The upper Columbia River in Washington State (main-stem and tributary habitat between McNary and Chief Joseph dams) is inhabited by two major lineages of Chinook Salmon (Oncorhynchus tshawytscha); endangered spring Chinook Salmon and summer Chinook Salmon which are not ESA listed. The lineages are highly genetically divergent from one another and historically spatial and temporal isolating mechanisms maintained these genetic differences. Both lineages occur in the Entiat River, a system where anthropogenic activity has changed habitat, flows, species composition, and the distribution of the two lineages over the past century. We examined the spatial and temporal overlap in spawning distributions between Entiat River spring and summer Chinook Salmon and we used genetic markers to assess the level of introgression between lineages. Redd surveys were conducted from 2003 to 2017 to describe spatial and temporal spawning patterns of both lineages. We genotyped sub-yearling juvenile Chinook Salmon captured in the Entiat River from 2009–2014 at 90 SNP loci to determine lineage and hybridization status. There was temporal overlap in spawning between lineages in several years and considerable spatial overlap in redd locations annually. Genetic analysis revealed hybridization between lineages does occur, albeit at relatively low rates (2.6% of sub-yearling juveniles genotyped). We detected hybrids each year samples were collected and they were distributed throughout the Entiat River basin. Hybridization between lineages of Chinook Salmon could result in introgression and a loss of genetic diversity between the lineages, and/or, a loss of production by ESA-listed spring Chinook Salmon. The presence of hybrids warrants concern for ESA-listed spring Chinook Salmon in both the Entiat River system and throughout the upper Columbia River basin.

The 96 SNP makers were processed using TaqMan® SNP Genotyping Assays (Life Technologies, Carlsbad, California) on a Fluidigm® EP-1™ System with 96.96 Dynamic Arrays following the manufacturer’s protocol (Fluidigm, San Francisco, California). Multi-locus genotypes of each individual fish were visualized and scored using Fluidigm® SNP Genotyping Analysis software and were confirmed by two researchers.

Genetic marker naming is defined on the "marker key" tab.  Definitions of allelic and missing data states are defined in the header on each tab.