# NOAA Tech Memo NWFSC-7: Part 5: Technological Contributions

#### Coded Radio Tag

Electronics personnel of the CZES Division developed and tested a radio telemetry system that provides individual coding of several tags on the same frequency with equal tag life. This system greatly increases the number of fish that can be tracked. The components include radio transmitter tags for juvenile and adult salmonids, a broad band radio receiver, a pulse decoding microprocessor, and paper and magnetic tape data output units. 

Radio transmitters are crystal controlled for frequencies between 30.170 and 30.250 MHz. Components for adult salmonid tags are miniature integrated circuits, and the juvenile tag utilizes hybrid chip technology. When pulsed at 600 ms, tag life is 30 days for the adult and 7 days for the juvenile. Individual codes for each tag are obtained by dividing the radio pulse into two parts, then setting the time between the parts differently for each tag on an assigned frequency. The code for an individual tag is a four digit number that begins with the frequency transmitted (Channel Number 1-9) followed by the time period between pulse parts. 

The receiver simultaneously monitors all channels and sets a flag when a channel is active. The monitor microprocessor scans the channels until a flag is found, then stops and checks the active channel for a period longer then the pulse period of the tag. The monitor then checks pulse length and sequence, measures the code period, and outputs the data to the recording devices. A paper data recorder provides real-time quality control for the system, and a digital cassette data recorder provides the permanent storage medium for computer entry and subsequent data analysis. Data recorded for each pulse includes date, time, channel number, code number, antenna number, and site location number. In situations where tags may be on the monitor for extended periods of time, there are provisions in the monitor to reduce the number of records stored and to delay monitor operation for a set period of time. 

There are three significant developments in the creation of this tracking system: coincident pulse circuitry, programmable read only memory (PROM) firmware for radio frequency (RF) noise reduction, and pulse reconstruction circuitry. First, the coincident pulse circuitry eliminates information when pulses from two or more tags overlap. As long as no two tags have the same pulse interval, the overlapping pulses will separate and the proper code will be recorded. Second, since RF noise on tracking frequencies can reduce the sensitivity of tracking monitors, even low level RF emissions can be a problem with a highly sensitive RF receiver. The monitor has three microprocessors producing low level RF noise. This RF noise combines with software-generated noise to produce noise with frequencies that may be the same as the tracking frequencies, thereby causing interference. Consequently, several of the program sequences for the monitor PROMs are specifically designed to eliminate RF noise or to shift the frequency to an area outside of the tracking frequencies. 

The third significant development is the pulse reconstruction circuitry. Tag signals from the limits of antenna range (distance or depth) are broken when checked by the pulse sequence logic. The pulse reconstruction circuitry removes breaks in the pulse to produce appropriate pulse characteristics. In effect, this circuitry adds 3 db of sensitivity to the monitor.

#### Bibliography

Monan, G. E.1985. Advances in tagging and tracking hatchery salmonids: Coded wire tags, multiple-coded and miniature radio tags, and the passive integrated transponder tag. In C. J. Sindermann (editor), Proceedings of the Eleventh U.S.-Japan Meeting on Aquaculture, Salmon Enhancement, Tokyo, Japan, 19-20 October 1982, p. 33-37. U.S. Dep. Commer., NOAA Tech. Rep. NMFS 27.

#### Genetic Stock Identification (GSI)

By 1980, the technical foundations were established for using allozyme characters for genetic stock identification (GSI) of salmon populations in mixed-stock fishery situations. Genetic stock identification depends on several attributes of a mixed-stock population: 1) a multilocus baseline for all of the major contributing stocks can be generated, 2) genetic differences can be identified between stocks in the baseline, 3) allele frequencies (e.g., the genetic baseline) are stable through time, 4) the alleles are evolutionarily neutral, and 5) an adequate number of fish can be sampled and studied electrophoretically from the mixed-stock fishery. By 1980, fishery managers had begun using GSI to estimate stock compositions for a few mixed stock fisheries: chinook salmon in the Columbia River; sockeye salmon in Cook Inlet, Alaska; and chum salmon in Puget Sound. 

