Western Fisheries Science News, April 2014 | Issue 2.4

Release Date:

Genetic Tools Help Managers Do More With Less

Klamath suckers

Genetic techniques make identifying endangered suckers in the Klamath Basin more efficient and more accurate. Photo by USGS.

The work of WFRC geneticist Carl Ostberg spans from Klamath sucker conservation to Elwha Dam restoration to gaining insight into the biology of hybridization between rainbow and cutthroat trout (Ostberg, C.O., et al. BMC Genomics, 14:570; 2013). His genetic tools and approaches help managers and scientists to be more efficient and more accurate while surveying and monitoring wildlife. 

Distinguishing Lost River suckers from shortnose suckers is critically important to U.S. Fish and Wildlife managers in the Klamath Basin so they can estimate population size and target and evaluate conservation efforts. Both species live together in Oregon’s upper Klamath River basin and are endangered, closely related, similar in appearance, and hybridize. Until recently, the standard method to tell whether a sucker was Lost River or shortnose involved using morphology or counting physical features such as vertebrae and gill rakers. In order to provide managers with a better conservation tool for identifying endangered suckers, Ostberg developed a technique to distinguish the species from small tissue samples. He used restriction-site-associated DNA (RAD) sequencing to develop a suite of DNA markers that differentiate the two species.  

Using these DNA markers, Ostberg and his team discovered that individuals were misidentified using the standard identification techniques. They also found the two species are breeding with each other at rates higher than previously suspected--a fact that has larger conservation and management implications. With the new genetic tools, managers can now identify Lost River and shortnose suckers more accurately. 

Ostberg’s genetic tools may also help scientists and managers monitor when and how rivers are recolonized after dam removal. Ostberg’s team is currently developing genetic tools to assess species presence or absence by testing water samples for traces of the DNA that fish shed into the bodies of water that they inhabit (environmental DNA).  The environmental DNA approach, or sampling water for DNA, has some advantages to traditional survey techniques such as electrofishing and netting, as it is non-invasive, non-disruptive and potentially much more sensitive to the early arrival of small numbers of fish. The approach is being used on the Elwha River, where two large dams are being removed. The watershed’s ecological response is now the subject of eager inquiry, as the effects of the dam removal will help inform decisions about whether to decommission aging dams in other areas. Ostberg’s environmental DNA approach will help track the return of Pacific lamprey and seven species of native salmonids including Chinook, coho and bull trout. His genetic tools may also help detect the spread of non-native brook trout into the upper reaches of the Elwha River where they have not been found previously. 

Newsletter Author: Lisa Hayward



USGS Scientists Provide Study Plan Assistance to Malheur National Wildlife Refuge Carp Coalition:  USGS scientists Eric Janney and David Hewitt from the WFRC Klamath Falls Field Station visited with biologists at Malheur National Wildlife Refuge during the week of March 17. They assisted with the design and implementation of a mark-recapture study for common carp, a nonnative species that has caused serious negative impacts to the Malheur Lake ecosystem. USGS will continue to provide technical assistance as research and carp control efforts ramp up at the refuge, including pilot studies to determine if commercial harvest of carp is feasible.  

USGS Scientist takes Job Detail with North Pacific Landscape Conservation Cooperative:  Fishery biologist Jill Hardiman from USGS WFRC - Columbia River Research Laboratory will be acting as Assistant Science Coordinator for the North Pacific Landscape Conservation Cooperative (NPLCC) for a detail starting in May.  The USGS is a partner with the USFWS and many other agencies involved in the NPLCC.  Duties include review of project data management plans, project deliverables, and project tracking.


USGS Scientists Present at Watershed Science Conference:  On April 15, USGS scientists Ian Jezorek and Jill Hardiman presented at the 7th annual Klickitat and White Salmon Rivers Fisheries and Watershed Science Conference, held at the Discovery Center in The Dalles, OR.

USGS Scientists Provide Educational Outreach to Students at Oregon Institute of Technology:  On April 14th and 15th, scientists at the WFRC's Klamath Falls Field Station contributed to a course on Wildlife Ecology and Research at the Oregon Institute of Technology.  Students were able to explore concepts and ideas that they had heard about in the lecture to a real world example of capture-recapture research.

USGS Hosted Visiting Norwegian Scientist: On April 10 and 11, the USGS WFRC hosted Professor Jorunn Jørgensen of the Artic University of Tromsø (UIT). Prof. Jørgensen presented a seminar on her research which focuses on immune strategies to improve the efficacy of fish vaccines. Prof. Jørgensen will return in September 2014 for a one year sabbatical at the WFRC. 


New Report Projects Climate Change Effect on Common Birds and Reptiles in Southwestern United States:  For more information visit https://dx.doi.org/10.3133/ofr20141050.

New USGS Open File Report Evaluates Commercial Fishing Gear:  For more information, visit https://doi.org/10.3133/ofr2014106.

Classic Textbook To Be Digitized: The 1996 fisheries textbook “Physiology of Fish in Intensive Culture” published as part of the WFRC, Fish Health Section research program, has recently been chosen by the Springer Book Archives project to be digitized and made available at little or no cost to researchers in developing countries worldwide.  Books in these Archives particularly benefit charitable organizations such as INASP (International Network for the Availability of Scientific Publications), and Research4Life that are working to achieve the UN's Millennium.