What four decades of canned salmon reveal about marine food webs
Combining ecology with spatial data: New book delivers toolbox for ecologists
In a new book providing a guided walkthrough and toolbox to conduct population and ecosystem modeling at high-spatial resolution, James Thorson (SAFS alum and affiliate faculty, and Statistical Ecologist at NOAA) has co-authored Spatio-Temporal Models for Ecologists with Kasper Kristensen. Coming up with the idea for the book during a meeting at SAFS almost a decade ago, we sat down with James to find out more about why it’s a useful tool for ecologists.
Tell us what was the impetus behind writing a book on this topic, and what new insights into ecology it provides?
Most efforts to determine whether ecosystems are managed sustainably in ecology and fisheries have tracked total abundance for specific populations, species, or communities. But the increased challenges presented by climate and its impact on spatial management means we need to transition from concepts of ecology measuring population abundance, to instead use fine-scale spatial information on population densities in different habitats.
Why is this work important? Because much of our policy is written to achieve sustainability for an entire population. These are blunt indicators for questions such as: are we catching too many fish, do we have too few wetlands, have we paved too many meadows for bees? However, these indicators then bring us to the solutions side. Problems are global, solutions are local. For most people, issues like changing sea ice in the Arctic are more impactful when they understand how it affects their local community. Ecology shouldn’t just be highlighting big trends, but also direct us to local solutions. Spatial analysis allow us to identify both local and regional solutions to issues of sustainability.
So, the book is intended to be a guided walkthrough using a minimal set of tools for people working in applied ecology that can be used to implement a wide range of real-world ecological problems. We use varied examples including fish species from Alaska, birds from the western United States, movement models of northern fur seals, and ozone concentrations on the east coast. For example, one example used a technique called “Empirical Orthogonal Functions” to show that declining summer sea ice in the Arctic could be explained by two dominant patterns, including a decrease in sea ice near Russia around 2005, and a separate pattern of decreasing sea ice in the Pacific gateway (north of Alaska) in 2007 and again in 2012 (Fig. 1). These high-level patterns aren’t so obvious when just looking at annual sea ice patterns (Fig. 2), and simplifying the patterns then moves the conversation forward by emphasizing different local impacts of a global pattern.
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- Empirical orthogonal function model components that explain summertime Arctic sea ice concentrations, including the average spatial component (top-left panel), the spatial response for both models (top-right and bottom-left), and the temporal index associated with each mode (bottom-right).
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- Predicted concentration of sea ice in September from 1997 to 2017 fitted using a spatio-temporal index model, based on satellite measurements and restricted to locations within 3000 km of the north pole.
Who did you write this book for?
There are plenty of textbooks on statistical theory written for graduate students in statistics, and others which focus on basic analyses using free software like R. However, for ecologists, we find that the former may be too complicated, and the latter can only implement a relatively small set of canned analyses. What our book aims for is the middle ground, where people can build custom tools using minimal code – snippets that people can snap together like Legos – and build exactly what they want out of a spatial model for their ecological questions. Custom-built tools such as these then allow ecologists to address the specific context and questions that local stakeholders care about. These custom-build models are widely used in managing fish, birds, and mammals, where they’re called stock assessments or integrated population models. In some sense, the book aims to do the same thing for spatial statistics, so ecologists can combine their ecological expertise with spatial data.
In every fisheries science lab across the country, there are numerous people working in specialized spatial analysis. I think that this book will be an essential tool for their work. It’s also useful for all realms of study – terrestrial and aquatic species, mobile animals and plants growing in fixed locations. And that’s because we’re presenting the math and then breaking it down into computer steps and code, all hosted in a GitHub repository, that people can reuse. For example, we show how to combine data from three different sampling programs, which measure presence/absence, numbers, and biomass of red snapper in different portions of the Gulf of Mexico (Fig. 3). Existing software packages aren’t available to deal with a complicated setting like this, but it’s straightforward when you can customize the model using high-level code. Spatial statistics isn’t something which most ecologists learn, but it’s very useful and widely applicable in fisheries science and ecology.
Share with us some of the things in your book that will be useful for ecologists?
