Polemoniaceae are often considered a model family for studying evolutionary processes, yet a reliable phylogeny for the family is only now beginning to emerge. To test the monophyly of this family and to elucidate intergeneric relationships, we employed comparative sequencing of the chloroplast gene matK. Parsimony analysis of matK sequences representing 18 genera of Polemoniaceae and nine families from Asteridae sensu lato places Polemoniaceae apart from Solanaceae near Fouquieriaceae, Ericaceae, Sarraceniaceae, and Diapensiaceae. Both this and a subsequent analysis of 59 species of Polemoniaceae indicate that Cobaea is derived from within Polemoniaceae, rather than being the sister to Polemoniaceae as suggested by some authors. The tropical genera Bonplandia, Cantua, and Cobaea form a clade, and the remaining, primarily temperate genera, excluding Acanthogilia, form a second monophyletic group. Acanthogilia is placed ambiguously as sister to either the tropical or temperate groups depending on the location of the root for Polemoniaceae. Within the temperate lineage, Polemonium is sister to three large clades: a well-supported clade comprising Phlox, Gymnosteris, Linanthus, Leptodactylon, and Gilia filiformis; a moderately well-supported clade comprising Allophyllum, Collomia, Navarretia, and several species of Gilia; and a weakly supported clade comprising Eriastrum, Ipomopsis, Langloisia, Loeseliastrum, Loeselia, and several species of Gilia. In addition to revealing the extreme polyphyly of Gilia, this analysis suggests that Ipomopsis and Linanthus are also polyphyletic.
