DELTA LEAD SCIENTIST REPORT: How different genetically are fall-run and spring-run chinook salmon?; Social science in the Delta; and activities of the Delta Science Program

At the January meeting of the Delta Stewardship Council, Delta Lead Scientist Dr. Laurel Larsen discussed the recent science publication, ‘A complex phenotype in salmon controlled by a simple change in migratory timing.’ She also introduced Dr. Jessica Rudnick, the new California Sea Grant Social Science Extension Specialist hired to work in the Delta and updated the Council on the Delta Science Program’s ongoing activities.

REPORT: A complex phenotype in salmon controlled by a simple change in migratory timing

Dr. Laurel Larsen began by discussing an article recently published in Science Magazine, titled, ‘A complex phenotype in salmon controlled by a simple change in migratory timing.’  The study was led by Neil Thompson et al., a team from UC Santa Cruz and NOAA. Funding for the primary author was in part provided by the California Sea Grant and the Delta Science Fellowship Program.

The word ‘phenotype’ is used to describe an outward appearance or a set of behaviors in an individual, which might be distinct from that individual’s genetic makeup, Dr. Larsen explained. “For example, in humans, the brown-eyed phenotype, which I exhibit, might result from having just one or two inherited genes for brown eyes from your parents,” she said. “Often, it is inferred that phenotypes that are very different from one another are indicative of significant differences in the underlying genotype or genetic makeup. Perhaps different enough that the organisms likely to not breed with each other and hence may be managed as different species, such as the case for Chinook salmon, for which the different phenotypes are referred to as ecotypes.”

Chinook salmon ecotypes are differentiated by their migration timing, such as spring-run or fall-run, and a host of other differences in appearance, including fat content. Spring-run salmon are much rarer and are protected under the Endangered Species Act, whereas fall-run salmon are not. This study questions the basis of the assumption that spring-run and fall-run salmon have genotypes that are different enough to justify managing them as separate species. 

The study involved the sequencing of the genomes of 160 fish collected from the Klamath and Sacramento river basins, and what they found is that the genetic differences between these salmon ecotypes were found only on a very small region on the genome, which they called the ROSA, or ‘region of strong association.’ The gene for migration timing is encoded with a simple pattern of inheritance analogous to that of eye color, so essentially, the whole suite of phenotypic differences, including the difference in appearance and fat content, are controlled by this one gene for migratory timing.

The authors inferred that the differences in appearance aren’t hardwired at all, but rather arise as a result of the different environmental conditions, including the food sources that are available to the fish at the timing of their migration,” said Dr. Larsen. “The authors found evidence that spring and fall-run chinook salmon do interbreed in the wild, which further supports the assumption that they aren’t different species at all. When they do interbreed, their offspring tend to have intermediate migration timing.”

These findings are important for several reasons, she said. “One is that they present a rosy picture for restoration and management. In places like the Klamath in Northern California, spring-run Chinook have almost been completely extirpated and parts of the watershed; however, loss of that spring-run population does not imply loss of all of the other genetic adaptations to the watershed that has evolved over long periods of time. Those adaptations are found on genes other than those in the ROSA and are held in common with the extant fall-run population. Thus, when ancestral parts of the watershed are reopened to the salmon upon removal of the dams, it’s possible that a robust spring-run population could reemerge, particularly with managed breeding with the few existing spring-run populations within the watershed.”

These findings in the Sacramento River basin challenge how we manage spring and fall-run populations separately. “The big question is, do we really need a separate San Joaquin restoration program focused on spring-run salmon if we know that the spring run and the fall run are hybridizing.”

The paper has been received with great interest by the Delta scientific community, but its interpretations are not without controversy, she said, noting that this paper is likely one that will undergo continued heated discussion, both within and outside of the scientific literature.

Delta Councilmember Don Nottoli asked about the restoration work and the removal of dams on the Klamath.  Does that presume that you still have remaining spring run Chinooks … ?

My understanding is that yes, there is still some hope for restoration mainly because of hatchery operations that maintain spring-run salmon populations,” said Dr. Larsen. “Now, if you’re only working with hatchery populations, there’s a danger of interbreeding and a host of genetic problems that come with interbreeding.  My understanding is that because these spring-run salmon do hybridize with the fall-run salmon, you could selectively breed with the wild pool and avoid some of those problems that come with inbreeding.  Eventually, you could select for individuals who exhibit that spring-run timing but do have the genetic diversity of the wild salmon pool.”

