Some terminology explained (with particular reference to fungi)

Classification: the assignment of objects to defined categories. Biologists classify species of organisms. Classification is focused on placing organisms within groups that show their relationships to other organisms. Modern classification was started by Carolus Linnaeus in the 18th century, who grouped species according to shared physical characteristics. Linnaean groupings were subsequently revised to make them consistent with the Darwinian principle of common descent. See https://en.wikipedia.org/wiki/Scientific_classification.

Systematics: the study of relationships and classification of organisms and the processes by which it has evolved and by which it is maintained. Systematics deals specifically with relationships through time. Used to understand the evolutionary history of life on earth and uses taxonomy as a primary tool in understanding organisms and existing classification systems.

Nomenclature: the allocation of scientific names to the taxons a systematist considers as meriting formal recognition. Nomenclature of fungi is governed by the International Code of Nomenclature for algae, fungi, and plants.

Taxonomy: the describing, identifying, classifying, and naming of organisms. Organisms are grouped according to their morphological and/or molecular characteristics into taxa of particular ranks: species, which are grouped into genera (singular: genus), and then higher taxa, like families, orders, classes, phyla (singular: phylum) or divisions, kingdoms, domains.

In phylogenetic taxonomy (or cladistic taxonomy), organisms are classified by clades, which are based on evolutionary grouping by ancestral traits. By using clades as the criteria for separation, cladistic taxonomy, using cladograms, can categorise taxa into unranked groups.   Visit the following webpages:

 https://en.wikipedia.org/wiki/Taxonomy

 http://taxonomicon.taxonomy.nl/

 http://sn2000.taxonomy.nl/

Taxonomy of fungi: at the time of writing the taxonomy of fungi is governed by the International Code of Nomenclature for algae, fungi, and plants; and although the rank of species is basic, there is no universally applicable definition! Corrections are afoot, however. Key changes were made in the rules relating to the nomenclature of fungi at the XIX International Botanical Congress in Shenzhen, China, in July 2017. The most significant being the decision to transfer decision-making on matters related only to the naming of fungi from International Botanical to International Mycological Congresses (IMCs) (Hawksworth et al., 2017). This was detailed in the Fungal Nomenclature Session on 18th July 2018 at IMC11 in Puerto Rico.

Also, a contribution to the definition of fungal species would be to allow DNA sequence data to serve as types for the names of fungi (Hawksworth et al., 2016).

MycoBank [http://www.mycobank.org/] is an online database designed as a service that documents new fungal names and combinations, and associated data such as descriptions and illustrations, sequence alignments and polyphasic identifications of fungi and yeasts against curated reference databases. The polyphasic approach uses genomic, chemotaxonomic, cultural, pathogenic and phenotypic methods of characterising the fungus, in combination, to establish its taxonomic position (Robert et al., 2013). Since 2013, all new fungal names have to be registered with MycoBank in order to be valid.

The Index Fungorum database and web site has moved and is now based at the Mycology Section, Royal Botanic Gardens Kew in association with Landcare Research-NZ (the New Zealand Crown Research Institute for terrestrial biodiversity and land resources, managing the national fungal collection) and the Institute of Microbiology, Chinese Academy of Science.The Index can be accessed at the URL: http://www.indexfungorum.org/.

Taxon (plural = taxa) is a taxonomic group of any rank.

Cladistics: a method of systematics which aims to reconstruct the genealogical descent of organisms through objective and repeatable analysis, leading to a natural classification or phylogeny. Cladistics is based on three basic assumptions: that taxa are united into natural groups on the basis of shared derived characters; that all groups recognised must be descended from a single ancestor (i.e. be monophyletic); that the most parsimonious pattern (the one requiring the fewest steps to account for relationships) is the one most likely to be correct.

The product of cladistic analysis is a tree-like branching diagram (called a cladogram or ‘phylogenetic tree’) which shows the pattern of relationships between the organisms based on the characters used.

In a cladogram, organisms form the leaves (extreme ends of branches), and each branching node (divergence) is ideally binary (two-way). The two taxa on either side of a divergence are called sister taxa or sister groups. Each subtree, whether it contains one item or a hundred thousand items, is called a clade.

A natural group has all its organisms sharing a unique ancestor (one which they do not share with any other organisms on the diagram) for that clade. See http://en.wikipedia.org/wiki/Cladistics.

Monophyletic groups, also called clades, are composed of a single ancestor together with all of its descendants and are generally considered as the only ‘natural’ grouping. They are very important in phylogenetic classification. In contrast, a paraphyletic group contains some, but not all, of the descendants of a common ancestor. The members included are those that have changed little from the ancestral state; those that have changed more are excluded.

