Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river

Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as one of 10 hybrid classes using 30 ‘diagnostic’ single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of cl..., This data was collected by sampling coastal cutthroat trout and steelhead in the Smith River. Fish were captured using night netting, hook and line, electrofishing, and weirs from mid-May through August 2013. A tissue sample, photograph, and fork length measurement were collected from 874 fish. Phenotypic characteristics of jaw slash color intensity, maxillary length compared to posterior margin of eye, and presence of hyoid teeth were also recorded for each fish in the field. We generated genotypes for 96 single-nucleotide polymorphisms (SNPs) using TaqManTM 5’ nuclease assays (Applied Biosystems Inc.) and 96.96 Dynamic Genotyping Arrays (Fluidigm Corporation), with imaging on an EP1 instrument l (Fluidigm). Genotypes were manually called using the SNP Genotyping Analysis Software (3.0.2, Fluidigm). NewHybrids was configured to assign fish to ten hybrid classes characterized by the expected frequencies of loci having 0, 1, or 2 alleles originating from each parental type. 
Body morphol...,