to retreat to, could not protect their nests or remain in their shallow-water breeding habitats. While the full extent of the damage is difficult to quantify, it raises concerns about how climate change might affect species like the midshipman, whose reproductive success is tied to specific environmental conditions.

Plainfin Midshipman and Ecosystem Health

The plainfin midshipman plays an important role in the food web of the Pacific Northwest. As a bottom-dwelling predator, they feed on invertebrates like shrimp, crabs, and small fish, while also serving as prey for larger marine mammals, birds, and even humans. Harbor seals, sea lions, and other large predators are known to feed on midshipman, particularly during their shallow-water breeding season when the fish are more vulnerable. This role as both predator and prey, connecting the nearshore sea floor to the open waters, makes the midshipman a key species in maintaining the balance of coastal ecosystems.

Climate-related challenges, like the 2021 heatwave, pose significant threats to this delicate balance. In addition to temperature stress, other changing ocean conditions might also make life difficult for midshipman. For instance, increasing ocean acidification could affect the availability of suitable nesting sites and the health of juvenile fish. Noise pollution from maritime traffic also poses a potential threat to midshipman communication. Research into how human-generated noise affects their ability to reproduce is an area of growing interest. Scientists have pointed to the delicate balance between natural and anthropogenic soundscapes, raising concerns about how noise pollution might disrupt the reproductive success of species like the plainfin midshipman. 

Looking Ahead: What’s Next for the Plainfin Midshipman?

Crab Team’s work—whether it’s tracking invasive crabs, recording unusual sightings like plainfin midshipman, or engaging the community in hands-on science—continues to be a critical part of marine conservation efforts in Washington. By keeping a close eye on ecosystem and biodiversity, monitoring helps to ensure that even peculiar residents, like the singing midshipman, are part of the larger conversation about the health of the Salish Sea.

As researchers continue to study the plainfin midshipman’s auditory capabilities and reproductive behaviors, new questions are arising about how the species will cope with future environmental changes. Whether humming away in the dark or quietly living beneath the surface, the plainfin midshipman reminds us that every species, no matter how small or strange, plays a crucial role in the ocean’s complex web of life. 

— P. Sean McDonald

*While we try to link you directly to the research we reference, some of the studies cited in this article are not open access. If you have any questions about any of the works cited here, please feel free to reach out to crabteam@uw.edu.

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Tokeland is a site with significant historical status, to the story of green crab in Washington and much deeper in time as well. Within the Crab Team monitoring network, this site plays an important role as it’s situated where Willapa Bay meets the Pacific Ocean, a location with a legacy longer than recorded history of supporting the peoples who have lived there.

A Deep History at the Mouth of the Bay

The Shoalwater Bay Indian Tribe has stewarded Toke Point, in northern Willapa Bay, and the surrounding area as part of their ancestral lands. However, by 1855 the tribe only retained a small parcel of land at the base of the peninsula (which would eventually be established as a reservation for the Shoalwater Bay Indian Tribe by President Johnson in 1866). This area is named after Chief Toke, who spent summers there with his family.

In 1885, as part of the settler displacement of the tribe from their ancestral lands, settlers Lizzie and William Kindred built a two-story farmhouse on the plot that would eventually become the Tokeland Hotel. The Kindreds have long since gone but the town of Tokeland remains, and several sites in the area are still associated with the name, including the slough on the north side of the peninsula, as well as the island that makes up the opposite shore.

These places have even older names, however, and prior to their removal, the Shoalwater thrived off rich and diverse foods living at the sea at the Nukaunlth village site. The Shoalwater Bay Indian Tribe continues to prosper in and steward the lands, waters, and shorelines of the region. As part of their partnership in Shoalwater Seafoods, the tribe carries on their legacy of first foods to farm and harvest oysters from the tribe’s tidelands in Willapa Bay, including their famed Toke Point oyster.

