The phylogenetic relationships of the genus Bryoria were examined using ITS, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and mitochondrial SSU rDNA sequence data in addition to 20 chemical and morphological characters. This first comprehensive molecular study to assess Bryoria phylogeny includes representatives from all the traditionally recognized four sections. Combined cladistic analyses of 88 Bryoria specimens representing at least 25 species resulted in highly resolved phylogenies. Based on the results, a new infrageneric classification for the genus is proposed. Five sections are recognized, largely corresponding to the existing classification, with the addition of section Americanae. The study shows that while most species with an erect growth-form are clearly monophyletic, current species status of many pendent taxa can be questioned.

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Bryoria fremontii and B. tortuosa are the only species in the lichenized ascomycete genus Bryoria known to contain the pulvinic acid derivative vulpinic acid. In B. fremontii this yellow pigment is restricted to the soralia and apothecia, while in B. tortuosa it can occur throughout the thallus. The actual amount of vulpinic acid produced by B. tortuosa is rather variable, however, with intermediate specimens bearing both white and yellow pseudocyphellae. We studied the relationship between the two species with parsimony analysis using four DNA regions: 1) the internal transcribed spacers of the nuclear rDNA including the 5.8S region (ITS), 2) partial sequences from the intergenic spacer of the nuclear rDNA (IGS), 3) partial sequences from the small subunit of the mitochondrial rDNA (mtSSU), and 4) partial sequences from the protein-coding glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH). Our phylogenetic analysis revealed that B. fremontii and B. tortuosa must be regarded as conspecific, but allowing for some genetic differentiation between European and North American populations. Bryoria tortuosa is therefore synonymized with B. fremontii.

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