We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.

Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that these inconsistencies stem from various causes, we reassessed the systematic placement of the most important fungal fossil, Paleopyrenomycites, and recalibrated internally unconstrained, published molecular clock trees by applying uniform calibration points. As a result the origin of fungi was re-estimated at between 760 million and 1.06 billion y ago and the origin of the Ascomycota at 500-650 million y ago. These dates are much more consistent than previous estimates, even if based on the same phylogenies and molecular clock trees, and they are also much better in line with the fossil record of fungi and plants and the ecological interdependence between filamentous fungi and land plants. Our results do not provide evidence to suggest the existence of ancient protolichens as an alternative to explain the ecology of early terrestrial fungi in the absence of land plants.

No abstract

We analysed patterns of habitat and microhabitat preferences of 19 families (comprising 135 genera and 950 species) of crustose, corticolous lichens in Costa Rica (Arthoniaceae, Arthopyreniaceae, Coenogoniaceae, Graphidaceae, Lecanoraceae, Letrouitiaceae, Monoblastiaceae, Pertusariaceae, Physciaceae, Pilocarpaceae, Porinaceae, Pyrenulaceae, Ramalinaceae, Roccellaceae, Strigulaceae, Teloschistaceae, Thelenellaceae, Thelotremataceae, Trypetheliaceae), in order to test whether Thelotremataceae are suitable predictors of undisturbed tropical rain forest and can be used as bioindicators of ecological continuity. The dataset consisted of 12,215 specimen samples and six environmental parameters recorded for each sample (altitude, degree of seasonality, vegetation type, disturbance level, substrate nature, light exposure), which were analysed by a multivariate approach using principal component analysis (PCA). The analysis showed that three of the 19 families, Letrouitiaceae, Porinaceae, and Thelotremataceae, showed significant preferences for undisturbed primary to old growth secondary forest, fully shaded to semiexposed microhabitats, and the bark of mature tree trunks, parameters assumed to be correlated with ecological continuity of closed rain forest habitats. Thelotremataceae had broader altitudinal range than Letrouitiaceae and Porinaceae and significantly higher genus and species diversity (16 genera, 130 species) compared to Porinaceae (4 genera, 40 species) and Letrouitiaceae (1 genus, 5 species). Our results support the hypothesis that Thelotremataceae perform best as predictors of undisturbed dry and lowland to montane