More recently, concerns are growing that the Toke Point oyster, along with the other shellfish and marine resources on which the tribe and region rely, is at risk from the increasing abundance of green crabs in Willapa Bay, where green crabs were first captured in Washington dating back to 1998.

Green Crabs Come … and Gone and Back Again?

Following that first detection of green crab, the focus of efforts were to figure out the scale of the problem. In the very first years of work to detect and eliminate green crab from Willapa Bay, most trapping centered on the Long Beach peninsula from Nahcotta to Stackpole. That stretch seemed to be a hotspot based on anecdotal accounts from shellfish growers, while growers in the Tokeland area rarely reported sightings. It wasn’t until a baywide trapping effort in 2000, that WDFW captured three green crabs in Kindred slough, a catch repeated the following year.

One of the first efforts to study green crab closely in the Tokeland area was led by Crab Team cofounder, Sean McDonald, at the time a graduate student in the UW School of Aquatic and Fishery Sciences. Sean and fellow grad student, Kirstin Holsman, spent the summer of 2002, conducting trapping surveys throughout the bay. They set up camp at My Suzie’s RV Park adjacent to the Tokeland Marina, which provided a good base for working the bay by boat. The Tokeland region itself remained relatively little explored with respect to green crabs, but given proximity, Sean and Kirsten took on a number of projects in Tokeland to learn how green crabs were using shorelines.

One example was trying to better understand green crab habitat preferences on the West Coast. Sean shared, “At the time, the highly invasive saltmarsh cordgrass Spartina alterniflora was widespread throughout the bay, and it was clear green crab were using it as a habitat. Our initial trapping work in Kindred Slough supported the pattern but it wasn’t possible to determine if they preferred Spartina over other habitats.” Using acoustic telemetry and other techniques, all observations they made indicated that green crab showed affinity for three dimensional structure that can provide protection, including Spartina and channeled shoreline. Today, focusing on structural features is central to the way trappers target green crab habitat, but was still a new insight at the time.

Though efforts to catch green crab in the marshes of Willapa Bay had been in full swing during the early 2000’s, the global “dot-com bubble” popped and funding for most green crab activities evaporated. By July 2003, WDFW had ceased all trapping activities. Somewhat fortunately, the timing appeared to coincide with what looked like a failure of green crabs to establish a self-recruiting population in the bay. This lull lasted for more than a decade, with years where green crabs were undetected, even by monitoring targeting the species. Numbers really started to heat up again following the 2015/2016 El Nino events, once again raising alarm and the need for coordinated action.

A Growing Crisis in Willapa Bay: The Shoalwater Bay Tribe Takes Action

In 2020, Larissa Ritzman, a longtime biologist for the Shoalwater Tribe, first encountered an unexpected and growing threat in Willapa Bay. Despite over a decade of working in the region and a deep connection to its marine ecosystems, she only became aware of European green crabs when Crab Team reached out as part of a coast-wide green crab assessment, and agreed to partner with WSG and WDFW in trapping the crabs in the Tokeland area, including a pilot monitoring site behind the Tokeland Hotel in Kindred Slough.

In short order, Ritzman went from surprised to alarmed. That August and September, initial Crab Team monitoring efforts with her crew in Kindred Slough, as well as trapping elsewhere on reservation and trust lands, found as many as 4 green crabs per trap, an abundance practically unheard of at the time in Washington. By 2021, the scale of the problem was undeniable. Trapping efforts across tribal tidelands yielded a staggering 5,000 crabs over the course of the season. 

The Shoalwater Bay Tribe quickly shifted from monitoring to active control, drawing on partnerships and innovative approaches to tackle the rapidly growing green crab population. Larissa and her team began experimenting with trap designs, bait types, and trapping schedules to improve their catch rates. They discovered that traditional Fukui and minnow traps could be greatly augmented by the use of shrimp traps. Using airboats, they accessed hard-to-reach areas with the highest crab densities, allowing them to expand their efforts. “It’s been eye-opening,” Larissa shared, “and an ongoing journey for sure. Whether it’s a good journey or a bad journey, I don’t know, but it’s a journey.”  

