Reference strains and synonymy: Atlas policy
For the construction of phylogenetic trees on the basis of sequence data, or other comparative studies, the species must be represented by a sequence that is truly typical of that species. Whenever possible, the strain derived from the permanently preserved type material should be used, i.e. an “ex-type” culture. The type is the actual name-bearer, and the single reference point of any species either upon its first introduction into the literature, or under certain circumstances by a later researcher.
The International Code of Nomenclature for algae, fungi, and plants, requires the type material to be permanently preserved and it cannot be living. Thus it should be a dried fungarium specimen or dried culture, microscopic preparation, a metabolically inactive culture (i.e. lyophilized or in liquid nitrogen), or in certain circumstances even a drawing. In case of centuries-old medical species, this material may be lost, or no longer be interpretable with today’s experimental methods. There are three ways to indicate a new specimen: (1) another part of the original collection of the author that described the species (lectotype), (2) if all material is lost, a completely new collection can be designated (neotype), or if the original material still exists but is not interpretable, an additional specimen can be indicated (epitype). Since January 2019, all later type selections must be published and registered in Index Fungorum, MycoBank, or Fungal Names in order to be accepted. Consult also the chapter “Nomenclature” in this Atlas.
In cases where no sequence from the type is available, because the original type is lost or does not yield DNA, mycologists often use a sequence deposited in a database under the name of the required fungus. But when not everyone picks the same sequence, or a sequence came from wrongly named material, the trees and the subsequent identifications based on it may be different. The availability of a fixed point of reference for each species is thus clearly essential. An epitype can be designated only once, and then functions as the new eternal reference point, instead of the original type material. Preferably the epitype a specimen is also available in culture, allowing contemporary analyses.
In the Atlas we now added the living strains that were derived from the name-bearing types, i.e. the ex-type culture. We mention this reference under the umbrella term “type strain”, irrespective of what kind of type it represents, either derived from the original type (holotype), or a replacement (lecto-, neo-, or epitype). The type strains are listed for every species below the description under the heading “Nomenclature”. We also provided the sequence of the primary barcode (ITS) of that strain, and eventually a secondary barcode if mentioned in the genus description.
In the literature, common species have a lot of synonyms. Many of these lack an interpretable type strain. Then we cannot be sure that this was a real synonym: it may have looked similar under the microscope 50 years ago, but now we know that observed similarity alone is not sufficient to recognize molecular siblings (so-called cryptic species). We therefore removed all synonyms without verifiable type strains to the chapter “Index of Doubtful Names”. All names can still be found by using “Global search” at the Atlas opening page. The button “Advanced search” provides the option to use several keywords at the same time.
Fungal names are currently changing quickly due to advances in phylogenetic taxonomy. Genera are taken as clades in the tree, and more precise sequencing usually leads to smaller genera. Dozens of species are given different genus names every year. In the Atlas, we aim to be somewhat conservative, preferably accepting name changes only when several taxonomic studies have come to the same conclusion. To find an eventually changed name, as used e.g. in GenBank or other databases, we added a MycoBank link at the bottom of the “General information” page of each species.