Puget Sound Study Shows E-DNA As Effective In Tracking Salmon Populations As Net Sampling

Scientists at NOAA Fisheries’ Northwest Fisheries Science Center, the University of Washington, and the Skagit River System Cooperative have shown that eDNA is just as effective in tracking threatened chinook populations as casting nets into the water to catch the fish swimming by.

The finding, published in Conservation Biology, is an important validation of eDNA as a tool for assessing the size and movement of fish populations, say the researchers.

Scientists collected environmental DNA by dipping 1-liter bottles into the Skagit River and estuary. Then they analyzed the samples for the DNA of Puget Sound chinook salmon. They simultaneously cast seine nets to collect fish in certain areas. They found that eDNA analysis identified the state of the population as well as seine net sampling — and sometimes even more accurately.

“What we found was that eDNA is a powerful tool for assessing populations of threatened animals that are otherwise difficult to trace,” said research scientist Andrew Shelton of the Northwest Fisheries Science Center and lead author of the new research. “At the population level, eDNA and seine surveys produced virtually identical information.”

That means that scientists can reliably use eDNA to assess the movement and habitat use of threatened and endangered fish populations. Scientists can use eDNA to examine and assess fish populations at a much lower cost than netting fish individually. There are tradeoffs, however. For example, eDNA does not provide some information that netting does, such as the age and size of the salmon detected.

Scientists at NWFSC are also exploring the use of eDNA to assess the reach of salmon populations in the ocean. They have shown in tests that eDNA results match up to when a research vessel nets salmon in the area. They have also shown that it is possible to detect killer whale DNA from water collected behind killer whales. It can also distinguish the type of killer whale, such as the endangered Southern Residents.

NOAA Fisheries is investing in the emerging genomics field as a way to enhance the agency’s science capability.

At the NWFSC, science teams are examining the potential for eDNA to support population surveys for Pacific hake off the West Coast, an important commercial fishery. Currently, the ship-borne surveys for hake use a mix of trawling and acoustic echo sounders.

This year, the survey has added sampling from an autonomous sail drone and eDNA analysis to test different methods for estimating the abundance of hake. Accurate stock assessments for hake help fisheries managers determine how many fish can be caught.

Highlights of the research:

• eDNA can be used for the quantification of a threatened, highly mobile marine species

• Patterns of variability within- and among-sites reveal precision of eDNA surveys relative to traditional sampling methods

• eDNA provides distinct and complementary information to traditional surveys for marine species

The study’s abstract:

Species of conservation interest are often rare or elusive, and often require labor-intensive population surveys for management. Sampling genetic traces of such species from environmental media such as water, air, or soil (environmental DNA; eDNA) can provide noninvasive and cost-effective means of monitoring. However, eDNA results may not align with traditional survey methods (e.g., visual, net) making it difficult to interpret eDNA results. We present the results of parallel beach seine and quantitative-PCR (qPCR) surveys of a threatened Chinook salmon (Oncorhynchus tshawytscha) from Skagit Bay, an estuary in Washington, USA. Our replicated design and hierarchical statistical model assesses the abundance, biomass, and DNA concentration at two spatial scales (site- and population-) over five months. We find both eDNA- and seine-derived abundance indices reflect the seasonal migration of salmon; at the population-scale, eDNA and seines provide virtually identical quantitative information. At the site scale, the methods are less correlated, suggesting the methods reveal different information about a patchily distributed species. Environmental DNA may act to smooth otherwise patchy biological signals in space and time. Reduced within-site variability for eDNA relative to seines suggests that eDNA may offer more precise population estimates. We partition sources of variability in space and time and compare eDNA and seine surveys – a first, to our knowledge – and so reveal the behavior of eDNA in the field. Our results underscore the value of using eDNA in conjunction with traditional surveys. Combining eDNA and seine estimates should improve the population data on which management of threatened species depends.

Also see:

— CBB, Jan. 11, 2019, COUNTING SALMON: STUDY USES DNA FROM SALMON TISSUES FOR ACCURATE COUNTS IN SPAWNING STREAMS https://www.cbbulletin.com/counting-salmon-study-uses-dna-from-salmon-tissues-for-accurate-counts-in-spawning-streams/

— CBB, Jan. 9, 2015, ENDANGERED UPPER COLUMBIA SPRING CHINOOK MONITORED WITH ‘E-DNA’ FOR FIRST TIME https://www.cbbulletin.com/endangered-upper-columbia-spring-chinook-monitored-with-edna-for-first-time/

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