Those who belong to the official lichen listserve, 'LICHENS-L', may remember a few months ago when someone threw out the fact that some biologists have adopted the notion that "There is nothing unique or special about the 'species' as a taxonomic rank". This idea is not in any way unique to lichenology, but within that forum I gave the following response:
There is no question that genetic recombination creates forces that maintain uniformity and keep members of 'species' morphologically and molecularly similar to one another; this is not the case for higher taxonomic ranks, where similarity within a group can generally be attributed only to common ancestry or ecology. When these forces break down permanently because of some reproductive barrier, we generally call that a 'speciation' event. This is obviously based on a Biological Species Concept (BSC) which says that a 'species' is essentially a group of interbreeding individuals reproductively isolated from other such groups. From my perspective, that is the only 'real,' justifiable species concept. However, other species concepts (e.g., phylogenetic, morphological) are perfectly valid in that they provide excellent insight into what the groups of interbreeding individuals are likely to be (this is usually very hard to demonstrate experimentally, so the BSC is often not practical from a scientific standpoint).
Of course, this leaves out asexual organisms, and those must be pigeon-holed because the species are not 'real' (i.e., they do not represent anything uniquely different from any other taxonomic rank). In these cases, species merely become names for phylogenetic entities possessing shared innovations that have altered the course of their evolutionary history (still valid, but no different from genera, families, etc.).
We must also not forget hybridization, polyploidy, etc., which can throw a wrench into the system. These events can have major effects and cause instant 'speciation' (reproductive isolation) even though they are seemingly quite rare. In some cases you can get new species with multiple progenitor species. We have good examples of this in plants, but I really wouldn't be surprised to find all sorts of crazy things that we just do not know about yet happening in the fungi!
If your perspective is only phylogenetic, then it is true that 'species' often do not show up clearly and distinctly as special units per se. However, if you can analyze a combination of molecular, morphological, ecological, and geographical features of organisms, then you can begin to infer 'biological species' by assuming that there are forces maintaining some degree of uniformity within each unit (but as I implied above, this is not always a sound assumption).
There is no doubt that the question of 'what makes a species' is a difficult one (the evidence for this is in the fact there there are so many well-accepted 'species concepts'), but it does not mean that we should throw out our species concepts and simply say that 'species' is just another taxonomic rank like any other. If we do this, we are likely to miss the significance of certain phenomena that take place all around us in the natural world.
-Brendan Hodkinson, Duke University