In recent years, the genus Bryoria (Parmeliaceae, Lecanoromycetes) has been the subject of considerable phylogenetic scrutiny. Here we used information on six gene regions, three nuclear protein-coding markers (Mcm7, GAPDH and Tsr1), two nuclear ribosomal markers (ITS and IGS) and a partial mitochondrial small subunit (mtSSU), to examine infrageneric relationships in the genus and to assess species delimitation in the Bryoria bicolor/B. tenuis group in section Divaricatae. For this purpose, phylogenetic analyses and several of the available algorithms for species delimitation (ASAP, GMYC single, GMYC multiple and bPTP) were employed. We also estimated divergence times for the genus using *BEAST. Our phylogenetic analyses based on the combined data set of six gene loci support the monophyly of sections Americanae, Divaricatae and Implexae, while section Bryoria is polyphyletic and groups in two clades. Species from Bryoria clade 1 are placed in an emended section Americanae. Our study reveals that section Divaricatae is young (c. 5 My) and is undergoing diversification, especially in South-East Asia and western North America. Separate phylogenetic analyses of section Divaricatae using ITS produced a topology congruent with the current species concepts. However, the remaining gene regions produced poorly resolved phylogenetic trees and the different species delimitation methods also generated highly inconsistent results, congruent with other studies that highlight the difficulty of species delimitation in groups with recent and rapid radiation. Based on our results, we describe the new species B. ahtiana sp. nov., characterized by its bicolorous, caespitose, widely divergent thallus, conspicuously thickening main stems, well-developed secondary branches, and rather sparse third-order branchlets. Another new lineage, referred to here as B. tenuis s. lat., is restricted to western North America and may represent a new species recently diverged from B. tenuis s. str., though further work is needed.

Hair lichens are distinctive for their capillary growth and typically arboreal occurrence, especially in temperate and boreal forests. They consist of two morphogroups based on cortical pigments: a brown-black group with fungal melanin and a pale yellow-green group with usnic acid. Here we test the hypothesis that these morphogroups are ecologically distinct and thus appropriately regarded as functional groups. We examine their respective horizontal occurrence in the lower canopy of 60-year-old conifer forests on a 250 m tall volcanic cone in south-central British Columbia. Trees on open south-facing slopes and near the summit were found to support mainly melanic hair lichens (Bryoria and Nodobryoria), whereas more densely spaced trees on north-facing slopes and at the base had higher cover values of usnic lichens (especially Alectoria sarmentosa and Ramalina thrausta). The cover of melanic hair lichens was strongly correlated with canopy openness but not for their usnic counterparts. We suggest that investment in light-absorbing melanic pigments is an extreme form of specialization for high light, favouring persistence in dry, sun-exposed canopies of otherwise cool forests. By contrast, the cortex of pendent usnic hair lichens appears to facilitate optimum light transmission to underlying photobionts in shaded sites, though at the cost of sensitivity to light in open habitats, especially in rather dry regions.

Maintenance of biodiversity in managed forested landscapes requires detailed knowledge of the ecological requirements of specialist organisms linked to key microhabitats. Here we examine the relationship of 37 lichenized and unlichenized epiphytic calicioid species to stand age and substratum type in seven pairs of mid-seral (70–165 y) and old (220–470 y) forest stands in humid east-central British Columbia. Based on our inventory of eight host tree species, total calicioid diversity and mean species richness are highest in old stands, with 12 species not detected and nine additional species much less frequent in mid-seral stands. Thuja plicata supports by far the highest level of total calicioid diversity, with 31 of 37 species; mostly associated with very old trees. Owing primarily to the late recruitment of lignicolous calicioids, stand-level calicioid richness continues to increase into the 5th century after stand initiation. Our study thus has two major findings pertinent to the maintenance of forest biodiversity in managed forests: first, stand-level calicioid richness increases slightly for at least three centuries past the acquisition of old-growth status; second, remnant trees and snags carried forward into mid-seral, regenerating stands enhance overall calicioid species richness. These results suggest that very old old-growth (= ‘antique’) forests might play an important role in the long-term maintenance of calicioid species richness, further suggesting that the standard practice of lumping all forests above a set age into a single old-growth category is not ecologically tenable for all taxonomic groups.

