Ocean Indicators Methods and Background Materials
Background materials including ocean indicator sampling methods, glossary, and references.
Hydrography, Zooplankton, and Ichthyoplankton
Much of the oceanographic data shown in this report came from sampling along the Newport Hydrographic Line (Figure HZI-01). We sample the coastal waters off Newport at biweekly intervals during the upwelling season in spring, summer, and fall. Sampling cruises are conducted monthly during stormy winter months. This program began in May 1996, but we also have data from these same stations from sampling conducted in 1973 (Peterson and Miller 1975), 1983 (Miller et al. 1985), and summer 1990-1992 (Fessenden 1995).
Cruises during May 1996-September 2001 occurred only during daylight hours. Our research vessel, the RV Sacajawea, was only 37 ft in length, rendering it unsafe to work at night. With the acquisition of a new and larger research vessel (RV Elakha; 54-ft.) in September 2000, we began sampling at night, collecting data for an adult euphausiid time series.
This work included measurements of copepod and euphausiid egg production and molting rates. We are also developing a long time–series of copepod and euphausiid production, which should prove useful in evaluating if there are measurable differences in zooplankton production in association with changes in sign of the Pacific Decadal Oscillation.
From 1998 to 2003, we sampled a group of transects from Newport, Oregon to Crescent City, California five times per year as part of the U.S. Global Ocean Ecosystem Dynamics (GLOBEC) program. Since the GLOBEC project ended, we have continued to sample these same transect lines as frequently as possible. We have sampled this region in 2004, 2006 and 2008-present. Also, we have extended the Newport Line out to 200 miles from shore.
Additionally, we also sample north of the Newport Line at least three times per year as part of the Juvenile Salmon sampling program. As a result, the Newport biweekly data are nested within larger-scale semi-annual to quarterly surveys. This approach helps us interpret locally derived data from the inner portions of the Newport Line.
We take a CTD profile (Conductivity, Temperature, and Depth; Seabird‡ SBE 19 CTD) at each station, and measure the surface water transparency (Secchi disc). We collect a bucket of seawater from the surface for analysis of chlorophyll-a and nutrients. The ship tows a vertical plankton net fitted with a flowmeter from near the seafloor to the surface (or from 100 m to the surface in deeper waters).
The plankton net is 0.5 m in diameter, with a mesh size of 202 µm. We make a double oblique tow for ichthyoplankton (0.6-m diameter bongo net with 333-µm mesh) over the upper 20 m. Since 2005, CTD casts have included fluorometry (WetLabs fluorometer) and oxygen (Seabird oxygen sensor).
We analyze nutrients using a Technicon Autoanalyzer. Chlorophyll-a is extracted from glass–fiber filters in 90% acetone then analyzed using a Turner Designs Fluorometer. We process zooplankton samples in the laboratory by subsampling with a Stempel pipette. We count species and note the developmental stages of copepods with the aid of a dissecting microscope.
We use appropriate conversion factors to convert our counts to the number of individuals per m³ of water. We estimate biomass by multiplying the number of individuals per m³ by the taxa's dry weight (using values from either literature or our measurements). We calculate carbon content assuming carbon is 40% of dry weight.
‡Reference to trade names does not imply endorsement by NOAA Fisheries.
Juvenile Salmon Sampling Program
Since 1998 we have sampled juvenile salmon at various stations from Newport, OR to Father and Son, WA. We collect pelagic fish from the upper 20 m of the water column using a 264 rope trawl (NET Systems, Inc.; 30 × 20 × 100 m).
We identify, count, and measure 50 randomly selected individuals from each trawl sample. We also measure and freeze up to 60 individual juvenile salmon of each species and size class (i.e., subyearling or yearling Chinook, based on size) for further examination in the lab.
The oceanographic data we collect at each station includes:
- Sea surface temperature and salinity.
- Depth profiles of salinity and temperature (collected with a Seabird SBE–19 and SBE-25 CTD).
- Water transparency (measured with a Secchi disk and/or a transmissometer).
We have collected samples over a wide range of ocean conditions each year since 1998. These data have provided many insights into ocean conditions' role in controlling the survival and growth of coho and Chinook salmon. For example, we sampled during:
- A very strong El Niño (June 1998) and a strong La Niña (cold water) (1999 & 2008).
- Very high Columbia River flows of June 1999, 2008, and 2010 – 2013 during extremely low flows of June 2001.
