SOS: Save Our (mud) Shrimps

Moving out of your parent’s house for the first time is not an easy thing to do. Especially if you move all the way across the country! But two weeks into my OSG Summer Scholars internship and I know I’m doing the right thing for myself. I’m excited to work live and in person with the animals and people that I’ve been working with for over a year. This summer I’m working on another piece of the 10+ year project trying to understand the relationship between a native burrowing mud shrimp, Upogebia pugettensis, and it’s invasive parasitic isopod, Orthione griffenis. Upogebia pugettensis populations up and down the west coast have drastically declined, with some local extinctions in California. Collapses in mud shrimp populations have been associated with infestations of Orthione and former pesticide use from oyster farmers.

Looking for juvenile mud shrimp in the lab (May 2021)

After taking a week to drive from North Georgia to the Oregon coast, I jumped right into my work duties. My lab partner, Joshua (an Oregon State REU intern), and I get the privilege of doing field and lab work this summer. Some of our field work includes trudging out onto the mudflats behind Hatfield Marine Science Center at low tides. On the mudflat, we take cores and sieve them down to collect the mud shrimp. We also get to bike out onto the fishing pier next to the Yaquina Bay Bridge after dark during high tides. On the pier, we are doing plankton tows, which are conical fine-mesh nets with a cod end that traps critters that are riding the incoming tides into the bay. Back in the lab, we sort and analyze the mud shrimp and the plankton tows. The mud shrimp are analyzed based on aspects like species, sex, carapace length, infested with Orthione, size of Orthione, and other important factors. The plankton tows get analyzed for juvenile mud shrimp (both Upogebia and Neotrypea) and Orthione cryptoniscans (one of the larval stages of Orthione).

Field sampling on the mudflat at low tide for Upogebia pugettensis (May 2021)

Through this project we are hoping to determine the life span and the settlement schedule of the cryptoniscans and to get large enough samples of mud shrimp to overcome sampling bias to ground truth the age/size relationship. Ultimately, accomplishing this project is putting another piece of the puzzle down into saving this mud shrimp from extinction. To do that, we need to know the relationship between the shrimp and the parasite better. That’s where my team and I come into play. With our work we can try and answer questions like: When do the shrimp become infested? Do the cryptoniscans settle on the shrimp or on other Orthione? Do cryptoniscans wait for a certain time to settle? What are they waiting for? Some kind of signal from the shrimp? Learning these answers will be one step closer to answering the big picture question “how can we turn this around or CAN we turn this around?”

Mud shrimp are native ecosystem engineers. They build permanent y-shaped burrows in the sediment that influence the estuarine benthic community by providing habitat and enhancing nutrient cycling. By saving these shrimp we are helping to advance OSG’s vision and mission to have thriving coastal communities & ecosystems. This research would also help to balance the forces of ecology and economy to inform oyster growers how to safely manage the burrowing mud shrimp populations without depleting them.

Getting Started


My name is Jessica and I am majoring in marine biology at Oregon State University. This summer I will be working with the Human Dimensions Project within the Oregon Department of Fish and Wildlife. I will travel to Oregon’s marine reserves to survey visitors about their awareness and opinions of Oregon’s marine reserve system. I will also be going to tourist-oriented businesses in nearby towns to ask about their awareness of marine reserves as well as how they think the reserves have impacted their businesses. Later in the Summer I will enter the data collected into a database so that it can be analyzed and used in a report due to Oregon’s legislature in 2023.

When the marine reserve system started in Oregon, the legislation required a report be submitted ten years after implementation describing the affect marine reserves have had on coastal communities and ecosystems. Baseline data was collected for two years before any restrictions were put in place so that the state of the ecosystem and the opinions of local communities before the reserves were fully up and running would be known. The data collected this Summer will be compared to the baseline data, allowing the Oregon Department of Fish and Wildlife to determine the impact of marine reserves on local communities.  

