The assembled Physcomitrella patens genome has been released. This provides a unique opportunity to identify and characterize new genes, and to compare moss genes with other plant genes from previously released plant genomes. Aldehyde dehydrogenases (ALDHs) comprise a protein superfamily of NAD(P) -dependent enzymes [EC 1.2.1] found in bacteria, animals and green plants capable of oxidizing a variety of aromatic and aliphatic aldehydes. ALDHs are key enzymes of abiotic stress-tolerance in a variety of organisms. In bryophytes, ALDHs are postulated to play a role in vegetative desiccation-tolerance. Using recently available genomic DNA sequence data, we have identified members of the ALDH gene superfamily in the marine picoeukaryote Ostreococcus tauri, the unicellular green algae Chlamydomonas reinhardtii and the moss Physcomitrella patens. The Arabidopsis thaliana genome has been shown to contain 14 unique ALDH sequences encoding members of nine ALDH protein families. The O. tauri genome contains six unique ALDH sequences encoding members of six ALDH protein families. The C. reinhardtii genome contains eight unique ALDH sequences encoding members of seven ALDH protein families. The P. patens genome contains 20 unique ALDH sequences encoding members of ten ALDH protein families. These three genomes encode members of ten previously identified protein families (ALDH2, ALDH3, ALDH5, ALDH6, ALDH7, ALDH10, ALDH11, ALDH12, ALDH21 and ALDH22) and two novel protein families (ALDH23 and ALDH24). We analyzed a sequence alignment of ALDH deduced amino acid sequences among plants using neighbor-joining and maximum parsimony methods. These analyses demonstrate that 1) at least eight ALDH protein families, as represented in the O. tauri and/or C. reinhardtii genomes were present prior to the evolution of land plants and each of these families have been maintained throughout land plant evolution, 2) novel ALDH families of as yet unknown function have evolved in several lineages of land plants including the mosses and flowering plants and 3) the moss P. patens exhibits a highly expanded set of sequences in three families, ALDH3, ALDH5 and ALDH11.

Bryophytes constitute important components of many ecosystems. However, the methods used to measure their dominance have remained unchanged during the last 25 years. Herein we compare accuracy, efficiency and objectivity among three methods used to estimate bryophyte cover: Braun-Blanquet cover classes, grid percentage and digital image processing. Using these methods, two observers determined bryophyte cover on 30 clay tiles planted with Neckeropsis disticha. Accuracy among methods was estimated by relating the cover values with the dry weight. Efficiency was estimated using the relation between time and data variability. Objectivity was estimated by comparing the variability between observers. The digital method resulted in less time in the field (F  =  272, p < 0.001) and lower variation among data (F =  0.55, p  =  0.02) than from the other two methods. Our results showed that the digital processing method was more reliable as it minimized observer effect in the cover values while providing higher efficiency in the field. The method is especially useful in monitoring studies that use repeated measurements because it helps to detect small variations in bryophyte cover. This method is particularly useful to improve the analysis in communities with low bryophyte cover, such as tropical epiphylls.

The lichen vegetation forming biological soil crusts is described for the first time for a semi-desert area of the Republic of South Africa (Knersvlakte, Namaqualand). Thirty-five terricolous lichen taxa were recorded. Fifty-two percent of the lichens are endemic to Namaqualand according to current knowledge. Squamulose and crustose lichens were the most common (over 60% of taxa) and most contained green algal photobionts. Three main communities were distinguished: 1) a widespread community composed by Collema coccophorum, Psora aff. crenata, Placidium tenellum and P. squamulosum; 2) a rare community characterized by foliose lichens belonging to Xanthoparmelia, Neofuscelia and Paraparmelia; and 3) a rare, crustose community formed by Caloplaca sp. (“C. sp. 1”), Toninia sp. (“T. sp. 1”), T. ruginosa and Buellia sp. (“B. sp. 2”). The lichen taxa and vegetation of the study area are unique and are threatened by land management practices and changing climate.

The Santa Monica Mountains, adjacent to the Pacific Ocean just west of Los Angeles, California, have low elevation, high relief and a Mediterranean climate. To date 122 species of bryophytes have been found, especially in the moist drainages. Species that were common (about half of the 122) were compared in terms of microhabitat variables (substrate softness, moisture, slope and shadiness) and in how they distinguished mesosites (varying vascular vegetation types, elevation, parent rock type, distance to the coast and insolation). This constitutes a descriptive comparison of the ecologies of the species in the flora. Acrocarpous mosses, pleurocarpous mosses and liverworts tended as groups to differ in some habitat preferences. Only a few bryophyte species were strong indicators of vascular vegetation type. The diversity of sampled mesosites was to a great extent explicable as a scaling-up of the variety of microsites that each contained, thereby allowing for a diversity of bryophytes in a biome that might generally be characterized as inhospitable.