One big leap on that journey was an emergency declaration made by the tribal council after the alarming observations of the 2021 trapping season. Along with similar statements made by other tribes, this set the stage for Washington to declare a Green Crab Emergency in 2022. Having such political will behind the management of a biological invasion is a very rare and valuable opportunity to bring substantial resources to the table, or the mud, in the efforts to control population growth and spread.

Reflecting on the progress made since 2020, Larissa remains realistic about the challenge as well as the resource constraints the tribe faces, but ultimately hopeful. “We’ve caught more crabs this year than in the first three years combined,” she says. With no dedicated staff for green crab management, the tribe relies on a dynamic team balancing other critical responsibilities, and adaptability has been crucial. “My staff have turned into engineers,” she jokes, referencing their work redesigning shrimp pots and other gear to improve efficiency. To maximize the impact her staff is able to have locally, Larissa has prioritized activities to focus on controlling the population. In the meantime, the Washington Department of Fish and Wildlife has taken on the role of monitoring the Crab Team network site. The information from monitoring efforts are vitally important to helping untangle changing population trends from the ever-improving trapping practices that groups like Shoalwater are developing.

Tokeland Trends and Tools

Unfortunately, observations from recent monitoring underscore an ever-growing invasion. This August, at the Tokeland Crab Team site, WDFW trapped the greatest number of green crabs ever captured in a single monthly survey – 99 green crabs in just 6 traps. They picked up one additional crab by hand from the slough, just to make a nice round hundo. WDFW Biologist Rachel Flannery reflects, “While the site increasingly caught more crab throughout the season, it feels incredibly worthwhile to put time and effort into collecting such important data and removing such aggressive species from our waters.”

Over the past five seasons, monitoring at this site has illuminated important regional patterns in the green crab invasion. Being so close to the mouth of Willapa Bay, Tokeland is particularly exposed to larvae being washed in from large source populations outside the bay. This pattern also shows up in the size of crabs seen at the site. The figure below shows four of the five Crab Team monitoring sites in Willapa Bay. Tokeland and Stackpole, as closest to the mouth, have many more small crabs than Nahcotta or Cutthroat. Most of the larvae that settle there are likely still coming from outside Willapa bay, but increasingly, as populations grow in southern portions of the estuary, larvae are being locally produced as well. 

The vulnerability of the region to larvae from other locations means that for the Shoalwater Bay Tribe, the fight against green crabs is an uphill battle. Depending on seasonal conditions, the work they do to trap and remove crabs can be offset by the arrival of more larvae. But the same monitoring data shows signs of progress at Tokeland. From 2021 to 2023, it became much less common to capture particularly large crabs in monitoring efforts – a signal that control trapping is impacting the population of green crabs by “crabbing down the population.”

The tribe’s commitment to preserving the ecological health of Willapa Bay remains steadfast. Larissa has secured grants to begin restoring shellfish beds but must now consider how green crabs could undermine these efforts. For Larissa, the fight against green crabs is personal. “It all started with Sea Grant. It was Alex and those guys who began our foray into everything green crab. I have to thank her for that.” While the road ahead is uncertain, the Shoalwater Bay Tribe’s dedication to their ancestral lands and waters continues to guide their response. For Larissa and her team, the battle against green crabs is about more than just numbers—it’s about protecting the heart of their community. 

— Lisa Watkins, Emily Grason, P. Sean McDonald, and Ben Rubinoff

Header image caption: Monitors from the Shoalwater Bay Indian Tribe trapping at the mouth of the channel at site #602 in 2020. Photo credit: Alex Stote

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Photo Gallery

We love to get the virtual experience of monitoring with all of the Crab Team volunteers. Do you have a photo to share? Send it to crabteam@uw.edu. (Click on arrows to scroll, and photos to enlarge for more detail.)