NOTE Purcell et al.: Genetic identification of salmonid prey from scat of Phoca vitulina nchardsi 



219 



Discussion 



This study focused on the development of tools for the 

 genetic identification of Pacific salmon skeletal remains 

 recovered from harbor seal scats. These tools help to deter- 

 mine the diet of marine mammals and can also be used to 

 address direct management questions regarding interspe- 

 cific interactions in rivers such as the Umpqua River where 

 salmonid species of concern (cutthroat trout (occur with pro- 

 tected marine mammal species. The harbor seal diet in the 

 Umpqua River consisted of nonsalmonid fish and chinook. 

 coho, and steelhead; no cutthroat trout were observed in the 

 scat samples (Orr et al., 2004). The majority of salmonid 

 species identifications were possible only by using genetic 

 methods because very few otoliths were recovered in the 

 Umpqua River scats. A number of other sites exist were this 

 technology may also be applicable. In Hood Canal ( WA) the 

 summer chum salmon run is listed as threatened under the 

 ESA. A report of seal diets in Hood Canal determined that 

 2T7c of the fish consumed by harbor seals were salmonids 

 (Jeffries et al. 3 ). The study used both bones and otoliths, 

 but only 25% of the samples contained otoliths that allowed 

 species-level identification. In the Alsea River (OR), coho 

 salmon are listed as threatened. A report by Riemer et al. 4 

 indicated that 69r of fish consumed by pinnipeds in the 

 Alsea River are salmonids; none of the salmonid remains 

 were morphologically identifiable to species. 



Extraction of DNA from bones can be done with a com- 

 mercially available kit with minor modifications. In our 

 study, only 67% of the bone DNA extracts could be ampli- 

 fied by PCR. PCR failure could be due to DNA degradation 

 during the digestive process or to environmental exposure 

 after defecation. However, multiple bones are often present 

 in scats and we were able to amplify DNA from at least one 

 bone representative from 35 out of the 39 scats examined. 

 Sequencing or RFLP analyses of the COIII/ND3 locus are 

 both viable methods of identifying the seven common On- 

 corhynchus species. This study used manual sequencing 

 with radioactivity and we did have better results using 

 this method compared to the RFLP method. A recently 

 published study also identified restriction enzymes in the 

 cytochrome B gene that distinguish among the salmonid 

 species (Russell et al., 2000). The study reported diagnostic 

 RFLP differences among these species but did not confirm 

 the lack of intraspecific variation in a wide geographic sur- 

 vey of each species. The goal of the cytochrome B RFLP as- 

 say designed by Russell et al. (2000) was to identify salmon 

 species found in processed food products but the primers 



3 Jeffries, S. J., J. M. London, and M. M. Lance. 2000. Obser- 

 vations of harbor seal predation on Hood Canal summer chum 

 salmon run 1998-1999. Annual progress report to Pacific 

 States Marine Fisheries Commission, 39 p. [Available from 

 WDFW, Marine Mammals Investigations, 7801 Phillips Rd. SW, 

 Tacoma, WA 98498.] 



4 Riemer, S. D., R. F. Brown, B. E. Wright and M. I. Dhruv. 

 1999. Monitoring pinniped predation on salmonids at Alsea 

 River and Rogue River, Oregon: 1997-1999. Oregon Depart- 

 ment of Fish and Wildlife, Marine Mammal Research Program, 

 Corvallis, OR, 36 p. [Available from ODFW, 7118 NE Vanden- 

 berg Ave., Corvallis, OR 97333.] 



may also prove useful in species identification of bone re- 

 mains. The 16s primer set is also valuable for bones that 

 are morphologically unidentifiable. However for salmonid 

 species identification, the 16s region contains fewer diag- 

 nostic nucleotide substitutions in relation to the d-loop and 

 the COIII/ND3 region. Overall, the techniques established 

 here would be useful for further study of marine mammal 

 diets and may have the potential for forensic application. 



Acknowledgments 



The authors acknowledge Robert Delong for suggesting 

 this study. Jon Baker at the Northwest Fisheries Science 

 Center and Paul Spruell at the University of Montana 

 kindly provided cutthroat DNA. James Shaklee at the 

 Washington Department of Fish and Wildlife kindly 

 provided pink salmon samples. Sam Wasser and Virginia 

 Butler provided advice on the recovery of DNA from scat 

 and bone samples. Gail Bastrup assisted in technical 

 aspects of this study. 



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