Classification & identification

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This section will explain a number of features and techniques that are used in fungal classification and identification so that you can get an idea of how a mycologist might go about studying fungi. There won't be a detailed discussion of the fine points of fungal classification - such as how different species or genera are defined. Nor will there be identification instructions.

If you would like explanations of the differences between the many families of fungi, The Fifth Kingdom is a good starting point, while the first chapter in Fungi of Australia, Volume 1A contains a history of fungal classification as well as a detailed discussion of the fundamental classificatory features used to differentiate major fungal groups. Some of the books mentioned in the {{REFERENCE SECTION}} will give you an introduction to fungal identification. You can find a brief warning about the limitations of many identification guides in the {{FIELD GUIDES - A WARNING SECTION}}.

A guide to what's here

This is a long section and you may not be interested in all the topics. To help you decide if there's something of interest to you, here are brief descriptions of the sub-sections. If nothing else - try Macroscopic features. If you haven't looked closely at fungi, the photos alone will show you a variety of features you can see with the naked eye or with a magnifying glass.

• Classification vs. identification
  An explanation of the difference between classification and identification.
• The classification hierarchy
  A brief outline of the classification hierarchy, with a link to more detail.
• Classification and identification again
  Why aren't just the "obvious" features used in fungal classification and identification?
• Macroscopic features
  Links to explanations and illustrations of many of the naked-eye features used in the study of fungi. If nothing else, it may make you look at common fungi from a new perspective.
• Microscopic structures
  An introduction to some of the basic microscopic features used in the study of fungi.
• Non-structural features
  You need more than macroscopic and microscopic structural features for a deeper understanding of fungi. Here are some other methods that can shed light on the fungal world.
• Relationships that are and are not
  Relationships aren't always obvious. Here are some examples.
• Classification and identification - final words
  A brief case study that brings us back to where we started.

Classification vs. identification

Before going further it is worth pointing out the difference between classification and identification.

Classification answers questions of the sort: How is this fungus related to other fungi?

Identification addresses the more immediate question: What's the name of the specimen in front of me?

To say that two organisms are related is the same as saying they have a common ancestor - perhaps in the fairly recent past or possibly in the distant past. Depending on whether that common ancestor lived in the recent or distant past we can talk of the two organisms as being closely or distantly related. This reflects the everyday idea of human relationships, for we say that two people are closely related if they have the same parents but talk of them as distant relatives if great-grandparents are their most recent common ancestors.

Classification therefore deals with evolutionary history and a good classification scheme should group evolutionarily close organisms near one another. This demands a good understanding of many different aspects of fungal structure (both macroscopic and microscopic) and fungal biology, since the different aspects provide different types of evidence regarding relationships. In order to develop a sound classification, all the evidence must be assessed.

In essence, classification involves the creation of pigeonholes into which related fungi will be placed. Once the different pigeonholes have been created, each is given a unique name to enable easy communication between mycologists.

Continuing with the pigeonhole analogy, identification is akin to picking up the specimen in front of you and putting it in the right pigeonhole. There are numerous fungal identification guides and, while they differ in scope and content, the actual identification procedure is much the same in each of them. You are asked a series of questions about the features of your specimen, with each successive question narrowing down the possible pigeonholes a bit more until you are left with just one. It's often a fairly mechanical process and mostly doesn't need any understanding of fungal classification. That is, you often don't need to understand how those pigeonholes were created. It's a bit like cooking - if you follow the instructions in the recipe you'll bake yourself a delicious cake. You must be able to recognize things such as eggs, flour, milk and yeast but you don't need to know the function of any of these ingredients. Of course, a good cook knows what the ingredients do and can then intelligently substitute ingredients or vary the recipe for particular purposes. Similarly, knowledge of fungal classification will give you a better grasp of the fungal world, allow you to take intelligent shortcuts in identification and help guard against misunderstandings.

The classification hierarchy

There are different degrees of relatedness in the living world and these varying degrees of relatedness lead to the concept of a hierarchy of different levels of classification - kingdom, division (or phylum), class, order, family, genus, species. That sequence goes from broad to fine. That is, a kingdom contains a number of divisions, each division contains a number of classes, each class contains a number of orders and so on.

If you are unfamiliar with the technical usages of any of the above terms, there's a simplified introduction to the essential concepts here CLASSIFICATION HIERARCHY, SPECIES NAMES AND IDENTIFICATION SECTION.

A species name is a unique combination of two Latin (or pseudo-Latin) words. That combination is called a binomial. When photos on this website are labelled with species names, those names (such as Schizophyllum commune in this instance) <<042>> are examples of binomials. Going back to the earlier pigeonhole analogy, we could say one of our pigeonholes has the label Schizophyllum commune on it.

