Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer r egion was sequenced in 47 species of Pinus, representing all recognized sub sections of the genus, and 2 species of Picea and Cathaya as outgroups. Par simony analyses of these length variable sequences were conducted using a m anual alignment, 13 different automated alignments, elision of the automate d alignments, and exclusion of all alignment ambiguous sites. High and mode rately supported clades were consistently resolved across the different ana lyses, while poorly supported clades were inconsistently recovered. Compari son of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pin us (=subsect. Sylvestres) and strong support for a clade of North and Centr al American hard pines. The Himalayan P. roxburghii may be sister species t o these "New World hard pines," which have two well-supported subgroups, su bsect. Ponderosae and a clade of the remaining five subsections. The positi on of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including: P . krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardian ae, Cembroides, and Balfourianae are poorly resolved. Support for the monop hyly of subgenus Pinus and subgenus Strobus is not consistently obtained. ( C) 1999 Academic Press.