Data from: Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases

Many salmonid fish populations are threatened by genetic homogenization,
primarily due to introgressive hybridization with hatchery-reared
conspecifics. By applying genomewide analysis using two molecular marker
types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts
of inadvertent gene flow via straying from hatchery releases on wild
populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16
years (1996–2012). Both microsatellites and SNPs revealed congruent
population genetic structuring, indicating that introgression changed the
genetic make-up of wild populations by increasing genetic diversity and
reducing genetic divergence. However, the degree of genetic introgression
varied among studied populations, being higher in the eastern part and
lower in the western part of Estonia, which most likely reflects the
history of past stocking activities. Using kernel smoothing and
permutation testing, we detected considerable heterogeneity in
introgression patterns across the genome, with a large number of regions
exhibiting nonrandom introgression widely dispersed across the genome. We
also observed substantial variation in nonrandom introgression patterns
within populations, as the majority of genomic regions showing elevated or
reduced introgression were not consistently detected among temporal
samples. This suggests that recombination, selection and stochastic
processes may contribute to complex nonrandom introgression patterns. Our
results suggest that (i) some genomic regions in Atlantic salmon are more
vulnerable to introgressive hybridization, while others show greater
resistance to unidirectional gene flow; and (ii) the hybridization of
previously separated populations leads to complex and dynamic nonrandom
introgression patterns that most likely have functional consequences for
indigenous populations.