Once again, if you are unfamiliar with the structure of scientific names, the basic facts are explained here CLASSIFICATION HIERARCHY, SPECIES NAMES AND IDENTIFICATION SECTION }}. That link also contains some examples of the hierarchy, by giving the various levels for a couple of fungal species and also contains some information on related topics.

All the (macro) fungi that are the subject of this website belong to one kingdom (called the Eumycota) and there's more to the Eumycota than that, but the rest of the Eumycota are beyond the scope of this website.

As noted in the {{ASCOMYCETES AND BASIDIOMYCETES SECTION}} those (macro) fungi can be divided into two groups, depending on whether spores are produced in asci or on basidia. Within the classification hierarchy, fungi that have asci constitute a Division called the Ascomycota and those with basidia constitute a Division called the Basidiomycota. These two technical names are obviously very similar to the ordinary English words ascomycete and basidiomycete. People often talk of "high level" or "low level" classificatory features. The former are used in the definition of higher groupings such as division and class while the latter are used at lower levels - for example, to define genera and species. In these terms asci and basidia are very high level classificatory features.

There are microfungal basidiomycetes and ascomycetes, but they are beyond the scope of this website.

While the (macro) fungi are contained within two divisions of kingdom Eumycota, the full range of organisms (macro and micro) that are likely to be called "fungi" are found in three kingdoms. An explanation of the features used in the high level classification of all those "fungi" is given in {{GET LINK TO ABRS WEBSITE WHEN IT'S UP}}.

There'll now be a brief detour on the subject of classification and identification. After that there'll be examples of the sorts of features that are used in classification or identification.

Classification and identification again

Omphalotus nidiformis (above) glowing in the dark Omphalotus nidiformis (left)

Many of the features or techniques used in classification are also used routinely in specimen identification and often that is inevitable. For example, luminosity is one of the defining characteristics of the genus Omphalotus, an example of which is shown in the accompanying photos. <<001, 002>> This easily observable classificatory feature is obviously a very useful identification feature as well.

However, classificatory features are not always necessary in day-to-day identification work. For example, DNA analysis is now in widespread use for the investigation of relationships between different organisms. DNA analysis is often in the news because of its use as a forensic tool in criminal investigations. There will be a little bit more about DNA analysis later. For the moment it is enough to know that DNA analysis is a powerful classification tool but it does require specialist equipment and is impractical in much routine identification work. So mycologists often use the more easily observed features for much of the day-to-day identification work.

If a specialised technique is essential for classifying fungi, how can you ever avoid using it for identification? The important thing is that, while our ideas of how we classify fungi will change (which will sometimes involve a change of name), the fungi themselves won't change. Some fungi are so distinctive, and with no look-alikes, that you can always recognize them by those distinctive features. Of course, the species name you give may change with time – but the identification features you look for remain unchanged. It's a bit like a friend who marries several times. You might need the marriage certificates to prove the changing relationships – but those bits of paper are irrelevant for identification. You’ll always recognize your friend by his distinctive appearance.

Calostoma fuscum

The species Calostoma fuscum <<070>> is immediately identifiable on the basis of naked eye features. However, its relationships to other fungi had been debated for a long time, until some fairly recent DNA studies. There’s more about this below in RELATIONSHIPS THAT ARE AND ARE NOT

People sometimes ask: If you can identify something using easily observed features, why not use those features for classification as well and forget about "impractical" techniques such as DNA analysis? Simply because reliance on the easily observed features can lead to incorrect conclusions about relationships. To take a trivial human example, suppose we have two brothers. One spends all summer indoors (and remains fair-skinned) while the other is on a sunny Australian beach each day (and develops a deep tan). Using just the easily observed feature of skin colour, an alien visiting earth at the end of summer could mistakenly conclude that the brothers are unrelated. On the other hand, a more detailed examination would have shown the alien that both brothers could produce dark skin pigments and that skin colour was a misleading classificatory feature. The darker skin on one brother was simply his body's response to a sunny environment.

Similarity in DNA reflects evolutionary closeness, hence the usefulness of DNA analysis. Of course, an organism's outward form is heavily dependent on its DNA but, as the tanned skin example shows, some aspects of outward form may be no more than responses to the surrounding environment, rather than being inherent features of the organism. A classification scheme should not use features that can be easily modified by the surroundings. Experience has shown that some outward features, once heavily relied on for classifying fungi, are as misleading as tanned skin in the above example.