Councilmember Maria Mehranian asked about the importance of knowing the type. I was unclear. Is this to help them survive? We’re trying to understand these differences; then we figure out why they are different, and the outcome of the study will be that we do certain things to preserve them?

That is the hope,” said Dr. Larsen. “The outcome helps us better understand how to manage for a diversity of migration timings, which is important because of the many distinct ecological values that are provided by maintaining populations with this diversity and migration timing. And then there are also cultural benefits, and native practices that rely on healthy populations of all of these ecotypes.”

Councilmember Mehranian asked what would be some of the measures that you would recommend that this finding will lead us to do?

One of the big recommendations is that we need to make the habitat available to each of these ecotypes of salmon,” said Dr. Larsen. “So we need to ensure that our flows … including temperature are going to coincide appropriately with the timing of these runs.  I think this also argues for the importance of continued hatchery operations and the urgency of managing these for these different ecotypes with the help of hatchery operations before some of these ecotypes are completely extirpated in the wild.”

FOR MORE INFORMATION: Click here to read the study.

Social science in the Delta

Dr. Larsen then introduced Dr. Jessica Rudnick, the new California Sea Grant Extension Specialist who recently began her position with the Council in December.  Dr. Rudnick holds a Ph.D. from the University of California Davis and the Center for Environmental Policy and Behavior.  In her position, she is tasked with leading the effort to integrate social science in the Delta. 

Dr. Rudnick’s background is in interdisciplinary environmental social sciences, where she focused on understanding human behavior and environmental governance. She recently finished her doctoral work, which incorporated multiple different social science disciplines, including sociology, psychology, and political science, to give both theory and tools for how to think about human decision making and behavior around complex environmental issues.

My previous research focused on understanding farmer decision making and behavior specifically around nitrogen fertilizer management, which is a critical challenge for both ecosystem and drinking water protection in California,” she said. “I had the chance to work both in the legal Delta as a Delta Science Fellow, as well as in the Sacramento and San Joaquin Valley. This work was extensively collaborative working with the state and regional water boards, local water quality coalitions, farm bureaus, and with different nongovernmental organizations, including environmental and environmental justice groups.”

She then gave an example of how behavioral science can inform future management and policy actions. One of her past research projects was identifying how to work with farmers to improve nitrogen management.  The research identified that private on-farm consultants were the most trusted source of information for farmers when deciding how to manage their nitrogen.  This information was then used to focus their efforts on working with the organization that trains and certifies the consultants to ensure that the consultants were informed on how to give the best farm practice recommendations that are protective of ecosystem and water protection goals. The work also informed the development of climate-smart agriculture incentive programs administered through the California Department of Food and Agriculture to direct the cap and trade monies to be used as efficiently and equitably as possible to the agricultural community in their climate adaptation efforts.

Humans are a central part of the complex system in the Delta, but more is known about fish population dynamics, invasive species impacts, or flood control models than what is known about the human communities living in and near the system and how they think, feel and behave.

For example, we have relatively crude understandings of how in Delta residents perceive different environmental issues,” said Dr. Rudnick. “We don’t understand well how Delta managers access and use scientific information or how they process and grapple with uncertainty. And we have relatively little understanding at sort of a complex governance level of where there are incentives or barriers to increasing cooperation and collaboration across the many different public, private and civil sector actors governing and managing the resources in the region.  Overlooking these human components or not having a great understanding of how these very diverse groups of people think, feel and behave can lead to unintended consequences in our management and policy solutions. These are the types of questions and issues that we hope social science can bring the tools to help develop more efficient, more effective, and more equitable policy and management going forward.”

The Delta Science Program and the Delta Stewardship Council staff have been working to identify where the gaps in social science knowledge are.  Their work over the past couple of years led to the development of a strategy for developing social science capacity in the Delta, which included the convening of a social science task force in 2018.  The task force produced a final report, released in early 2020, which included some high-level recommendations for how to go about integrating social sciences into the Delta, science policy, and management landscape. 

