The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module (“Hypha”) of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

The genus Lecidea Ach. sensu lato (sensu Zahlbruckner) includes almost 1200 species, out of which only 100 species represent Lecidea sensu stricto (sensu Hertel). The systematic position of the remaining species is mostly unsettled but anticipated to represent several unrelated lineages within Lecanoromycetes. This study attempts to elucidate the phylogenetic placement of members of this heterogeneous group of lichen-forming fungi and to improve the classification and phylogeny of Lecanoromycetes. Twenty-five taxa of Lecidea sensu lato and 22 putatively allied species were studied in a broad selection of 268 taxa, representing 48 families of Lecanoromycetes. Six loci, including four ribosomal and two protein-coding genes for 315- and 209-OTU datasets were subjected to maximum likelihood and Bayesian analyses. The resulting well supported phylogenetic relationships within Lecanoromycetes are in agreement with published phylogenies, but the addition of new taxa revealed putative rearrangements of several families (e.g. Catillariaceae, Lecanoraceae, Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae). As expected, species of Lecidea sensu lato and putatively related taxa are scattered within Lecanoromycetidae and beyond, with several species nested in Lecanoraceae and Pilocarpaceae and others placed outside currently recognized families in Lecanorales and orders in Lecanoromycetidae. The phylogenetic affiliations of Schaereria and Strangospora are outside Lecanoromycetidae, probably with Ostropomycetidae. All species referred to as Lecidea sensu stricto based on morphology (including the type species, Lecidea fuscoatra [L.] Ach.) form, with Porpidia species, a monophyletic group with high posterior probability outside Lecanorales, Peltigerales and Teloschistales, in Lecanoromycetidae, supporting the recognition of order Lecideales Vain. in this subclass. The genus name Lecidea must be redefined to apply only to Lecidea sensu stricto and to include at least some members of the genus Porpidia. Based on morphological and chemical similarities, as well as the phylogenetic relationship of Lecidea pullata sister to Frutidella caesioatra, the new combination Frutidella pullata is proposed here.

We studied the tree communities in primary forest and three different land use systems (forest gardens, ca. 5-year-old secondary forests, cacao plantations) at 900-1200 m elevation in the environs of Lore Lindu National Park, Central Sulawesi. The primary forests had ca. 150 tree species !10 cm diameter at breast height (dbh) per hectare, which is unusually high for forests at this elevation in southeast Asia. Basal area in the primary forest was 140 m 2 ha À1 , one of the highest values ever recorded in tropical forests worldwide. Tree species richness declined gradually from primary forest to forest gardens, secondary forests, and cacao plantations. This decline was paralleled by shifts in tree family composition, with Lauraceae, Meliaceae, and Euphorbiaceae being predominant in primary forests, Euphorbiaceae, Rubiaceae and Myristicaeae dominating in the forest gardens and Euphorbiaceae, Urticaceae, and Ulmaceae in the secondary forests. Cacao plantations were composed almost exclusively of cacao trees and two species of legume shade trees. Forest gardens further differed from primary forests by a much lower density of understorey trees, while secondary forests had fewer species of commercial interest. Comparative studies of birds and butterflies demonstrated parallel declines of species richness, showing the importance of trees in structuring tropical forest habitats and in providing resources.

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most published family phylogenies are incompletely sampled, generally contain massive polytomies, and/or show incongruent topologies between datasets. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life, or BrassiToL) based on nuclear (>1,000 genes, almost all 349 genera and 53 tribes) and plastome (60 genes, 79% of the genera, all tribes) data. We found cytonuclear discordance between nuclear and plastome-derived phylogenies, which is likely a result of rampant hybridisation among closely and more distantly related species, and highlight rogue taxa. To evaluate the impact of this rampant hybridisation on the nuclear phylogeny reconstruction, we performed four different sampling routines that increasingly removed variable data and likely paralogs. Our resulting cleaned subset of 297 nuclear genes revealed high support for the tribes, while support for the main lineages remained relatively low. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene icehouse origin of the family. Finally, we propose five new or re-established tribes, including the recognition of Arabidopsideae, a monotypic tribe to accommodate Arabidopsis. With a worldwide community of thousands of researchers working on this family, our new, densely sampled family phylogeny will be an indispensable tool to further highlight Brassicaceae as an excellent model family for studies on biodiversity and plant biology.

Runge, M. (2002). Site factors determining epiphytic lichen distribution in a dieback-affected spruce-fir forest on Whiteface Mountain, New York: stemflow chemistry. Retrieved from http://repository.upenn.edu/ees_papers/1Site factors determining epiphytic lichen distribution in a dieback-affected spruce-fir forest on Whiteface Mountain, New York: stemflow chemistry AbstractEpiphytic lichen diversity in a dieback-affected forest of red spruce (Picea rubens Sarg.) and balsam fir (Abies balsamea (L.) Mill.) on Whiteface Mountain, New York, U.S.A., was higher on dead compared with living trees and on fir compared with spruce. Diversity differed more between living and dead spruce than between living and dead fir. Cover of all lichen species that occurred on more than 50% of the sample trees, except for two species, decreased with increasing mean concentration of NO Cover of all lichen species that occurred on more than 50% of the sample trees, except for two species, decreased with increasing mean concentration of NO 3 -in stemflow. Concentrations of NO 3 -were higher on living spruce compared with dead spruce and with living and dead fir. The negative correlations between lichen cover and NO 3 -concentration may reflect either a decrease of lichen abundance caused by toxic effects of higher NO 3 -concentrations or a removal of NO 3 -from stemflow by epiphytic lichens. Experimental exposure of Hypogymnia physodes to NaNO 3 reduced chlorophyll concentrations. This result, together with estimations of lichen and needle biomass, indicates that a dependence of lichen cover on NO 3 -concentrations in stemflow may be the cause for the negative correlations. The sulphur concentration in stemflow did not affect lichen abundance on Whiteface Mountain. The manganese concentration in stemflow may have an effect on single species.Key words: forest dieback, manganese, nitrate assimilation, nitrate toxicity, precipitation chemistry, sulphur.Résumé : Dans une forêt d'épinette (Picea rubens Sarg.) et de sapin (Abies balsamea (L.) Mill.) de la Whiteface Mountain, New York, E.U., affectée par un dépérissement, la diversité des lichens épiphytes est plus importante sur les arbres morts que sur les arbres vivants, et sur le sapin que sur l'épinette. La diversité est plus marquée entre les épinet-tes vivantes et mortes qu'entre les sapins vivants et morts. La couverture par l'ensemble des espèces de lichen qui se retrouvent sur de 50 % des arbres échantillonnés, sauf pour deux espèces, diminue avec l'augmentation moyenne de la teneur en NO 3 -dans le lessivat de l'arbre. Les teneurs en NO 3 --sont plus élevées sur l'épinette vivante que sur l'épinette morte, et sur le sapin vivant que sur le sapin mort. Les corrélations négatives entre la couverture lichénique et la teneur en NO 3 -pourraient refléter soit une diminution de l'abondance des lichens causée par les effets toxiques des hautes teneurs en NO 3 -ou soit une élimination du NO 3 -du lessivat de l'arbre par les lichens épiphytes. Une exposition expérimentale de l'Hypogymnia phys...