Microsatellite DNA analysis of population structure in Atlantic herring (Clupea harengus), with direct comparison to allozyme and mtDNA RFLP analyses.

Previous attempts to test for small-scale stock structuring within Atlantic herring (Clupea harengus L.) with molecular markers have been hampered by uninformative levels of genetic variation. Here we report the first application of microsatellite DNA markers to investigate population subdivision in Atlantic herring from Norwegian waters and the Barents Sea, and also examine microsatellite differentiation between C. harengus and Pacific herring (C. pallasi). Results from four microsatellite loci indicate high, and informative, variation compared to molecular markers used previously: number of alleles per locus=18-41; mean expected heterozygosity within samples=0.90-0.93. Significant genetic differences were detected between almost all samples representing postulated Icelandic summer-spawner, Norwegian spring-spawner and Norwegian fjord stocks, using Fisher's exact test, FST and RST values. Levels of allele frequency differentiation between Atlantic and Pacific herring overlapped the range seen among Atlantic herring samples, indicating that microsatellites are poor indicators of the degree of species differentiation. Comparison with allozyme and mitochondrial DNA restriction fragment length polymorphism (RFLP) datasets from the same samples suggests that microsatellites may detect structuring at a finer scale, but are less informative at larger scales of divergence.