Nomenclature & Taxonomy Notes

NOTICE- aspects of this page is “under construction” to update nomenclature based on current scientific findings.

You will separately find our index to fungal names, fungal synonyms, and teleomorph-anamorph relationships. Providing an organizational scheme for the world of the fungi is a complex challenge. If all things were known about the fungi, it would be easy! But, this is not the case. Any naming scheme must deal with the multiple growth forms of many fungi, and the fact that some organisms have been incorrectly considered to be fungi.

The history of the names of the fungi is a major source of confusion. Scientists have, over the years, often inadvertently given the same fungus different names. Once it is ultimately realized that Whatafungus burgerii is actually the same as Anotherfungus macus, a decision must be made about which name to use. The name first correctly described receives precedence. But, not always: sometimes a newer name has achieved such prominence in the literature that reversion to the older name would produce major confusion. A good example of this is the genus Candida. If the rules of precedence were followed strictly, then we would actually have to refer to it as Torulopsis. But, making such a change at this point would be impossible, and the International Botanical Congress has specifically made an exception for the name Candida by designating it as nomen conservandum (nom. cons.).  For additional reading on this topic we recommend reviewing this paper by Dr. John Taylor (One Fungus = One Name).

If you are really interested in learning more about the whole area of fungi, their life cycles, and more, we highly recommend the (E):online introductory mycology course notes at (E):Tom Volk’s fungus website. Another useful resources is the general discussion of fungal taxonomy provide by Bryce Kendrick’s (E):Mycologue website.

The DoctorFungus View

In these pages, we have applied a consistent scheme to the classification of the fungi. Here is our approach.

  1. All genera belong to one of three broad groups: Yeast, Mould, or Other. Yeast reproduce principally by budding (or fission) and moulds reproduce principally by elongation at the tips of filamentous growth forms. The group Other contains genera that aren’t technically fungi but that are, for various reasons, often studied along with the fungi.
  2. All fungal genera of medical importance can be placed into one of five sexual groups, even if sexual reproduction has not been observed. These groups correspond to the five phyla of the Kingdom Fungi and are the ascomycetes (Phylum Ascomycota), basidiomycetes (Phylum Basidiomycota), zygomycetes (Phylum Zygomycota), chytridiomycetes or chytrids (Phylum Chytridiomycota), and Fungi Imperfecti. The first four groups are the true sexual groups (or phyla) because they are characterized by the production of sexual spores known as ascospores, basidiospores, zygospores, and oospores, respectively. Fungi that infect people come from all the groups except the chytridiomycetes. The chytrids are important as causes of diseases in agriculture and in lower cold-blooded animals.The asexual genera of the Fungi Imperfecti (also sometimes known as the phylum Deuteromycota) are different from the known sexual genera in that a sexual form is not known. Genera in the Fungi Imperfecti are form genera because they are recognized without the use of sexual characteristics such as ascospores. Also unlike the sexually reproducing fungi, the Fungi Imperfecti are not classified based upon evolutionary relationships. These genera may at times be associated with a sexual genus (e.g., Aspergillus fischerianus is the anamorph of Neosartorya fischeri). But, we leave the genus as a whole in the Fungi Imperfecti unless we want to talk about the sexual stage or all of the forms and properties of a given fungus.The issue of sexual and non-sexual states of the fungi produces much confusion. The sexual form is known as the teleomorph and the asexual form is the anamorph. As these are often physically quite distinct forms, the teleomorph and the anamorph of the same fungus will have different names. This has happened because many of the asexual forms were discovered without evidence that they could reproduce sexually. Members of the Fungi Imperfecti are only known by their anamorphic name. When we want to discuss the whole fungus, which includes all of its forms regardless if they are sexual or asexual, we use the name based upon the sexual form because a fundamental goal of all classification systems is to have a system that shows evolutionary relationships among its members. Evolutionary relationships are based upon sexual reproduction, not asexual reproduction.
  3. Some genera are classified as dematiaceous, meaning that melanin in the cell walls of its conidia, hyphae, or both results in a darkly colored fungus.
  4. Three genera are classified as dermatophytes. These fungi attack hair, nail and skin on the living patient.
  5. Dimorphism is coded at the species level. Genera that contain dimorphic species are coded as moulds. For example, the genus Coccidioides is coded as a mould which contains a pair of dimorphic species.

Special Terms

The following terms have very specific meanings. Note especially our definition of the term Obsolete. This term can be independently attached to any given genus or species.

  • (A):anamorph (ANAtomic MORPHology): An asexual form of the fungus that is recognized based on its anatomic morphology. A fungus can have several anamorphs–the hyphae, alternating arthroconidia, and spherules with their endospores are the three anamorphs of Coccidioides immitis. These forms could also be referred to as synanamorphs.
  • nomen confusum (nom. conf.): A name based on two or more different components.
  • nomen conservandum (nom. cons.): A name authorized for use by the International Botanical Congress (IBC).
  • nomen dubium (nom. dub.): A name of uncertain sense.
  • nomen illegitimum (nom. illegit.): A validly published name, but one that contravenes some of the articles of the IBC.
  • nomen invalidum (nom. inval.) A name that is not valid.
  • nomen nudum (nom. nud.) A name that lacks a description.
  • obsolete: A synonym of a published name that is no longer acceptable for use. Possible reasons for being invalid are coded as nom. conf., nom. dub., nom. illegit., or nom. nud.
  • (A):synanamorph: Two or more distinct anatomic forms (anamorphs) produced by one fungus.
  • teleomorph: A form based on a sexual state.

Extended Discussions of Selected Topics

Anamorph and Synanamorph

Anamorph means an asexual anatomic morphological form. The word can be used in several ways. We can say that Coccidioides immitis has several anamorphs. These are hyphae, alternating arthroconidia, and spherules containing endospores. Collectively, the fungus has several anamorphs. The term synanamorph could be used here because it means that the fungus produces more than one anatomic form, or anamorph. The anamorphs of interest are arthroconidia and spherules. Hyphae formed by the moulds are generally not used to make taxonomic decisions as is done in the yeasts. Because anamorph refers to an asexual anatomic morphological form, we can say that Coccidioides immitis is an anamorphic fungus and that the genus and species names are anamorphic genus and species names.

The fact that Coccidioides immitis can make at least two different anamorphs is also used for its identification. If we use an ecology species concept where the fungus is producing different anamorphs in response to different environmental conditions, the spherule anamorph is one of the bases of the name Coccidioides immitis. If we were to use the anamorph consisting of alternating arthroconidia, we would have to note that these are characteristic of the genus Malbranchea. Based on this morphology, the proper name for the fungus would be as a species of Malbranchea! What we do in medical mycology is say that the whole asexual fungus is Coccidioides immitis, because the ability to change anamorphs depending upon environmental conditions (dimorphic) is the key characteristic in recognizing this fungus. We can also say that Coccidioides immitis forms a synanamorph consisting of alternating arthroconidia. This synanamorph is characteristic of the genus Malbranchea. Therefore, to confirm the identity of a fungus as Coccidioides immitis, we must demonstrate that it is dimorphic, or use some other method like exoantigens, PCR, or animal studies. This is why the identification of dimorphic fungi must always be confirmed. By definition, they all produce more than one type of anamorph which is growth environment dependent.

This discussion also illustrates one last critical idea. The key to any fungus is its species name. Even though we may move it from genus to genus during debates about which of its many features make it most recognizable, the species name is preserved. The only time we would change a species name would be if a change of genus resulted in an overlap with a pre-existing species of that genus. In this case, a new species name must also be assigned.