The assumptions made in making fungal identifications using molecular methods are the same as those made using traditional methods. The concept of a species (or any other taxonomic level) is ultimately what those working in the field agree it to be. These decisions are based on available data, but there is always some degree of subjectivity in the process, especially when considering closely related species.
None of the current molecular methods used in fungal identification can screen more than a minute portion of the genome. There is no single method that can be used to distinguish all species or all genera from one another. Generally, if the data provided by a molecular method support current taxonomic thought on a taxon, they are used.
A molecular method appropriate for identification of one species or genus (or part thereof) may not be useful for species in other genera or even for all portions of one genus.
Molecular methods provide powerful new tools to aid in fungal identification, but they have not provided (and probably will never provide) a universal solution to problems associated with fungal identification. They are tools, not panaceas, for taxonomists. Currently molecular methods are more labor-intensive and more expensive than many of the traditional methods of fungal identification, but the field is evolving and more rapid and affordable methods will probably become available.
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