Highly Discordant Nuclear and MitochondrialDNA Diversities in Atka Mackerel

—Levels of neutral genetic diversity largely reflect effective population size (N e ), which is influenced by physical and biological environmental variables. While large populations of marine fishes generally harbor higher diversities than freshwater species, historical demography or the effects of natural selection may significantly reduce N e and differentially affect genomic diversities. Here, we surveyed levels of genetic diversity and examined genetic structure among populations of the Atka mackerel Pleurogrammus monopterygius across most of its geographic range by screening variation at nine nuclear microsatellite DNA markers (n 1⁄4 745) and in a 468-base-pair segment of the mitochondrial DNA (mtDNA) control region (n 1⁄4 119). Samples from Japan to the western Gulf of Alaska were collected between 2004 and 2006 at six locations, including temporal replicates at two sites. Microsatellite allele frequency homogeneity across the North Pacific indicated an apparent lack of genetic population substructure. While levels of polymorphism at microsatellite loci were typical for marine fishes (haplotype diversity h 1⁄4 0.34–0.96), mtDNA control region diversity was extremely low (nucleotide diversity1⁄4 0.00007; h1⁄4 0.033). Only three mtDNA haplotypes, two occurring as singletons, were detected among 119 individuals. The strong contrast between microsatellite and mtDNA diversities appears to be due to the smaller N e for mtDNA, perhaps resulting from population bottlenecks during postglacial colonizations of the central North Pacific or the effects of natural selection on