Asymmetric Introgression Between Coastal Cutthroat Trout and Coastal Rainbow Trout within the Smith River (CA) Basin

Coastal Cutthroat Trout (Oncorhynchus clarki clarki) (CCT) and steelhead (Oncorhynchus mykiss) (SH) naturally hybridize throughout their sympatric range from Alaska to Northern California. Prezygotic and postzygotic barriers to introgression have maintained species boundaries of CCT and SH in seven sub-basins of the Smith River, California. A panel of 66 diagnostic single nucleotide polymorphisms (SNPs) was used to assess individual, population, and genomic introgression for 876 individuals. Invasive SH alleles were found in 135 individuals, whereas invasive CCT alleles were found in only five individuals, suggesting strong asymmetric introgression. Genomic clines were fit to determine if loci deviated from a neutral model of gene flow. Significance testing of genomic clines revealed non-neutral introgression at 32% of the loci (n=21). Genomic patterns of introgression were further investigated using a linkage map created for F1 hybrids of Yellowstone Cutthroat Trout and Rainbow Trout. Variable patterns of introgression across the genome produced strong similarities among loci within the same linkage group. Linkage groups expressing reduced or absent gene flow, suggests suppression of recombination by chromosome rearrangements. Analysis of first-generation (F1) hybrid mitochondrial DNA (14 of 15, SH mtDNA) showed that hybridization was driven by male CCT sneaking fertilizations with female SH.