One of the main goals of the Human Dimensions Project is to ensure conservation efforts are not negatively impacting coastal communities. Without community support ODFW would not be able to carry out its mission of, “protecting and enhancing Oregon’s fish and wildlife and their habitats for use and enjoyment by present and future generations.” The coastal community focus of the project also helps to further Oregon Sea Grant’s mission by supporting a management approach to marine resources that prioritizes thriving coastal communities as well as a healthy ecosystem.

The first day of surveying visitors to the Otter Rock Marine Reserve in Newport, Oregon.
Joe the sea Lion was not bad company between visitors to Cascade Head Marine Reserve.

Let the Summer Begin!!

Hello everyone!

My name is Phoenix A. McFarlane and I am a Doris Duke Conservation Scholar who is going to spend the summer right alongside Oregon SeaGrant’s Summer Scholars! I am a junior at the University of Idaho and am majoring in Environmental Science. Though I thoroughly enjoy the outdoor recreation and wilderness aspects of Idaho, I was ready for a change! Spending the summer on the Oregon Coast is going to be an unforgettable adventure!!! 

Fishing @ Lucky Peak Lake. Boise, ID.

For my summer internship, I am working with the Oregon Department of Fish and Wildlife (ODFW) within their Marine Reserves division. My summer will be spent conducting visitor surveys in hopes of assessing awareness of Oregon’s marine reserves amongst the visitor population. Also, I will be surveying coastal businesses and determining if they have faced any socioeconomic impacts from the implementation of the marine reserves. Though my summer will mostly consist of interactions amongst the public, I will also be tasked with the responsibilities of data entry and interpretation. So far I am realizing that it sounds easier said than done! However, I have no doubt I will overcome the obstacles and develop new skills that will help me in my future as a scientist. 

Day hike in the Sawtooth Wilderness. Stanley, ID.

Overall, the exploring I have accomplished up to this point has been a much needed change of scenery. Slowly in the process of getting familiar with the coastal species and their common names. I am so grateful for this opportunity and the connections I am making! Shoutout to my roomies Grace Roa and Lisette Perez for making this summer experience that much more meaningful!

More adventures to come!                          


Start of the Summer with Eat Oregon Seafood

I am just one week into my Oregon Sea Grant Summer Scholar position and I am already starting to get a clearer idea about my role as a Summer Scholar! One thing I have started to figure out is how my work fits into the broader picture of Sea Grant. This summer I am working for Eat Oregon Seafood (EOS) which is an initiative created by Oregon Sea Grant. EOS was created after a survey asked individuals in the Oregon fishing community about the effects of COVID-19 on their income. The survey reported that 95% of respondents had suffered negative impacts due to the pandemic. In response, the EOS mission was created: “to give the coastal seafood economies a boost as they recover from restaurant closures and other issues related to COVID-19”. My goal this summer is to participate in smaller projects that help advance the larger EOS mission.

I have a few different projects I will be working on this summer. The first is creating a social media campaign to boost the reach of EOS content. Part of this campaign will include short videos to highlight different members of the fishing community. I will also be working on creating a way to analyze the effectiveness of the outreach program “Shop at the Docks”. Shop at the Docks provides tours of the Newport fishing docks every Friday. The goal of these tours is to show the public how to purchase seafood directly from fishers. All of these duties aim to increase the public’s awareness of issues facing coastal communities.

The project I am starting on right away is the social media campaign. I will post infographics and seafood recipes on a weekly basis on the EOS social media. Hopefully, this will increase the number of people these resources reach. If you’re interested in keeping up with our social media you can follow us on Twitter or Instagram @EatORSeafood! If we are able to reach more people and increase the number of people buying seafood from fishermen, then we may be able to slightly offset the other negative impacts these coastal communities are facing. Hopefully, these projects will help the community enough so individuals can bounce back from COVID-19 impacts and reach a pre-pandemic economy.

The EOS goal ties directly into the broader goals of Oregon Sea Grant. Oregon Sea Grant’s mission is to be “a catalyst that promotes discovery, understanding, and resilience for Oregon coastal communities and ecosystems”. EOS is directly impacting the resilience of Oregon coastal communities by increasing financial buy-in. EOS also increases interactions between fishers, scientists, policymakers, and the public. My hope for the summer is to use my projects to strengthen the connection of fishermen with other community members. Then fishers can use these connections to help build a more resilient fishing community. I am excited to see where this summer goes and will keep you all updated throughout my journey as a Summer Scholar!


