School of Aquatic and Fishery Sciences

Sockeye salmon are found in many lakes and rivers in the northern Pacific Ocean, and have radiated outwards into regions formerly under glaciers during the most recent ice age. There are three main ecotypes: river-spawners (that migrate directly from the ocean to spawn in rivers); beach-spawners (that spawn on beaches in lakes) and tributary-spawners (that spawn in river tributaries that feed into lakes). Now, a new genetic study examines sockeye salmon from these 3 ecotypes that come from 32 separate populations in 7 major river systems. For each fish, key regions of the DNA were genotyped (reading the DNA letters) that are not subject to selective pressure, that are likely involved in adaptive divergence among populations from a single drainage (“genomic islands”), and that are important for the immune system. There was strong evidence of selection, but this did not vary systematically by ecotype. The resulting data show links between distant populations of river-spawning sockeye salmon, which provides evidence that river-spawners are the ancestral form of sockeye salmon, and that other ecotypes arose from adaptive radiation into areas that came available as glaciers receded. The work was led by current and former SAFS students and postdocs Wes Larson, Tyler Dann, and Garrett McKinney, and SAFS professors James Seeb and Lisa Seeb, and appears in the journal Molecular Ecology.

Rivers are crucial components of human well-being, contributing water, food, hydroelectric power, and transport for millennia. Yet an estimated 2.8 million dams now divide up rivers world-wide, threatening healthy river ecosystems and reducing biodiversity in stream systems, in addition to impacts on inland fisheries that supply protein to 158 million people worldwide. Now, the first global assessment of free-flowing rivers has just been published in the journal Nature. The new study finds that as river length increases, so do human impacts. Indeed, only 37% of rivers over 1000 km in length still flow uninterrupted from source to sea, and these are found only in most remote parts of the world: the Arctic, Amazon basin, and the Congo basin. Free flowing rivers are important suppliers of nutrients, sand, and species to deltas and estuaries in particular; and some of the longest remaining (the Irrawaddy and Salween Rivers) produce 1.2 million tons of fish catch annually. Given the global degradation of the natural flow of these long rivers, protection is needed to prevent further declines in their health. The new study was conducted by a global collaboration of 34 scientists from 16 countries led by Günther Grill of McGill University, and included SAFS professor Julian Olden among the coauthors.

The Deepwater Horizon oil spill, starting 10 April 2010 and lasting until 15 July that year, was the largest in US waters in history. This highly impactful event offers lessons that can be used to train the next generation of marine scientists. In a pair of new articles in Current: The Journal of Marine Education a group of authors that include SAFS communications specialist Dan DiNicola outlines ways in which marine educators can bring the story of the oil spill to life, including assessing the impact of oil on fish swimming behavior and vision using “fish treadmills” with the aid of an online virtual laboratory; and highlighting new technological advances that came out of research on the effects of the oil spill.

“For the virtual lab, the RECOVER team wanted to create an online resource for teachers that put them in control of the same experiments we were performing in the lab,” said Dan DiNicola. “It’s really amazing to hear from educators who are using it in places like Colorado and Ohio, where they are introducing new marine species, concepts, and even the lasting impacts of the oil spill to students. It also allows the scientists to communicate their work and present the actual data from their experiments to students in a new way.”

Dan DiNicola

Mapping the distribution of mobile species is a long-standing problem in ecology. For many species, there are multiple types of data available, roughly categorized into surveys of many individuals at a snapshot period in time (e.g. a systematic spatial survey recording all individuals at a point in time) compared to tracking devices that follow individuals over time as they move through space (e.g. satellite tracking tags). Now, a new study on common murres shows how the two methods can be combined to give detailed information about the space that these birds inhabit. The results from systematic ship-based and aerial surveys show that common murres are present in great densities close to their coastal colonies, and are rare further away. However, satellite tags on individuals demonstrate that some individuals are not at all tied to the colony areas, and can roam far afield. This the study population can comprise residents that are tied to colonies and tourists that travel far afield. The new work was led by former SAFS PhD student Elizabeth Phillips, SAFS professor John Horne, Jeannette Zamon of NOAA Fisheries, and USGS researchers Jonathan Felis and Josh Adams, and appears in the journal Ecology and Evolution.

Complex fisheries models are like weather forecasts for fish populations: they gather together all the available data about fish trends in numbers over time, numbers at each age, and other information, and then predict the level of sustainable catch that can be taken from the population. Over time, as computing power has grown, these models have also become more complex, and run time has remained consistently high. Explaining all of the data in such models can be done using two methods: maximum likelihood methods, which approximate the uncertainty around model estimates, and Bayesian methods, which more directly measure the uncertainty. Although Bayesian models perform better, the time to run them to completion has been prohibitive, and most fisheries are managed with models in the maximum likelihood framework. Now, a suite of new advances has been combined including new and more efficient Bayesian algorithms, parallel processing, and restructuring so that models are more amenable to Bayesian methods. The new methods offer a 50 to 50,000-fold improvement in run time over existing methods: in one case allowing a model that would take more than 15 years to complete to be run in just over 12 hours. The new work was led by Cole Monnahan as part of his PhD dissertation, and completed while he was a research scientist at SAFS. Coauthors include SAFS professor Trevor Branch, NOAA scientist Jim Thorson, IPHC scientist Ian Stewart, and Cody Szuwalski. The paper is published in the ICES Journal of Marine Science.

Tuna fisheries supply nutrients, food, employment, and other economic benefits to coastal states and global industrial fleets. A new analysis now examines the causes for variability in economic performance among regions and management types through Fishery Performance Indicators, which score performance on 68 questions answered on a scale from 1 (worst) to 5 (best). Benefits were greatest for tuna caught for canning and for sashimi (raw fish) markets, since these were the highest quality fish, and had access to the most valuable markets; and success was largely determined by the post-harvest sector. Thus foundations and NGOs seeking to improve livelihoods of those living in coastal states will achieve the greatest economic benefit in these states by investing in infrastructure that enables tuna fishers to improve fish quality and access to markets. The new work was conducted by Jessica McCluney of McCluney Seafood Marketing Strategies, SAFS professor Chris Anderson, and James L. Anderson at the University of Florida, and is published in the journal Nature Communications.

Recent advances allow for the editing of any part of the DNA of individuals (their genome), offering a chance for ecologists and conservationists to radically transform individuals and ecosystems, as outlined in a new review. The new genome-editing tools are being driven by technology called CRISPR that allows for the precise editing of DNA letters coding for key genes within an organism. Among the many applications of CRISPR are the creation of gene drives that result in the rapid spread of either beneficial genes (to rebuild populations) or deleterious genes (to halt the spread of invasive species) throughout populations. Other applications include rapid sequencing of genomes, the removal of unwanted DNA, high-sensitivity detection of pathogens, the alteration of an organism’s adaptive capabilities, and the correction of disease using gene therapy. CRISPR can even be used to insert a genetic barcode into the genome of individuals to allow for different populations to be tracked as they mingle within broader aggregations. While there is still understandable reluctance to change the DNA of individuals in their natural habitat for ethical reasons, genome-editing will soon become an integral part of biology that needs to be tailored to solve conservation problems around the world. The review appears in the journal Conservation Biology, and is authored by Michael Phelps of the Department of Pathology at the University of Washington, and SAFS professors Lisa Seeb and Jim Seeb.