Chapter 1  Kingdoms and  Classification

The Fifth Kingdom - Chapter 1  

KINGDOMS, CLASSIFICATION

NOMENCLATURE,   CLADISTICS,

BIODIVERSITY,  

IDENTIFICATION
 - Species bar codes

(The words above are hotlinked to chapter sections)

Kingdoms - now there are (at least) Seven!

New vocabulary! 

As you read the text that follows, you may come across words that are new to you.   But most of them should be in colour and underlined. This means that they are hotlinked to definitions, with or without pictures. All you have to do is click on them, then click the back arrow to return to the main text.  If even the definitions and pictures leave you scratching your head, I suggest you find and read a first year University Biology textbook before going much further.

You may not know it, but you are about to become a member of an elite group. Although many people are aware that there are millions of different kinds (species) of living organisms on Earth today (although our own species is doing its best to drive many of them into extinction), surprisingly few people are aware that these organisms are now divided up among no fewer than seven Kingdoms. Before I can effectively develop the theme of this book I must explain these major patterns, and those of some of the almost 100 distinctive evolutionary pathways (phyla) which make up those Kingdoms.

Archaebacteria, Eubacteria and Eucaryotes

The really basic division among life forms is between the simpler Bacteria and the more complex Eucaryotes. Look at the diagram below (after Patterson & Sogin 1992): it shows the way in which we think the Kingdoms evolved. It is based on molecular evidence: base sequences from ribosomal RNA.

Phylogeny.gif (44070 bytes)

The earliest forms of life, which appeared about 3,500 - 3,800 million years ago, were bacteria. We tend to define them by their relative morphological simplicity, and by the absence of many features found in more modern cells. Although their modern descendants have a single chromosome, this is not found inside a nucleus, and their cytoplasm contains no mitochondria or plastids (cytoplasmic organelles). These organisms make up the baseline Kingdoms Archaebacteria and Eubacteria (These are sometimes called Domains, and regarded as having equal 'rank' with the whole of the Eucaryota). It is also now believed that the earliest cells swapped genes in lateral transfers before the three domains became distinct.  Most gene-swapping now takes place within, rather than among, domains, which is one reason they are still recognizable entities.

Multiple symbiosis = Eucaryota

The bacteria had the world to themselves for 1,500 million years (they did, however, invent photosynthesis during that time). Not until about 2 billion years ago did life take the next giant step, the evolution of the eucaryotic cell. Many, perhaps most, biologists now believe that this arose as a result of the mutually beneficial symbiotic union of several different kinds of bacteria within another host bacterium.  At least two kinds of modern organelle have been found to retain some of their original independent DNA: (1) Mitochondria, which  specialize in the oxidation of 3-carbon organic acids (the Krebs cycle), providing an immediately available energy supply in the form of ATP; and (2) Plastids, which may contain photosynthetic pigments and enzymes (chloroplasts), or may store food.  Some biologists also think that flagella were once free-living bacteria.

Eucaryotic cells also have their DNA organized into a number of discrete chromosomes, which are found inside a membrane-bounded nucleus. Cell division in eukaryotes involves a complex process called mitosis. The nuclear membrane breaks down, a mitotic spindle of microtubules develops, and the chromosomes are duplicated. Then the daughter chromosomes separate and are pulled to opposite poles by the contracting spindle fibres. Each set of chromosomes then becomes enclosed by a new nuclear membrane, and the cell finally divides into two.

Bacterial cells have only a single, usually circular chromosome, and do not undergo mitosis. They usually divide by a much simpler process called binary fission. Mitosis, with its very accurate duplication and sharing of the genetic material, seems to have been a crucial invention. Only eucaryotic cells, with their precisely regulated genetic mechanisms, apparently had the potential to evolve into more complex, multicellular organisms in which cells are organized into different tissues and organs.

Now look at the Kingdom diagram again (above). The eucaryotes encompass the other five Kingdoms, and it is in these other Kingdoms that the dazzling evolutionary explosion of new taxa has occurred. The diagram shows five eucaryote Kingdoms: (1) Protista (now often called Protozoa), (2) Chromista (sometimes called Stramenopila), (3) Plantae, (4) Animalia and (5) Eumycota.

New information on the fully sequenced genome of an amoeboid (Protozoan) pseudofungus, Dictyostelium discoideum, has now thrown some light on the timing of the origin of the Kingdoms.  You can read about it in Chapter 2a.