Differences I observed going from academia to government

As I transitioned from academia to a government agency, I noticed some similarities between the two. In both places I have worked with an incredible lab/team that are always willing to help figure out why some R code isn’t working or review a paper. Also, in both places I have been constantly learning new things and testing my skills. On the other hand, I have noticed many differences between my experience as a graduate student at the University of Florida and as a fellow with the Marine Reserves Program at the Oregon Department of Fish and Wildlife (ODFW).

One major difference between the two places is how I speak about my research. As a student I was allowed to be an advocate. I could speak about wanting to expand protected areas and conserve all species to my heart’s content. It was practically expected of me to have these strong opinions about conservation and discuss them openly. Working for a state agency, the expectation is exactly the opposite. I now must be impartial in my word choice both in person and in writing. Though I work for the Marine Reserves Program, I am not an advocate for marine reserves. I am simply studying how the marine reserves may have impacted communities and presenting these results in a straightforward manner. If I take a strong position on marine reserves, the public may lose trust in my ability to conduct unbiased research. If the public loses this trust, they are less likely to support the agency and follow agency regulations. This trust is crucial, but also fragile.

Another difference between academia and government is the type of research being conducted. In academia, the focus is more on what is interesting and would advance the field. In government, the focus is on achieving the mandate. Therefore, our research options are limited and must be strictly applied research rather than theoretical. We also must be transparent about our research and where funds are going since we are a largely tax-funded agency. This is another important component of building that trust.

Government agencies typically work on projects with larger scale timeframes than what graduate students are involved in. While long-term monitoring projects are typically considered boring and unpublishable in academia, these types of data are the bread and butter of ODFW reports. We are constantly monitoring fish stocks, commercial fishing pressure, license sales, oceanographic conditions, etc. Most of these data are written up in annual reports and used to inform management. While long-term monitoring is generally not considered “sexy” research, it is extremely useful to have these historical datasets to understand how things have changed over time. I am using many of these historical datasets in my current work looking at how marine reserves may have impacted factors like recreational anglers’ Catch Per Unit Effort (CPUE), commercial fishing employment, and coastal communities’ socioeconomic conditions.

Lastly, one of the best changes I experienced when going from academia to government was an increased focus on having a work-life balance. In graduate school I was applauded for staying in the lab late and working on weekends. In my current position, I am expected to only be working 40-hour weeks and taking weekends off. We spend time in our weekly meetings discussing general life announcements that aren’t marine reserves related in the slightest. We even share good places to hike, mountain bike, snowshoe, camp, etc. because we know we will all have time to do these fun hobbies.

These are some of the major differences I observed in my life going from academia to government. These are solely based on my personal experience and are likely not applicable to everyone that made this transition.

How do we know if marine reserves influence recreational fishing communities?

We’ve almost made it! The year 2020 is just about to end and 2021 is right around the corner. Though many issues that were highlighted in 2020 won’t be going away in 2021 and need to continue to be addressed, there are some things to look forward to. Just this month, healthcare workers started receiving the first round of the COVID-19 vaccine. As more and more people get vaccinated, we will hopefully see the end of strict quarantine measures in the near future. Maybe we will even be able to spend the 2021 holidays with family without a mask in sight! 2021 will also bring a new administration with climate change as a top priority, which will likely influence ocean policies and management. So, while 2020 was an important year and we should not forget what we learned in it, here’s to hoping that 2021 doesn’t throw us any detrimental curveballs.

Now that you’re up to date on some of what’s happening in the USA, let me update you on what I’ve been working on. In my last blog post I outlined how I’m using the Oregon Department of Fish and Wildlife’s (ODFW) daily angling license sale data to determine if marine reserves have influenced recreational fishing. Since people are no longer able to fish in the marine reserve sites, we might expect this to result in fewer licenses purchased in towns near the reserves post implementation. This might also be observed by an increase in licenses purchased in towns further from the reserves.