I’ve always loved how ecosystems change across landscapes and have been very interested in how spatial patterns change with climate change. Spatial information is extremely important when asking and answering questions around conservation science and resource management. But these fields usually use stock assessment models and integrated population models to take a bunch of data and make it into policy-relevant information. I think our toolbox should be co-equal with that effort, by assisting with spatial knowledge on how to help humans do their activities sustainably in different parts of the landscape. This is the first book to show how we can conduct this custom-built spatial analysis that’s driven by questions versus what software is available and accessible.
My co-author, Kasper Kristensen, build the Template Model Builder (TMB) software which is reused in many different applications. A big chunk of this book is laying out how to use their powerful piece of software in an understandable way. The first two chapters in particular are a guided introduction to TMB. Another useful part of the book is that it uses entirely open source, free-to-use software such as R, and computational heavy work with TMB. This addresses part of the need for this book, which is that many ecologists use accessible software like R, versus tools only existing behind paywalls.
What was the process like for you, writing a book?
One of the special things we’ve found about writing a book is we can take a decade of work and amalgamate it in one book – this isn’t always possible in research papers which have to be a lot shorter, each emphasizing some novel advance in isolation. With this book, which was a really fun and rewarding process to brainstorm and write over the last decade, we have a lot more discretion in telling the whole story around our topic. This book brings together lots of terminology and software and condenses it into a minimal set of principles and numerical techniques for ecologists in different fields. Our previous developments have been scattered across over 100 papers in a wide range of journals, and it can take years for new students or researchers to put the story together. We hope that our book provides a fun and gentle introduction to both the statistics and ecology involved in finding local solutions for global environmental problems.
Carey Kuhn, MMPA Permit No. 14327
Letting nature be nature: restoring Puget Sound’s shoreline
Stretching from Admiralty Inlet to the city of Olympia, Puget Sound has 1330 miles of shoreline. Home to 4 million people along its shores, armor covers over 25% of the region’s shoreline. In the summer of 2023, we caught up with University of Washington School of Aquatic and Fisheries Sciences (UW SAFS) researcher, Jason Toft from the Wetland Ecosystem Team, who has been working for over 10 years on monitoring the impact of shoreline restoration when armor is removed. Installed throughout the last century to minimize erosion risk in the uplands, science has actually revealed the opposite is the case waterward of the armor: armor disrupts the natural ecosystem of shorelines that support habitat for much of Puget Sound’s fish, wildlife and vegetation.
In a new paper published in Restoration Ecology, Simone Des Roches, a UW SAFS Research Scientist, led a team of researchers studying the impact of armor removal and other restoration activities on shorelines through time in Puget Sound locations. “Part of the issue with evaluating the most effective shoreline restoration strategy is that it’s very hard to pinpoint only one thing, as the actions are so interactive,” shared Simone. “In general, other restoration activities such as planting native vegetation and log placement aren’t as effective without armor removal, so that remains the most important shoreline restoration strategy to start with. Everything else follows from there.”
Simone Des Roches
With armor removal gaining momentum in the last decade, almost 30 restoration sites monitored by the Wetland Ecosystem Team in collaboration with their partners are covered in the new publication. “A major impetus for the removal of shoreline armor was the Puget Sound Chinook salmon being listed as threatened under the Endangered Species Act in 1999,” Jason shared. “This led to subsequent exploration of the impacts of armor on shorelines in the region.”
Once armor is removed, planting endemic, native vegetation, such as dunegrass, is one of the most important ‘living shoreline’ strategies. “When armor is initially removed, you inevitably get some erosion as the natural processes come back into play. By planting things like dunegrass that grow and establish quickly and has a lot of fine root systems that retain sediment, this is a great way to reduce a massive amount of erosion,” Simone noted. “It also has a higher chance of success as it occurs naturally in our Puget Sound region. By planting it in restoration projects, we give this flora a head-start on invasive species such as blackberry bushes. In essence, we’re kickstarting the natural endemic function before invasive ones have a chance to establish.”
