title: Evolution of a perfect simple sequence repeat locus in the context of its flanking sequence.
abstract: 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.
authors.affiliation: Bodega Marine Laboratory. Department of Animal Science, University of California-Davis, Occidental, 95465, USA. szscottb@yahoo.com
authors.forename: Scott M
authors.initials: SM
authors.lastname: Blankenship
authors.forename: Bernie
authors.initials: B
authors.lastname: May
authors.forename: Dennis
authors.initials: D
authors.lastname: Hedgecock
mesh_terms: D000483:Alleles; D000818:Animals; D001483:Base Sequence; D002140:California; D002170:Canada; D018900:Dinucleotide Repeats / Q000235:genetics*; D019143:Evolution, Molecular; D005787:Gene Frequency; D014644:Genetic Variation / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics; D011110:Polymorphism, Genetic / Q000235:genetics; D012474:Salmon / Q000235:genetics*; D012621:Seasons; D012689:Sequence Homology, Nucleic Acid