Population genetics and Genetic Stock Identification of anadromous Salmo trutta from the Irish Sea and adjacent areas, using microsatellite DNA loci

Paulo Prodöhl, A. Antoniacomi, Caroline Bradley, Jens Carlson, Gary R. Carvalho, Jamie Coughlan, J. Coyne, Mary C. Cross, Maud E. Cross, C. A. Davies, E. Dillane, P. Gargan, Rose Hynes, Philip McGinnity, Nigel Milner, Thomas Reed, William Roche, Martin Taylor, N. Tysklind, Tom F. Cross

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)peer-review


The management and conservation of anadromous sea trout (Salmo trutta L.) during the marine phase of their life history depends on a better understanding their ecology and migratory behaviour in the sea. To address this knowledge gap, a Genetic Stock Identification (GSI) exercise using Individual Assignment (IA) was undertaken. A panel consisting of 18 microsatellite nuclear DNA loci was used for the construction of a genetic baseline for sea trout from river systems flowing into the Irish and Celtic Seas. Sampling design involved the collection of over 5,000 juvenile fish, from putative sea trout spawning areas in 99 riverine locations. This comprehensive sampling programme of Irish, Manx, Scottish, English and Welsh rivers was designed to include the majority of the larger rivers contributing sea trout to the Irish and Celtic Seas. Genomic DNA extracted from these specimens was genotyped and analysed, to examine patterns of population structure, and produce a genetic baseline for assignment of marine-caught individuals (post smolts and adults) of unknown origin. A highly genetically-distinct trout group from SW Ireland was included as an outlier. STRUCTURE analysis of riverine genetic data revealed complex patterns of population structuring, which was best explained by nine major genetically-distinct regional groups within the Irish and British database. A self-assignment exercise, based upon identified populations, using the ONCOR algorithm, demonstrated the applicability of the database for assignment, particularly at the regional level. Assignment to regional reporting groups, rather than specific populations, was then utilised for marine-caught samples. Marine sampling, mainly in the Irish Sea, secured over 1,000 adult sea trout for individual assignment analysis, using the programme ONCOR. Marine-captured fish were used for spatial distribution mapping purposes when they could be scored for 14 or more loci, and were assignable to one of the nine regional groupings, with assignment probability scores equal or greater than 0.7. Results indicate that sea trout in the Irish Sea originate from a large number of rivers throughout the sampling area, and constitute substantially mixed marine aggregations. Individual assignment suggests that most inferred movement is region specific, the majority of fish being captured in the proximity of their natal rivers. However, there was strong evidence for long range migrations, with some fish traversing the Irish Sea or moving between the Irish and Celtic Seas.
Original languageEnglish
Title of host publicationSea Trout: Science and Management
Subtitle of host publicationProceedings of the 2nd International Sea Trout Symposium
EditorsGraeme Harris
Place of PublicationLeicestershire
PublisherTroubador Publishing Ltd.
Number of pages26
ISBN (Print)978 1788035 354
Publication statusPublished - 2017


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