So, what is considered a successful restoration of a shoreline? “The answer isn’t so simple,” said Simone. “Along with initial erosion, the removal of armor along a shoreline can make a previously tidy shoreline look, quite frankly, messy. But this is because restoring ecosystems is a process, and natural systems are dynamic. Restoration is not a one and done activity.” In many cases, scientists might not know what a successful restoration project looks like for many years as natural processes take time to adjust to armor removal.
Simone Des Roches
The added effects of climate change also have unprecedented consequences that are still being studied, and so the removal of armor might not result in a shoreline looking the same as it did pre-armor. “One of the key things we deal with in our new paper is that shoreline restoration is happening at different timescales and therefore it’s difficult to look at these projects and make definitive judgements on what success looks like,” Simone noted. “Armor removal hasn’t happened on every Puget Sound shoreline on one day. And the timescales we’re looking at – spanning 10s of years – are still undergoing transitions that may even outlive us.”
A vital part of armor removal and shoreline restoration projects is public education and participation in restoration projects. “The Shoreline Monitoring Database has been essential for combining data from multiple groups, including community scientists,” Jason said. A collaborative project developed by a team including community science groups, the Washington Department of Fish and Wildlife (WDFW) and UW, the Shoreline Monitoring Database provides publicly accessible, standardized protocols to allow for widespread shoreline monitoring and training.
“There are a lot of nuances in restoration, and I would love to emphasize, especially to the public, that natural systems are messy and variable,” Simone added. “One of the things that shoreline armor and river dams are doing is constraining natural processes so there is less variability. By removing this, we end up with a wild, messy, natural system, which looking at in comparison to a neat and tidy beach, can be quite uncomfortable for many people. But I like to say: trust the process!”
Niamh Owen-McLaughlin
A huge amount of diversity exists in the types of shorelines found in Puget Sound, from pebbly beaches and sandy beaches, to sheer cliffs and rockpools. “This means there is no one ideal shoreline to aim for in restoration projects,” said Simone. “The many types of beaches depend on where the water is flowing from, how far it flows, what direction the beach is facing, how much sediment comes in. But all these characteristics contribute to a functioning shoreline ecosystem. Because of this, the ideal functioning shoreline looks messy, with lots of logs and vegetation, the presence of beach wrack, and different types of bugs living in the washed-up seaweed and in the sand. And all of this contributes to the presence of other species such as birds, fish, and even whales that the ecosystem is supporting.”
This brings us to an important question – how far into the water does an effective, functioning, restored shoreline stretch? The answer is quite far. “The farther down the shoreline you build armor, the more naturally sloping beach you’re removing. This is an important shallow habitat and safety zone for small fishes and other marine organisms that are significant food sources for bigger species that don’t go into shallow water, such as orcas,” Simone noted. “So, shoreline restoration doesn’t just impact the small bit of visible coastline that we can see, but instead has huge implications for the entire ecosystem that makes up Puget Sound.”
“My ultimate takeaway for people interested in shoreline restoration is to embrace the disorderly – that’s what nature is,” Simone shared. “Letting nature be nature is something we should be applying not just to our shorelines, but also to our rivers and other spaces. It means we should look to creative solutions for our living spaces to be in synergy with nature, and part of this is accepting that these spaces might not be neat, tidy, predictable, and homogenous.”
An ambassador for diversity in marine science: a conversation with Xochitl Clare
Recently contributing to a special Oceanography issue titled ‘Building Diversity, Equity, and Inclusion in the Ocean Sciences’ was Dr. Xochitl Clare, a postdoctoral scholar at SAFS. We caught up with Xochitl about her journey to becoming a marine biologist, her background in Film and Theatre, and what inspires her to be a mentor working towards diversity, equity and inclusion (DEI). In the special issue, Xochitl contributed her own autobiography about her identity as a first-generation Afro-Latina Marine Biologist and Performing Artist, and co-authored a paper on an initiative to support inclusive mentoring practices. Xochitl is a member of the Padilla-Gamiño Lab at SAFS and is conducting her research on sea cucumbers in the Pacific Northwest and Belize, an important bio-indicator species for marine ecosystems. Her work is supported by the Washington Research Foundation.
Tell us some more about the importance of being involved in the special Oceanography issue looking into inclusion in ocean science?
