Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

This is the opening paper in the special issue of Fungal Diversity, which collates the data on
defining species. Defining and recognizing species has long been a controversial issue …

This article provides an outline of the classification of the kingdom Fungi (including fossil
fungi. ie dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi …

Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from
erroneous inference of homology and saturation of substitutions, are thought to negatively …

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly
changing technologies and expanding data volumes make evaluation of completeness a …

Transcription factors (TFs) that bind common DNA motifs in vitro occupy distinct sets of
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …

The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes
characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities …

Phylogenomic studies using genome-scale amounts of data have greatly improved
understanding of the tree of life. Despite the diversity, ecological significance, and …

In this review, we discuss the current status and future challenges for fully elucidating the
fungal tree of life. In the last 15 years, advances in genomic technologies have …