Taxonomy

Time for another ‘science basics‘ post and this time out I’m tackling the often complex and misunderstood field of taxonomy, quite simply the naming of things. It is quite possibly the most fundamental and important part of biology as a field and yet seems to be glossed over in the few undergraduate courses that even bother to mention it, which is both a shame and a worry. Why is it so fundamental? Well for the quite simple reason that if you do not know what species any given organism belongs to, then it becomes very hard to say anything meaningful about it. How do you protect a given species if you don’t even know what is and what is not a member of that species? Want to treat a snake bite? What species was it? Got a new drug from a rare frog, great! What frog was it? Are you working on a single species of a bunch of them in your lab that have just not been revised properly? You can see the issues – there is a basic one of clarity (all scientists want to be able to communicate clearly about what they are dealing with) but the consequences of making sure that is the case go far beyond that and touch every branch of biology.

Taxonomy is basically a filing system that allows us to find and identify any given species (and of course higher ranks like families, genera and even kingdoms). A good analogy is a literal filing system where each hierarchical rank contains others (for those that don’t know the major ranks are in order: kingdom, phylum, class, order, family, genus, and species, though there are plenty of minor ones too). So a kingdom could be a building, with the floor number the phylum, the right room telling you which class, the filing cabinet the order, the drawer of the cabinet the family, each files as a genus and in each file the sheets of paper represent a species. Each of those has a biological definition and a formal name to avoid confusion, so as opposed to building 5, floor 2, room 3, cabinet 4, drawer 2, file 13, species 3 we have Animalia, Vertebrata, Mammalia, Primates, Hominidae, Homo and sapiens for humans. Hopefully that all quite straight forward and simple, and of course the analogy should also make it clear why good taxonomy is essential – if you file something in the wrong place, not only will you have trouble finding it, but you will also make mistakes by referring to it when it shouldn’t be there. A stretch perhaps, but it works well enough. If something is in the wrong place through because it has the wrong definition then not only might you lose it, but you might also compare it to other things that you shouldn’t and come to the wrong conclusion.

The whole process of naming a species may seem simple (find the organism, makes sure it’s new, bung a name on it) but in fact is actually quite complex. The primary problem being the age old issue of what is actually a species? Many if not most readers will know what is typically called the ‘biological species concept’ which roughly runs as “a species can interbreed with other members of the species to produce fertile offspring”. This is a great working concept and is both important and common, but it is one of many (for a start it obviously can’t be applied to organisms that reproduce asexually and there are plenty of them). Bacteria have all tricks to shift genes between spies that might be considered parts of different *orders* let alone the same strain, so a definition based on even conservation of genetic material would even be problematic. I wont’ get dragged into species concepts here as there are far too many, but it is an interesting field and an increasingly important one. The reason that there are so many is the simple fact that some work well for some species and not others, and life is nothing if not crammed with exceptional and extraordinary variation. It is very hard to objectively compare a virus, a fish, a coral, a lichen, a fungus, a tree, a bacterium and a whale with just one definition and thus we need a whole box of tools to deal with these complexities and of course life itself is actually a continuum. We have things like ring species and lichens (themselves a combination of two organisms, some of which can exist independently of the ‘parent’) that make a confusing mess of any straight lines we might want to make.

While generally avoiding specis concepts, I will add a brief note on the morphological species concept, as it is so important to palaeontology. Obviously we can’t conduct breeding experiments on fossils or check their DNA and so species are identified acording to their shape and form, with taxonomists using differences in the bones, or shells, or whatever to distinguish and categorise different taxonomic groups.

Returning to the main theme, the concept of species (and other ranks) is one that is completely artificial and is simply being applied to a fluid and ever changing pattern of life simply for our convenience. We simply have to apply our own rules and ideas about species as best we can to reality, and rely largely on convention and understanding of the researchers to paper over the cracks that will naturally exist. A bacterium species is *not* the same as a mammal species, and nor is a species of extant mammal the same as that of an extinct one. (Incidentally this is also part of the reason why comparing species across major groups is incredibly problematic for example using rates of mammalian extinction to estimate the same in other clades). Each research group largely has their conventions and essentially species concepts are largely arrived at by consensus. After all, if an avian taxonomist can’t tell you whether or not a new bird is a new species is, then who can? The old adage that a species is “what a good taxonomist says it is” might seem trite, but it is also largely true. One simply cannot conjure up rules and blanket apply them to all organisms, life is sadly not that obliging. How then, can we define a species satisfactorily? The answer lies in how descriptions, or more properly the diagnoses of new (and actually old) species are produced.