Here we incorporate molecular sequence data (ITS, IGS, mtLSU, RPB2) to test the hypothesis of strict clonality in the lichen-forming fungus Thamnolia vermicularis. Recombination was rejected by most methods, though, a small number did detect recombination. We intepret these analyses as mostly supporting the hypothesis of strict clonality. We were unable to determine if the recombination detected was the result of rare recombination events in recent time, historic recombination, or false positives by certain methods. In addition, we investigated whether chemotypes in T. vermicularis formed monophyletic groups. Molecular sequence data suggest that the two chemotypes do not form well-supported, monophyletic lineages. Chemotypes were found with identical haplotypes and some populations were composed of more than one haplotype. Our data suggest that there is not a simple dichotomy between chemotypes in T. vermicularis, which may be due to rare or historic recombination, repeated chemotype evolution or incomplete lineage sorting.

In this study, the occurrence of Dermatocarpon meiophyllizum, Leptogium rivale and Peltigera hydrothyria on federal land in western Oregon and Washington, and northern California is documented using a large-scale random sampling approach amplified by historical site data, frequency, distribution and habitat “preferences,” including water quality, forest age and land use allocations. A total of 256 sites were surveyed, of which 216 were randomly selected. All three species were distributed throughout the study area in all three states, and mostly in interior mountain ranges. Only L. rivale was widespread, and both D. meiophyllizum and P. hydrothyria appear to be rare in the region but can become locally common in some watersheds. All three lichens probably benefit from older streamside forests, but association with forest age was inconclusive at the watershed level. Federal protective land use allocations and Aquatic Conservation Strategy components appear to play a minor role in protecting existing populations for the three aquatic lichens. Climate factors appear to be of major importance to habitat suitability for the three aquatic lichens. Results from this study suggest the following habitat summaries for the three aquatic lichens. Higher elevation, exposed streams with large rocks or bedrock appear to be important habitat for D. meiophyllizum. This lichen was also often found above the stream water level. Leptogium rivale was found most frequently in shallow, partially shaded streams and submerged or just above the water level. For P. hydrothyria, this study suggests that cool, partially shaded small mountain streams are important habitat; however, this only appears to be habitat characteristics for this lichen from southern Washington and southward in the study area. In Washington's North Cascades and in to British Columbia, P. hydrothyria is often observed in colder, higher elevation exposed sites. Upper 95% confidence interval values for stream sites suggests good water quality across the region: dissolved oxygen  =  9.60 mg^−l, conductivity  =  78 µS/cm, pH  =  7.51, nitrogen  =  0.07 mg^−l and phosphorus  =  0.024 mg^−l. Benthic diatom-based indices suggest that these aquatic lichens are subject to siltation and high flow stream scouring. Results from this study can be used to guide management in the face of global climate change and research needs are discussed.

Through laboratory experiments I showed that ants (Lasius platythorax) may play the role of a passive vector for dispersing asexual propagules (gemmae) of Aulacomnium androgynum. Both species are commonly found on dead wood in Swedish forests. Two experiments were performed: one in which ants were allowed to run over a moss tuft and another where gemmae were attached manually to the ants. The first experiment clearly showed that gemmae adhered to the body of the ants as they moved freely over the moss tuft. In total, gemmae adhered to 33% of the ants within less than 2 minutes of exposure to the moss. The second experiment was conducted to determine how long the gemmae stayed adhered, revealing that under laboratory conditions half the gemmae stayed attached for approximately 4 hours before falling off. The results indicate that dispersal of asexual species may be mediated by animal vectors, thereby explaining why seemingly dispersal-limited species may in fact be target-oriented dispersers through animal vector assistance.