The burst of eucaryote evolution was made possible by, among other things, a modified form of mitosis called meiosis or reduction division. In many organisms this produces special sex cells called gametes. Each of these cells has a single set of chromosomes (we say that the cells are haploid). When two gametes from compatible parent organisms fuse, the resulting cell (the zygote) has two sets of chromosomes (we call this condition diploid). In plants and animals, zygotes develop into diploid, multicellular organisms, but in most fungi the vegetative phase is always haploid, so meiosis must take place in the zygote. Whether meiosis happens in the zygote, or at the other end of the life cycle, during the formation of gametes, it is responsible for the reassortment of the genetic information built into the chromosomes. New features are constantly being added to the pool of genetic material by the process of mutation, but sexual reproduction is the mechanism by which this pool is recombined each generation in most eucaryotic organisms, producing an endless supply of variation upon which the processes of natural selection can work. This is one of the key secrets of eucaryote diversity.

The radiation of the two largely unicellular Kingdoms (Protozoa and Chromista) shows how the evolution of the eucaryotic cell expanded life's horizons. But the full potential of the new teamwork -- I call it that, since several bacteria (most as endosymbionts) cooperate to make one functional eukaryotic cell -- was not realized until cells, as well as cell components, began to cooperate. When organisms became multicellular, different cells could assume different, specialized functions. This division of labour eventually led to the development of tissues and organs, and ultimately permitted the evolution of complex beings like ourselves, beings with almost infinitely expanded capabilities (both wonderful and terrible).

Multicellular kingdoms

Three new multicellular Kingdoms arose, exemplifying three different ways of life. Multicellular organisms which could photosynthesize -- make their own food from simple inorganic precursors -- were eaten by other multicellular organisms that lacked this talent, and both were recycled after death by a third group. These groups we call producers, consumers and decomposers -- which roughly correspond to the plants, the animals and the fungi. We recognize about 9 phyla of plants, about 32 phyla of animals, and...

6 phyla of fungi (2 chromistan and 4 eumycotan).

The world being what it is, the picture is not as simple as we might like. Some of the divergent paths of evolution have come together again, almost as they did at the birth of the eucaryotes, and many organisms that seem unitary are in fact partnerships or even consortia. Lichens, for example, always incorporate both an alga (eucaryotic or cyanobacterial) and a fungus. (Other examples -- reef-building corals, animals mof the Phylum Cnidaria, always have endosymbiotic dinoflagellates, many sponges have endosymbiotic algae, plants often have systemic endophytic fungi, and in most cases also have mycorrhizal fungi associated with their roots).

How can fungi fit into two Kingdoms? The answer lies in the way we define the term fungus (plural: fungi). 

Fungi are eucaryotic (their cells have nuclei), heterotrophic (they can't make their own food), osmotrophic (they absorb, don't ingest, food), develop a rather diffuse, branched, tubular body (radiating hyphae making up mycelia or colonies), and reproduce by means of spores.
 

This happens to describe, not a single phylogenetic line, but rather a way of life shared by organisms of different evolutionary backgrounds.  The concepts just mentioned are fleshed out in the chapters that follow: for example, look at Chapter 3A to find out about hyphae. We recognize chromistan fungi (pseudofungi with cellulosic hyphal walls) as well as eumycotan fungi (true fungi with chitinous hyphal walls).

If you find this strange, consider the 'algae' for a moment -- they include representatives of three Kingdoms: the blue-green cyanobacteria, chromistans (diatoms, kelps), and protozoans (green algae, red algae, dinoflagellates, euglenids). Both algae and fungi are often defined functionally or ecologically, rather than phylogenetically.

At this point it becomes clear that this book does not, as its title implies, deal exclusively with the fifth Kingdom, Eumycota, but also discusses some elements of Kingdom Chromista.  But these latter are relatively minor players on the biosphere when compared with the huge numbers and biomass of the Eumycota.

For a more detailed discussion of the fungi and their relatives, as defined by ultrastructural and molecular characters, please click here.

According to R.K. Noyd, who has published a set of mycology reference cards, the main line of evolution leading to the fungi gave off various side branches en route.  First to branch off were members of Kingdom Protozoa -- the Myxostelida (slime moulds), then the aggregating amoebae of the Dictyostelida (cellular slime moulds), then the red algae, then the Kingdom Chromista (Stramenopila) which include the Oomycota.  Next Kingdom Plantae diverged, then Kingdom Animalia. Later (we have now arrived at Kingdom Eumycota), the Phylum Chytridiomycota branched off, followed by the Phylum Zygomycota.

Fungi have been around for hundreds of millions of years.  The next picture shows one recently recovered from 400 million-year-old rocks of the Rhynie chert in Scotland. This the new genus Hassiella, described by Taylor et al. (2006). It is amazingly well preserved.