- Anomalously warm conditions in the coastal ocean due to lack of upwelling in June 2005.
During this period, the Pacific Decadal Oscillation moved from a warm phase (pre-1999) to a cool phase (1999–2002), then to a warm phase again (2003-2007) and then back to a cool phase (2008-2013). Nature has handed us a grand experiment. We can observe how salmon and other ecosystem components respond to short-term climate variability and time taken for these responses to occur.
We observed the highest average juvenile Chinook and coho salmon abundance during May cruises in the Columbia River vicinity. We rarely caught subyearling (fall) Chinook salmon in May Figure JSS-02).
In June, we see the highest average abundance in the vicinity of the Columbia River and off the Washington coast (Figure JSS-02).
Distributions of coho salmon have been more widespread, whereas both yearling and subyearling Chinook salmon were far less common off Oregon than Washington.
We observed the lowest overall salmon catch in September. Their distributions shifted to the north except for fall Chinook, which was found mainly inshore throughout the study area. September sampling ended in 2012.
Catches in all months were very patchy. We generally caught half of the fish in ~5% of the trawls per cruise and did not catch any fish in 40% of the trawls (Peterson et al. 2010). Patches most generally occurred for both yearling Chinook and coho salmon off the Columbia River and the Washington coast in May and June (Figure JSS-02) and very near shore for yearling and subyearling Chinook salmon in September.
Annual Variation in Salmon Abundance
The lowest June catches of Chinook and coho salmon were associated with:
- An El Niño event in 1998.
- Anomalously low upwelling period during May-June 2005.
- The warm “Blob” in 2017 (Figure JSS-03).
Conversely, the highest June catches occurred during years with a negative signal (cold phase) of the Pacific Decadal Oscillation (1999-2003 and 2008-2013).
In June 2019, we noted higher catches of subyearling Chinook salmon, average catches of yearling Chinook and coho salmon, and below-average catches of mixed-age juveniles. Subyearling Chinook salmon catch were the 5th highest of the 22 years, yearling Chinook salmon were ranked 9th, yearling coho salmon were the 12th highest catches, and mixed-age juvenile Chinook salmon were the 26th highest of the 22 June survey catches.
Age at maturity, which may differ among fish of the same year class. For example, among wild Snake River spring Chinook born in 2003, 8% may mature as jacks, 73% after two years in the ocean, and 19% after three years.
A semi-permanent, subpolar area of low pressure located in the Gulf of Alaska near the Aleutian Islands. It is a generating area for storms, and migratory lows often reach maximum intensity in this area. It is most active from late fall to late spring. During summer, it is weaker, retreating toward the North Pole and becoming almost nonexistent. During this time, the North Pacific High-pressure system dominates (NOAA National Weather Service). Courtesy of NOAA National Weather Service.
The California Current System (CCS) is a southward–flowing ocean current found along the west coast of North America, beginning at the northern tip of Vancouver Island, Canada, and ending near the southern tip of Baja California/Mexico. It is one of four elements of the anticyclonic North Pacific Gyre. The North Pacific Gyre includes the southward–flowing California Current, the westward–flowing North Pacific Equatorial Current (which flows toward Japan), the Kuroshio Current (which flows north along Japan) and the North Pacific Current (which flows eastwards towards North America).
We define catch per unit effort (CPUE) as the number of a particular species caught per kilometer traveled with the trawl under tow. However, CPUE is a relative and indirect measure of fishing effectiveness or species abundance. "Catch" can mean weight or numbers of total catch or a particular species. "Units of effort" can be measured as individual cruises, the number of sets of a fishing net (or casts of a line), or units of time or distance.
A wind that is affected by Coriolis force, blows parallel to isobars and whose strength is related to the pressure gradient (i.e., spacing of the isobars). Courtesy of NOAA National Weather Service.
For salmon, the proportion of a population returning as an adult to spawn in the natal stream (having "escaped" the catch in ocean fisheries).
Ichthyoplankton are the eggs and larvae of fish. They are usually found in the sunlit zone of the water column, less than 200 meters deep, which is sometimes called the epipelagic or photic zone. Ichthyoplankton are planktonic, meaning they cannot swim effectively under their own power, but must drift with the ocean currents.