The first thing that comes to mind when I think about that paper, is that I represent a lot of identities and peoples. I’m from a first-generation immigrant family – my mother is from Jamaica and my father is from Belize. I’m the first in my family to pursue higher education in marine science and embark on ocean exploration.
I never had access to the ocean growing up as a child in Glendale, California. I learned to swim in college and became certified as a scientific diver in under 5 years…that’s a pretty unusual timeline! This was a huge and intense experience for me, going from not spending much time in the ocean to doing lots of marine biology fieldwork in the ocean.
Chris Knudson
Because of that, being a mentor is really important to me. To conduct marine biology fieldwork, you need to feel welcome in the outdoors. To reach this goal of welcoming people of all backgrounds into nature, I’ve become a strong advocate for diversifying outdoors. And that’s what this publication is all about—building mentors up to support people in their first experiences working in nature. Many mentors involved in diversifying outdoors for early career scientists were doing things in the Diversity, Equity, Inclusion, and Justice (DEIJ) space but organically— because they happened to be from underrepresented backgrounds themselves.
But now, we’re actively advancing our ability to make these resources more widespread to those who don’t share the same backgrounds with their mentees. This way, we can share what we have learned in a more official capacity. I like to say we’re mentoring the mentors.
Can you share some of the specific initiatives you’re involved in to advance the diversification of the outdoors?
What’s special about this publication is that it is focused on a mentoring series for a program called Field-based Undergraduate Engagement through Research, Teaching, and Education (FUERTE), aiming to get people more comfortable working in nature. These can be unwelcome places – either directly or indirectly – for a lot of BIPOC people. And so we’re undertaking this effort to train the mentors as we believe that when people are better prepared as mentors, then more people will come into the field, especially from diverse backgrounds. We leaned on the expertise of mental health and social services workers to develop a set of integrated one-hour workshops to help mentors take the time to cultivate their intentional mentoring approaches, and for the program to advocate for self-care and self-awareness in the mentoring space.
It’s not often that scientists band together to write a reflective paper like this. It is common, however, to see reflective papers on mentoring and outdoor education strategies in other disciplines (e.g. Humanities, Social Sciences). However, we are seeing more and more findings from DEI intervention programs being shared in scholarly journals in our Geoscience disciplines.
This is great because the outdoors is not only the only thing needing to diversify. We have to diversify marine science as a whole. Marine science issues are global and have direct, widespread, and massive impacts on so many people and communities. And there are so many different perspectives that need to be taken into consideration when conducting marine science research. This meta-mentoring is a first step to begin to combat that.
How does your background in performing arts tie into all of this?
I always couch my work, both in marine science and in being a mentor for others in the BIPOC community, with science communications and theatre work. I feel like the creative medium allows people to embrace perspectives and narratives in a meaningful and personal way, but also in a way that others can relate to.
From designing science communications lessons with improvisation, to attending and engaging with small film festivals, to encouraging students to make Tik Toks about their research, these are all ways to enhance expression and build a sense of belonging in the marine science community. We know that if people can experience marine science in an authentic way, it means they’re more likely to feel included and it increases the longevity of people in the field.
Spring into Spring Quarter with SAFS Cafe
Spring into Spring Quarter with SAFS Cafe, back every Wednesday at 3.30pm.
Whether you’re a student, researcher, faculty, or member of staff, all are invited for cookies, coffee, and conversation every week.
Join us in the 3rd floor kitchen in the Fishery Sciences Building.
To tweet or not to tweet: three-year experiment finds no citation bump from Twitter promotion
In a controlled experiment spanning three years and involving 11 scientists from a range of life science disciplines, a new study published in PLOS ONE demonstrates that sharing a paper on Twitter did not increase citations.
It has long been asserted that papers shared on social media platforms, such as X (formerly called Twitter), receive a higher number of citations. However, a team of leading science communicators, led by University of Washington School of Aquatic and Fishery Sciences Professor Trevor Branch, with a combined total of 223,000 followers at the end of the experiment, wanted to explore whether increased citations was actually caused by tweeting about them, or was a correlation due to other factors such as the quality of the paper and the importance of the information in the paper. In other words, some papers may simply be unusually good or important, resulting in both more shares on social media and more citations.
