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Asymmetric introgression between Coastal Cutthroat Trout and steelhead: variable introgression by linkage group
I assessed introgression between sympatric Coastal Cutthroat Trout (Oncorhynchus clarki clarki, CCT) and steelhead (Oncorhynchus mykiss irideus, SH) from 7 sub-basins of the Smith River in northern California. Population, individual and genomic level introgression was determined using a panel of 65 diagnostic single nucleotide polymorphisms, of which 59 are mapped to 26 of 28 known linkage groups. Among hybrids, first-generation (F1) hybrids were rare (2%) and the frequency of backcrosses was asymmetric, with backcrosses to SH infrequent (<1%), and backcrosses to CCT relatively common (17%). Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven by sneak-mating of male CCT with female SH. Genomic clines analysis located nine loci across three known linkage groups that deviated from a neutral model of introgression. Genome-wide differential introgression was documented along with non-random patterns of introgression among linkage groups. These findings suggest genomic blocks are inherited in recent CCT and SH hybrids and subsequently undergo decay as repeated rounds of recombination break up linkage group associations. Chromosome rearrangements known to suppress recombination are suspected in CCT and SH hybrids, and may preserve genomic regions fundamental to isolation. Analysis of geometric morphometrics and phenotypic characteristics revealed distinct CCT and SH morphologies. However, first-generation hybrids and backcrosses expressed non-distinct morphologies that overlapped with parental types, creating challenges in visual field identification.