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

• Published in: Molecular Ecology
• Main Authors: Ozerov, M. Y., Gross, R., Bruneaux, M., Vähä, J.‐P., Burimski, O., Pukk, L., Vasemägi, A.
• Other Authors: Suomen Akatemia, Eesti Teadusfondi, Estonian Ministry of Education and Research, Estonian Environmental Investment Centre
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2016
• Subjects: Atlantic salmon
• Online Access: http://dx.doi.org/10.1111/mec.13570; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.13570; https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13570

Abstract 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 SNP s 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 SNP s 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.