Lead author Branch said “A group of us (on Twitter, of course) agreed that a controlled experiment was needed to test this idea, and we had a ton of fun doing the experiment and writing up the paper. But it definitely tested our patience waiting for the results.”
The team conducted their experiment every month over more than a year starting in December 2018: randomly selecting five articles published in the same month and journal and tweeting about only one while retaining the others as controls, then waiting three more years for citations to accumulate. By recording information such as number of tweets, Altmetric scores (a measure of online attention from social media and news articles), and citation counts, the results demonstrate that although downloads and online attention both increased substantially for the tweeted articles, there was no detectable difference in the number of citations after three years. The authors note that there can be a long lag before additional citations manifest, perhaps longer than the three year study.
Social media remains an important way to bridge the gap between scientific research and educating the public. It allows scientists across the globe to not only share their work with other scientists working in their areas of expertise, but also to reach a diverse audience from the non-scientific community. From the public to policy-makers, communicating about science in an engaging, understandable way is useful to demonstrate the importance of conducting research across a number of topics that have global impact and interest. However, as the team found out, doing so does not bump up citation counts, and this should be considered when thinking about the role of science communication. Is the goal to share work to broadly educate or to increase the profile of scientific papers?
“It’s important for scientists and technical experts to break out of the ivory tower and engage with the public, and social media tools are a powerful way to do that. Public science engagement results in a lot of good things for science and for society,” David Shiffman, research associate at Arizona State University shared. “However, tweeting about your published papers does not result in more citations for those papers, despite many people claiming otherwise. It turns out that the relationship between citations and social media shares is not causative – some papers are shared more on social media and cited more for other reasons, which a colleague calls the “good papers are good” hypothesis. If you want to talk about your research using social media, there are lots of reasons why I think you should do that, but don’t think it’ll get you more citations for your research.”
The scientists and science communicators involved in the study spanned three continents from the following institutions:
- David Shiffman, Arizona State University
- Melissa Márquez, Curtin University
- David Steen, Florida Fish and Wildlife Conservation Commission
- Isabelle Cȏté, Simon Fraser University
- Joshua Drew, State University of New York, College of Environmental Science and Forestry
- Michelle LaRue, University of Canterbury
- E. C. M. Parsons, University of Exeter
- Solomon David, University of Minnesota
- Alexander Wild, University of Texas at Austin
- Trevor Branch, University of Washington
- D. Rabaiotti, Zoological Society of London
Being an ecological detective: modeling population dynamics for humpback whales
Since 2017, Kristin Privitera-Johnson has been working with André Punt on creating a population model for North Pacific humpback whales as part of the work of the Scientific Committee of the International Whaling Commission. This population is modeled using various datasets – new, old, hidden, lost. Working with other members on their team, they’re uncovering new ways to deliver deeper insights into this population of humpbacks, including use of genetic and photo IDs data on population connectivity.
With a migratory lifestyle, North Pacific humpbacks breed in the warmer waters of Asia, Hawaii, Southern California, and Mexico, with data even showing movement even further down into Central America. When they feed, they move northwards, everywhere between Russia, Alaska and the Aleutian Islands to Oregon and California. In Kristin’s words, they are loyal to where they feed and breed, and return to the same places year after year.
IWC-POWER
Now a PhD student in the Punt Lab at the University of Washington School of Aquatic and Fishery Sciences (SAFS), part of Kristin’s work is to build models to test biologically driven hypotheses posed by her collaborators, related to the population structure of this species. Kristin describes this as being an ecological detective – how do we model who is where, and where do they keep coming back to? And do we have enough data to test the hypotheses? Part of the artfulness of this work is, if we assume some of these hypotheses about breeding and feeding habits, how can mathematical and statistical models be built to reflect this?
The data available to Kristin and her collaborators come from all over the North Pacific and various sources: old whaling records, bycatch, abundance surveys, photo ID mark-recapture, genetic analyses, and even tagging studies. The data is collected by academic scientists who conduct tagging and genetic studies, and organizations such as the National Oceanic and Atmospheric Administration (NOAA). This massive effort from a variety of groups giving time and data feeds into the development of models of the North Pacific humpback whales.
