Oaks (Quercus: Fagaceae) hybridize relatively readily within sections yet maintain species identity despite ongoing gene flow. This feature, coupled with frequent differences in microhabitat distribution among coexisting species, make Quercus communities model systems for the study of forest tree hybridization, speciation, and local genetic adaptation. In this study, we tested EST-SSR markers previously developed in Q. robur (section Quercus) for transferability and utility in five sympatric North American red oak (section Lobatae) species. While less polymorphic than simple-sequence repeats, EST-SSRs often show greater transferability among taxa and are located in putatively adaptive genes. A total of 86 EST-SSR primer pairs were screened in two Quercus rubra individuals. Of these, 80% amplified a product of expected size and 40% showed polymorphism in at least one individual. Eighteen of these polymorphic primers pairs were selected on the basis of linkage group position and putative gene function for characterization in 18 to 26 (total = 84) individuals from each of a Q. rubra, Q. ellipsoidalis, Q. coccinea, and Q. velutina population previously characterized by AFLP markers. Mean expected heterozygosty (He= 0.65) was slightly lower than previously observed in Q. robur. The number of alleles per locus across all four populations ranged from 3 to 12 with a mean of 6.91. Genetic
differentiation among the four species was moderate (Fst= 0.089), but four EST-SSRs markers, including one locus putatively associated with drought tolerance, significantly deviated from neutral expectations. Future research will involve sequencing these outlier loci to identify functional SNPs within these genes.