Estuary provides refuge after dam removal for bull trout

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Bull trout use a bewildering array of strategies to aid in their survival, from remaining in streams their whole lives, like rainbow trout, to spending part of their lives in the ocean before returning to streams to spawn, just as salmon do. Bull trout are present in only one of two neighboring rivers in the Olympic peninsula, Washington state, and in this one (the Elwha River), two large dams were removed during the period 2011-2014. Dam removal resulted in massive outflow of sediments, reducing the clarity of the water and also building up a large delta and expanding the size of the estuary at the mouth of the Elwha River. Standardized sampling for bull trout before, during, and after dam removal was used to detect whether bull trout changed their use of the Elwha River estuary, or moved into the adjacent Salt Creek stream where they were formerly absent. Sampling revealed no movement into Salt Creek, but numbers of bull trout in the Elwha River estuary increased greatly during and immediately after dam removal, coinciding with large sediment outflow, before returning to their original low levels. Thus bull trout appear to have used the enlarged estuary as a refuge from the effects of dam removal, then returning to the river when the river water cleared up from the sediment, although confirmation is needed from tagging studies from other rivers experiencing dam removal. Of additional interest is the long-term response of bull trout to the additional habitat opened up above the former dams. The new research by SAFS graduate student Alexandra Lincoln, Anne Shaffer of the Coastal Watershed Institute, and SAFS professor Thomas Quinn, appears in the journal Environment Biology of Fishes.

(a) Map showing the Salt Creek watershed and Elwha River watershed, (b) aerial photo showing Elwha River estuary sampling sites, (c) aerial photo of Salt Creek estuary sampling sites.

 

Increase in bull trout sampled during surveys of the Elwha River estuary before (white), during (gray) and after (white) dam removal.

How far do river fish move?

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For decades, fish researchers believed in Gerking’s “restricted movement paradigm”, thinking that river-dwelling fish largely stay in the same place and rarely venture forth. But in recent decades, ecologists have harnessed the power of both advanced tags and improved genetic methods to directly estimate movement distances and average home ranges of different fish species. Now, a new paper has gathered in one place data from more than 200 direct movement studies and more than 200 genetic studies to estimate how far river fish more on average. The findings show that while some fish in each population stays largely in the same place, other individuals of the same species move vast distances—in one case, more than 1,000 km (600 miles). Median movements from the direct studies were 12 km, while genetic studies based on changes in DNA estimated median dispersal to be 1 km. Across species, both method were closely correlated, but some species dispersed very little (69 meters based on direct methods; 19 m based on genetics), while others were champion movers. The new research by Lise Comte of U.C. Berkeley, and SAFS professor Julian Olden, appears in the journal Fish and Fisheries.

Whole DNA sequences should be used to improve conservation decisions

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The U.S. Endangered Species Act has saved or recovered many species, and is recognized as one of the most powerful laws in the world for protecting the environment. The primary aim of the Act is to ensure that populations and species persist, and to conserve genetic variation in population. But little attention is paid to the adaptive potential of populations—the capability of populations to evolve when faced with new selective pressures—even though new genetic methods of sequencing the entire DNA of organisms are now cheaper and easier than ever before. These new “genomic” methods offer the unprecedented ability of measure how much adaptive potential each population contains. In a new paper, scientists explain how managers, policy makers, and conservationists can harness the power of genomic methods to ensure that protected populations have as much capacity as possible to adapt to a rapidly changing world. The new paper by W.C. Funk and others, including SAFS professor Sarah Converse, appears in the journal Conservation Genetics.

Illustration of adaptive potential for a population with genes that are adapted to cold (c) or hot (h) conditions. In panel a, all individuals contain a mixture of genes and can adapt to either hot or cold conditions. In panel b, one population has only the genes for cold (cc) and the other population for hot (hh) conditions; both lack the adaptive potential to exist in a different thermal regime. In panel (c), environmental conditions follow a gradient from cold on the left to warm on the right, and there are more cc individuals in cold regions, and more hh individuals in hot regions, illustrating how adaptive potential allows populations to live in a variety of conditions in a changing environment.