We explored molecular data in order to establish the phylogenetic relationships of the Thuidiaceae. We sampled nine genera and 13 species of Thuidiaceae, and included representatives of 15 families that have been considered related to Thuidiaceae at some point. We used two chloroplast codifier genes (rbcL and rps4) and the rps4-trnS intergenic spacer. Our combined parsimony analyses retrieved a clade containing 12 exemplars of Thuidiaceae representing eight genera (Thuidium, Thuidiopsis, Pelekium, Aequatoriella, Abietinella, Rauiella, Haplocladium and Actinothuidium) but with the inclusion of Leskea polycarpa and exclusion of Hylocomiopsis making the Thuidiaceae non-monophyletic as currently defined, and the Leskeaceae polyphyletic. The name Thuidiaceae is retained for the informal “thuidioid” group of taxa. The Rhytidiaceae (Rhytidium rugosum) was found sister to the clade of Thuidiaceae s.lat and Leskea polycarpa. The rps4-trnS spacer added characters that improved resolution and may be of value for similar studies at family level in other pleurocarpous mosses.

Hypogymnia minilobata is described as a new species of lichenized fungi from the coast of southern California and the Channel Islands. Previously lumped under H. occidentalis, H. minilobata is distinguished from that species by its small size, consistently appressed growth form, slightly smaller and more elongate spores, and distinct ITS and GPD sequences. So far H. minilobata is known from coastal scrub and woodlands, and is especially common in the Los Osos and Baywood areas of San Luis Obispo County, California.

Ten species of lichenicolous fungi on Collemataceae in the Iberian Peninsula are recorded. A new species, Pronectria pilosa, on Collema furfuraceum is proposed and three new records from the Iberian Peninsula are indicated, Endococcus pseudocarpus, Nectria brutia and Toninia leptogii. The known distribution of several treated species is enlarged notably.

Recent surveys of the inland rain forests of British Columbia and adjacent regions have brought to light an unexpectedly rich epiphytic lichen flora, including several species apparently new to science. In the first of a series of papers, we describe eight species discovered during these surveys as new: Absconditella amabilis T. Sprib. (Ostropales), Bacidina contecta S. Ekman & T. Sprib., Biatora aureolepra T. Sprib. & Tønsberg, Biatora ligni-mollis T. Sprib. & Printzen (all Lecanorales), Collema coniophilum Goward (Peltigerales), Pertusaria diluta C. Björk, G. Thor & T. Wheeler (Pertusariales), Schaereria brunnea C. Björk, T. Sprib. & T. Wheeler (Ostropomycetidae incertae sedis) and Scoliciosporum abietinum T. Sprib. (Lecanorales). We also call attention to a ninth species, Bacidina sp. A, a poorly known and possibly undescribed colonizer of moribund cyanolichens. A majority of the above species appear to be confined to old-growth forests, while two (Biatora ligni-mollis and Schaereria brunnea) are currently known only from “antique” forests older than about 500 years. Many additional undescribed epiphytic lichens are known from inland rain forests, underscoring the need for further baseline biodiversity research in light of its ongoing disappearance as a result of resource extraction. In addition to the eight new species, we report Absconditella celata as new to North America, Absconditella lignicola as new to Canada and Montana, Bacidina chloroticula as new to British Columbia and Gyalideopsis piceicola as new to Montana.

In recent years, Alectoria in the Acharian sense has been shown to contain several discordant elements, now recognized as separate genera, including Bryoria, Nodobryoria, Pseudephebe and Sulcaria. Here we describe a new segregate genus Gowardia. At present, Gowardia contains two species: G. arctica sp. nov. and G. nigricans (Ach.) comb. nov. (syn. Alectoria nigricans). In addition to several morphological and chemical characters, our decision to recognize Gowardia as distinct from Alectoria is supported by phylogenetic analysis based on combined ITS and GAPDH data. Gowardia arctica is known from Arctic regions of Canada and Russia, while G. nigricans has a wider range. Alectoria vancouverensis is documented from Finland, which is the first report of the species outside the Pacific coast of North America.

Acarospora nicolai is revised and a lectotype designated. Acarospora caesiofusca is made a synonym of A. nicolai and a lectotype is designated. Acarospora nicolai is a pruinose brown crustose species containing gyrophoric acid and occurs in Mexico (Puebla) and the United States (Kansas, Oklahoma, Texas) on sandstone.

Four new taxa of the lichenized, foliicolous ascomycete genus Chroodiscus are described from Southeast Asia: Chroodiscus defectus Papong & Lücking, Ch. homchantarae Papong & Lücking, Ch. khaolungensis Papong & Lücking and Ch. khaosokensis Papong & Lücking. Chroodiscus argillaceus (Müll. Arg.) Lücking & Papong ( = Chroodiscus parvisporus Kalb & Lücking) is introduced as new combination. The genus as currently circumscribed now includes 14 taxa, which are keyed out here. A short discussion on the putative evolution and taxonomic treatment of species pairs in this genus is included.