Building on classes at SAFS where she had to build fairly complex models using software, Kristin enjoys being able to continue using her quantitative skillsets, while also learning how the production of scientific advice works on a global scale, outside of the US. The projects she works on also demonstrate how researchers can come together from across the world to gather data, produce scientific advice, and how this is then used for real-world applications such as supporting the provision of management advice.
Describing her experience being advised by André as an apprenticeship, she gets to be a part of community-based, team-based work that pairs marine biology and fisheries science with quantitative ecology tools, weaving this all together to provide scientific advice for decision-makers.
There are many factors that potentially impact the North Pacific humpback population, from ship strikes and entanglements, to climate change and sea ice regression opening new travel pathways. During a March 2024 workshop in Seattle, Washington led by Debra Palka form NOAA Fisheries, the biological hypotheses to be tested were finalized, data sources were assembled, and André and Kristin refined earlier models for the North Pacific humpback whales. André and his collaborators will present and refine the model results during the meeting of the International Whaling Commission Scientific Committee in Bled, Slovenia, in April-May 2024.
IWC-POWER
Science diplomacy at work: tackling illegal, unreported and unregulated fishing
In her role as a US Science Envoy, SAFS Assistant Professor Jessica Gephart was selected as one of seven distinguished scientists in January 2023, with this position extended through 2024. Through this role, Jessica is part of a team which helps inform various US institutions and the scientific community about opportunities for science and technology cooperation abroad.
“Science diplomacy creates an opportunity for knowledge exchange across borders and allows the US to model scientific independence,” Jessica shared. “Although I travel with members of the US State Department, I attend these meetings as a private citizen and my opinions are my own. It’s a great opportunity to learn from the local embassy staff and in-country groups working on aligned issues and hear other perspectives of the issues experienced on the ground”.
Chosen for her expertise in illegal, unreported, and unregulated (IUU) fishing and trade and how this intersects with international supply chains, Jessica recently traveled to the West African countries of Senegal and Gambia in January 2024 with a more local focus in mind: the processing of small pelagic fish into fishmeal.
Why is this such a major issue? Sardinella, the primary species going into fishmeal in the region, is an important local food source and has reportedly doubled in price and become scarce. With fishmeal primarily used for aquaculture, estimated at 86%, this fishery issue is having a big impact not only on consumption, but on local fish processors and traders, who are also often women. Currently working on a paper looking into this exact issue, Jessica is delving into who benefits nutritionally from aquaculture production systems.
During her visit to Dakar, Senegal and Banjul, Gambia, Jessica was able to meet with a wide range of local people including students, conservation groups, fisher organizations, women processors, and fisheries managers. “There is a lot of enthusiasm on the ground to tackle issues of overfishing and associated impacts on availability, prices, and supply chain distribution,” Jessica shared. “When it comes to combating these issues is not a lack of willing people with the know-how, but instead resource constraints”. Issues such as limited capacity to patrol waters, inadequate systems for reporting fishing interactions, and a lack of vessels and equipment for monitoring are some key areas of constraint.
The need for regional coordination to organize priorities around fishery management, such as the nutritional use of small pelagic fish, is something Jessica noted would be useful during her trip. Regional coordination would also have positive impacts on negotiating foreign fishing access, support for training of local people, and introducing regional stock assessments. “Fish don’t recognize our political boundaries, necessitating regional cooperation for their sustainable management, which will only become more urgent as fish stocks shift under climate change,” Jessica said.
This was Jessica’s first trip in her role as a US Science Envoy, with her next trip taking her to Greece in April 2024 for the Our Ocean conference.
New paper: Shellfish aquaculture farms as foraging habitat for nearshore fishes and crabs
As interest and investment in shellfish aquaculture have expanded both locally and globally, so has interest in how these farms modify intertidal habitat and whether the complex structure created by the shellfish and shellfish growing gear provides ecosystem services that are comparable to those of unfarmed areas, such as mudflats and eelgrass meadows.