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 applica tion of microsatellite DNA markers to investigate population subdivision in Atlantic herring from Norwegian waters and the Barents Sea, and also exami ne microsatellite differentiation between C. harengus and Pacific herring ( C. pallasi). Results from four microsatellite loci indicate high, and infor mative, 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 s amples representing postulated Icelandic summer-spawner, Norwegian spring-s pawner and Norwegian fjord stocks, using Fisher's exact test, F-ST and R-ST values. Levers of allele frequency differentiation between Atlantic and Pa cific herring overlapped the range seen among Atlantic herring samples, ind icating that microsatellites are poor indicators of the degree of species d ifferentiation. 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.