The final, or most recent split, was into ascomycetes and basidiomycetes.  Noyd treats each of these large groups as a separate phylum, but given their almost parallel sexual development, and many other similarities, I used to keep them together in the Phylum Dikaryomycota as the subphyla Ascomycotina and Basidiomycotina.  But I have been outvoted, and the Phyla Ascomycota and Basidiomycota are now generally recognized, in a subkingdom Dicarya. All of these groups -- from Myxostelida to Basidiomycota -- are dealt with in some detail in the chapters that follow.

Although the outline of the Kingdoms seems relatively sound, the classification of fungi at the lower levels - class, order, family and genus, is being shaken up by an influx of molecular data.  The classification presented in the chapters that follow is still to some extent based on the ideas first proposed by the great biologist, Anton de Bary, in the 19th century, and refined by many subsequent generation of mycologists using morphological, anatomical and developmental characteristics.  But it now seems that a true phylogenetically based classification has become possible as a result of molecular studies.

This new system is still fragmentary, and not entirely consistent, but it holds out hope of a truer understanding of the fungi than we have ever had before.  The full outline, as well as the fine details, will become clearer in the next few years, and I will try to incorporate them in future versions of this CD-ROM.  Notes on recent taxonomic changes are already to be found at several points in the chapters that follow, and these will be augmented as the story unfolds.

If you want to learn a little more about the techniques used to extract, amplify and sequence fungal DNA, go to Chapter 25.

How old are the fungi?  
How important were they during the critical
Precambrian-Cambrian transition?

The fungi have a poor fossil record, so can be dated (albeit rather approximately) only by molecular clock extrapolations based on DNA sequence data.  In advancing the most recent estimate, Lucking et al. (2009) suggest that the fungi evolved between 1.06 billion years ago and 760 million years ago.  A first step toward colonization of the land may have been the establishment of  lichen-like symbioses. These associations may have been partly responsible for the increase in global oxygen levels.  Land plants are thought to have arisen about 600-700 Myr ago (also probably as symbioses between fungi and the plant-like algae) and to have paved the way for the explosion of animal taxa during the Cambrian. The diagram below is from Lucking et al. (2009).

The deep time history and origins of the fungi are still rather obscure. Many of the attempts to build calendars using rates of genetic change come up with dates far older than any known fossils, so are impossible to confirm.  A recent review of this subject is given by Berbee and Taylor (2010). Don't expect any early resolution of this problem.

Biological Classification

The first part of this book deals with the classification of the fungi. You can certainly ignore chapters 2-7, and move quickly to the more accessible and, to many people, more interesting chapters later in the book which deal with the many ways in which fungi impact on human existence. However, I don't think I am overstating the case if I say that unless you understand something about how the main groups of fungi differ in morphology and behaviour, you will not be able to make much sense of the more 'relevant' sections of the book. If you can develop a sort of 'cognitive map' of the main classes, recognizing them on sight, and understanding the unique abilities of each, you will find the study of fungi -- mycology -- infinitely more rewarding.

 

A NEW PHYLOGENETIC CLASSIFICATION OF TRUE FUNGI - 2007

 

This new system has just been completed.  It is based on all available information, but especially on molecular data.  It is contained in a paper to appear in Mycologia, entitled "A Higher-Level Phylogenetic Classification of the Fungi" by no fewer than 66 authors (Hibbett et al.)  Note that it does not deal with the Oomycetes, nor with the various kinds of slime moulds, none of which are true fungi.

I am adding it here as a preliminary to reorganizing the first several chapters of the CD-ROM. 

Please consult these tables so that you can place the taxa discussed later in their 'correct' places...

This first table deals with the older and simpler groups, including the chytrids, the Zygomycetes, and the Glomeromycota


This second table deals with the Ascomycetes (including most lichens)


This third and last table covers the Basidiomycetes, including rust and smut fungi.

 

Biological Nomenclature

Every species of living organism is a collection of individuals which are very similar (genetically, if not always in appearance), and each species has a unique name made up of two words, which may actually be from the ancient Latin lexicon, but are far more often new, pseudo-Latin words coined for the occasion. This two-epithet name is the binomial. You and I belong to the species Homo sapiens. The supermarket mushroom belongs to the species Agaricus brunnescens. In each case the first of these two Latin words is the generic name or epithet (this places the organism in a genus, a collection of similar and/or related species). The second Latin word is the epithet applied to one particular species of the genus. But notice that the name of the species always consists of both epithets together. This is because only the two-word combination is actually unique to that species. The generic epithet is shared by all other species in that genus. The same species epithet may also be applied to species in other genera (for example, many Canadian spring flowers, though belonging to different genera, have the same species epithet, canadensis, as does the national animal of Canada, the beaver). So remember that only the two epithets together -- the binomial -- properly specify a species. Homo sapiens is the only extant species in the genus Homo, but most genera contain more than one species, and some, for example the mushroom genus Cortinarius, are made up of hundreds of species.