A "Jack" is a male Chinook or coho salmon that returns to spawn prematurely, before growing to a normal adult's size. Jacks stay in the ocean from a few months to a year, returning to the natal stream 1–2 years before normal adults of their age class. Thus numbers of returning jacks are sometimes used as a basis to predict run size the following year.
A sampling station located 5 miles offshore along the Newport Hydrographic Line, a transect of established stations used in oceanographic sampling by Northwest Fisheries Science Center research teams since the mid-1970s (Figure 1). Findings at this station are often used as a reference point for ocean ecosystem indicator data.
Northern California Current
The Northern California Current (NCC) is generally taken to be that part of the California Current that lies between the northern tip of Vancouver Island and the Oregon–California border, between Cape Blanco OR/Cape Mendocino CA. This portion of the CC shows a generally weak meandering flow year-round, which more–or–less flows parallel to the coast. It is characterized by strong seasonality in winds, upwelling, and biological productivity. Winter winds in the NCC are usually from the south or west, whereas summer winds are from the north and cause coastal upwelling.
North Pacific High
The North Pacific High-pressure system is a region of high sea-level pressure over the subtropical eastern North Pacific Ocean (Kenyon 1999). This dominant atmospheric pressure system influences the northern California Current during the summer months, whereas the Aleutian Low is dominant from late fall to late spring.
A tow made by pulling the net at a slow tow speed from the seafloor to the surface. Under this configuration, the angle between the net and seafloor is maintained at 45 degrees.
Oceanic Nino Index (ONI)
The temperature anomaly within the Niño 3.4 region, averaged over three months. Values, and additional information, can be found at NOAA’s Climate Prediction Center.
OPIH (Oregon Production Index, Hatchery)
For coho, an estimate of the total freshwater escapement, adjusted for ocean and freshwater catch, for public hatchery fish throughout the Oregon Production Index Area. Private hatchery production is removed from this estimate, so it reflects only public hatchery fish. Used as the numerator in calculating SARs for the OPIH.
The factors influencing salmon marine survival or adult return numbers are numerous. We recognize that the primary drivers of mortality may vary from year to year. Although any given indicator may be correlated with survival, there may be years where the correlation does not hold (i.e., years when the primary driver of mortality is a set of conditions unrelated to this indicator). Therefore, we expect many of the indicators to have outlier years, where the indicator's value does not reflect the mechanisms of mortality. Because we do not know the exact mechanism driving mortality each year, we chose a statistical measure to identify and remove outlier years from many of our analyses. Specifically, we calculated Cook's Distance (Cook 1979) and used a cutoff of 4/N (Bollen and Jackman 1990) to identify outlier years. Although we show these years in our plots, we excluded them from analyses when creating outlooks.
Number or proportion of biomass added to a fish population as a result of growth or reproduction, especially for a given year class.
A device to measure the turbidity (transparency) of the upper water column. A 30–cm diameter white disc is lowered slowly through the upper water column to the point at which the pattern is no longer visible. The depth of the disk is then taken as a measure of transparency or turbidity.
SAR (smolt–to–adult ratio)
For a salmon population, the number from a given year class that survived to the smolt stage (i.e., migrated as juveniles) divided by the total number of returning adults from that year class (all age classes combined).
The term "teleconnection pattern" refers to a recurring and persistent, large–scale pressure and circulation anomalies that spans vast geographical areas. Teleconnection patterns are also referred to as preferred modes of low–frequency (or long time–scale) variability. Courtesy of the NOAA National Weather Service Climate Prediction Center.
A device for measuring beam attenuation, which can be used as a measure of turbidity in water. A beam of light is cast through the water. A transmissometer records the measure of light at a given point past the source of the beam.
Fish of the same species and stock that are born in the same year.
- Achord, S., G. M. Matthews, O. W. Johnson, and D. M. Marsh. 1996. Use of passive integrated transponder (PIT) tags to monitor migration timing of Snake River Chinook salmon smolts. North American Journal of Fisheries Management 16:302–313.
- Achord, S., J. R. Harmon, D. M. Marsh, B. P. Sandford, K. W. McIntyre, K. L. Thomas, N. N. Paasch, and G. M. Matthews. 1992. Research related to transportation of juvenile salmonids on the Columbia and Snake Rivers, 1991. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers, Walla Walla District.
