Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various ‘relaxed clock’ scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen–forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non–lichenized Ascomycota, many of which had not been previously dated.

The high richness of epiphytes in moist tropical montane forests is continuously decreasing due to deforestation and habitat loss. Lichens and bryophytes are important components of epiphyte diversity on trunk bases and play an important role in the water balance and nutrient cycling of tropical montane forests. As lichens and bryophytes are very sensitive to microclimatic changes, we hypothesized that their species richness and composition would change with forest alteration. We also expected their response patterns to be different given the capability of lichens to photosynthesize using water vapour. In this study, we assessed the richness and composition of epiphytes (lichens and bryophytes) on the trunk bases of 240 trees in primary and secondary forests of southern Ecuador. We found that diversity was higher in primary forests and lower in monospecific secondary forest stands. Total diversity was negatively affected by habitat loss and by the reduction of canopy cover for bryophytes. Shade epiphytes were replaced by sun epiphytes in open secondary forests. We conclude that lichen and bryophyte diversity of tropical montane forests are negatively affected by the removal of large trees and canopy disruption. The different species compositions of primary and secondary forests and the high number of species exclusive to primary forests indicate that secondary forests are of limited importance in compensating for the loss of non-vascular epiphyte species associated with primary forests.

Although the high degree of non-monophyly and parallel evolution has long been acknowledged within the mazaediate Caliciaceae (Lecanoromycetes, Ascomycota), a natural re-classification of the group has not yet been accomplished. Here we constructed a multigene phylogeny of the Caliciaceae-Physciaceae clade in order to resolve the detailed relationships within the group, to propose a revised classification, and to perform a dating study. The few characters present in the available fossil and the complex character evolution of the group affects the interpretation of morphological traits and thus influences the assignment of the fossil to specific nodes in the phylogeny, when divergence time analyses are carried out. Alternative fossil assignments resulted in very different time estimates and the comparison with the analysis based on a secondary calibration demonstrates that the most likely placement of the fossil is close to a terminal node rather than a basal placement in the Calicium clade. Our dating analysis show two successive events giving rise to main clades of mazaediate taxa within the Caliciaceae, in the Upper-Lower Cretaceous boundary and in the Paleocene. As a result of this study, Cyphelium is synonymized with Calicium, Acolium is resurrected, and the new genera Allocalicium and Pseudothelomma are described. Twelve new combinations are proposed: Acolium karelicum, Acolium marcianum, Allocalicium adaequatum, Calicium carolinianum, Calicium lecideinum, Calicium lucidum, Calicium notarisii, Calicium pinicola, Calicium trachyliodes, Pseudothelomma occidentale, Pseudothelomma ocellatum and Thelomma brunneum. A key for the mazaedium-producing Caliciaceae is included.