For purposes of classification (which is actually a method of information storage and retrieval), related genera are grouped into families, families are grouped into orders, orders into classes, classes into phyla, and phyla into Kingdoms. Here is a sample of how an organism is classified in this hierarchical (boxes within boxes) system. Note that the binomial is in italics, as it is in most scientific publications, while the names of higher-ranking taxa (families, orders, etc.) are not in italics. If you refer to a binomial in writing, it should be underlined, to show that it would be printed in italics.


Kingdom: EUMYCOTA (some prefer FUNGI)

  Phylum: Basidiomycota

    Subphylum: Agaricomycotina

      Class: Agaricomycetes

        Order: Agaricales

          Family: Agaricaceae

            Genus: Agaricus

              Species: Agaricus brunnescens -- the edible (supermarket) mushroom.


Why do we use this binomial nomenclature, which is so unfamiliar to the man-or-woman-in-the-street? Why not use common names wherever they exist? 
For three good reasons:
(1) the common names of many organisms differ from country to country, and even from district to district;
(2) the same common name is sometimes applied to different organisms -- for example, the British, North American and Australian "Robins";
(3) common names can be downright misleading: Irish moss is a red alga, Spanish moss is a flowering plant, clubmoss is a fern ally, and reindeer moss is a lichen.
Let's face it, common names are too unreliable and confusing to be of much use to scientists, who rely heavily on international communication and cooperation. Please take the time to learn the proper scientific names of the more important organisms you encounter in these pages. If you ever want to know more about any of them, you'll find that their binomials are the key to almost everything that has been written about them.

Having said that, I must admit that I can occasionally remember the common name of an organism when I can't pull the scientific name out of my memory banks (this is increasingly true with advancing years as of November 2008 I am almost 75)Google and Wikipedia are wonderful memory aids which I (and I am sure all of you) use often. Many identification manuals list common names, so they can in times of forgetfulness be one way to get at the scientific name.  But that's as far as I am willing to go, unless you have to give a talk to non-scientists or small children, when common names are all they will be able or willing to accept.

"But why Latin or pseudo-Latin binomials?" I can hear you saying plaintively. That's easy too:
(1) Latin is officially a dead language, so although scientists do coin new words, the grammar, vocabulary and usage will change much more slowly than those of all living languages. In a changing world, we need the relative stability of Latin for our scientific names.  
(2) The use of Latin for names and diagnoses of all new taxa also means that no-one can be offended by being forced to use someone else's language. Latin has again become a useful international standard.

I do have one problem with the Latin terminology: it is that the same generic names can be used in different Kingdoms.  For example, there is a hyphomycete genus called Graphium (an asexual phase of an ascomycete - see picture, below, left, and Chapter 4b).  There is also a genus of butterflies called Graphium (below, right).  I do not think that this is necessary or reasonable, and I personally would disallow it - especially since the affiliations of kingdoms may change: the fungi are now considered quite closely allied with the animals, rather than the plants. 

It is unlikely that anything will be done about this in the near future, but you should be aware of the problem...

Cladistics

In recent years, followers of Willi Hennig have forcefully advanced a challenge to the traditional Linnaean hierarchical system.  Their approach is called cladistics from the Greek word clados for branch.  There is quite a bit of terminology to learn before we can understand this newish taxonomic philosophy.

Characters inherited from a common ancestor are homologies.
Similarities  developed independently or separately as adaptations to a common way of life (say flying or swimming) are homoplasies.  Homologies reflect true relationships while homoplasies don't.

Primitive features are plesiomorphies
Primitive features shared by different organisms are symplesiomorphies.
Such features do not imply close (recent) relationship.
Features shared by some organisms but not found in others are recent or derived, as opposed to primitive, and are called apomorphies.
Shared derived features are called synapomorphies.

In order to establish a classification based on true relationships we must learn to distinguish between apomorphic (derived) homologies and plesiomorphic (primitive) homologies.  Synapomorphies are more indicative of close relationship than are symplesiomorphies.  (Rather like learning a new language, isn't it?)