From 1981 to 1982, two studies were completed by Division personnel that were instrumental in the development and initial acceptance of GSI as a management tool. First, the reliability of the method was demonstrated. In this study, the GSI model was used to accurately estimate the contributions of 14 spring chinook salmon hatchery stocks in the Columbia River to four "blind" mixtures. Second, a 31-locus baseline was constructed from 81 stocks ranging from Sacramento River, California, through Vancouver Island, British Columbia. This extensive baseline allowed the application of GSI to a commercial troll fishery off the Washington coast in May 1982. This also marked the beginning of an extended period of cooperative GSI projects by the CZES Division and the Washington Department of Fisheries (WDF). Each year since 1982, GSI has been instrumental in the management of chinook salmon fisheries in the Columbia River and off the Washington coast. 

In 1983, GSI was used to monitor the stock composition of commercial, treaty, and sport fisheries of chinook salmon. Areas monitored ranged from the Strait of Juan de Fuca southward along the Washington coast through the mouth of the Columbia River to the northern coast of Oregon. Beginning in 1984, and continuing through 1986, the west Vancouver Island troll fishery was also added. The Canadian Department of Fisheries and Oceans (CDFO) became an active collaborator with the Division and WDF in these studies. Improvements in data handling and statistical procedures and expansion of baseline development in southern Oregon, the Columbia River Basin, and British Columbia were also emphasized during these years. 

From 1980 to 1985, the Division worked with the NMFS Auke Bay Laboratory (ABL) on related GSI issues in southeast Alaska. ABL was interested in baseline development for sockeye and chum salmon stocks in southeast Alaska, and they supplied the Division with tissues for electrophoretic study. In 1985, a multilocus description of allozyme variability in sockeye salmon in North America was published by Division personnel. Sockeye salmon have few polymorphic (multi-allelic) loci, and the Division worked with ABL biologists in augmenting a GSI baseline with other characters (e.g., scales and parasites) for use in mixed fishery situations. The chum baseline was presented jointly with ABL at a GSI meeting. 

In 1987, Division personnel cooperated with CDFO and WDF in a project to estimate stock contributions to sport fisheries in Georgia Strait. 

Various papers published by CZES Division authors in the late 1980s summarized the general nature and use of GSI technology and related topics in population genetics. These documents provide the following: explanation of the GSI model in general terms and demonstration with three simple applications; laboratory interpretations of allozyme banding patterns of salmon; description of statistical/mathematical advances in mixture analyses; provision of technical details for staining billions of enzymes in salmon; interpretation of temporal changes in allele frequencies; distribution of alleles in chinook salmon populations in North America; description of three areas of genetic research that flow from genetic baselines; and description of levels of genetic variability in Columbia River Basin stocks with respect to conservation and management issues. 

With the general increase in GSI activities throughout the 1980s, an interagency group was formed to help standardize techniques and data base applications. Two to three GSI coordinating meetings are held per year, with the host responsibility rotating among the participating laboratories. Meetings were held by the University of California at Davis; WDF; CZES Division; the Pacific Salmon Commission (Vancouver, British Columbia); ABL; and the U.S. Fish and Wildlife Service in Anchorage, Alaska. Important results of these meetings include a process for "sponsoring" new loci or alleles to be included in standardized scoring protocols (chinook and chum salmon only) and standardized locus, allele, and, to some degree, buffer nomenclature. The CZES Division is responsible for the standardized chinook salmon baseline. This includes tabulating the new baseline data yearly and entering these data into the coastwide data set following statistical evaluations. The current baseline for chinook salmon uses 23 loci and includes 183 stocks or stock groups. Division personnel are also responsible for coordinating the Asian portion of a specieswide data set for chum salmon. 

From 1987 to 1990, the CZES Division worked with CDFO biologists to expand the chinook salmon baseline in the Fraser River. The CZES Division now has data for about 40 loci from 63 stocks in the Fraser River. Test fisheries were conducted from 1987 to 1989 in the lower Fraser River and analyzed by the Division (1988 data only). The results have provided useful information about the presence of upper, middle, and lower river stocks in this test fishery. 

The present status of CZES GSI research can be summarized as follows:

