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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In this study we examined photobiont identity, diversity and selectivity in the genus Bryoria. We focused on B. fremontii and section Implexae in order to determine whether secondary chemistry is correlated with photobiont identity. DNA from two loci for photobionts and three loci for mycobionts was sequenced for both parsimony and Bayesian phylogenetic analyses. A comparison of photobiont and mycobiont phylogenies reveals that most Bryoria species associate exclusively with lineages of the Trebouxia simplex group; only B. smithii was associated with a different photobiont. We conclude that most Bryoria species included in our study are highly selective in their choice of algal partners and that the presence/concentration of different secondary compounds does not correlate with photobiont identity either in section Implexae or in B. fremontii.

Bryoria pseudocapillaris and B. spiralifera are currently treated as members of Bryoria section Implexae although conspicuous, long and depressed pseudocyphellae characterizing both species resemble those found in the genus Sulcaria. Both genera belong in Parmeliaceae and form an alectorioid group together with Alectoria, Gowardia and Pseudephebe. Parsimony and Bayesian analyses of ITS, partial GAPDH and partial Mcm7 sequence data were used to examine the phylogenetic position of B. pseudocapillaris and B. spiralifera, and in light of these results evaluate the generic delimitation of Bryoria and Sulcaria. A total of 110 specimens of 53 species containing representatives from alectorioid and closely related genera were included in the analyses. The results clearly show first, that both B. pseudocapillaris and B. spiralifera belong in Sulcaria rather than in Bryoria, and second, that they should be considered conspecific. Bryoria pseudocapillaris is proposed as a synonym under B. spiralifera and the name Sulcaria spiralifera comb. nov. is introduced.

Two new species of Bryoria are described based on morphology, chemistry and molecular phylogeny (ITS and Mcm7). Both species belong in section Bryoria, which was resolved as a polyphyletic group in the ITS+Mcm7 phylogeny. Bryoria alaskana belongs to a clade restricted to South-East Asia and north-west North America, and is so far known from south-east Alaska and the Sino-Himalayan Mountains. This highly variable species is most reliably recognized by its pendent, esorediate thallus, its production of fumarprotocetraric acid, and the combination of isotomic branching, abundant, whitish, predominantly fusiform pseudocyphellae, and sparse, short perpendicular side branches. Black emorient patches are lacking. Bryoria irwinii is endemic to north-west North America and is closely related to B. araucana from South America, B. poeltii from South-East Asia, as well as B. nadvornikiana and B. trichodes, both widely distributed in the Northern Hemisphere. It is a subpendent, esorediate species recognized by its predominantly anisotomic branching, olivaceous hue, black emorient patches, conspicuous pale brownish, fusiform pseudocyphellae, and numerous perpendicular, more or less basally constricted, side branches.

Molecular studies have revealed the presence of yet another species in the Bryoria bicolor complex in China, which confirms that the mountains of SE Asia to be an evolutionary centre for Bryoria sect. Divaricatae. The new species B. rigida is formally described. It is characterized by a stiff and coarse thallus, which contains fumarprotocetraric acid and often protocetraric acid as the main substances. A key to the divaricate species of Bryoria in the Himalayan region is provided.