Estimation of phylogenetic relationships within the Ascomycota on the basis of 18S rDNA sequences and chemotaxonomy

Lichenopeltella mizerniana sp. nov. from the upper Pliocene of Mizerna (southern Poland)

Fungal sporocarps having ostiole with setae were found in the upper Pliocene deposits from Mizerna (borehole Mizerna-Nowa), southern Poland. These remains morphologically correspond to the fossil-genus Trichothyrites Rosend., although the structure of the ostiolar collar with non-septate setae seems unique and is typical for sporocarps (catathecia) of some modern species of the genus Lichenopeltella Höhn. Other contemporary fungal genera with setose sporocarps differ considerably from Lichenopeltella in respect of their morphology. Taking this into consideration, a new fossil-species Lichenopeltella mizerniana G. Worobiec is proposed. Morphologically, Lichenopeltella mizerniana is similar both to some modern lichenicolous [L. peltigericola (D. Hawksw.) R. Sant., L. rangiferinae Brackel, and L. uncialicola Brackel] and non-lichenicolous species [L. ammophilae (J.P. Ellis) P.M. Kirk & Minter, L. palustris (J.P. Ellis) P.M. Kirk & Minter] of this genus. The presence of Lichenopeltella mizerniana suggests that the Pliocene climate of the Mizerna locality was probably at least moderately humid.

Assessment of phylogenomic and orthology approaches for phylogenetic inference

MOTIVATION

Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology.

RESULTS

Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content.

CONCLUSIONS

Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.