- Chinook Salmon: The coastwide baseline extends to the northern coast of   British Columbia. It is anticipated that the Skeena River area will be   finished in the next 3 years with the cooperation of CDFO and WDF.   
- Coho Salmon: This species is a focus of concern under U.S.-Canada   negotiations. Allozymic variation in coho salmon is being evaluated and   baseline work continues.   
- Chum Salmon: CZES Division personnel are initiating field and laboratory   research with Japanese and Russian scientists to fill out an Asian baseline   for use in high seas fisheries. This work will be coordinated with WDF and ABL   to establish a standardized genetic baseline for the species.   
- Sockeye Salmon: An allozyme survey is being completed for the first two   brood years of sockeye salmon in the Lake Cle Elum restoration project.   
- Steelhead: Work continues with steelhead stocks in the Snake River Basin   to evaluate hatchery supplementation. The CZES Division is the lead agency in   setting up a coastwide standardized baseline for this species.   
- High Seas Application: The Asian portion of the specieswide baseline for   chum salmon will be expanded in 1989-90. Data have been gathered for about 155   stocks or stock groups, and it is anticipated that data will be added for 70   loci for up to 15 Japanese populations and several Russian populations. Chum   salmon data have been used for several mixture analyses and will be used more   in the future. The future also includes working with the Fishery Agency of   Japan and CDFO to do GSI estimates on samples from test fisheries on the high   seas.   
- DNA Research: A proposal has been submitted for consideration under the   High Seas Project to establish a DNA research laboratory at the Northwest   Fisheries Science Center. 

#### Bibliography

Bermingham, B.1990. Mitochondrial DNA and the analysis of fish population structures. In D. H. Whitmore (editor), Electrophoretic and isoelectric focusing techniques in fisheries management, p.197-221. CRC Press, Boca Raton.

Grant, W. S., G. B. Milner, P. Kransnowski, and F. M. Utter.1980. Use of biochemical variants for identification of sockeye salmon (Oncorhynchus nerka) stocks in Cook Inlet, Alaska. Can. J. Fish. Aquat. Sci. 37:1236-1247.

Milner, G. B.1977. Biochemical variation: Its use in mixed fishery analysis. Proceedings of the Genetic Implications of Steelhead Management Symposium, 20-21 May 1977. Calif. Coop. Fish. Res. Unit, Spec. Rep. 77-1.

Milner, G. B., D. J. Teel, P. A. Aebersold, and F. M. Utter.1986. Genetic stock identification. Report to Bonneville Power Administration, Contract DE-A-79-85BP23520, 90 p. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Milner, G. B., D. J. Teel, and F. M. Utter.1983. Genetic stock identification study. Report to Bonneville Power Administration, Contract DE-A179-85BP23520, 33 p. + Appendix. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Milner, G. B., D. J. Teel, F. M. Utter, and C. L. Burley.1981. Columbia River stock identification study: Validation of genetic method. Report to Bonneville Power Administration, Contract DE-AI79-80BP18488, 35 p. + Appendix. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Milner, G. B., D. J. Teel, F. M. Utter, and G. A. Winans.1985. A genetic method of stock identification in mixed populations of Pacific salmon, Oncorhynchus spp. Mar. Fish. Rev. 47(1):1-8.

Parker, N. C., A. E. Giorgi, R. C. Heidinger, D. B. Jester, Jr., E.D. Prince, and G. A. Winans.1990. Fish-marking techniques. International Symposium and Educational Workshop on Fish-marking Techniques. Am. Fish. Soc. Sympos. 7, 879 p.

Pella, J. J., and G. B. Milner.1987. Use of genetic marks in stock composition analysis. In N. Ryman and F. Utter (editors), Population genetics and fishery management, p. 247-276. Univ. Washington Press, Seattle.

Ryman, N., and F. M. Utter (editors).1987. Population genetics and fishery management. Univ. Washington Press, Seattle, 418 p.

Smouse, P. E., R. S. Waples, and J. A. Tworek.1990. A mixed fishery model for use with incomplete baseline data. Can. J. Fish. Aquat. Sci. 47:620-634.

Teel, D. J.1987. Fishery simulation: Fraser River chinook example. In R. Lincoln (editor), Genetic stock identification (GSI) of chinook salmon: Status, needs, and future, p. 8-9. Pacific Salmon Commission Joint Chinook Technical Committee Report, Pacific Salmon Commission, Vancouver, B.C.

Teel, D. J.1987. Vancouver Island Troll Fishery Pilot. In R. Lincoln (editor), Genetic stock identification (GSI) of chinook salmon: Status, needs, and future, p. 13-14. Pacific Salmon Commission Joint Chinook Technical Committee Report, Pacific Salmon Commission, Vancouver, B.C.

