Pinus subsection Cembroides (the pinyon pines) is a group of palaeo- and neo-endemics confined to the western United States and Mexico. Both ancient, and recent speciation are apparent causes of taxonomic disagreement in the group. We used nuclear ribosomal DNA internal transcribed spacer (ITS) region sequences to reconstruct a molecular phylogeny for subsection Cembroides and representative species from other subsections of Pinus. The ITS1 is approximately 2.6 Kb in Pinus, thus providing more variable sites for phylogenetic reconstruction than typically expected for the ITS region. Restriction digests of ITS region amplified either directly from genomic preparations or from clones revealed polymorphism within individuals. ITS pseudogenes were detected by examining the rate and pattern of substitution, and by a relaxation of secondary structure. Although pseudogenes could be distinguished and removed from the phylogenetic analysis, inclusion of multiple clones that were not pseudogenes resulted in topological conflicts that we attribute to deep coalescence of paralogous copies. ITS polymorphism may limit the utility of the ITS for phylogenetic reconstruction among closely related species in Pinus. However, agreement with cpDNA phylogenies at the level of subsection and above suggests that the ITS is useful for higher level phylogeny in the genus.

Key words: concerted evolution, ITS region, Pinus subsection Cembroides, pseudogenes