Workpackages

We will use microsatellite loci to determine (i) genetic differentiation between adult herring from distinct spawning aggregations from waters west of the British Isles. Samples of spawning fish will be taken over 2 years to (ii) determine whether any temporal variation exists in the genetic structure of herring stocks in western European waters. Juvenile herring will be sampled from inshore nursery and overwintering areas to determine (iii) the contribution that each spawning stock makes to each nursery ground. Fishery aggregations (non-spawning adults) will be sampled and the data from objectives (i) and (ii) will be used to (iv) evaluate the contribution of each spawning stock to the present herring fishery. Since the above data are obtained by genotyping individual fish, which limits sample size through cost and time, we will investigate whether it is possible to increase sample size and reduce cost simultaneously by (v) comparing data obtained from objectives (i-v) with those obtained by amplifying samples of pooled DNA using quantitative PCR.

DNA will be extracted from fin clips (preserved in ethanol) using standard methods. We will use microsatellites since these are typically more variable than other genetic markers, with a sample size of 50-100 individuals sufficient to describe a population. Genetic variation of herring in western European waters will be assayed at 15 microsatellite loci on 100 individuals (50 males & 50 females) from each of the designated spawning sites and nursery areas. Genotyping will be cross-validated between laboratories using 50 individual herring from 3 sample sites. For mixed-stock analysis, 500 herring will be sampled and genotyped from 3 areas. All sampling will be repeated over 2 years. Data from spawning stocks will be used to determine the degree of stock separation using standard population genetic statistical packages. These data will then be used to classify individuals from nursery areas and the mixed stocks to their original spawning stock by discriminant function analysis and principal components. The genetic data set will also feed into the multivariate analysis of herring stocks (WP7). Quantitative PCR will be used to estimate sample allele frequencies using a single PCR of a sample of pooled DNA. All individual genotype data will be compared to those generated from quantitative PCR of pooled DNA. We will investigate the accuracy of estimated allele frequencies generated with pooled samples of 10, 20, 50 and 100 individuals. We will also investigate the use of real-time PCR for rapid genotyping pooled DNA samples. We are not aware of these techniques being employed for genetic analyses of fish stocks in this way, but believe that, once established, it will become the industry standard given the potential for reducing time and expense required for genetic analysis of fish stocks.

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