But synapomorphies exist at different levels.  For example, feathers are a synapomorphy for all birds - they are found only in birds -  but they don't tell us how to separate a sparrow from a starling.  So groups at all levels are established by different synapomorphies.
Mammals are defined by hair made of keratin, warm-bloodedness, suckling their young, etc.  One subgroup is the placental mammals [Eutheria] (as opposed to those which don't produce a placenta, such as the marsupials).  The Primates are a subgroup of the placental mammals defined by synapomorphies including a pair of pectoral breasts, nails instead of claws, complete bony eye sockets, etc.  The Hominoidea differ from other primates in such synapomorphies as reduction of the tail to an internal coccyx.  Members of the genus Homo share synapomorphies such as large brain size, flat face, high forehead, etc.

All classifications can be presented as nesting tree diagrams, but those produced by cladists, which are based on synapomorphies, are called cladograms.  Each node or branching point in the tree represents the common ancestor of the branches arising from that point.  Cladists emphasize the importance of what they call clades, each of which consists of the common ancestor and all of its descendants.

All recognized taxa are clades.  The primates are a clade containing all men, apes, monkeys, lemurs and tarsiers right back to their common ancestor who existed about 65 million years ago.  The mammals are a larger clade, including all primates, horses, rodents, etc., right back to the first mammal, which lived in the Triassic, about 210 million years ago. 

But a problem surfaces when you look at reptiles.  Traditional taxonomists recognize the class Reptilia (tortoises, turtles, snakes, lizards, crocodiles and the tuatara), but it is NOT a clade, because the reptiles gave rise both to the birds, which traditional taxonomists put in another class, Aves, and to the mammals.  So birds and mammals have to be placed in the same clade with what we call reptiles.   We seem to need some kind of compromise in the naming of such groups.   There does not yet seem to be a universally accepted one.  But reptiles, since they can't be a clade (they can't be defined by synapomorphies), are often called a grade. They are 'non-avian, non-mammalian reptilia'.  In practice, reptiles are often called a paraphyletic group (in this case, it is a monophyletic group with two subsets removed), and this looser usage for some familiar groups is signaled by the insertion of an asterisk after the formal name of the taxon - Reptilia*.

Since birds arose from a group of dinosaurs, it is common to hear cladists speak of 'non-avian dinosaurs' when referring to the older group.

If we want to separate reptiles and mammals, we need to compare both to an outgroup, for example a salamander, which is related to both groups but not part of either.  Cladograms always include an outgroup.

All of this theory is now gradually being applied to the fungi, especially as new molecular data come in to supplement (or in some cases, conflict with) morphological and developmental data.


Biodiversity

Different strokes for different folks.  For some people, place names are evocative, calling up vivid memories of past experiences.   For me it is the names of organisms I have seen that bring back those experiences.   Metrosideros excelsa conjures up Christmas in Auckland, New Zealand, where the red flowers of this tree adorn beaches in December.  Protea cynaroides takes me back to the amazingly rich Fynbos plant community in South Africa, where this flamboyant shrub flourishes, and has been adopted as the national flower.  Amphiprion places me on the Barrier Reef in Australia, where these agile little damselfish with blue-white stripes live unscathed among the tentacles of large sea anemones.    Such organisms, and the communities and ecosystems of which they are parts, are the real reasons I leave home.   I hope that some of you will also come to think of the biodiversity you encounter as a measure of your quality of life.

Biodiversity was one of the buzz-words of the nineties, and I for one hope that it will continue to be a newsmaker in the new millennium.  Biologists know from the earliest years of their training that the Earth is blessed with an amazing number of different living things.  As you have just read, systematists have tried to catalogue and describe all these riches, but with widely varying degrees of success.  We know practically all the birds, and almost all the mammals, that inhabit the earth. But we know only a small fraction of the arthropods and fungi.  How can I make those two statements so confidently?  Because although there are many ornithologists and mammalogists scouring the globe for new taxa, they rarely find any.   At the other end of the scale, entomologists and mycologists find new taxa every day.  They have so far described approximately a million insects and about 100,000 fungi, but it is obvious to the professionals who work in these areas that huge numbers of both groups have not yet been described.    I began my mycological career examining the sequence of fungi involved in the slow decomposition of Scots pine needles.   Almost immediately I found several microscopic fungi which turned out to be new to science, and I had the privilege of describing these fungi (You can see some of them in Chapter 11 of this book).  Since I moved to Vancouver Island, off the west coast of Canada, in 1994, I have seen many mushrooms that could not be identified using the existing literature.  I am convinced that many of these fungi are actually undescribed. 

