Taxon distinction and relationships are based primarily on morphological characters, DNA sequence data and, more recently, on divergence time estimates. However, the rank of any taxon at any level can be very subjective. This is especially true for fungi because of their morphological plasticity and the existence of the same taxon as different morphs (asexual and sexual states). To overcome limitations associated with morphology, estimating divergence times from molecular data have been used in the ranking of plants and animals by molecular clock analysis, allowing a better understanding of evolutionary relationships and to bring more objectivity in taxon level recognition.
Recently, some fungal groups were dated, and this led to improving their taxonomy, assisting in revising their classification and was directly used in their taxonomic ranking. The first attempt at establishing a taxonomic system among Fungi based on divergence time was a reconstruction of a taxonomic system for Agaricus, based on a multigene phylogeny using the BEAST software. This helped to standardize the ranking of taxa into subgenera and sections. The following criteria were used to recognize taxa above species level: (i) they must be monophyletic and statistically well-supported in the molecular dating analyses; (ii) their respective stem ages should be roughly equivalent, and higher taxa stem ages must be older than lower level taxa stem ages; and (iii) they should be identifiable phenotypically, whenever possible. Based on those criteria some subgenera or sections were split or rejected, and new ones were discovered and named. Following the Agaricus work, many other fungal groups, including Ascomycetes and Basidiomycota, have been rapidly dated.
In this context, the goal of this Research Topic is to further expand the ranking of fungi based on the divergence times approach.
Factors which may affect the reliability of divergence time estimates are (i) the limitation of accurately identified fossils, (ii) modelling rate heterogeneity in highly diverse groups, and (iii) the uncertain evolutionary rates within morphological distinct groups. Although challenges in dating analysis are apparent, the use of divergence times into systematics, coupled with a robust phylogeny, will provide extra evidence to better assign taxa to specific taxonomic ranks and revise their classification. Presently, they may not be perfect clocks which reflect perfect lineages, but they provide extra quantitative evidence as compared to morphology-based system and molecular phylogenetic classification.
This article collection mainly focuses on cutting-edge research inputs which use divergence time estimates to revise or reconstruct taxonomic systems among fungi at any level. It also welcomes broader recent research work, based on divergence times in synergy with multigene phylogenetics that addresses not only taxonomic aspects but other broader areas, such as evolutionary, phylogeography or biogeography issues.
Taxon distinction and relationships are based primarily on morphological characters, DNA sequence data and, more recently, on divergence time estimates. However, the rank of any taxon at any level can be very subjective. This is especially true for fungi because of their morphological plasticity and the existence of the same taxon as different morphs (asexual and sexual states). To overcome limitations associated with morphology, estimating divergence times from molecular data have been used in the ranking of plants and animals by molecular clock analysis, allowing a better understanding of evolutionary relationships and to bring more objectivity in taxon level recognition.
Recently, some fungal groups were dated, and this led to improving their taxonomy, assisting in revising their classification and was directly used in their taxonomic ranking. The first attempt at establishing a taxonomic system among Fungi based on divergence time was a reconstruction of a taxonomic system for Agaricus, based on a multigene phylogeny using the BEAST software. This helped to standardize the ranking of taxa into subgenera and sections. The following criteria were used to recognize taxa above species level: (i) they must be monophyletic and statistically well-supported in the molecular dating analyses; (ii) their respective stem ages should be roughly equivalent, and higher taxa stem ages must be older than lower level taxa stem ages; and (iii) they should be identifiable phenotypically, whenever possible. Based on those criteria some subgenera or sections were split or rejected, and new ones were discovered and named. Following the Agaricus work, many other fungal groups, including Ascomycetes and Basidiomycota, have been rapidly dated.
In this context, the goal of this Research Topic is to further expand the ranking of fungi based on the divergence times approach.
Factors which may affect the reliability of divergence time estimates are (i) the limitation of accurately identified fossils, (ii) modelling rate heterogeneity in highly diverse groups, and (iii) the uncertain evolutionary rates within morphological distinct groups. Although challenges in dating analysis are apparent, the use of divergence times into systematics, coupled with a robust phylogeny, will provide extra evidence to better assign taxa to specific taxonomic ranks and revise their classification. Presently, they may not be perfect clocks which reflect perfect lineages, but they provide extra quantitative evidence as compared to morphology-based system and molecular phylogenetic classification.
This article collection mainly focuses on cutting-edge research inputs which use divergence time estimates to revise or reconstruct taxonomic systems among fungi at any level. It also welcomes broader recent research work, based on divergence times in synergy with multigene phylogenetics that addresses not only taxonomic aspects but other broader areas, such as evolutionary, phylogeography or biogeography issues.
