Phlox, the largest genus in the Polemoniaceae, comprises approximately 65 species and has a center of diversity in western North America. It is a valuable experimental system for a variety of evolutionary studies, yet the taxonomy is difficult, and phylogenetic relationships within the genus as a whole have remained poorly understood. A high diversity in eastern North America (22 species) and the Rocky Mountains (23 species) relative to most genera of the Polemoniaceae raises questions regarding patterns of diversification relative to geography. Sequence data from the nuclear genome were gathered as part of a larger study to develop a strong phylogenetic framework for the genus (based on data from the nuclear genome, the chloroplast genome, and morphology) and a thorough taxonomic revision. A phylogeny based on the ITS region of the nrDNA and including representative sampling for the entire genus has several important implications: the sections and many of the subsections are artificial; the eastern species comprise at least two lineages; and the eastern mat-forming species occur in a clade with several western species. There is weak support for some of the interior branches on the ITS tree; to strengthen the nuclear-based phylogeny, part of chloroplast-expressed glutamine synthetase (ncpGS; including seven introns) was sequenced. Despite the challenges of working with this low-copy gene, the preliminary ncpGS tree demonstrates the utility of this marker for phylogeny reconstruction in Phlox; ultimately, appropriate combination of ITS and ncpGS data may yield a much improved nuclear-based phylogeny. An overview of our current understanding of relationships of Phlox is presented, with a note of caution on the need for a future comparison with a chloroplast-based phylogeny, as previous work on the eastern species demonstrated some incongruence that may be related to hybridization.

Key words: chloroplast-expressed glutamine synthetase, ITS, Phlox, phylogeny, Polemoniaceae