Pacific Rim Population Structure of Chinook Salmon as Determined from Microsatellite Analysis TERRY D. BEACHAM,* KIMBERLY L. JONSEN,JANINE SUPERNAULT,MICHAEL WETKLO, AND LANGTUO DENG Department of Fisheries and Oceans, Pacific Biological Station, Nanaimo, British Columbia V9T 6N7, Canada NATALIA VARNAVSKAYA Kamchatka Fishery and Oceanography Research Institute, 18 Naberezhnaya Street, Petropavlovsk-Kamchatsky 683000, Russia Abstract.—The Pacific Rim population structure of Chinook salmon Oncorhynchus tshawytscha was 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 (F ST ) 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. The Chinook salmon Oncorhynchus tshawytscha is a Pacific salmonid that has a wide geographic spawning range. In Asia, the most abundant stocks are located on the Kamchatkan Peninsula, but in North America historically or currently abundant stocks range from the Yukon River in the north to the Sacramento River in California. Considerable life history variation is observed within the spawning distribution. One major component of life history variation is related to juvenile life history in freshwater. Some populations are considered to be stream type, in which juveniles rear at least 1 year in freshwater before migrating to the ocean (Healey 1983). Other populations are considered to be ocean type, in which the juveniles migrate directly to the ocean upon fry emergence, or they may rear for a period in freshwater before migrating to the ocean in their year of emergence. The stream-type life history is dominant in large, northern rivers like the Yukon, and in populations spawning in the headwaters of more southern large rivers, like the Fraser and Columbia. The ocean-type life history is common in smaller coastal rivers south of 568N latitude, as well as in larger rivers in the extreme southern portion of the spawning distribution such as the Klamath and Sacramento rivers (Healey 1991). Although these two life history types have been considered as separate races (Healey 1983, 1991), no clear genetic demarca- tion exists between these two life history types over a wide geographic area (Waples et al. 2004). Chinook salmon populations also display a wide variation in timing of return to freshwater for spawning, which may occur during almost any month of the year (Healey 1991). As outlined by Waples et al. (2004), these run times are typically characterized as spring (March–May), summer (June–August), fall (September–November), and winter (December–Feb- ruary). Populations can also differ in spawning locations within a river drainage, with some popula- tions migrating to the headwaters of major rivers like the Columbia, Fraser, and Yukon rivers to spawn, whereas other populations spawn in locations not far removed from salt water. Conservation of Chinook salmon genetic diversity around the Pacific Rim requires an understanding of * Corresponding author: beachamt@pac.dfo-mpo.gc.ca Received March 28, 2006; accepted June 21, 2006 Published online November 13, 2006 1604 Transactions of the American Fisheries Society 135:1604–1621, 2006 Ó Copyright by the American Fisheries Society 2006 DOI: 10.1577/T06-071.1 [Article]