Pacific Rim Population Structure of Chinook Salmon as Determined from Microsatellite Analysis

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Abstract
The Pacific Rim population structure of Chinook salmonOncorhynchus tshawytschawas examined with a survey of microsatellite variation. Variation at 13 microsatellite loci was surveyed for over 52,000 Chinook salmon sampled from over 320 localities ranging from Russia to California. The genetic differentiation index (FST) over all populations and loci was 0.063; individual locus values ranged from 0.026 to 0.130. The most genetically diverse Chinook salmon were observed from northern British Columbia, Washington (Puget Sound and coastal populations), and the upper Columbia River (spring run). Chinook salmon from the Alsek River, northern British Columbia, and the Klamath River, California, displayed the fewest number of alleles relative to Chinook salmon in other regions surveyed. Differentiation in Chinook salmon allele frequencies among river drainages and populations within river drainages was approximately 13 times greater than that of annual variation within populations. We observed a general pattern of regional structuring of populations, and Chinook salmon spawning in different tributaries within a major river drainage or in smaller rivers within a geographic area were generally more similar to each other than to populations in different major river drainages or geographic areas. Population structure of Chinook salmon on a Pacific Rim basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation. The distribution of microsatellite variation of Chinook salmon on a Pacific Rim basis reflects the origins of salmon radiating from refuges after the last glaciation period.

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