Taxonomy: Part 2. The Tree of Life

In Part 1 we established that the taxonomy of organisms is a very useful and essential human concept if we are going to study biology, and we started to get a grasp of how that taxonomy works. We can also see why it changes from time to time as new information and scientific methods come to hand. In fact, an updated outline of fungi and fungi-like organisms has recently been published (Wijayawardene et al. 2020).

By Barry Muir

Let’s start at the top of the present classification system, not with species at the bottom, but at Life. This excellent diagram, borrowed from Wikipedia, shows how the subdivisions work. “Life” requires that the organism, whatever it is, is carbon-based and can reproduce itself.

 This rules out rocks, metals, water and other non-living things – fairly intuitive but even this gets tricky if you think too hard! Certain computer viruses, for example, can reproduce themselves, but they are not carbon-based, so can’t be called life.

Next comes domain. The domain category was only established in 1990, so is a new idea. According to the domain system, the tree of life consists of either three domains – Archaea, Bacteria, and Eukarya, or just two domains consisting of Archaea and Bacteria, with Eukarya included in Archaea, so even this is prone to interpretation. Archaea and Bacteria are mostly single-celled organisms whose cells have a nucleus that does not have a membrane around it. The Eukarya, in contrast, all have a distinct cell nucleus bound by a membrane, e.g., us. They also have organelles, tiny structures in their cells involved in special functions, an example being, say, plastids, organelles that contain the chlorophyll in plants. Fungi are also Eukarya; they have nuclei with membranes, lots of internal goodies like mitochondria (energy factories), and parenthosomes (the things that stop them leaking when you chop them with a shovel), etc.

Below domain comes the kingdoms. In the olden days, when your grandma was a baby, there were only three kingdoms: animal, vegetable and mineral, with fungi being included in the vegetable kingdom. As you have seen, mineral is now excluded from “Life” because it is non-living. However, the concept of kingdom is still unclear! In the United States and Canada they have six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea/Archaebacteria, and Bacteria/Eubacteria). In Great Britain, India, Greece, Brazil and Australia we have only five kingdoms (Animalia, Plantae, Fungi, Protista and Monera). Just to top it off, some recent classifications based on modern genetic research have abandoned the term kingdom completely, arguing that the kingdoms do not consist of the descendants of a common ancestor. If you think that is important, put your hand up! In the last few years, the terms flora (for plants), fauna (for animals), and funga (for fungi) have become popular. The kingdoms, whichever version floats your boat, are then divided into phyla.

In biology, a phylum (plural phyla) is a level of classification below kingdom and above class. Traditionally, in botany and mycology the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts the terms as equivalent. Depending on whose definition you are enamoured with, the animal kingdom Animalia contains about 31 phyla, the plant kingdom Plantae contains about 14 phyla, and the fungus kingdom Fungi contains about 19 phyla, but probably a different number next week.

The term phylum was coined in 1866 by Ernst Haeckel from the Greek phylon (“race, stock”) because he noted that when species evolved into new species some seemed to retain a few consistent features that distinguished them as a group, e.g., backbones. A phylum can thus be defined as a group of organisms with a certain degree of structural or developmental similarity, or a group of organisms with a certain degree of evolutionary relatedness. Here is just one version relating to fungi. There are many more, and, even at this high level of classification there are many versions and ideas about what belongs where.

PHYLUM BIOLOGY (very summarised)
Chytridiomycota Produce spores that can swim, mostly saprobic (recyclers) but some parasites (e.g., chytrid disease of frogs)
Mucoromycota and Zoopagomycota (previously called Zygomycota) Saprophytes (recyclers), parasites or living in association with plants
Microsporidia Mostly single-celled parasites of animals such as bees
Blastocladiomycota Saprobes (recyclers) and parasites of insects and other animals
Neocallimastigomycota Live in the digestive system of herbivores and in landfill sites
Glomeromycota Form mycorrhizal symbiosis with plant roots – the endomycorrhizae
Ascomycota Spores are enclosed in a minute sac-like structure called an ascus. Recyclers, parasites, and symbionts with lichens
Basidiomycota Spores are formed on the end of a microscopic pillar-like structure called a basidium (plural basidia). Most common mushrooms belong to this group, as well as rust and smut fungi and some human pathogens

Next comes the class. This term is gradually becoming obsolete. Linnaeus suggested class purely as a convenience in classifying animals and plants – class was never intended to represent natural groups, but rather to provide a convenient “artificial key” according to his Systema Sexuale, largely based on the arrangement of flowers. In botany and mycology, classes are now rarely discussed.

