Tee! et al.: Genetic analysis of juvenile Oncorhynchus kisutch 



641 



late summer samples to detect seasonal shifts in stock 

 compositions along the coast and make comparisons with 

 earlier tag-recovery studies to search for decadal shifts 

 in the marine distributions of particular stocks. Recent 

 efforts at Pacific Northwest hatcheries to mark the major- 

 ity of their releases of coho salmon with a fin clip provide 

 new opportunities to estimate proportions of hatchery and 

 wild coho salmon in ocean samples (Beamish et al., 2000; 

 Lawson and Comstock, 2000). We therefore report genetic 

 estimates for hatchery-marked and unmarked fish in ocean 

 samples and use these estimates to identify hatchery and 

 wild population origins of ocean juvenile coho salmon. 



Materials and methods 



To establish an allele-frequency baseline, populations of 

 coho salmon were sampled from 89 hatcheries, streams, 

 and rivers between 1984 and 1999 (Fig. 1, Table 1). Samples 

 of skeletal muscle, eye, liver, and heart tissues were col- 

 lected from adults during spawning operations in hatcher- 

 ies or from whole juvenile fish in hatchery rearing ponds. 

 All hatchery broods sampled were the progeny of al least 

 50 adult fish. Wild juveniles were sampled in natal streams 

 and rivers by electroshocking. Wild adult fish were sampled 

 in spawning areas by gaffing and dip-netting. 



Samples of juvenile coho salmon in marine waters were 

 collected during NMFS coastal pelagic trawl surveys 

 (Emmett and Brodeur, 2000). Trawls consisted of one- 

 half-hour long surface tows with a 264 Nordic rope trawl 

 along nine transects perpendicular to shore ranging from 

 La Push, Washington (47°55'N) to Cape Perpetua, Oregon 

 (44°15'N) (Fig. 1). Sampling stations began 1-5 nautical 

 miles offshore and continued, in about 5 nautical-mile 

 (nmi) increments, to about 30 nmi offshore. Marine ju- 

 veniles were sampled 16-24 June and 21-30 September 

 1998, 16-24 June and 21 September-1 October 1999, and 

 17-25 June and 19-24 September 2000. Fish were mea- 

 sured and examined for the presence of fin clips and coded 

 wire tags (CWTs). Juveniles in their first ocean summer 

 were separated from older coho salmon by length by using 

 a modification of the criteria of Pearcy and Fisher (1990). 

 Fish with fork lengths less than 330 mm (June) and 450 

 mm (September-October) were considered to be juveniles 

 in their first year in the ocean. Fish with CWTs, and there- 

 fore of known brood year, provided supporting evidence for 

 these criteria with the assumption that growth of hatchery 

 and wild fish was similar 



Tissue samples or whole juvenile fish were frozen on 

 dry ice or in liquid nitrogen and stored at -80°C prior to 

 electrophoretic analysis. We used the methods of Aeber- 

 sold et al. (1987) for sample preparation and horizontal 

 starch-gel protein electrophoresis. Electrophoretic condi- 

 tions for 30 enzymes, for which we obtained reliable and 

 interpretable data for 59 loci, are reported in an appendix 

 that can be retrieved at the Northwest Fisheries Science 

 Center website [http://www.nwfsc.noaa.govl. Guidelines 

 by Utter et al. (1987) were used to infer genotypes from 

 banding patterns. Locus and allelic nomenclature follows 

 Shakleeetal. (1990). 



Figure 1 



Locations of ocean sampling transect lines ( + ) and 89 coho salmon 

 populations in California, Oregon, Washington, and British Colum- 

 bia. Numbers correspond to population names in Table 1. 



Genotypic frequencies of polymorphic loci for each base- 

 line sample were examined for departures from expected 

 Hardy-Weinberg proportions with a Fisher's exact test 

 (Guo and Thompson, 1992) by using GENEPOP version 

 3.1 (Raymond and Rousset, 1995). Hardy-Weinberg tests 

 were performed on isoloci (comigrating protein products of 

 duplicated loci) following Waples (1988). 



We estimated allelic frequencies for each sample. Allelic 

 frequencies for isoloci were calculated as mean frequen- 