There are multiple ways of thinking about endangered species classification

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To protect and recover species, most countries have laws that mandate particular actions when species are classified as threatened or endangered. These classifications can have an enormous impact on industries that impinge on the species in question, for example the declaration of northern spotted owls as endangered led to large-scale shutdowns in logging on old-growth forests. This process of classifying a species as threatened, endangered, or neither constitutes a difficult decision, and difficult decisions can usefully be approached using the theory and tools of decision analysis. In the analysis of a decision, framing the decision correctly is key: we are better off when we are precise in defining the decision to be made, as it helps everyone involved and invested to be on the same page. The perspective of policy makers (“framing”) around whether to declare species as threatened or endangered has substantial influence on the final decision, and a new paper outlines five possible ways in which this can occur. (1) Putting species in the correct bin: applies scientific methods to decide if the species falls below specified thresholds. (2) Doing right by the species over time, which adds a dimension of future time to the decision. (3) Saving as many species as possible given budget limits, which requires classifying suites of species at the same time to ensure the best possible trade-offs. (4) Weighing extinction risk against economic or social objectives, thus explicitly balancing costs and rewards of classification. (5) Strategic aims to advance conservation goals, thus requiring negotiation as an integral part of classification. Policy makers that are clear about which framing they are using will make decisions that are easier to defend, reduce confusion, and minimize conflict, as well as leading to closer collaboration with scientists. The new paper authored by Jonathan Cummings and others at the U.S. Geological Survey and U.S. Fish and Wildlife Service, was coauthored by SAFS professor Sarah Converse, and appears in the journal Conservation Biology.

Far smaller fishing footprint than previously believed

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A new and more accurate study reveals that about 4% of the ocean area experiences fishing each year, a far smaller estimate than previous studies that relied on very large grid sizes. Two recent studies estimated that fishing takes place in 55% of the ocean and 90% of the ocean each year. But these estimates divide the ocean into 0.5°×0.5° grid cells, which are ~3100 km² in size at the equator, and assume each cell is fished if a single fishing location is recorded in the entire cell. The higher estimate additionally assumes that catches occur in areas inhabited by a fished species, not just in fished locations, potentially placing actual fishing locations into multiple grid cells. Now, researchers using the same dataset have examined what happens if the estimates are recomputed using high resolution data, to get a more accurate estimate of the ocean area fished. When the grid cells are reduced to 0.1°×0.1°, only 27% of the ocean area is fished; and when the grid cells are 0.01°×0.01°, then only 4% of the ocean area is fished. Furthermore, even for the tiniest grid cells they examined, half of the grid cells could not have been fully covered by fishing even if fishing uniformly covered the grid cells. The authors also showed that large areas where fishing is banned in Alaska appear to be completely fished when using 0.5°×0.5° grid cells, but are not fished when using fine resolution 0.01°×0.01° cells. The results overturn the main tenet of one of the original papers, that the area footprint of fishing is larger than the footprint of agriculture; instead, the opposite is true. The new results appear in Science magazine, and were authored by an international group of scientists headed by SAFS postdoc Ricardo Amoroso.

Using smaller grid cells results in a much more accurate estimate of fishing footprint. Shown here are estimates for Alaska and southern South America. Fishing is banned in the red area in Alaska, but appears to be fully fished when using large grid cells.

The recovery of whooping cranes is threatened by black fly harassment

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Whooping Cranes are highly endangered. To improve their recovery chances, a new migratory population was reintroduced into the wild in 2001, but their hatching success has been very low. A new study examines three possible hypotheses for this failure: harassment by black flies of nesting birds, effects of captive rearing, and inexperience of breeding birds. The overwhelming finding was that black fly harassment is the cause of poor hatching success: for example, when black fly numbers were reduced experimentally, breeding success doubled. In addition, as black fly numbers went up, especially of the Loon Blackfly (Simulium annulus), survival of chicks declined strongly. The other two hypotheses (effects of captivity and breeding inexperience) only weakly explained patterns in survival. Although black fly harassment was pinpointed as the key issue affecting hatching, other factors such as inexperience and the rearing environment still are suppressing the recovery of Whooping Cranes, so that black fly mitigation alone is insufficient for the population to grow at hope-for rates. The new paper was led by Jeb Barzen of the International Crane Foundation and coauthors included SAFS professor Sarah Converse. It appears in the journal The Condor: Ornithological Applications.

