Genetic Diversity and Population Structure of Spring Chinook Salmon from the Upper Willamette River, Oregon

Effective management of Pacific salmon requires an accurate understanding of both population genetic diversity and structure. Spring Chinook Salmon Oncorhynchus tshawytscha from the upper Willamette River (UWR), Oregon, are listed as threatened under the U. S. Endangered Species Act, and although this evolutionarily significant unit is recognized to be distinct from other Columbia River stocks, genetic relationships among its constituent hatchery and wild populations remain obscure. We used genotypic data from 13 microsatellite loci to test whether hatchery populations of UWR spring Chinook Salmon are most similar to wild populations within the same subbasin, or whether hatchery populations from different subbasins are more similar to each other than to local wild populations. We also tested for differences between the genetic diversities of hatchery and wild populations, as measured through heterozygosity and allelic richness. Our results suggest that populations are weakly structured among subbasins and, in all cases, hatchery populations are genetically most similar to local wild populations. We also found heterozygosity to be higher (P = 0.009) in hatchery populations (median, 81.5%) than in wild populations (median, 75.2%), but observed no significant difference with respect to allelic richness (P = 0.406). We conclude that hatchery-origin UWR spring Chinook Salmon represent genetically appropriate founder populations for ongoing reintroduction programs and recommend that the conservation and recovery of this stock proceed through management actions developed specifically for each subbasin. We further recommend that current restrictions on hatchery stock transfers among UWR subbasins be continued to preserve extant population genetic structure.