Molecular methods for the genetic identification of salmonid prey from Pacific harbor seal (Phoca vitulina richardsi) scat

Twenty-six stocks of Pacific salmon and trout (Oncorhynchus spp.), representing evolutionary significant units (ESU), are listed as threatened or endangered under the Endangered Species Act (ESA) and six more stocks are currently being evaluated for listing. The ecological and economic consequences of these listings are large; therefore considerable effort has been made to understand and respond to these declining populations. Until recently, Pacific harbor seals (Phoca vitulina richardsi) on the west coast increased an average of 5% to 7% per year as a result of the Marine Mammal Protection Act of 1972 (Brown and Kohlman2). Pacific salmon are seasonally important prey for harbor seals (Roffe and Mate, 1984; Olesiuk, 1993); therefore quantifying and understanding the interaction between these two protected species is important for Morphobiologically sound management strategies. Because some Pacific salmonid species in a given area may be threatened or endangered, while others are relatively abundant, it is important to distinguish the species of salmonid upon which the harbor seals are preying. This study takes the first step in understanding these interactions by using molecular genetic tools for species-level identification of salmonid skeletal remains recovered from Pacific harbor seal scats.

Genetic differentiation among Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals

This study examines genetic variation at five microsatellite loci and at the vesicle membrane protein locus, pantophysin, of Atlantic cod (Gadus morhua) from Browns Bank, Georges Bank, and Nantucket Shoals. The Nantucket Shoals sample represents the first time cod south of Georges Bank have been genetically evaluated. Heterogeneity of allelic distribution was not observed (P>0.05) between two temporally separated Georges Bank samples indicating potential genetic stability of Georges Bank cod. When Bonferroni corrections (α=0.05, P<0.017) were applied to pairwise measures of population differentiation and estimates of FST, significance was observed between Nantucket Shoals and Georges Bank cod and also between Nantucket Shoals and Browns Bank cod. However, neither significant differentiation nor significant estimates of FST were observed between Georges Bank and the Browns Bank cod. Our research suggests that the cod spawning on Nantucket Shoals are genetically differentiated from cod spawning on Browns Bank and Georges Bank. Managers may wish to consider Nantucket Shoals cod a separate stock for assessment and management purposes in the future.

The geographic basis for population structure in Fraser River chinook salmon (Oncorhynchus tshawytscha)

We surveyed variation at 13 microsatellite loci in approximately 7400 chinook salmon sampled from 52 spawning sites in the Fraser River drainage during 1988–98 to examine the spatial and temporal basis of population structure in the watershed. Genetically discrete chinook salmon populations were associated with almost all spawning sites, although gene flow within some tributaries prevented or limited differentiation among spawning groups. The mean FST value over 52 samples and 13 loci surveyed was 0.039. Geographic structuring of populations was apparent: distinct groups were identified in the upper, middle, and lower Fraser River regions, and the north, south, and lower Thompson River regions. The geographically and temporally isolated Birkenhead River population of the lower Fraser region was sufficiently genetically distinctive to be treated as a separate region in a hierarchial analysis of gene diversity. Approximately 95% of genetic variation was contained within populations, and the remainder was accounted for by differentiation among regions (3.1%), among populations within regions (1.3%), and among years within populations (0.5%).Analysis of allelic diversity and private alleles did not support the suggestion that genetically distinctive populations of chinook salmon in the south Thompson were the result of postglacial hybridization of ocean-type and stream-type chinook in the Fraser River drainage. However, the relatively small amount of differentiation among Fraser River chinook salmon populations supports the suggestion that gene flow among genetically distinct groups of postglacial colonizing groups of chinook salmon has occurred, possibly prior to colonization of the Fraser River drainage.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

An examination of spatial and temporal genetic variation in walleye pollock (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data

We used allozyme, microsatellite, and mitochondrial DNA (mtDNA) data to test for spatial and interannual genetic diversity in wall-eye pollock (Theragra chalcogramma) from six spawning aggregations representing three geographic regions: Gulf of Alaska, eastern Bering Sea, and eastern Kamchatka. Interpopulation genetic diversity was evident primarily from the mtDNA and two allozyme loci (SOD-2*, MPI*). Permutation tests ˆindicated that FST values for most allozyme and microsatellite loci were not significantly greater than zero. The microsatellite results suggested that high locus polymorphism may not be a reliable indicator of power for detecting population differentiation in walleye pollock. The fact that mtDNA revealed population structure and most nuclear loci did not suggests that the effective size of most walleye pollock populations is large (genetic drift is weak) and migration is a relatively strong homogenizing force. The allozymes and mtDNA provided mostly concordant estimates of patterns of spatial genetic variation. These data showed significant genetic variation between North American and Asian populations. In addition, two spawning aggregations in the Gulf of Alaska, in Prince William Sound, and off Middleton Island, appeared genetically distinct from walleye pollock spawning in the Shelikof Strait and may merit management as a distinct stock. Finally, we found evidence of interannual genetic variation in two of three North American spawning aggregations, similar in magnitude to the spatial variation among North American walleye pol-lock. We suggest that interannual genetic variation in walleye pollock may be indicative of one or more of the following factors: highly variable reproductive success, adult philopatry, source-sink metapopulation structure, and intraannual variation (days) in spawning timing among genetically distinct but spatially identical spawning aggregates.