Allelic diversity in alligator microsatellite loci is negatively correlated with GC content of flanking sequences and evolutionary conservation of PCR amplifiability.

Microsatellites are short tandem arrays of simple DNA sequences, having a basic repeat unit of l-5 bp (Tautz and Schlbtterer 1994). Microsatellite loci are abundant in most complex genomes (Tautz and Schliitterer 1994) and are usually highly polymorphic when the basic repeat unit is duplicated more than 10 times (Weber 1990). Alleles at a locus differ in length due to variation in the number of repeats, and slipped strand mispairing is considered to be the major mechanism by which length variants (new alleles) are generated (Levinson and Gutman 1987; Strand et al. 1993). Variation at microsatellite loci can be assayed by PCR amplification using primers complementary to unique sequences flanking specific repetitive arrays, followed by electrophoretic sizing of the PCR products (Tautz 1989). Because microsatellites are highly polymorphic and amenable to PCR, multiplex PCR, and automated scoring, they often are the molecular genetic marker of choice (e.g., Bruford and Wayne 1993). Although microsatellites occur in all eukaryotes (Tautz and SchlGtterer 1994), their distribution and overall frequency varies widely (e.g., Langercrantz, Ellegren, and Andersson 1993). Because primer development can be time-consuming and costly, many investigators attempt to use primers developed in one species to amplify orthologous loci in closely related species (e.g., Moore et al. 1991). Some of these studies show that this strategy can be quite successful, even in distantly related species (e.g., FitzSimmons, Moritz, and Moore 1995). Most such cross-species comparisons, however, have tested either a small number of primer pairs (e.g., FitzSimmons, Moritz, and Moore 1995) or a small number of taxa (e.g., Moore et al. 1991). Additionally, only loci that are polymorphic in the species from which they are developed are used in most studies. The selection and use of such loci biases cross-taxa comparisons (Ellegren, Primmer, and Sheldon 1995). In general, primers that exhibit low levels of variation, as well as those that yield complex or unclear patterns, are discarded without much investigation or hesitation. Thus, it is not known how a reasonably large random sample of microsatellite sequences evolves within a group of taxa. We have developed primers to amplify microsatellite loci from American alligators (Alligator mississippiensis). Details of the lab work will be published else-