In contrast to European and US oak species, there are no molecular studies addressing the relationships of the diverse Mexican taxa. In this study we use the ITS-1 and -2 regions to study the phylogeny of red oaks (Quercus sect. Lobatae), focusing on Mexican and selected North American species. Previous studies addressing the phylogeny of oak species using ITS have reported results from only one putatively orthologous ITS locus. Utilizing additional species, we found that PCR amplification of the ITS-1 and -2 regions resulted in products of several sizes for some Mexican oak species. Two of these products have been characterized: one of them is about 600 bp and the other is approximately 500 bp long. A comparison of our sequences with those from previous studies indicates that most of the published sequences are most similar to our 600 bp copy. Analyses of our sequences from the 500 bp copy show regions of similarity to the 600 bp copy, however, there is an average divergence of 15% between those copies. Since multiple ITS loci have been reported for some angiosperm taxa and unexpected phylogenies have been obtained in some previous oak studies, the possibility of finding other ITS paralogues in Quercus should not be ruled out.

Key words: ITS, Mexican species, paralogous, Quercus, red oaks