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Classification

So far we have looked mostly at various fruiting body structures (both macroscopic and microscopic) that are used to classify or identify fungi. A little earlier a few non-structural features were mentioned amongst the list of macroscopic features in fungal classification and identification – for example smell and what the fruiting bodies are growing from. These non-structural features are easily noticed and require neither technical knowledge nor specialised techniques. We will now look briefly at a few non-structural features that are a little more complex.

Internal chemistry and chemical tests

The complex organic compounds produced by fungi are another source of classificatory information. In common with numerous other living organisms, any particular such compound is produced via a series of steps or "pathways". Two compounds can be considered closely related if their pathways are similar. Slight genetic changes (such as a mutation at one gene) may lead to slight changes in a chemical pathway. Thus chemical relatedness can be used as an indicator of genetic closeness.

Those familiar with the study of lichens will know that chemistry plays an important role in lichen classification, with chromatography a standard tool in lichen investigation. While chromatography has been used to study the pigments of various fungal genera (such as Dermocybe, where many of the species produce brightly coloured mushrooms <<GET RED OR YELLOW DERMOCYBE PIC>>), chemistry is not yet used to the same degree as it is in the study of lichens.

The chemical classification referred to above requires a detailed analysis of chemical structures with the analytical tools and laboratory facilities of the organic chemist. At a much simpler level a small number of chemical tests are in regular use for the identification or classification of fungi. Sometimes a small drop of a chemical may be applied to some part of the fruiting body and any reaction observed. For example, the white flesh of some boletes turns pink when exposed to ammonia fumes. However, more often a drop of chemical is put on a microscope slide, with spores or a tiny fragment of fungal tissue soaked in that drop and then observed through a microscope for any reactions between the chemical and the spores, hyphae, basidia, asci, cystidia, etc.

Mycelium growth characteristics

Mycelia of many species (especially the saprotrophs) can be grown in artificial environments, such as agar-filled petri dishes. Mycelia of different fungi, when grown under standard conditions (of agar composition, temperature and light levels - for example) show variations in growth or chemical production that can help determine relationships between species. Mycelia may grow as a fairly flat mat across the petri dish, or produce more "bushy" growth; some mycelia are white while others are coloured; some mycelia are slow growing, others fast. These (and other) growth characteristics provide another tool to help classify different species, but can also be used to help in identification - especially identification of wood-rotting fungi, if fruiting bodies aren't present.

Developmental studies

Some features, present in the young stages of a fruiting body, may disappear at maturity and, conversely, some features appear only late in the fruiting body development. So, studies of fruiting body development provide another insight into fungal classification. For example, basidia are present in immature puffballs but absent from the mature puffball. Without knowledge of the young stage we wouldn't know that puffballs are basidiomycetes. Developmental studies have proven very useful in all groups of fungi.

Mating tests

A frequent question is whether two widely separated fungi, of similar appearance, are the same species. You may be examining two specimens, collected thousands of kilometres apart - perhaps separated by barriers such as desert, sea or mountain range. You find that, while there are slight differences under the (light or electron) microscope, those differences don't seem to justify calling these two different species. In order to help determine if you have just one species you decide to try a mating test. Essentially, the procedure is as follows. Take a spore from one of your specimens and let it germinate on an agar plate. Do the same with a spore from the other specimen. You then have two haploid mycelia. Then bring the two mycelia together to see if they form a dikaryotic mycelium. If they do, the two specimens must be of the same species. Note that mating tests are not always possible, for a number of fungi are very hard (or so far impossible) to grow artificially.

DNA evidence

Studies of DNA are increasingly being used to investigate many groups of organisms. It's well known that an organism's genetic identity and "operating instructions" are contained in the DNA that is found in every cell.

Each DNA molecule is built up from four simple building blocks, used over and over again to build up the long chain of any particular individual's DNA. The important point is that different individuals have different sequences of those building blocks. In a similar way any book (no matter how long), that is written in the English language, is built up from just 26 letters and a small number of punctuation marks. Different books have different sequences of letters and punctuation marks.

Two features make DNA very useful for investigating relationships. First, an individual's DNA is inherited from parents and, second, DNA is fairly resistant to change. It's true that many factors can easily modify DNA in laboratory experiments. To give a few examples, ultraviolet radiation, radioactivity and various chemicals will readily cause mutations in DNA. However, within the cells of living organisms there are efficient and effective monitoring and repair mechanisms that work to maintain the integrity of the DNA. Of course, sometimes those mechanisms fail, so over time there are changes in the DNA of living organisms, but these occur at a much lower rate than in test tube experiments.

Since a good classification scheme would group evolutionarily close species together, the evolutionary information contained in fossil evidence would be exceedingly helpful. Unfortunately, most types of fungi don't fossilise well and the fungal fossil record is very poor, but DNA evidence can help. Remember that as DNA is passed down through the generations, it does change and research has produced estimates of this rate of change. Once you know the composition of the different DNA sequences from two different fungi, you might ask yourself: "Starting from these two sequences, how many changes do I have to make to turn one sequence into the other?" Using that information and the rate-of-change estimates mentioned just now, you could come up with an estimate of the time needed for the two fungi to have evolved from a common ancestor. By doing such analyses for a large number of fungi, you'd begin to see when different divisions, families, genera or species evolved. In this way, DNA evidence helps compensate for the lack of fossils.

Note that the rate-of-change estimates are critical to the use of DNA as a fossil substitute and there are uncertainties involved when calculating those rates. Hence, whenever possible the DNA evidence would be compared with fossil evidence, as an independent check of the conclusions reached by DNA analysis.