However, whether or not people decide to go fishing is just one aspect of measuring a potential reserve effect on recreational fishing communities. For those that do decide to go fishing, how much they catch and over what time period is another crucial component. This metric is referred to as Catch Per Unit Effort (CPUE). For our analysis, we calculate CPUE by dividing the total number of fish caught by the number of anglers aboard the vessel and by the number of hours fished. This creates a standardized metric whereby we can compare fishing trips with varying numbers of anglers and hours fished. Specifically, we can compare CPUE reported at docks near marine reserves pre- and post-marine reserve implementation. We might expect that marine reserve site closures could increase effort, thereby decreasing CPUE, by forcing anglers to spend more time traveling further to avoid the reserves. On the other hand, we might expect site closures to increase catch, thereby increasing CPUE, due to spillover effects whereby a greater abundance of fish inside the reserves leads to a greater abundance of fish outside the reserves.

Lucky for me, ODFW has been collecting the information I need to calculate CPUE through the Ocean Recreational Boat Survey (ORBS).  This is an annual survey of Oregon’s marine recreational fishery that estimates both catch and effort at the top 10-11 ocean access points. This survey was first developed in 1979, but the original focus was on generating accurate salmon estimates in a timely manner. The ORBS survey has since expanded and provides valuable data on stock abundance and health for many species, which is used for management purposes.

By looking at both daily angling license sales as well as CPUE on charter boats, we should be able to uncover any potential marine reserve effects on the recreational fishing community. Of course, there are many covariates to take into account that could influence CPUE, such as catch regulations and environmental variables. I won’t dive into this right now, but maybe another blog post detailing the difficulties of finding downloadable historical buoy data without huge gaps is in order. Signing off for now, happy New Year!

Working with the data you have

Amid the chaotic nature of this summer with COVID-19, protests, wildfires, and an upcoming election, I have managed to seamlessly transition into my second year as a Natural Resource Policy Fellow with the Oregon Department of Fish and Wildlife (ODFW). Over the next year, I will continue to evaluate the impacts of marine reserves on coastal communities, communities of interest (e.g. commercial fishers), and ocean users (e.g. tourists).

Over the last year working on this mandate I have discovered that there are no perfect data sources to answer this question. Data often have errors associated with insufficient sampling in small communities, issues with changes in methodology, or are simply not available for the years or communities of interest. However, we can’t let these issues stop us. Therefore, we are gathering and analyzing relevant data from as many sources as possible while documenting the limitations of the data.

One source of data we have used are ODFW’s one- through seven-day fishing and shellfishing license sales. Implementing marine reserves closes off any extractive activities within that area. Therefore, we might expect that daily fishing and shellfishing license sales in communities located near marine reserves would decrease following reserve implementation. However, we also need to control for the historical trend in license sales on the coast. If license sales are decreasing in towns located near reserves, but also decreasing across the entire coast, then this reduction may be caused by something other than the reserves, such as a change in culture.

License sales are just one example of the data we are using to analyze marine reserve impacts. While we don’t always have perfect data to work with, using the best data available from multiple sources should be sufficient to understand if and how marine reserves have impacted communities.

Reflections of a remote intern

As the end of my internship encroaches I am feeling like I have accomplished my goals and completed my tasks. I learned a lot this summer and as I reflect on my last 8 weeks I am very happy with who I have met and worked with, and what I learned from them. I am also happy that I got to learn a little bit more about myself and how I might respond to a remote position in the future.

Our three dogs: Wolf the chocolate brown Pomeranian-Poodle, Kona the merle Pomeranian, and Einstein the white Pomeranian.

I was surprised about how productive I can be at home. There are so many distractions for me to get tangled up in like the pile of laundry in my closet, the dogs (we have 3!), or even the sudden urge to clean out my refrigerator but I was able to manage my needs and get my work done. Some days I was more productive than others and I definitely didn’t work a M-F, 9-5 either. I put in a full eight hours of work some days and other days I didn’t. I was lucky because although my organization operated on standard business hours, I could complete my tasks outside of the work day if I pleased.