When a species is formally named and described a diagnosis must be produced. This is essentially a list of characteristics that can be used to identify this species and indeed differentiate it from others. These can either be unique (i.e. this species has it and nothing else does) or a unique combination of characters (e.g. some birds have black wings, some have red beaks, but only this one has black wings and a red beak) and typically there will be a fair few of them. You want lots of characters so you can avoid making mistakes with later identifications and of course to make sure that what you are describing is distinct from everything else. As a vertebrate palaeontologist I only really have to deal with morphological features (shape and structure) of bones and teeth, but of course these can include behaviours, colours or patterns, muscles, or even molecular data (DNA sequences, the composition of venom or other complex chemicals and so on). One final thing is that the description must be accompanied by an actual physical specimen (in a museum). This is called the holotype specimen and basically acts as the registration for the species so all future researchers can (in theory anyway) compare their specimens to this one to ensure they are the same thing.

[It is actually rather more complex than this, but these are the essentials. It's so complex in fact that there are entire organisations devoted to the micro ins and outs of taxonomy and huge volumes of rules and regulations that run over to over a thousand pages, with different divisions for different kingdoms. I deal with the ICZN (International Code for Zoological Nomenclature) which is rather an easy one compared to say plants or bacteria that can reproduce in all kinds of weird ways and cause still more problems].

The diagnosis will of course be part of a formal scientific paper (actually it doesn’t have to be – another problem that badly needs to be corrected) and must pass through peer review. LINK So again the consensus idea comes into play as obviously it will be other specialist taxonomists who will decide if your diagnosis is good enough and suitable in the context for naming a new species (or any rank of course). One obvious flaw here is that not all descriptions are long and detailed, or reviewed by specialists if the description is attached to a larger paper that also deals with other issues (something I have railed against before). Another one is that things can date incredibly quickly and need constant revisions.

You can describe a new species with a whole list of interesting features that makes it clearly different to everything else, and then someone comes and finds something else, also new and definitely different, but that has all of your features too. So now you need to not only described and diagnose the second species, but the diagnosis of first one needs to be updated so it can be told apart from the other one. Then a third is found…  This is especially true of many palaeontological descriptions where characters are far fewer in number (less fundamental information for just bones and of course you might only have a bit of the skeleton to work from as well) and so new discoveries can often match all the details you were able to provide while clearly being new and different forcing revisions of the old one and a description of the new. You also get synonymy too – where two (or more) things have been given different names, despite being the same species and these have to be sorted out as well.

Thus taxonomists are constantly fighting what is in many ways a losing battle, having to rewrite and revise old definitions as well as describe new species, and as new methods are employed (look at the revisions that have occurred since the advent of genetic sequencing which was unknown only 10 or 20 years ago). It is basically impossible to keep up to date and keep everything accurate, yet it is essential.

Without the basic work being down or what is and is not a species, every branch of biology has immense difficulties with dealing with even the simplest bits of research. If you have two organisms in front of you and cannot confidently answer the question of “are they the same species or from two different ones?” there is only so much work you can do.

Sadly taxonomy is increasingly dying out as a specialist subject and it is only a matter of time before this becomes a serious problem. There are simply fewer and fewer people being formally trained as taxonomists and fewer and fewer research positions for them to fill. At the same time with the increase in funding for conservation are captive breeding programmes and the ‘goldrush’ or bioprospecting more and more species are being found, but these efforts are fundamentally undermined without good taxonomy. The subject seems to be seen as unexciting and even unnecessary compared to fields like ecology, evo/devo, gene sequencing and so on (both by researchers themselves and more worryingly by research funding bodies) but these can only go so far without the basics. We are building an increasingly high tower of new finds and new areas of research without firm foundations, and the problem is getting worse on an almost daily basis. Still, could be worse. Probably.

Well there you have it as briefly as I could manage, a fundamental outline to how taxonomy is practiced and why it is so essential to every aspect of biology. I do wonder how far astrophysicists would get if they could not classify star types, or the problems chemists would have if there were no fixed definitions for the elements or molecules they work with, yet this is effectively what we are doing in biology. Hopefully this goes a little way to explaining not just why this is important, but also why it is important that it is done *well*. If not, people will make mistakes based on the information they are given and it will all have to be done again. I’d be more positive if I could but the fact is that money is draining away from this field and eventually we will reach a genuine crisis in biology, and it is the very field of conservation that it will probably hit most dramatically and yet I the one (in terms of the global environment) that most needs protection.

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