We will discuss the usefulness of one nuclear and three chloroplast regions for inferring phylogenies in Pinaceae, with emphasis on the pinyon pines (Pinus subsections Cembroides, and Nelsoniae) from the western United States and Mexico. The ITS region of nuclear ribosomal DNA is exceptionally long in conifers, particularly in Pinus, Picea, and Podocarpus, and is often heterogeneous within individuals. Although analysis of ITS region sequences yields reasonable results approximately at the level of subsection and above, ITS1 shows much length variation and is difficult to align among genera. Orthology/paralogy problems are evident in pinyon pine ITS and confuse relationships among closely related species. Sequences from the chloroplast regions rbcL, matK, and rpl16 reveal fewer differences among species, but yield subsectional relationships that are consistent with ITS in pines (including the separation of P. nelsonii from subsect. Cembroides). Furthermore, cpDNA sequences also confirm more dubious relationships seen in ITS data, such as a sister relationship between P. maximartinezii and P. pinceana and a sister relationship between P. monophylla and P. quadrifolia (plus the latter's likely synonym, P. juarezensis). All three chloroplast genes support the hypothesis that P. cembroides includes three subspecific taxa: subspecies cembroides, lagunae, and orizabensis. Several haplotypes have been identified for P. johannis and its possible synonym, P. discolor. No differences were found between P. remota and its possible synonym, P. catarinae. Considering the effort of sequencing each of the four regions, the chloroplast genes rbcL and matK, which together are about the same length as the more variable ITS region (over 3 kbp), did not suffer from polymorphism and sequencing difficulties resulting from secondary structure, and gave better tip resolution than rpl16.

Key words: ITS region, matK, phylogenetics, Pinus, rbcL, rpl16