The model treats allelic states as integers, and proposes that mutations cause a change in allele class by adding or subtracting one unit of charge, in the case of proteins, or a repeat motif unit, in the case of microsatellites. Interest in the model waned, however, as it is difficult to associate numbers of amino acid substitutions with mobility differences. The SMM was revisited in the early 90's with the discovery of microsatellite markers and the mechanisms of their evolution. Empirical evidence supporting stepwise mutation as a model for microsatellite evolution comes from modeling efforts and direct observations. In practice this means that microsatellite marker fragments observed on an electrophoretic gel may not necessarily be identical even though they are of identical size.
Chinook salmon are an important species both economically and culturally.
Microsatellites are used on these runs, as well as other populations along the West Coast, for management and conservation purposes. Inferences derived from these markers have far reaching impacts. The proposed project may also find single nucleotide fixed differences between salmon runs, which would lend itself to more efficient means of run-discrimination. The question will be answered given the molecular phylogeny of microsatellite alleles determined by flanking sequence identities. Approach I propose to assess the level of homoplasy present at a microsatellite locus in the Chinook salmon by a straightforward sequence analysis of microsatellite alleles and their adjoining flanking regions.