Methods

• Allozymes
  Allozyme data will link the microsatellite results with extensive genetic data published in the scientific literature and with information available in the database of partner 3. Partner 3 has access to data bases of individual allozyme genotypes for samples from spawning aggregations collected 15-20 years ago (hundreds of individuals typed at 17 loci, 13 of which were variable). Those spawning aggregations will be re-sampled within the present project, and the resulting estimates of the amount of temporal change over 15-20 years will contribute unique and critical information on the relative importance of temporal heterogeneity to genetic variability patterns observed. Some methodological details on alozyme electrophoresis can be found here.

• Mitochondrial DNA
  For mitochondrial DNA (WP-5) the partners will conduct RFLP analyses on a 2.3 kb fragment containing the ND3 and ND4 gene. Partner 5 has recently shown that this region has considerable potential for the discrimination of North East Atlantic herring populations (Hauser et al. 2001). Furthermore, these data will again be used to investigate the temporal stability of observed patterns. And this is how RFLP work.

• Microsatellites
  Microsatellite DNA is central to achieving the objective of estimating proportional contribution by spawning populations to mixed aggregations. Because of their high variability, microsatellites are currently the most powerful markers for the detection of population differentiation in pelagic fish (Hauser & Ward 1998). Microsatellites will also be the main tool for the quantification of stock contributions to the mixed fishery in central North Sea and the Skagerak.

• Major Histocomptibility Complex
  MHC genes in fish are comprised of those coding for class I alpha chain and class II alpha- and beta-chains. The research will attempt to compare population analyses based on "neutral markers", such as anonymous microsatellites and non-neutral markers such as the MHC genes. Such an approach would require an expedient technique to detect MHC polymorphism. Cloning and sequencing alleles from both class I and class II genes of a large number of individuals would be unfeasible. However, it has been shown that MHC genes contain satellite markers in a number of fish species. A recent study on farmed Atlantic salmon MHC polymorphism identified 8 microsatellite alleles in class I and 8 in class II alpha gene in a group of 80 broodstock fish. In addition a study on wild brown trout (n=60) revealed a large number of microsatellite markers embedded in class I (n=17) and class II alpha gene (n=47). The presence of similar repeats in herring MHC genes would provide the possibility to compare the relative roles of neutral and adaptive processes in generating population differentiation through comparative studies between microsatellites in neutral and selected regions of the genome.

• Otolith microstructure