One of the early actions identified in the report was hiring for the position Dr. Rudnick now holds, so her task is to figure out how to operationalize the other goals identified in the task force report and the priorities that the Council has.

Dr. Rudnick’s vision for this work builds off the foundation from the task force and the other Council staff efforts to develop specific recommendations and objectives for the upcoming years. She will be organizing her time and effort around three goals:

Integrating more social science theory, methods, and tools into ongoing Council work. “For example, I have started to work with the team developing the Science Action Agenda to think about how social science questions can contribute to that effort. I’ve also started to work with the Delta Adapts team to brainstorm on how we integrate more human dimensions and issues of Delta as a place into the adaptation phase of that ongoing climate change project.”

Sustained outreach and engagement with communities in the Delta and with the social science community in the region.I am looking forward to supporting the development of more equitable public participation best practices, to developing long-lasting relationships with the environmental justice communities and community-based organizations working in this area, and to initiating a collaborative community of social science, academic scientists, and practitioners across the region, who can contribute to building large scale longitudinal studies where we begin to understand how the population in and around the Delta is changing over time.  We’re planning a kickoff event for this social science network that will take place at the Bay-Delta Science Conference in April, and encourage anyone interested to attend that.”

Initiating long term collaborative applied social science research studies.The first project that I’m excited to get underway is a study on how Delta communities perceive climate change risks that will affect them, how this perception of risk aligns with the risks that have been identified through the Delta Adapts vulnerability assessment study, and where there is willingness or capacity to engage with different adaptation strategies. I’m hopeful that this understanding of the human dimension around climate change will help us bridge the gap between the biophysical science and implementing adaptation actions going forward.”

Dr. Rudnick then closed by saying that she is here to be a resource on the human dimension issues in the region. “I’m hoping that we’ll develop useful and relevant understandings of the key stakeholders that are influencing and influenced by the decision making in the Delta. My philosophy in doing this work is to be as cooperative and engaged as possible. And I’m hopeful that these efforts can be multipurpose and leveraged to inform multiple projects both within the Council and happening externally across the rest of the region.”

Activities of the Delta Science Program

The Delta Science Proposal: The solicitation for letters on intent was successful; they received requests for double the amount of funding.  This enables the science program to fund new work that will address key uncertainties in implementing the Delta Plan. Dr. Larsen attributed the popularity of the solicitation to the growing visibility and competitiveness of our science funding program on both a national and international stage. The full proposals are due on February 12.

Adaptive Management Forum:  The adaptive management forum will be held February 3 through 5th.  One of the recommendations from the Delta Independent Science Board’s adaptive management review in 2016 was to convene a regular forum that brings together scientists and adaptive management practitioners from multiple agencies and institutions.  The biannual Adaptive Management Forum is a direct response to that recommendation.  The themes for this year’s forum include revisiting the foundations and planning for the future of adaptive management, the practice of adaptive management planning, closing the adaptive management loop, adaptive management, surprises and successes, mechanisms of adaptive management, and the future of adaptive management.

Steelhead Trout Workshop: The steelhead trout workshop will be held from February 16 through 18th. This workshop represents a collaborative effort between the Council, the US Bureau of Reclamation, the National Oceanic and Atmospheric Administration, Metropolitan Water District, the Department of Water Resources, the Department of Fish and Wildlife, and US Fish and Wildlife Services. The impetus for the workshop was the biological opinion on the long term operation of the Central Valley Project and State Water Project that directed that the US Bureau of Reclamation coordinate with the Collaborative Science and Adaptive Management Program to sponsor a workshop for developing a plan to monitor steelhead populations within the San Joaquin basin and the San Joaquin River downstream of the confluence of the Stanislaus River. This includes steelhead and rainbow trout on non-project San Joaquin tributaries.  Click here to register.

Bay-Delta Science Conference: The 11th biannual Bay-Delta Science Conference will be held virtually from April 6 to 9th.   The conference is jointly sponsored by the Delta Stewardship Council and the US Geological Survey.  Over 300 abstracts were submitted, which is more than twice the amount of available speaking slots. Click here for more information and to register.

This response, together with the PSN, it was illustrates the growing visibility of our Delta Science Program and its growing competitiveness,” said Dr. Larsen.

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