Tracings of the north of Europe: Robert Chambers in search of the Ice Age.

Scottish publisher and naturalist Robert Chambers pursued an amateur interest in geology through much of his life. His early measurements of raised beaches in Scotland earned him membership in the Geological Society of London in 1844, a recognition much appreciated by the anonymous author of the 'scandalous' Vestiges published the same year. Although familiar with emerging ice age theories, Chambers remained with most British geologists a sceptic through the 1840s, even after a trip to the glaciers of the Alps in 1848, which nevertheless prepared him for the turning point, which came in 1849 during an extensive field trip in Norway and Sweden. Here a wealth of observations left him in no doubt that vast glaciers had formerly covered Scandinavia, polishing cliffs, scouring striations, depositing old moraines and erratic boulders. This also led him to a new glacial reading of the British landscape, and with the ardent conviction of a fresh convert he became one of the most vocal supporters of glacial theory in Britain in the 1850s at a time when the iceberg drift theory for boulder transport was still favoured by most prominent British geologists. While Chambers through his popular Chambers's Edinburgh Journal communicated his travels and ice age vision to a wide audience, and also pointed out ice age evidence on guided excursions around Edinburgh, he did not enter this new vision into subsequent editions of Vestiges, probably in order not to reveal its author. This paper explores Chambers's contributions to the ice age debate, his field trips and the genesis of his convictions, and evaluates his impact on the scientific debate.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

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.

Single origin and subsequent diversification of central Andean endemic Umbilicaria species.

We studied an Andean endemic group of species of the lichen-forming fungal genus Umbilicaria from the subalpine and low-alpine zone, with their biogeographic center in Bolivia and Peru. A number of species and varieties have been described from this element, but apparent instability in several morphological traits has made it difficult to precisely delimit taxa. Based on DNA sequences of nuclear ITS, LSU and mitochondrial SSU from extensive collections from Argentina, Bolivia, Chile, Colombia, Ecuador and Peru, we present here a molecular phylogenetic analysis of this Andean endemic element within genus Umbilicaria. All analyses (MP, ML and Bayesian) support a single origin for the element and a division into two major groups characterized by different apothecium types: the Umbilicaria dichroa group and U. calvescens group. Taxa U. krempelhuberi, U. peruviana and U. subcalvescens are nested withinn U. calvescens and are treated as conspecific with the latter species. The endemic element shares a most recent common ancestor with the Umbilicaria vellea group, which has a worldwide distribution and contains several asexually reproducing (sorediate) species. Independent reversals to sexual reproduction might explain the evolution of two types of apothecia in this monophyletic endemic lineage. A number of cosmopolitan, mostly high-alpine, species of Umbilicaria also present in the central Andes are related only remotely to the endemic element and do not exhibit speciation into endemics. Because the An-dean element dominates the Umbilicaria habitats of the low- and subalpine zones we propose that the founder colonized the Andes at a time when the mountains had not yet reached their current elevation while the high-alpine species arrived more recently.

Competition on the rocks: community growth and tessellation.

Crustose lichen communities on rocks exhibit fascinating spatial mosaics resembling political maps of nations or municipalities. Although the establishment and development of biological populations are important themes in ecology, our understanding of the formation of such patterns on the rocks is still in its infancy. Here, we present a novel model of the concurrent growth, establishment and interaction of lichens. We introduce an inverse technique based on Monte Carlo simulations to test our model on field samples of lichen communities. We derive an expression for the time needed for a community to cover a surface and predict the historical spatial dynamics of field samples. Lichens are frequently used for dating the time of exposure of rocks in glacial deposits, lake retreats or rock falls. We suggest our method as a way to improve the dating.

Early recruitment equals long-term relative abundance in an alpine saxicolous lichen guild.

The relative abundance within a guild of six species of the lichen-forming fungal genus Umbilicaria was studied during primary colonization of rock surfaces in a chronosequence of ca. 245 y in an alpine glacier foreland in southern Norway. Although the density of the guild grew from zero to more than 1000 thalli/m2 and the species differ substantially in life history traits such as initial growth rate, maximal size, maturation rate and propagule types, the relative abundance among the species remained almost unchanged through those years. The relative abundance of species is correlated with their life history parameters, such as initial growth rate and size-related maturation. The pattern of relative abundance was also similar in the saxicolous communities outside the foreland, which are potentially several thousand years old. Outside the foreland however the density of the guild is only 1/10 of that in the oldest parts of the foreland, due to soil formation and vegetation growth that have covered many of the low profile rock habitats. Thus the areas affected by the disturbance of glacier expansions and retreats provide temporary opportunities for large increases in the population sizes of the members of the saxicolous community. The observations support the view that pre-emption of habitat rather than competitive exclusion is common in saxicolous lichen communities and that "succession" consists in the addition but rarely the loss of species.

A higher-level phylogenetic classification of the Fungi.

A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.

A five-gene phylogeny of Pezizomycotina.

Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.

The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.

Competitive behaviour of umbilicate lichens - an experimental approach.

The lichens Lasallia pustulata and Umbilicaria spodochroa grow in dense monospecific or mixed populations on the coastal cliffs of southern Scandinavia. Attached to the substrate by only a thin central holdfast, their shield-shaped thalli compete for light and space for growth by overlapping each other. Matched pair experiments in the laboratory and field observations of interacting pairs show that different behavioural responses to precipitation tend to result in the margins of U. spodochroa overlapping those of L. pustulata within a few minutes. The behaviour is apparently caused by different capacities for water absorption in the upper and lower cortices of the species. An initial period of repeated encounter caused by thallus expansion and contraction during precipitation will be followed by a period in which U. spodochroa grows to overlap L. pustulata more and more. When the overlapping lichens are wet, flexible and photosynthetically active, the thallus above rests directly on the upper surface of the one below. Very little light is transmitted through thalli of U. spodochroa, and the shaded parts of L. pustulata are retarded in their growth and die off.

Sex, size, competition and escape-strategies of reproduction and dispersal in Lasallia pustulata (Umbilicariaceae, Ascomycetes).

The lichen Lasallia pustulata has a mixed strategy of asexual and sexual reproduction. Close-dispersed, asexual, symbiotic isidia are produced early, when the thalli are small. The asexual propagules are subsequently supplemented by far-dispersed, sexually generated ascospores when the thalli grow larger. This observation is consistent with evolutionary stable strategy (ESS) models of dispersal allocations in heterocarpic plants accordin to which the production of far-dispersed propagules should increase as clutch size and sibcompetition in the local habitat increases. The observation is also consistent with the "tangled bank" or "elbow room" hypothesis for the maintenance of sexuality, according to which sex, by generating genetic variation, represents an escape from competition in biologically saturated environments. Thus the advantage of sex is density dependent. L. pustulata grows in densely packed populations where intraspecific competition results in self-thining and the development of distinct sizehierarchies.