School of Aquatic and Fishery Sciences

A new genetic analysis of Pacific cod has identified more than 6000 genetic markers, and demonstrates that their DNA diverges steadily with distance, which is termed “isolation by distance”. The results allow researchers to identify where Pacific cod are caught to within 220 km, even if the unknown Pacific cod come from a population that was not included in the original analysis. This is the first time that this particular technique has been applied to any marine species, following from its original application to identify where poached ivory originated. The new analysis also found pronounced differences in DNA between offshore cod, and the cod in the more sheltered waters of the Salish Sea off Seattle and Vancouver. The new paper was written by SAFS postdocs Daniel Drinan and Kristen Gruenthal, SAFS MS student Mary Fisher, SAFS professor Lorenz Hauser, together with their coauthors from NOAA and WDFW, and appears in the journal Evolutionary Applications.

Sablefish is a highly valuable wild-caught fish on the west coast of North America that can also be easily cultured in aquaculture facilities. However, when reared at high densities in pens, disease outbreaks can be a problem, especially a bacteria that causes a disease named furunculosis. A new study examines the effectiveness of a vaccine developed by the company AquaTactics, to test whether this vaccine protects against furunculosis when injected into fish, or when the fish are immersed for one minute in a vaccine solution. Injected vaccine proved to be both highly effective and long-lasting against both typical and atypical forms of the disease, but immersion provided no protection compared to controls. The research was authored a team led by Mary Arkoosh of NOAA, including SAFS professor Graham Young, and appears in the journal Aquaculture Research.

Many scientific fields require long-term monitoring of regions using sensors that are fixed in place, such as weather stations or acoustic stations that monitor fish abundance. These sensors produce high-quality streams of data in time, but typically over a small proportion of the study area. A long-standing sampling design problem is calculating how many sensors should be deployed to accurately estimate amounts of monitored variables such as rainfall. After a review of methods to scale point measurements to area, a new decision tree has been developed to help users decide which techniques should be used to scale time to space, and how many sensors to deploy to monitor an area of interest. The work by SAFS professor John Horne and SAFS Master’s graduate Dale Jacques, appears in the journal Environmental Monitoring and Assessment.

A new analysis of DNA differences between populations of pink salmon in the North Pacific reveals some fascinating insights into how these populations first arose and how they are related. Pink salmon all come back to spawn exactly two years after their parents spawned, which means that pink salmon coming back in even years (2014, 2016, 2018, etc.) are distinct from those coming back in odd years (2013, 2015, 2017, etc.). The new analysis is the latest confirmation of the surprising result that even year salmon all across the North Pacific are more closely related to each other, than to odd year pink salmon spawning in the same rivers. In every region examined, the odd-year pink salmon were more genetically variable than the even-year salmon. The results suggest that the last glacial maximum separated pink salmon populations, with one group surviving in Asia and North Alaska, and another group extending from southcentral Alaska to Washington. The new paper was authored by SAFS MS student Carolyn Tarpey, SAFS postdoc Garrett McKinney, and SAFS professors James Seeb and Lisa Seeb, as part of an international collaboration, and was published in the Canadian Journal of Fisheries and Aquatic Sciences.

Fishing removes parasite species that rely on multiple hosts, according to a comparison of fish parasites on three fished islands and three unfished islands in the central Pacific. The new research also finds that the positive relationship between parasite diversity and fish diversity is eliminated on fished islands. However, it remains an open question whether the impacts of fishing on parasite species increase or decrease disease in host fish. The new research was led by SAFS professor Chelsea Wood and is published in the journal Global Change Biology.

In recent years (2009-2015) polar bears in Baffin Bay come on to land about one month earlier than they did in the 1990s, largely owing to early sea ice breakup. This has reduced the duration of maternity denning by approximately 27 days. Maternity dens are now at higher elevations than they were in the 1990s as pregnant bears seek places with deep snow. In Kane Basin sample sizes were too few to make similar assessments of changes, but the impact of climate warming in Baffin Bay leaves little doubt of its effect on polar bears. The research was conducted by SAFS student Erica Escajeda and SAFS professor Kristin Laidre and appears in the journal Polar Biology.

Complex computer models are used to estimate sustainable catches in fisheries, by finding the best values for dozens or hundreds of variables so that the models explain data such as trends in abundance and the number of fish at each age and length. Traditionally, software packages are used for this kind of model fitting, most commonly a package called AD Model Builder (ADMB), but more recently a package called Template Model Builder (TMB). These models work well when trying to find the very best values for model fitting, but may take days or weeks to estimate uncertainty using what are called Bayesian methods. Recently, a new Bayesian algorithm was developed that is much faster at solving the uncertainty problem, called the No-U-Turn-Sampler (NUTS), which is implemented in a third software package called Stan. In a new paper, the NUTS algorithm is adapted for use in ADMB and TMB, allowing all of the models already written in these packages to make full use of this faster method for assessing uncertainty. The paper finds that the speed can be comparable to Stan, and is likely to allow widespread usage of Bayesian methods in fisheries stock assessments, so that catch setting can be more precautionary when the models are more uncertain. The paper, by SAFS research scientist Cole Monnahan, and Kasper Kristensen of the Technical University of Denmark, appears in the journal PLoS One.

A section of DNA in each species determines sex, and it is usually assumed that the many differences between sexes are due to DNA variability in this section. However, fresh evidence suggests that other parts of the genome also contribute to differences between sexes in many species from humans to fruit flies. A new study examines what parts of the DNA result in males and females reaching sexual maturity at different ages in coho salmon, and what influences their growth rates at young ages, finding that indeed there is some sex-specific control over these traits that comes from DNA outside of the sex-determining section of DNA. The research by former SAFS PhD student Miyako Kodama, NOAA researcher Jeffrey Hard, and SAFS professor Kerry Naish appears in the journal Marine Genomics.

The deadly fungal disease Bd (Batrachochytrium dendrobatidis) is a major cause of the wave of recent extinctions of frogs and toads, but it is difficult to decide how to best save amphibian populations from its ravages. Now a new framework has been developed that helps managers decide which actions are the most beneficial. A combination of a model of multiple boreal toad breeding sites, and expert judgment, was used to assess 35 possible actions that either preserve habitat, reduce Bd prevalence, or reintroduce boreal toads to areas where they no longer exist. The resulting strategy balanced toad survival against cost, and was predicted to reduce toad decline from 53% over 50 years to 21%. The paper, coauthored by SAFS professor Sarah Converse, appears in Conservation Letters.