Polyphyletic groups are formed when two lineages convergently evolve similar characters. Organisms classified into the same polyphyletic group share observable similarities rather than phylogenetic or evolutionary relationships.

Common ancestor: a group of organisms is said to have common descent if they have a common ancestor. In biology, the theory of universal common descent proposes that all organisms on Earth are descended from a common ancestor or ancestral gene pool. See https://en.wikipedia.org/wiki/Common_descent.

Deep time: Deep time is the concept of geological time. See http://www.pbs.org/wgbh/evolution/change/deeptime/index.html.

Deep divergences: Divergence between taxons inferred to have occurred in deep geological time, typically at least 1 billion years ago.

DNA barcoding is a taxonomic method that uses a short (about 700 nucleotides in length) genetic marker in the DNA of an organism to identify it as belonging to a particular species. The DNA marker you choose is amplified by PCR in DNA extracted from ‘your’ tissue sample and the amplified sequence is submitted for sequencing. Capillary sequencers have now largely displaced slab gel instruments, and short DNA barcodes can be quickly processed from thousands of specimens and unambiguously analysed by computer programs. The sequencer generates a ‘barcode’ because it detects the four bases that make up the sequence using fluorescent dyes and the sequencer’s colorimeter reports the sequence by printing appropriately coloured peaks (or bars) that designate the sequence. If the sequence contains a run of the same base, then the peak (or bar) is broad; where the sequence has a single base, the peak (or bar) is narrow. So, just as the unique pattern of bars in a universal product code (UPC) in commerce identifies each consumer product, a ‘DNA barcode’ is a unique pattern of DNA sequence that identifies each living thing (providing you’ve made the right choice of DNA marker!). Botanists tend to use a portion of the chloroplast DNA of plants, those interested in animals can use mitochondrial cytochrome c oxidase subunit I or 16S rRNA. Recent research is demonstrating that the nuclear ribosomal internal transcribed spacer (ITS) region could serve as a universal DNA barcode marker for fungi (Schoch et al., 2012; Truong et al. 2017) although even high-fidelity DNA polymerases have per nucleotide error rates of about 4 × 10^-6 per replication and can cause PCR artifacts (Zhou et al., 2019). If you refer to Alan Rockefeller’s YouTube lecture describing his method of DNA barcoding and PCR testing for wild mushrooms [URL: https://youtu.be/JoltDnGYn3g] you’ll learn all you need to know to accomplish DNA barcoding for yourself in your home, car or bathtub (listen to the lecture!); [See also the following related URLS: https://wiki.counterculturelabs.org/wiki/DNA_sequencing, and https://mushroomobserver.org/ and https://facebook.com/groups/FungalSequencing]. 

Capillary sequencers have now largely displaced slab gel instruments, and short DNA barcodes can be quickly processed from thousands of specimens and unambiguously analysed by computer programs. The sequencer generates a ‘barcode’ because it detects the four bases that make up the sequence using fluorescent dyes and the sequencer’s colorimeter reports the sequence by printing appropriately coloured peaks (or bars) that designate the sequence. If the sequence contains a run of the same base, then the peak (or bar) is broad; where the sequence has a single base, the peak (or bar) is narrow.

So, just as the unique pattern of bars in a universal product code (UPC) in commerce identifies each consumer product, a ‘DNA barcode’ is a unique pattern of DNA sequence that identifies each living thing (providing you’ve made the right choice of DNA marker!).

Botanists tend to use a portion of the chloroplast DNA of plants, those interested in animals can use mitochondrial cytochrome c oxidase subunit I or 16S rRNA. Recent research is demonstrating that the nuclear ribosomal internal transcribed spacer (ITS) region could serve as a universal DNA barcode marker for fungi (Schoch et al., 2012; Truong et al. 2017).

A little fungal taxonomy: Principal taxonomic ranks (and the characteristic word-endings) in use for fungi today are as follows (the current practice recommended in the International Code is to print all of these taxon names in italics, or underline in typescript (Thines et al., 2020)):

 Domain Eukarya

Kingdom Fungi

Phylum …mycota

 Subphylum ...mycotina

 Class …mycetes

 Order …ales

 Family …aceae

 Genus

Species

Several similar kingdoms may be clustered into a supergroup, but this is intentionally not formally defined because it is intended as a temporarily convenient collection awaiting more data.

Refer to Hyde et al. (2017), Varga et al. (2019) and He et al. (2019) for information about current ideas for the development of classification schemes and ranking of taxa in fungi, and the evolution and most likely historical divergence times of those taxa.