How many fungi are waiting to be discovered?    David Hawksworth (1991) came up with an ingenious answer.   Noting that Britain is among the most intensively investigated areas on Earth for plants and for fungi, he pointed out that almost all the flowering plants are known, and that there are about 2,000 species.  Although the fungi of Britain are definitely not as fully known, since new ones are still being described, about 12,000 species have been recorded there.   This gives a ratio of about 6 fungi to each plant species.  Extrapolating (perhaps rather ambitiously) from Britain to the entire globe, Hawksworth suggested that since there appear to be about 250,000 species of flowering plants in the world, there are probably six times as many fungi - about 1,500,000 fungi, in fact. Even if this figure is an over-estimate, and there are only half-a-million fungi, we have still described only 20% of the total, and a huge task lies before us.

But if we accept this figure as a working approximation (and no-one has yet come up with a different formula), it brings us to a realization that about two centuries of mycology have so far succeeded in describing only about 7% of the world's mycota -- a pretty shocking state of affairs.   Over the years I have been involved in describing probably three hundred fungal taxa, and have now basically run out of steam in this area of mycology.  But even if all the mycologists alive today were to publish 100 species apiece, they would still manage to describe only about 300,000 taxa.

Where are all the undiscovered fungi?  Hawksworth returned to the fray in 2004, and suggested that:  (1) many of them live in tropical forests - for example, mycorrhizal fungi associated with leguminous trees; (2) many will be found in as yet only partially explored habitats - for example the guts of arthropods, or the soil of Australia, where many new taxa of hypogeous fungi are just now being discovered; (3) some are lost or hidden (lost inside broadly defined taxa, or collected but as yet unidentified) for example, the presumably well-known Fusarium graminearum has been found to embrace nine separate species.

Recently, the use of molecular techniques to detect fungal DNA has shown that soil contains many fungi that do not reveal themselves to normal microscopic investigation (at least, not in an identifiable form), and do not grow on ordinary culture media. Some are similar to known species, and may simply be new (undescribed) species, but others are novel, and may exemplify new and unknown higher taxa.  It has also been pointed out that only about 20% of the approximately 1,000 new fungal taxa formally described every year have been added to public databases such as GenBank.  So there is a growing disjunct between our morphological knowledge of fungi and our genetic knowledge of DNA sequences which will undoubtedly take many years to bridge.

The preceding discussion assumes a steady state, in which no species are added, and none subtracted, from the global total.  But we know that this is not the case.   New species are arising constantly, albeit at an unknown rate, as results of the combined effects of selection pressure and genetic recombination.  Our own species, by sticking its fingers into every existing niche and ecosystem, as well as creating new ones, is undoubtedly providing the fungi with new challenges at every turn, and they are surely responding to those challenges by spawning new taxa.

But now we come to the tragic bit.  Human activities are undoubtedly driving some fungi into extinction.  We don't know which or how many are being lost, and it is absurd for anyone to suggest that we are losing two species each week or twenty each day. Information on extinctions is extremely hard to obtain: How can you tell when a particular microscopic fungus, which can be detected only by culturing the soil, or a macroscopic fungus that may fruit only once in 20 years, has finally succumbed?   Nevertheless, we have good reason to suspect that these things are happening.   For example, the huge fruit bodies of Bridgeoporus (Oxyporus) nobilissimus, a polypore that grows only in old-growth forests on the west coast of North America, are seen less and less frequently, and (along with the forests in which it lives) this species may certainly be considered endangered. 

But our problem in North America is that we do not have extensive records of the mycota from the past -- a base-line with which present-day comparisons can be made.  Fortunately. some European countries, with centuries of data collection to draw upon, have been able to document the decline in numbers of many fungi, and have published what they call Red Lists.   These lists highlight the increasing rarity of many fungi, and the apparent disappearance of some. 

1 fire-bellied toad.jpg (43490 bytes) So what does a fire-bellied toad from North Vietnam have to do with preserving fungal diversity?  Read on...

Dr. Bob Murphy, Director of the Royal Ontario Museum's Centre for Biodiversity and Conservation Biology, reports in the Globe and Mail for July 12th 1999 that he has just returned from collecting herpetiles (amphibia and reptiles) in the North Vietnam rainforest.  His comments about his animals are worth repeating here. "Because they're beautiful, aesthetically appealing, wonderful animals, you can get them protected.  If you can get them protected, you protect the forest.  If you protect the forest, you protect everything that's there, especially the fungi (my italics), which are producing the majority of new pharmaceuticals that are coming out."   You will find an echo of that statement in Chapter 24, in the discussion of antibiotics, immunosuppressants and other fungal metabolites.

Are there still exciting new fungi out there waiting to be discovered?  Terry Henkel knows the answer.  He has found a new fungus so radically different from anything that had ever been seen before that it was almost filed in the wrong subphylum.  Here is a picture of this strange fungus, which he discovered when surveying the ectomycorrhizal partners (see Chapter 17) of Dicymbe trees in the Pakaraima mountains of Guyana.  

