GERNANDT, DAVID S., AARON LISTON*, AND DANIEL PIÑERO. Instituto de Ecología, Universidad Nacional Autónoma de México, México D.F. 04510, Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331. - Nuclear ribosomal DNA internal transcribed spacer region polymorphism and its implications for phylogenetic inference in Pinus subsection Cembroides.
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