By the way, don't think that colour is unimportant in fungal classification (or identification). Often it is a crucial feature - but not always. As in the example of the two brothers, it is important to know the reason behind the colours. Each of the following photos shows the species Flammulina velutipes. In the wild this mushroom has the slightly sticky, orange cap. The white form appears when it is grown in the dark, in an atmosphere with a high carbon dioxide level and with the developing clusters of mushrooms forced to grow out through long tubes. You can see that cultivated form in many supermarkets or Asian grocery stores, where it is sold under the name enokitake.

GET FLAMMULINA VELUTIPES PHOTOS

• Macroscopic features
  Links to explanations and illustrations of many of the naked-eye features used in the study of fungi. If nothing else, it may make you look at common fungi from a new perspective.
• Microscopic structures
  An introduction to some of the basic microscopic features used in the study of fungi.
• Non-structural features
  You need more than macroscopic and microscopic structural features for a deeper understanding of fungi. Here are some other methods that can shed light on the fungal world.
• Relationships that are and are not
  Relationships aren't always obvious. Here are some examples.

Classification and identification - final words

This section has given you a quick tour of some tools of fungal classification and pointed out a few non-intuitive relationships between various fungi. Over the past three centuries fungal classification has changed, with microscopic features now of great importance and there's a brief account of the timing of some of the basic microscopic discoveries in the {{CLASSIFICATION HISTORY SECTION}}. Various other aspects of fungal behaviour provide additional information. Each investigatory tool, whether it be fruiting body shape, spore features, mating tests or DNA analysis provides a different way of looking at fungi. In order to come up with a robust classification scheme, it is necessary to approach fungi with these different tools and assess the information that each provides.

Sometimes the evidence from one approach may contradict the evidence from another approach. For example, the old classification (relying on "inkiness" as an important feature) put all the Inkcaps into the genus Coprinus - but DNA analysis says the Inkcaps don't all belong in the one genus - in fact, not even in the one family. What do you do when you get conflicting evidence? Obviously, re-check the methods to see if there have been any mistakes. If not, you can either accept one lot of evidence as more reliable than the other or leave the issue unresolved. Not necessarily a very happy result, but sometimes it's necessary to put a problem aside and wait for future developments to resolve the issue.

In the case of Coprinus, people redid the DNA analysis, using improved techniques, and still came up with the same conclusion. One thing to note is that the DNA evidence didn't come as a great surprise to some mycologists, since there had been considerable debate (over a hundred years) about the correct relationships between the Coprinus species. The DNA results prompted re-examination of the macroscopic and microscopic structures in various Coprinus species.

The DNA evidence indicates that Coprinus comatus and a few other species form a closely related group, so there's a good argument for grouping those species into a genus of their own. Apart from the DNA evidence, the species in this group share some microscopic and macroscopic features that aren't found in other Coprinus species. One macroscopic feature is very easy to see. The stem of Coprinus comatus is pipelike, rather than solid, but the pipe isn't empty. There's a wispy cord, composed of a bundle of hyphae, that runs the length of the hollow centre and has no known purpose. This photo shows a dried specimen of Coprinus comatus, with the stem cut open to reveal the wispy central cord. The cord is present in the other species that the DNA evidence groups with Coprinus comatus - but the cord is absent from those Coprinus species that are not grouped with Coprinus comatus.

<<PHOTO OF COMATUS CORD>>

It's interesting to note that in a painting of Coprinus comatus, published in 1781 in a book by the French naturalist Jean Baptiste Francois 'Pierre' Bulliard (1752-1793), this cord showed very clearly. However inkiness was thought to be an important feature and so it was used in the original definition of Coprinus. If (and the 'if' must be stressed) the species in the Coprinus comatus group are separated from the rest of the Coprinus species and put into a genus of their own, that hyphal cord will be a very useful and easy-to-use identification feature for the new genus. Inkiness would still remain a very useful feature, but one that needs to be augmented. While inkiness would no longer take you to just one genus, it would take you to a small group of genera, after which you'd use additional evidence (such as the hyphal cord) to determine the genus.

At present, the status of the species in Coprinus is being debated and more work is needed before the debate is settled and any new genera agreed to.

However the Coprinus work does show that whenever a specialised technique is used to help classify fungi, it is essential to re-examine other features to see if there is anything that is correlated with the results from the specialised technique. That may not always happen but, in the current example, the cord in the hollow stem is an easily observed feature that is correlated with the genetic evidence. Therefore the cord would be ideal for identification purposes, assuming the Coprinus comatus group is placed in its own genus.

This brings us back to where we started. Remember that classification and identification are two different things. While classification must bring together many different strands of evidence (using a variety of methods), for identification we use whatever features make it easiest to answer the question: "What's the name of the specimen in front of me?".