This fungus was almost described as a new genus of basidiomycetes not far from Tulostoma, which it resembles in many ways.  But molecular work on a succession of specimens pointed to the ascomycetes, and eventually it was realized that this was a totally new and different member of the Elaphomycetales (see Chapter 4b) which usually fruit underground.  Pseudotulostoma obviously has a volva and a stalk, unlike any other member of the Elaphomycetales.  But it clearly belongs to that order, and has developed these adaptations to get its spore mass above an extremely wet forest floor. It has been called, perhaps with some hyperbole, the find of the century, but it is certainly a dramatic new kind of fungus which eluded mycologists until the year 2001.  It has now been discovered to be ectomycorrhizal with the tree Dicymbe, a member of the Caesalpiniaceae.

So our efforts to collect and describe the world's mycota need to be redoubled.  As you will learn from many of the other chapters in this book, and perhaps most accessibly from Chapter 24, many fungi confer enormous benefits on Mankind.   I am not just referring to the producers of antibiotics such as penicillin and immunosuppressants like cyclosporine, but also to the myriad species which recycle organic matter, especially plant debris, and to the others that establish obligate mutualistic symbioses with many of our most important plants.

Another reason for learning more about the fungi lies in the problems they cause for us and other organisms in which we are interested (for whatever reason).  If you will consult the web site:  http://www.issg.org/database/welcome  (the global invasive species database) you can easily find out that of the 100 invasive taxa (usually aliens introduced to new areas) considered to cause the worst problems, 5 are fungi.

Awareness of our ignorance of biodiversity has generated proposals to compile what are called "All-Taxa Biodiversity Inventories" or "ATBI" for short.   A meeting to discuss such an ATBI for a forested area in Costa Rica came up with a figure of $20 million for the fungi alone.    Although the Costa Rican venture didn't fly, it spawned a marginally less ambitious project for the Great Smoky Mountains National Park in Tennessee.  Setting other organisms aside, it has been estimated that there are 20,000 fungi in the Park, of which only 2,250 have so far been described. (Hey, that's more than 10%, so we are already ahead of the game.)   A two-year pilot project aimed at refining sampling methods and data protocols was begun in March 1999, and mycologists everywhere will be watching with interest (or will be co-opted) as this unfolds.   To learn more about this project, visit the web site http://www.discoverlife.org

Finally, the last few years have seen the emergence of a global project aimed at cataloguing all known biodiversity.  "Species 2000," based in Britain,  is attempting to produce a database containing the names of all known organisms.  You can check your favourite taxa at this web site:  http://www.sp2000.org/AnnualChecklist.html

Give it a test drive...
 

Identification and "Species bar codes"
 

For many people, the whole point of this chapter is not to give them an insight into the grand scheme of things, but to allow them to gain entre to a taxonomic system that will help them to identify particular organisms.  The following six chapters are aimed, not simply at displaying the grand taxonomic scheme, but at helping you to put a name on an organism you haven't seen before.  Over the past few hundred years, the way in which organisms have been identified involved detailed morphological comparisons (assisted more recently by developmental and perhaps physiological or biochemical features). 

But in recent years, molecular techniques have been increasingly used to pin down relationships and identities (see Chapter 25 for the ways in which these molecular techniques are carried out).  Now it seems that DNA 'fingerprints' will soon be used to separate species. Paul Hebert, of the University of Guelph, found that he could easily identify all 260 species of butterfly and moth encountered where he lives, on the basis of sequencing the nucleotides in a small part of the mitochondrial DNA.   He has called this a 'species bar code', and many other scientists are now trying to apply this technique across the biological spectrum.

Basically, DNA is obtained from each organism, the mitochondrial DNA is separated from that, then the first 648 base pairs of one mitochondrial gene, the CO1 (cytochrome C oxidase 1) are amplified by the polymerase chain reaction (PCR) before being sequenced.  Each species is believed by Hebert and his colleagues to have a unique sequence for this gene.  So far, differences within species have not generally exceeded 2%, while interspecific differences are much larger.  Many biologists have been surprised that this choice of gene works so well, and there is still scepticism about its universal application.

The next target is a hand-held 'species detector'.  The idea is being worked on, but I'm not sure when these devices will become generally available.  In the meantime, remember that it will always be important to know what an organism looks like, how it behaves, and how it interacts with other organisms and the environment.  The DNA is only a blueprint - not the whole story.  

