The relative ages of ectomycorrhizal mushrooms and their plant hosts estimated using Bayesian relaxed molecular clock analyses

Background Ectomycorrhizae (ECM) are symbioses formed by polyphyletic assemblages of fungi (mostly Agaricomycetes) and plants (mostly Pinaceae and angiosperms in the rosid clade). Efforts to reconstruct the evolution of the ECM habit in Agaricomycetes have yielded vastly different results, ranging from scenarios with many relatively recent origins of the symbiosis and no reversals to the free-living condition; a single ancient origin of ECM and many subsequent transitions to the free-living condition; or multiple gains and losses of the association. To test the plausibility of these scenarios, we performed Bayesian relaxed molecular clock analyses including fungi, plants, and other eukaryotes, based on the principle that a symbiosis cannot evolve prior to the origin of both partners. As we were primarily interested in the relative ages of the plants and fungi, we did not attempt to calibrate the molecular clock using the very limited fossil record of Agaricomycetes. Results Topologically constrained and unconstrained analyses suggest that the root node of the Agaricomycetes is much older than either the rosids or Pinaceae. The Agaricomycetidae, a large clade containing the Agaricales and Boletales (collectively representing 70% of Agaricomycetes), is also significantly older than the rosids. The relative age of Agaricomycetidae and Pinaceae, however, is sensitive to tree topology, and the inclusion or exclusion of the gnetophyte Welwitschia mirabilis. Conclusion The ancestor of the Agaricomycetes could not have been an ECM species because it existed long before any of its potential hosts. Within more derived clades of Agaricomycetes, there have been at least eight independent origins of ECM associations involving angiosperms, and at least six to eight origins of associations with gymnosperms. The first ECM symbioses may have involved Pinaceae, which are older than rosids, but several major clades of Agaricomycetes, such as the Boletales and Russulales, are young enough to have been plesiomorphically associated with either rosids or Pinaceae, suggesting that some contemporary ECM partnerships could be of very ancient origin

Phylogenetic Relationships Among Species of Phillipsia Inferred from Molecular and Morphological Data

The internal transcribed spacers (ITS) of the nuclear ribosomal DNA have been sequenced from 29 collections of Phillipsia, mainly from the New World. The P domingensis complex, collections with a range of colors but otherwise referable to P domingensis s.l. based on spore ornamentation, were studied. Three distinctive species of Phillipsia also were included. The sequences were analysed to infer phylogenetic relationships within Phillipnsia, using parsimony. Morphological features were studied separately, and then evaluated in the context of the ITS phylogeny. Four distinct rDNA lineages, supported by ascospore ornamentation, were identified: the P. crispata the P. domingensis, the P. olivacea and the P. carnicolor lineages. SEM photographs of the ascospores are presented. Phillipsia lutea and another yellow form were nested within the P. dominagensis complex, of those with reddish hymenial colors. Color has been emphasized in taxonomy of Phillipsia, but these results suggest that individuals with strikingly different coloration may be closely related. Levels of ITS sequence divergence in the P. domingensis lineage were low. Based on these data, and morphology as studied thus far; there is no justification for recognizing segregate species within the P. domingensis complex. The Old World collections of the P. domingensis complex were nested within the New World collections, which implies that the P. domingensis lineage is geographically widespread. Phillipsia rugospora is plated in synonymy with P. olivacea and a detailed description of this taxon is given. A lectotype is designated for P. olivacea.Organismic and Evolutionary Biolog

Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi.

Fungi that decay wood have characteristic associations with certain tree species, but the mechanistic bases for these associations are poorly understood. We studied substrate-specific gene expression and RNA editing in six species of wood-decaying fungi from the 'Antrodia clade' (Polyporales, Agaricomycetes) on three different wood substrates (pine, spruce, and aspen) in submerged cultures. We identified dozens to hundreds of substrate-biased genes (i.e., genes that are significantly upregulated in one substrate relative to the other two substrates) in each species, and these biased genes are correlated with their host ranges. Evolution of substrate-biased genes is associated with gene family expansion, gain and loss of genes, and variation in cis- and trans- regulatory elements, rather than changes in protein coding sequences. We also demonstrated widespread RNA editing events in the Antrodia clade, which differ from those observed in the Ascomycota in their distribution, substitution types, and the genomic environment. Moreover, we found that substrates could affect editing positions and frequency, including editing events occurring in mRNA transcribed from wood-decay-related genes. This work shows the extent to which gene expression and RNA editing differ among species and substrates, and provides clues into mechanisms by which wood-decaying fungi may adapt to different hosts

