Localized Genetic Structure Persists in Wild Populations of Chinook Salmon in the John Day River Despite Gene Flow from Outside Sources

Samples of Chinook salmon Oncorhynchus tshawytscha collected front four spawning areas in the Joint Day River, Oregon (n = 330), were genotyped with 13 microsatellite loci to test for bottlenecks and temporal stability within sites as well as genetic differentiation among sites. and to estimate gene flow front outside populations. Since the John Day River has never been stocked with hatchery-reared fish, this study provided the opportunity to evaluate the genetic integrity and structure of Chinook salmon in a wilderness area amid many hatchery-supported populations in the Columbia River. No tests for bottlenecks (Wilcoxon tests for heterozygosity excess) were significant, and the temporal variation was slight and not significant within any spawning reach except for the collections from the Middle Fork John Day River. Overall, the genetic distance estimates suggest that there are three distinct subpopulations in the John Day River, namely, those in (1) the North Fork John Day River (including Granite Crock), (2) the Middle Fork John Day River, and (3) the upper main-stem John Day River. These genetic relationships were supported by results from a neighbor-joining dendrogram. Assignment tests indicate thin out-of-basin straying occurs throughout the John Day River. the largest percentage of strays going to the North Fork John Day River. Immigration may have acted to avert genetic bottlenecks and maintain genetic diversity in populations with fluctuating census size. Yet file genetic substructure of the Chinook salmon in the John Day River indicates natural reproduction from philopatric individuals, possibly with higher reproductive success than immigrants. The evidence presented here elucidates the balance of philopatry and dispersal acting to maintain genetic diversity and localized structure among the Chinook salmon of the John Day River.