A new cyanolichen, Peltigera islandica sp. nov. in the section Peltigera (‘P. canina group’) is described from Iceland. This species is similar in general appearance to P. rufescens and P. membranacea, but may be recognized by its downturned lobe tips and narrow lobes, respectively. Most thalli are bright emerald green in colour when moist, although a dark khaki green colourmorph is also documented. Monophyly of P. islandica s. lat. (i.e. including P. sp. A sensu O’Brien et al., from Canada) is significantly supported based on ITS sequences and corroborated by molecular synapomorphy (absence of the ITS1 hypervariable region). Analysis of the rbcLX locus indicates the cyanobiont of P. islandica (Nostoc sp.) comprises strains belonging to a pool of Icelandic genotypes, some of which are present in other Peltigera species, including P. “neorufescens”, another taxon new to Iceland collected during this study. Association with photobionts that are shared by other local species suggests P. islandica may be well established in Iceland, but a review of herbarium collections as well as broader field surveys are needed to better characterize its geographical distribution.

Western North America is the global centre of diversity for Letharia, a distinctive and cryptically diverse genus of lichenized fungi belonging to the Parmeliaceae. The genus is characterized by a shrubby, fruticose habit and presence of vulpinic acid. Previous studies using multiple fungal nuclear loci revealed the existence of two distinct species-level lineages within the traditional concept of L. vulpina and four such lineages within L. columbiana. Here we use molecular sequence data in an attempt to settle long-standing taxonomic issues in the genus. Our results confirm the widespread existence within L. vulpina s. lat. of two distinct species-level groups, each forming a mutually exclusive partnership with a separate algal clade within Trebouxia jamesii s. lat. Accordingly, we formally describe the segregate species L. lupina sp. nov. Our results also support the evolutionary independence of four candidate species previously circumscribed from L. columbiana s. lat. One of these lineages, L. ‘gracilis’, has already received species recognition as L. gracilis, while a second, L. ‘lucida’, is epitypified here against L. columbiana s. str. Based on results from species delimitation analyses under the multispecies coalescent model, the two remaining lineages, L. ‘barbata’ and L. ‘rugosa’, also warrant formal taxonomic recognition; however, we refrain from describing these species pending additional studies of diagnostic characters, ecological preference, and distributions.

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.

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.

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.

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.

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.

Nephroma occultum is a COSEWIC listed cyanolichen of “Special Concern”. It is endemic to old-growth cedar-hemlock forests in western North America. This is the first study to place N. occultum into a phylogenetic framework using nucleotide sequence and secondary structure data. It also addresses the phylogenetic relationship between N. occultum and N. arcticum. Analysis of fungal Internal Transcribed Spacer (ITS) ribosomal DNA (rDNA) produced four major clades. The cyanobacterial transfer RNALeu intron (tRNALeu) from N. occultum was separated from that of N. isidiosum and fell between the Eurasian and North American epiphytic taxa. Examination of length and complexity of the folded secondary structures revealed different trends in the ITS1 and ITS2 rRNA regions. Even though N. occultum is endemic to North America, it seems more closely related to South American temperate rainforest species than to the sympatric N. arcticum. Nephroma occultum is alone among the studied species of Peltigerales in having an exceptionally long ITS1 region, and a different tRNALeu intron DNA sequence of the photobiont suggesting association with a unique genotype of Nostoc. It may be argued that the fitness of N. occultum may be influenced by the complex ITS1 RNA structure, a unique photobiont genotype undergoing a genetic bottleneck, no sexual reproduction to generate variation, and the inability to associate with different photobionts to adapt to changing habitats.