Evolutionary biology for the 21st century

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.Molecular and Cellular BiologyOrganismic and Evolutionary Biolog

Transcriptomics of Temporal- versus Substrate-Specific Wood Decay in the Brown-Rot Fungus Fibroporia radiculosa

Brown-rot fungi lack many enzymes associated with complete wood degradation, such as lignin-attacking peroxidases, and have developed alternative mechanisms for rapid wood breakdown. To identify the effects of culture conditions and wood substrates on gene expression, we grew Fibroporia radiculosa in submerged cultures containing Wiley milled wood (5 days) and solid wood wafers (30 days), using aspen, pine, and spruce as a substrate

Climate, decay, and the death of the coal forests

After death, most of the biological carbon in organisms (Corg) is returned to the atmosphere as CO2 through the respiration of decomposers and detritivores or by combustion. However, the balance between these processes is not perfect, and when productivity exceeds decomposition, carbon sequestration results. An unparalleled interval of carbon sequestration in Earth’s history occurred during the Late Carboniferous (Pennsylvanian) and Permian Periods (ca. 323–252 Ma), when arborescent vascular plants related to living club mosses (Lycophytes), ferns (Monilophytes), horsetails (Equisetophytes) and seed plants (Spermatophytes) formed extensive forests in coastal wetlands. On their death, these plants became buried in sediments, where they transformed into peat, lignite, and, finally, coal

Polypores and genus concepts in Phanerochaetaceae (Polyporales, Basidiomycota)

Correction DOI:10.3897/mycokeys.19.11562We explored whether DNA-phylogeny-based and morphology-based genus concepts can be reconciled in the basidiomycete family Phanerochaetaceae. Our results show that macromorphology of fruiting bodies and hymenophore construction do not reflect monophyletic groups. However, by integrating micromorphology and re-defining genera, harmonization of DNA phylogeny and morphological genus concepts is possible in most cases. In the case of one genus (Phlebiopsis), our genetic markers could not resolve genus limits satisfactorily and a clear morphological definition could not be identified. We combine extended species sampling, microscopic studies of fruiting bodies and phylogenetic analyses of ITS, nLSU and rpb1 to revise genus concepts. Three new polypore genera are ascribed to the Phanerochaetaceae: Oxychaete gen. nov. (type Oxyporus cervinogilvus), Phanerina gen. nov. (type Ceriporia mellea), and Riopa (including Ceriporia metamorphosa and Riopa pudens sp. nov.). Phlebiopsis is extended to include Dentocorticium pilatii, further species of Hjortstamia and the monotypic polypore genus Castanoporus. The polypore Ceriporia inflata is combined into Phanerochaete. The identity of the type species of the genus Riopa, R. davidii, has been misinterpreted in the current literature. The species has been included in Ceriporia as a species of its own or placed in synonymy with Ceriporia camaresiana. The effort to properly define R. davidii forced us to study Ceriporia more widely. In the process we identified five closely related Ceriporia species that belong to the true Ceriporia clade (Irpicaceae). We describe those species here, and introduce the Ceriporia pierii group. We also select a lectotype and an epitype for Riopa metamorphosa and neotypes for Sporotrichum aurantiacum and S. aurantium, the type species of the anamorphic genus Sporotrichum, and recommend that teleomorphic Riopa is conserved against it.Peer reviewe

Lost Branches on the Tree of Life

Failure to archive published data can impede reproducibility and inhibit downstream synthesis. Alarmingly, we estimate that ∼70% of existing DNA sequence alignments/phylogenetic trees, representing much of the underpinning of modern phylogenetic analysis, are no longer accessible. The evolutionary biology community needs to adopt policies ensuring that data are publicly archived upon publication