Tortella bambergeri (Schimp.) Broth. is reported for the first time from northern and central-eastern Spain in the Iberian Peninsula. Diagnostic characters and differentiation from other closely related Iberian Tortella taxa are discussed. Furthermore, a map of the currently known distribution of T. bambergeri in Spain, illustrations of the species and an updated key to Iberian Tortella are provided.

Bryum cyclophyllum is reported from two new localities in the Iberian Peninsula and added to the Portuguese bryophyte flora. The habitat and worldwide distribution of this species are discussed: it shows a mainly Arctic-boreal distribution, widespread but not frequent; it is considered a rare or threatened moss in several European regions and with relict occurrences in more southern areas of North America. The ecology and distribution probably reflect migratory events during the last glacial period of the Pleistocene.

In developing a revision of Syntrichia in the Neotropics, seven names are newly synonymized based on morphological data. Syntrichia ciliata, S. prostrata, S. ruralis var. spiralis and S. viridula are considered to be conspecific with S. andicola, S. serrulata, S. princeps and S. lacerifolia, respectively. Tortula goudotii var. boliviana is transferred into Syntrichia and synonymized with S. andicola. Syntrichia bipedicellata and S. linguifolia are newly synonymized with S. fragilis. Lectotypes for three names currently included in Syntrichia are designated here.

Pohlia flexuosa is reported from a single California site as new for the North American moss flora. This species is otherwise found in central and eastern Asia, where it is one of the most common gemmiferous Pohlia species, and in western Europe. A key is provided for the six gemmiferous species of Pohlia currently known from California.

A new species of Leskeaceae, Pseudoleskea tribulosa, is described and illustrated from limestone outcrops in subalpine coniferous forests of Yosemite National Park in the central Sierra Nevada of California.

Pseudocrossidium linearifolium (Barbula subrevoluta var. linearifolia Müll. Hal.) is a new combination and status proposed for a neglected South American taxon. This distinctive moss has been known only from the type locality in the mountains around Córdoba, Argentina. It is newly reported for the moss floras of Ecuador and Bolivia. The species is described, lectotypified, illustrated and its distribution is mapped. Diagnostic characters and distinction from some closely related South American taxa, with which it may be confused, are discussed. Pseudocrossidium perrevolutum is reduced to the synonymy of P. replicatum.

A new Orthotrichum species, O. karoo, is described. The moss has a gametophyte similar to that of O. diaphanum, from which it mainly differs in its peristome lacking exostome teeth. It is known from three localities in western South Africa, and from one more in southern Namibia. In all these localities it was found growing on shrubs and trees, rarely on rocks, in succulent karoo and related types of vegetation.

Diagnosis and illustrations are given for Braunia squarrulosa. Relevant to the taxonomy of the species, three names needed lectotypification. A Schlechtendahl specimen at bm is the lectotype for B. squarrulosa. A collection by Ehrenberg (bm) is the lectotype for B. sphaerocarpa. The lectotype for B. liebmanniana is a Liebmann specimen located at bm. The last two names are retained as synonyms of B. squarrulosa. The worldwide distribution of the species is documented in Mexico, Guatemala, Honduras, Costa Rica and Panama.

The Orthotrichum strangulatum complex in eastern and interior North America has three species: O. strangulatum P. Beauv., O. parvulum Mitt. and O. lescurii Austin. All three form blackish green, rigid tufts and are restricted to calcareous substrates. Orthotrichum strangulatum has oblong-lanceolate leaves with partially thickened laminae and multistratose, recurved margins. Its oblong-elongate capsules have 16, reticulate-papillose, free exostome teeth. Orthotrichum lescurii has a more narrowly lanceolate leaf shape than O. strangulatum with unistratose laminae and revolute margins. Its ovate capsules have eight pairs of finely papillose exostome teeth. Orthotrichum parvulum has oblong-lanceolate leaves with unistratose laminae and plane leaf margins. It has oblong capsules with 16, reticulate-papillose, free exostome teeth. Orthotrichum peckii Sull. & Lesq. in Austin, O. porteri Sull. & Lesq. in Austin, and O. strangulatum var. missouricum Holz. ex Grout are synonyms of O. strangulatum. Orthotrichum strangulatum var. missouricum is lectotypified with a specimen from Holzinger's herbarium in minn.