   Go to Chapter 2a
   Go to Table of Contents

Mycologue Publications 2010

Web Sites and Further Reading on 
Classification and Biodiversity

http://phylogeny.arizona.edu/tree/phylogeny.html   contains information about the phylogenetic relationships and characteristics of organisms, to link biological information available on the Internet in the form of a phylogenetic navigator.

http://www.ucmp.berkeley.edu/chromista/chromistasy.html  gives a taxonomic overview of the phyla placed in the Kingdom Chromista.

http://environment.miningco.com/msubbio.htm?rf=ma&COB=home
&TMog=15251325924750&Mint=15251325924750
has pages on biodiversity.

http://tectonic.nationalgeographic.com/2000/biodiversity/   has pages and maps that document loss of biodiversity (though not in fungi).

Berbee, M.L. and J.W.Taylor (2010) Dating the molecular clock in fungi - how close are we?  Fungal Biology Reviews 24: 1-16.

Cavalier-Smith, T. (2001) What are Fungi? Chapter 1 (pages 3-37) in The Mycota, Vol VIIA. (Eds.) D.J. McLaughlin, E.G. McLaughlin & P.A. Lemke. Springer, Berlin.

Crowson, R.A. (1970) Classification and Biology. Heinemann, London.

Dawkins, R. (1995) River out of Eden: a Darwinian view of life.  Harper-Collins.  Paperback edition 1996, publ. by W.W. Norton.

Hawksworth, D.L. (1991) The fungal dimension of biodiversity: magnitude, significance and conservation. Mycological Research 95: 641-655.

Hawksworth, D.L. (2004) Fungal diversity and its implications for genetic resource collections. Studies in Mycology 50: 9-18.

Heckman, D.S., D.M. Geiser, B.R. Eidell, R.L. Stauffer, N.L. Kardos and S.B. Hedges (2001) Molecular evidence for the early colonization of land by fungi and plants.  Science 293: 1129-1133.

Hibbett, Binder, Bischoff, Blackwell, Cannon, Eriksson, Huhndorf, James, Kirk, Lucking, Lumbsch, Lutzoni, Matheny, McLaughlin, Powell, Redhead, Schach, Spatafora, Stalpers, Vilgalys, Aime, Aptroot, Bauer, Bergerow, Benny, Castlebury, Crous, Dai, Gams, Gaiser, Griffith, Gueidan, Hawksworth, Hestmark, Hosaka, Humber, Hyde, Ironside, Koljalg, Kurtzman, Larsson, Lichtwardt, Longcore, Miadlikowska, Miller, Moncalvo, Mozley-Standridge, Oberwinkler, Parmasto, Rogers, Roux, Ryvarden, Sampaio, Schussler, Sugiyaa, Thorn, Tibell, Untereiner, Walker, Wang, Weir, Weiss, White, Winka, Yao and Zhang.  (2007)   A Higher-Level Phylogenetic Classification of the Fungi.  Mycologia: in press.  (see http://www.clarku.edu/faculty/dhibbett/index.html and click on AFTOL Classification Project)

Jaques, H.E. (1946) Living Things: How to Know Them. Wm.C. Brown, Dubuque.

Kirk, P.M., P.F. Cannon, J.C. David and J.A. Stalpers (Eds) (2001) Ainsworth and Bisby's Dictionary of the Fungi, 9th Edition. CABI Bioscience, UK Centre, Egham, UK. 624 pp.

Lucking, R., S. Huhndorf, D.H. Pfister, E.R. Plata and H.T. Lumbsch (2009) Fungi evolved right on track. Mycologia 101: 810-822.

Margulis, L. and R. Guerrero (1991) Kingdoms in turmoil. New Scientist, 23 March 1991, 46-50.

Margulis, L. and K.V. Schwartz (1982) Five Kingdoms. Freeman, San Francisco.

Miller, O.K. Jr., T. Henkel, T.Y. James & S.L. Miller (2001) Pseudotulostoma, a remarkable new volvate genus in the Elaphomycetaceae from Guyana. Mycological Research 105: 1268-1272.

Patterson, D.J., and Sogin, M.L. (1992) Eukaryote origins and protistan diversity. in The Origin and Evolution of Prokaryotic and Eukaryotic Cells. (Eds.) H. Hartman and K. Matsuno. World Scientific Pub. Co., NJ . pp. 13-46.

Ross, H.H. (1974) Biological Systematics. Addison Wesley, Reading.

Taylor, T.N., M. Krings, and H. Kerp (2006) Hassiella monospora gen. et sp. nov., a microfungus from the 400 million year old Rhynie chert. Mycol. Res.110: 628-632.

Woese, C.R., O. Kandler and M.L. Wheelis (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Science 87:4576-4579.