- Achord, S., B. P. Sandford, S. G. Smith, W. R. Wassard, and E. F. Prentice. 2012. In-stream monitoring of PIT-tagged wild spring/summer Chinook salmon juveniles in Valley Creek, Idaho. Pages 163-176 in J. McKenzie, B. Parsons, A. Seitz, R. K. Kopf, M. Mesa, and Q. Phelps, editors. Advances in fish tagging and marking technology. American Fisheries Society Symposium 76, Bethesda, Maryland.
- Adams, N. S., D. W. Rondorf, E. E. Kofoot, M. J. Banach, and M. A. Tuell. 1997. Migrational characteristics of juvenile chinook salmon and steelhead in the forebay of Lower Granite Dam relative to the 1996 surface bypass collector tests. Report of the U.S. Geological Survey to the U.S. Army Corps of Engineers, Walla Walla District.
- Adams, N. S., D. W. Rondorf, and M. A. Tuell. 1998a. Migrational characteristics of juvenile spring and fall chinook salmon and steelhead in the forebay of Lower Granite Dam relative to the 1997 surface bypass collector tests. Report of the U.S. Geological Survey to the U.S. Army Corps of Engineers, Walla Walla District.
- Adams, N. S., D. W. Rondorf, M. A. Tuell, and M. J. Banach. 1998b. Migrational characteristics of juvenile spring chinook salmon and steelhead in Lower Granite Reservoir and tributaries, Snake River. Report of the U.S. Geological Survey to the U.S. Army Corps of Engineers, Walla Walla District.
- Beigel, M. 1999. Dynamic performance of inductive RFID systems. Technical paper presented at the European Conference on Circuit Theory and Design, Stresa, Italy. (February 2009).
- Connolly, P. J., I. G. Jezorek, and E. F. Prentice. 2005. Development and use of in-stream PIT-tag detection systems to assess movement behavior of fish in tributaries of the Columbia River Basin, USA. Pages 217-220 in L. P. J. J. Noldus, F. Grieco, L. W. S. Loijens, and P. H. Zimmerman, editors. Proceedings of measuring behavior 2005, 5th international conference on methods and techniques in behavioral research. Noldus Information Technology, Wageningen, The Netherlands.
- Connolly, P. J., I. J. Jezorek, K. D. Martens, and E. F. Prentice. 2008. Measuring the performance of two stationary interrogation systems for detecting downstream and upstream movement of PIT-tagged salmonids. North American Journal of Fisheries Management 28:402–417.
- Downing, S. L. , E. F. Prentice, R.W. Frazier, J. E. Simonson, and E. P. Nunnallee. 2001. Technology Developed for Diverting Passive Integrated Transponder (PIT) Tagged Fish at Hydroelectric Dams in the Columbia River Basin. Aquacultural Engineering 25:149–164.
- Downing, S. L. , E. F. Prentice, E. P. Nunnallee, and B. F. Jonasson. 2004. Development and evaluation of passive integrated transponder tag technology, 2000-2002. Report of the National Marine Fisheries Service to the Bonneville Power Administration.
- Downing, S. L. , E. F. Prentice, B. F. Jonasson, and G.T. Brooks. 2008. Development and evaluation of passive integrated transponder tag technology, December 2006–November 2007. Report of the National Marine Fisheries Service to the Bonneville Power Administration.
- Eppard, M. B., E. E. Hockersmith, G. A. Axel, and B. P. Sandford. 2002. Spillway survival for hatchery yearling and subyearling Chinook salmon passing Ice Harbor Dam, 2000. Report of the National Marine Fisheries Service to the U.S. Army Corps of Engineers, Walla Walla District.
- Horton, G.E., T. L. Dubreuil, and B. H. Letcher. 2007. A model for estimating passive integrated transponder (PIT) tag antenna efficiencies for interval–specific emigration rates. Transactions of the American Fisheries Society 136:1165–1176.
- ISO (International Organization for Standardization). 1996. Radio frequency identification of animals. ISO TC 23/SC 19: Agricultural electronics. See ISO catalogue items 11784, 11785, 14223, and 24631.
- Knudsen, C. M., M. V. Johnston, S. L. Schroder, W. J. Bosch, D. E. Fast, and C. R. Strom. 2009. Effects of passive integrated transponder tags on smolt-to-adult recruit survival, growth, and behavior of hatchery spring Chinook salmon. North American Journal of Fisheries Management 29(3)658–669.