Utter, F. M., P. B. Aebersold, J. Helle, and G. A. Winans.1984. Genetic characterization of populations in the southeastern range of sockeye salmon. In J. M. Walton and D. B. Houston (editors), Proceedings of Olympic Wild Fish Conference, Peninsula College, Port Angeles, WA, p. 17-32. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Utter, F. M., P. B. Aebersold, and G. A. Winans.1987. Interpreting genetic variation detected by electrophoresis. In N. Ryman and F. Utter (editors), Population genetics and fishery management, p. 21-45. Univ. Washington Press, Seattle.

Utter, F. M., D. J. Teel, G. B. Milner, and D. McIsaac.1987. Genetic estimates of stock compositions of 1983 chinook salmon, Oncorhynchus tshawytscha, harvests off the Washington coast and the Columbia River. Fish. Bull., U.S. 85:13-23.

Waples, R. S.1989a. A generalized approach for estimating effective population size from temporal changes in allele frequency. Genetics 121:379-391.

Waples, R. S.1989b. Temporal stability of allele frequencies: Testing the right hypothesis. Evolution 43:1236-1251.

Waples, R. S.1990a. Temporal changes of allele frequency in Pacific salmon populations: Implications for mixed-stock fishery analysis. Can. J. Fish. Aquat. Sci. 47:968-976.

Waples, R. S.1990b. Conservation genetics of Pacific salmon. II. Effective population size and the rate of loss of genetic variability. J. Heredity 81:267-276.

Waples, R. S.1990c. Conservation genetics of Pacific salmon. III. Estimating effective population size. J. Heredity 81:277-289.

Waples, R. S., and D. J. Teel.1990. Conservation genetics of Pacific salmon. I. Temporal changes in allele frequency. Conservation Biol. 4(2):144-156.

Winans, G. A.1987. Status of chinook baseline data. In R. Lincoln (editor), Genetic stock identification (GSI) of chinook salmon: Status, needs, and future, p. 17-18. Pacific Salmon Commission Joint Chinook Technical Committee Report, Pacific Salmon Commission, Vancouver, B.C.

Winans, G. A.1990. Genetic variability in chinook salmon stocks from the Columbia River Basin. N. Am. J. Fish. Manage. 9:47-52.

Winans, G. A., P. B. Aebersold, S. Urawa, and V. G. Markovstev.1990. Genetic stock identification of chum salmon: New data for 16 populations in Asia. Int. N. Pac. Fish. Comm. Doc. 3604, 23 p. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Winans, G. A., P. B. Aebersold, and R. S. Waples.In press. Genetic stock identification of chum salmon in high seas fisheries using allozyme data from stocks in the Pacific Basin. Proceedings of Pacific Salmon International Symposium, Sept. 1989, Yuzhno-Sakhalinsk, USSR.

#### Passive Integrated Transponder (PIT) Tag

In 1984, juvenile and adult salmon were injected with sham (nonfunctional) PIT tags to determine suitable anatomical areas for tag placement, to develop tag injection techniques, and to determine the effect of the tag on growth and survival. The body cavity was selected as the best area for tag placement for most applications. 

Work continued in 1985 to evaluate the effect of the tag on growth and survival of juvenile fish and to further refine tagging techniques. Functional polypropylene-encapsulated PIT tags were used for the first time. In addition, prototype juvenile and adult PIT-tag monitoring systems were evaluated in field tests in the Columbia River Basin. Although these studies supported the feasibility of the PIT-tag system, an unacceptable tag failure rate (10%+) and a high tag rejection rate (to 15%) were noted. This poor performance was attributed to the polypropylene shell of the tag. 

In 1986, a new glass encapsulated PIT tag having a smooth, leak proof, and seemingly biologically inert case was evaluated. This glass-encapsulated version proved to be highly reliable in tagging fish weighing as little as 3 g. Results of laboratory tests indicated a high tag retention rate (99%+) and a low tag failure rate (1% or less). Behavioral tests showed no measurable effect of the tag on juvenile salmonids. 

Field testing of PIT-tag systems to monitor the in-river movements of juvenile and adult salmonids continued in 1986. The monitoring systems were installed and tested at McNary Dam on the Columbia River and Lower Granite Dam on the Snake River. Results showed that fish injected with the PIT tag and released into the river can be individually recognized by detecting/recording devices when passing fish collection facilities at hydroelectric dams. Since 1986, additional PIT-tag monitoring systems have been installed at Little Goose Dam on the Snake River and Prosser Dam on the Yakima River. 

