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Molecular Biology and Evolution 19:1943-1951 (2002)
© 2002 Society for Molecular Biology and Evolution

Evolution of a Perfect Simple Sequence Repeat Locus in the Context of Its Flanking Sequence

Scott M. Blankenship*, Bernie May{dagger} and Dennis Hedgecock*

*Bodega Marine Laboratory
{dagger}Department of Animal Science, University of California–Davis

Microsatellites, which have rapidly become the preferred markers in population genetics, reliably assign individual chinook salmon to the winter, fall, late-fall, or spring chinook runs in the Sacramento River in California's Central Valley (Banks et al. 2000 . Can. J. Fish. Aquat. Sci. 57:915–927). A substantial proportion of this discriminatory power comes from Ots-2, a simple CA repeat, which is expected to evolve rapidly under the stepwise mutation model. We have sequenced a 300-bp region around this locus and typed 668 microsatellite-flanking sequence haplotypes to explore further the basis of this microsatellite divergence. Three sites of nucleotide polymorphism in the Ots-2 flanking sequence define five haplotypes that are shared by the Californian and Canadian populations. The Ots-2 microsatellite alleles are nonrandomly distributed among these five haplotypes in a pattern of gametic disequilibrium that is also shared among populations. Divergence between the winter run and other Central Valley stocks appears to be caused by a combination of surprisingly static evolution at Ots-2 within a context of more rapidly changing haplotype frequencies.


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