Phylogenetics ofPinus(Pinaceae) Based on Nuclear Ribosomal DNA Internal Transcribed Spacer Region Sequences

Abstract

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species ofPinus,representing all recognized subsections of the genus, and 2 species ofPiceaandCathayaas outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement includingPinus nelsoniiandP. aristata.Within subgenusPinus,there is moderate support for the monophyly of a narrowly circumscribed subsect.Pinus(=subsect.Sylvestres) and strong support for a clade of North and Central American hard pines. The HimalayanP. roxburghiimay be sister species to these “New World hard pines,” which have two well-supported subgroups, subsect.Ponderosaeand a clade of the remaining five subsections. The position of subsect.Contortaeconflicts with its placement in a chloroplast DNA restriction site study. Within subgenusStrobusthere is consistent support for the monophyly of a broadly circumscribed subsect.Strobi(includingP. krempfiiand a polyphyletic subsect.Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects.Gerardianae, Cembroides,andBalfourianaeare poorly resolved. Support for the monophyly of subgenusPinusand subgenusStrobusis not consistently obtained.