During the 1987, 1988, and 1989 field seasons, tests were conducted on the Columbia River comparing the PIT tag to both traditional coded wire tag and freeze-brand fish identification systems. These studies indicated no statistical differences in the survival, growth, or behavior of PIT-tagged fish. In addition, it was shown that because of high precision, accuracy, and efficiency in tag-reading, many studies could be conducted with 95 to 98% fewer fish than those using traditional tagging or marking systems. This reduction in numbers of fish required for research projects is an important advantage and reflects the unique characteristics of the PIT tag. 

Additional tests of monitoring systems at dams were made during 1987-89 to improve tag reading efficiency, equipment reliability, and functionality. Results of tests showed that tag reading efficiency was over 95% and that reading accuracy was over 99% (correct tag code read). A prototype system was developed, installed, and evaluated at Lower Granite Dam to separate PIT-tagged from non-PIT-tagged fish. The system, which functioned satisfactorily, is considered critical to fish transportation and many other proposed studies. Modifications to the separation system were made in 1990 that improved its performance. Alternative means of monitoring PIT-tagged fish on release from hatcheries or other holding or rearing areas (e.g., pumping fish or passing fish volitionally through monitors) were developed and are being evaluated. 

A prototype data base, for Columbia River Basin PIT-tag information, was established in 1988. A permanent data base was established with the Pacific States Marine Fisheries Commission in Portland, Oregon, in 1990. The new system will be functional in 1991. A PIT-tag technical work group was formed in 1988 to establish data and procedural specifications and to make recommendations pertaining to overall PIT-tag system development. Both software and hardware modifications were made to PIT-tag monitoring and tagging programs. These changes, coupled with the development of a semiautomatic tag injection system, resulted in a standardized tagging system. The system is universal in that it can be operated on either AC or DC power. 

Research on the PIT tag is continuing and will focus on extending the monitoring range of the system, evaluating long-term tag retention and operation, and determining possible tag effects on behavior of fish. New PIT-tag monitoring sites (e.g., other Columbia River Basin dams) are being planned to expand the usefulness of the system. 

The juvenile salmon PIT-tag system is now considered to be in its final developmental stages. Currently, the system is being used by state, federal, tribal, and private fishery managers and researchers concerned with salmonid stocks throughout the Columbia River Basin. Several project elements, including data base management and systems operation and maintenance, are being transferred to other agencies as the system is refined.

#### Bibliography

Prentice, E. F.1990. A new internal telemetry tag for fish and crustaceans. In A. K. Sparks (editor), Marine farming and enhancement: Proceedings of the Fifteenth U.S.-Japan Meeting on Aquaculture, Kyoto, Japan, 22-23 October 1986, p. 1-9. U.S. Dep. Commer., NOAA Tech. Rep. NMFS 85.

Prentice, E. P., T. A. Flagg, and C. S. McCutcheon.1987. A study to determine the biological feasibility of a new fish tagging system. Report to Bonneville Power Administration, Contract DE-AI79-84BP11982, 113 p. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Prentice, E. F., T. A. Flagg, and C. S. McCutcheon.1990. Feasibility of using implanted passive integrated transponder (PIT) tags in salmonids. 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, International Symposium and Educational Workshop on Fish-marking Techniques. Am. Fish. Soc. Sympos. 7:317-322.

Prentice, E. F., T. A. Flagg, C. S. McCutcheon, and D. F. Brastow.1990. PIT tag monitoring systems for hydroelectric dams and fish hatcheries. 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, International Symposium and Educational Workshop on Fish-marking Techniques. Am. Fish. Soc. Sympos. 7:323-334.

Prentice, E. P., T. A. Flagg, C. S. McCutcheon, D. F. Brastow, and D. C. Cross.1990. Equipment, methods, and an automated data entry station for PIT tagging. 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, International Symposium and Educational Workshop on Fish-marking Techniques. Am. Fish. Soc. Sympos. 7:335-340.

Prentice, E. P., and D. L. Park.1984. A study to determine the biological feasibility of a new fish tagging system. Report to Bonneville Power Administration, Contract DE-AI79-84BP11982, 38 p. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Prentice, E. P., D. L. Park, T. A. Flagg, and C. S. McCutcheon.1986. A study to determine the biological feasibility of a new fish tagging system. Report to Bonneville Power Administration, Contract DE-AI79-84BP11982, 89 p. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

Prentice, E. P., D. L. Park, and C. W. Sims.1985. A study to determine the biological feasibility of a new fish tagging system. Report to Bonneville Power Administration, Contract DE-AI79-84BP11982, 36 p. (Available from Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112-2097.)

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