Me on vacation last week in North Bend, WA visiting the Snoqualmie Falls on an early morning hike.

If I could start the summer over again before the internship, I would have dedicated a space for me to complete my work. This summer I worked on the back patio, the living room couch, my bed and even in the basement. Having a desk where I can keep my computer and notes would have been ideal to keep me focused for a longer period of time. I would also have planned my vacations after the internship because although my internship was remote, it was a little difficult to stay on the computer while everybody else is relaxing!

A future in Science Policy

Learning about science policy is one of the main reasons I applied to the Oregon Sea Grant Summer Scholars program. I am so happy that I was selected to work with the Oregon Coastal and Oceanic Information Network (OCOIN) because bringing science to policy makers and natural resource managers is what they do!

The OCOIN network is a series of partnerships and just to name a few, they work with Portland State, Oregon State, Oregon Coastal Management Program and a new partnership this summer with the PNW Consortium on Plastics. The network also has a large variety of politicians, natural resource managers and researchers.

Working with OCOIN has taught me two very important things. The first is that policy makers actually use published science to help inform policy and second, there isn’t enough (especially oceanic) research published and/or distributed to policy makers. OCOIN tries to make the research as accessible as possible to decision makers and other researchers. 

I have had the opportunity to attend agency meetings with the Institute of Natural Resources (INR), the Department of Land Conservation and Development (DLCD) Ocean Management Program (OMP) and the Oregon Marine Reserves (ODFW). One of my main goals this summer was to learn about as many different careers in natural resource management as possible and with at least 8-10 people in agency meeting all specializing in different work, I think I achieved my goal!

Science Policy and the Organization of the South Slough National Estuarine Research Reserve

Before I get to the real substance of this blog post, try saying “South Slough National Estuarine Research Reserve” five times fast… It takes some practice, so good luck!

Once you have mastered saying “South Slough National Estuarine Research Reserve,” you can move on to the remainder of this post.

Okay, games aside… For this week’s blog, I have answered questions related to science policy that can be seen below in bold.

Now that you’ve been on the job for several weeks, how has your view of science policy changed (if at all)?

My views on science policy haven’t really changed, though working for a state-run organization has given me a better understanding of the resources available to organizations like the South Slough National Estuarine Research Reserve (SSNERR). I’ve also heard more about what it takes to get additional funds through grants for various projects (and it doesn’t seem easy).

Do you have a better understanding of how policy organizations work?

One of my goals for this summer is to have an in-depth understanding of how the SSNERR is run. As of now, I have not had time to learn more about how it works on a macro-level, but I have definitely developed a better understanding of how the SSNERR team works on a micro/local level. I have had the opportunity to work with both the science and education teams this summer; as a result, I feel I have a solid understanding of how similar programs may be organized. I also have a better understanding of what positions are necessary to run a state-guided science organization.

Have you had a chance to attend any agency-level meetings?

I meet frequently with the education team, but have not yet attended an all-staff meeting or meeting of higher status. I will be attending the next all-staff meeting in order to learn about how the meetings and agenda-setting work, though my role at the South Slough (given my limited time) has not made it imperative for me to attend such meetings. I believe I will get to attend a National Estuarine Research Reserve (NERR) meeting this summer as well, which will help me understand the larger system as a whole. 

Does your agency have ties to other states, and/or to national-level organizations?  

The South Slough was the first location designated as a National Estuarine Research Reserve (NERR) and is affiliated with the National Estuarine Research Reserve System (NERRS). This system functions under NOAA. As seen on NOAA’s website, “The National Estuarine Research Reserve System is a network of 29 coastal sites designated to protect and study estuarine systems. Established through the Coastal Zone Management Act, the reserves represent a partnership program between NOAA and the coastal states. NOAA provides funding and national guidance, and each site is managed on a daily basis by a lead state agency or university with input from local partners.”

Logo for South Slough National Estuarine Research Reserve
Our logo at the South Slough!