- Marvin, D. M. and J. Nighbor, editors. 2009. Columbia Basin PIT Tag Information System: 2009 PIT Tag Specification Document. Report of the Pacific States Marine Fisheries Commission to the PIT–Tag Steering Committee, Portland, Oregon.
- Muir, W. D., S. G. Smith, J. G. Williams, E. E. Hockersmith, and J. R. Skalski. 2001. Survival estimates for migrant yearling chinook salmon and steelhead tagged with passive integrated transponders in the lower Snake and lower Columbia Rivers, 1993-1998. North American Journal of Fisheries Management 21:269–282.
- Prentice, E. F., T. A. Flagg, and C. S. McCutcheon. 1990a. Electronic tags. Pages 317–322 in N. C. Parker, A. E. Giorgi, R. C. Heidinger, D. B. Jester, Jr., E. D. Prince, and G. A. Winans, editors. Fish-marking techniques. American Fisheries Society, Symposium 7, Bethesda, Maryland.
- Prentice, E. F., T. A. Flagg, C. S. McCutcheon, and D. F. Brastow. 1990b. PIT-tag monitoring systems for hydroelectric dams and fish hatcheries. Pages 323–334 in N. C. Parker, A. E. Giorgi, R. C. Heidinger, D. B. Jester, Jr., E. D. Prince, and G. A. Winans, editors. Fish-marking techniques. American Fisheries Society, Symposium 7, Bethesda, Maryland.
- Prentice, E. F., T. A. Flagg, and C. S. Clinton. 1990c. Equipment, methods, and an automated data-entry station for PIT tagging. Pages 335–340 in N. C. Parker, A. E. Giorgi, R. C. Heidinger, D. B. Jester, Jr., E. D. Prince, and G. A. Winans, editors. Fish-marking techniques. American Fisheries Society, Symposium 7, Bethesda, Maryland.
- PSMFC (Pacific States Marine Fisheries Commission). 1996-. PIT tag information system for the Columbia River Basin (PTAGIS). Available at www.ptagis.org (February 2009).
- Roni, P., T. Bennett, R. Holland, G. Pess, K. Hanson, R. Moses, M. McHenry, W. Ehinger, and J. Walter. 2012. Factors affecting migration timing, growth, and survival of juvenile coho salmon in two coastal Washington watersheds. Transactions of the American Fisheries Society 141:4, 890-906.
- Ryan, B. A., S. G. Smith, J. M. Butzerin, and J. W. Ferguson. 2003. Relative vulnerability to avian predation of juvenile salmonids tagged with passive integrated transponders in the Columbia River Estuary, 1998-2000. Transactions of the American Fisheries Society 132:275–288.
- Skalski, J. R., S. G. Smith, R. N. Iwamoto, J. G. Williams, and A. Hoffmann. 1998. Use of passive integrated transponder tags to estimate survival of migrant juvenile salmonids in the Snake and Columbia Rivers. Canadian Journal of Fisheries and Aquatic Sciences 55(6):1484–1493.
- Wigington Jr., P.J., J.L. Ebersole, M.E. Colvin, S.G. Leibowitz, B. Miller, B. Hansen, H.R. Lavigne, D. White, J.P. Baker, M.R. Church, J.R. Brooks, M.A. Cairns, and J.E. Compton. 2006. Coho salmon dependence on intermittent streams. Frontiers in Ecology and the Environment 4(10):513–518.
- WSDE (Washington State Department of Ecology). 2009. Joint aquatic resource permits application (JARPA). Accessed March 2009.
- Zydlewski, G. B., G. Horton, T. Dubreuil, B. Letcher, S. Casey, and J. Zydlewski. 2006. Remote monitoring of fish in small streams: a unified approach using PIT tags. Fisheries 31(10):492–502.
Many individuals contributed to the work found on these pages. We thank the scientists and ship's crew who participated in the ocean sampling programs. Special thanks to JoAnne Butzerin for the initial design and editing, and Jo Ann Akada for the IT support.
Funding for data collection and data analysis came from the U.S. GLOBEC program NOAA–Center for Sponsored Coastal Ocean Research; grants NA 67RJ0151 and NA 86OP0589 and from the NOAA Fisheries and the Environment (FATE) Program. Grants from the National Ocean Partnership Program (NA97FE0193), the National Science Foundation (9907854–OCE), and the Bonneville Power Administration support this work.