Orders are, however, widely used. What does and does not belong to each order is determined by a taxonomist, as is whether a particular order should be recognized at all. Often there is no exact agreement, with different taxonomists each taking a different position. There are no hard rules that a taxonomist needs to follow in describing or recognizing an order. Some taxa are accepted almost universally, while others are recognized only rarely. For some groups of organisms, their orders may follow consistent naming schemes. Orders of plants, fungi, and algae use the suffix -ales (e.g., Dictyotales). Orders of birds and fishes use the Latin suffix -(i)formes meaning ‘having the form of’ (e.g., Passeriformes – the songbirds), but orders of mammals and invertebrates are not so consistent (e.g., Artiodactyla, Actiniaria, Primates). In some groups of animals, the order names are widely used, e.g., Lepidoptera for the order of moths and butterflies; Diptera for the order of flies, mosquitoes, midges, and gnats).

Use of order in plants and fungi is less consistent. One fungal order with which we are all familiar is the Agaricales. The Agaricales, or gilled mushrooms, are named for their distinctive gills, although there are a few less obvious, such as Filoboletus with pores! It also depends very much on whose taxonomy you use. For example, DNA research has demonstrated that the Agaricales, in a narrow-sense, is valid. On the other hand, another study showed that most species tested could be put into six groups (genetically termed clades) that were named the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid, Hygrophoroid and Plicaturopsidoid clades. Further, chanterelles, although they have gills, are substantially different. The genera Russula and Lactarius have been put in a separate order Russulales, and other gilled fungi, including such species as Paxillus involutus and Hygrophoropsis aurantiaca show a closer affinity with Boletes and have been put in the order Boletales. Some puffballs, truffles, and some coral-like fungi, e.g., Typhula, have recently been shown to also lie within the Agaricales although they don’t have gills and look nothing like mushrooms!

Genus and species, of course, we are all familiar with, although there have been over 30 differing definitions of what is considered a species (Lucking et al. 2020). I will leave those for another time.

All this aside, the strength of a system of taxonomy is that it can be used to organize different kinds of living organisms. Every species (once we have decided what a species is) can be given a unique (and, one hopes, stable) name, as compared with common names that are often neither unique nor consistent from place to place or language to language. There are many examples amongst plants, where a single species can have dozens of vernacular names, but they never have more than one taxonomic name. This uniqueness and stability are, of course, a result of the acceptance by working biologists specializing in taxonomy, not merely of the names themselves, but of the rules governing the use of those names, which are laid down in formal nomenclature codes.

So, what have we learned? Firstly, and very importantly, taxonomy is highly fluid – in the past largely because of what individual taxonomists considered important and what they did not consider important. Today, using DNA techniques, relationships between organisms are becoming clearer, but observations in the field are just as confused because some of what we now know as close relatives are, visually and structurally, very different.

Secondly, establishing species using DNA sequencing is confusing field ecology because we can no longer be certain that a fungus we are observing in two different localities is really the same species. Then we must convince ourselves that the sequences are sufficiently similar as to be comparable. If they are not, the field observations, which are often un-repeatable, become meaningless.

It must also be borne in mind that the classifications being proposed for fungi today are based on perhaps only 3-8 % of the fungal species present on Earth (Hawksworth & Lücking, 2017). Thus, you can bet your life that many changes will occur in the future as we learn more. Simple – isn’t it?

I recommend Wikipedia for more information on many of these taxonomic groups. Also see:


Hawksworth, DL. & Lücking, R. (2017). Fungal diversity revisited: 2.2 to 3.8 million species. Microbiology Spectrum 5. doi: 10.1128/microbiolspec.FUNK-0052-2016

Lucking, R. et al. (2020). Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11:14 32pp.

Wijayawardene et al. (2020). Outline of fungi and fungus-like taxa. Mycosphere 11(1): 1060–1456. doi 10.5943/mycosphere/11/1/8