Multiple levels of single-strand slippage at cetacean tri- and tetranucleotide repeat microsatellite loci

Between three and six tri- and tetranucleotide repeat microsatellite loci w ere analyzed in 3720 samples collected from four different species of balee n whales. Ten of the 18 species/locus combinations had imperfect allele arr ays, i.e., some alleles differed in length by other than simple integer mul tiples of the basic repeat length. The estimate of the average number of al leles and heterozygosity was higher at loci with imperfect allele arrays re lative to those with perfect allele arrays. Nucleotide sequences of 23 diff erent alleles at one tetranucleotide repeat microsatellite locus in fin wha les, Balaenoptera physalus, and humpback whales, Megaptera novaeangliae, re vealed sequence changes including perfect repeats only, multiple repeats, a nd partial repeats. The relative rate of the latter two categories of mutat ion was estimated at 0.024 of the mutation rate involving perfect repeats o nly. It is hypothesized that single-strand slippage of partial repeats may provide a mechanism for counteracting the continuous expansion of microsate llite loci, which is the logical consequence of recent reports demonstratin g directional mutations. Partial-repeat mutations introduce imperfections i n the repeat array, which subsequently could reduce the rate of single-stra nd slippage. Limited computer simulations confirmed this predicted effect o f partial-repeat mutations.