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Deliverable: microsatellite classification of harvest location of cod

For most of the location investigated, we did not observe any temporal genetic differentiation (first and second spawning seasons). Moreover, in most of the sampling areas we did not observe differences between harvest and spawning locations. Therefore, the samples could be combined for the analysis, which renders the assignment analysis stronger.

The total percentage of individual assignment to their population of origin greatly varied from 43% (North Sea) to 83% (Baltic Sea). Even if the obtained percentage of assignment is very high in this study for a marine species, it will nonetheless be difficult to assign properly individuals coming from Irish, Celtic and North as well as individuals from Norway and Iceland. This is mainly due to the lack of genetic differentiation of population living in those areas. Celtic, Irish and North Seas are geographically relatively closed to each other and no obvious barriers to migration are present. The absence of genetic differentiation between those areas could merely be due to migration events between the populations living in those areas, thus rendering correct individuals assignment difficult. On the contrary, because of the large geographical distance involved between Norway and Iceland, it is unlikely that migration, which reduces the level of genetic differentiation between two populations, is responsible for the lack of genetic divergence between these two populations. On the contrary, recent common shared could explain the lack of genetic dissimilarity between Icelandic and Norwegian populations.

Concerning the assignment of individuals to their origins, the observed genetic pattern was stable over the investigated seasons e.g. for the spawning and harvested locations: for the assignment and the origin of fish, the first spawning season was slightly different from the other seasons. In fact, during the first season, 14.61% of the individuals were not correctly assigned (17.14% unexplained, 30% because of potential migration and 52.86% because of potential common ancestor). For the second spawning and the harvest location, around 25% of the individuals were not correctly assigned among which 35% were due to migration, 58% to common ancestry and 7% were unexplained. This slight difference can in fact be due to sampling effect. Indeed during the first season, the number of individuals we caught per sampling location was not constant and could have induce a bias in the different percentage of individuals assigned. For example we only caught 29 fishes in North Sea for the first spawning location in this area and 60 during the second spawning period. Moreover, most of the fish caught in this area during the second spawning season could be considered as migrant, thus increasing the percentage of wrongly assigned individuals.

Our results clearly demonstrated that individual assignment to population of origin may be, in some cases, particularly accurate, while in other cases individual origin can not be assessed. Microsatellite loci are useful genetic markers for traceability of individuals and assignment to population of origin, but genetic differentiation should be pronounced between the considered units. Here, at the individual base, the assignment was reasonable for Icelandic samples (farm and wild), the Baltic Sea, The Irish-North-Celtic Seas and the Scottish farm. The sample size of the Norwegian samples was probably too small to give an accurate estimate of the position of this population in this genetic pattern. Finally, 76.25% of the individual analysed could be assigned to the correct group.
However, some individuals were not correctly assigned with STRUCTURE while the basic genetic analysis, especially the PCA-gene analysis clearly separated the investigated groups, except the Irish and Celtic Seas. Therefore, the traceability of individuals may not be clear, mainly because of common shared ancestor between the population considered, but the combination of the group (PCA) and individual (STRUCTURE) assignment should allow correct determination of fish origins.

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