Photo of Whooping Crane
Whooping Crane. Credit: Sarah Converse

 

Restoration of mountain whitefish to the upper Cedar River

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Dams and river crossings often block the migration routes of stream-dwelling fish in addition to their better-known effects preventing salmon from spawning in upper river reaches. Relatively little is known about the movements of mountain whitefish (Prosopium williamsoni) in the Pacific Northwest, despite their widespread distribution. In the upper Cedar River, Washington, mountain whitefish had been absent above the Landsburg Dam, constructed in 1901, until a fish ladder was built in 2004 that allowed their upstream passage. Mountain whitefish undergo extensive migrations within larger rivers, and the fish ladder was expected to open up more than 33 km of suitable habitat, especially in deeper stretches of the river. Immediately after the fish ladder was installed, small numbers of mountain whitefish were observed above the dam, and numbers continued to increase for seven years before leveling off. These results show that wild fish can rapidly re-establish in areas above dams, when stream barriers to migration are removed, providing hope for river restoration in other regions. The paper was led by Peter Kiffney of the Northwest Fisheries Science Center, NOAA, included two SAFS coauthors, Ben Cram and Thomas Quinn, and appeared in the journal Ecology of Freshwater Fish.

Number of mountain whitefish observed per km above the Landsburg Dam, Cedar River, in the years immediately after a fish ladder was installed. No mountain whitefish had been observed in these stretches before the fish ladder was installed.

Migrations of whooping cranes converge with age

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Whooping cranes are endangered and slowly recovering from a low point of just 15 birds and one migratory population in the wild. New efforts have established an eastern second migratory population from captive-bred birds, although not without some difficulty, since migration routes are learned from other adults. In the eastern population two methods were used to teach a new migration pathway: imprinting cranes on ultralight aircraft on the ground, which would lead the cranes to an overwintering destination; or imprinting them to follow older whooping cranes or wild sandhill cranes when they migrate. After the first season, whooping cranes are no longer guided, and gradually change their migration pathways, shortening the migration distance each year. A comparison of the two methods of imprinting (ultralights vs. other cranes) finds big differences in the first few years of age in migration distance, but by age 6, the migration paths of the two groups had converged and shortened to similar distances and locations. The new research by Claire Teitelbaum and Thomas Mueller of Goethe University, Germany, and SAFS professor Sarah Converse, appears in Conservation Letters.

Detecting smallmouth bass in a stream using a sampled glass of water

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Smallmouth bass are native to much of the midwestern USA and central Canada, but have been introduced to 41 states and 20 countries. While they are sought-after angling targets, they also are voracious predators of small fish and crayfish, which is of particular concern given their taste for baby salmon and trout. Thus it is crucially important for management and conservation to detect which streams have been occupied by smallmouth bass. Current methods involve snorkeling through streams, but this is expensive, time-consuming, and not guaranteed to detect all occurrences. In a new study, the methods of environmental DNA (eDNA) is trialed that involves taking a water sample and testing it for cast-off bits of DNA from smallmouth bass. The eDNA tests detected smallmouth bass in streams at similar or greater rates than snorkel surveys, and was able to distinguish between smallmouth and largemouth bass DNA, but could not distinguish between smallmouth bass and a couple of other closely related species occurring outside the Pacific Northwest. Thus the new method is perfectly suited for surveying streams in the Pacific Northwest for smallmouth bass, with much less environmental impact than snorkel surveys. The study was conducted by Thomas Franklin and colleagues at the U.S. Department of Agriculture, together with SAFS PhD student Erika Rubenson and SAFS professor Julian Olden, and appears in the journal Northwest Science.

Fish that learn migration from their elders are more susceptible to fishing

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Many fish species repeatedly migrate from feeding areas to spawning areas, and their migration pathways could be innate or learned. Two possible models are examined for learning of these migration pathways: the Diffusion Model holds that fish head to spawning site near where they themselves hatched; while the Go With the Old Fish Model involves young fish joining schools of older fish, and learning migration pathways from the older fish. In a new paper, the implications of these two models are examined. Following older fish results in much great variability in fish numbers from one place to another, and when fish numbers decline, this strategy results in some spawning sites being abandoned while other spawning sites have much higher fish numbers. In addition, the Go With the Old Fish Model results in lower sustainable catches and a less productive fishery overall. Such patterns mimic observed herring population changes, highlighting the importance of research that identifies how fish learn migration pathways. The new paper by Alec MacCall of the Farallon Institute for Advanced Ecosystem Research, and his coauthors, which include SAFS postdoc Margaret Siple, SAFS director André Punt, and Tessa Francis, who is a Research Scientist at the Puget Sound Institute/UW Tacoma and Managing Director of the Ocean Modeling Forum, was published in the ICES Journal of Marine Science.