"Taxonomy is classification, as well as the how-to of classification, and its rationale" (Groves, 2004:1105). That is to say, it is the study of why we classify organisms, and how best to do it; "a taxonomy" is often used to mean simply a classification. It is, in its more theoretical aspect, nearly the same as Systematics, which is generally taken to encompass much more about evolution and biodiversity.
The basis of taxonomy is the species. Species are the units of the living world -- but how we define and recognize these units is controversial to perhaps an unexpected degree. What we mean by species affects genetics, biogeography, population biology, ecology, and ethology, in the present-day sphere; palaeontology and palaeoanthropology; and, in an era in which threats to the natural world and its biodiversity are ubiquitous and accelerating, it affects conservation strategies (Rojas, 1992). And so we have the flourishing field of "species concepts". Mayden (1997) distinguished as many as 24 different species concepts; as many of these are simply variants of each other, I will talk only about five.
The Evolutionary Species Concept (ESC) was proposed by Simpson (1961): “A lineage… evolving separately from others and with its own evolutionary role and tendencies”. Commentators such as Mayden (1997) and Groves (2001) agree that this definition goes to the heart of the matter, and encapsulates what a species really is, but of course it is no help in a practical sense. What we need, in effect, is a way of recognising an evolutionary species when we see one.
Under the Biological Species Concept (BSC), species are defined as “groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups” (Mayr, 1963). Hence what distinguishes a species is its reproductive isolation. The nature of reproductive isolating mechanisms (RIMs) was discussed by Dobzhansky (1937), who first coined the term; they may be either premating or postmating. Premating RIMs include those that prevent potential mates from meeting (seasonal or ecological), or from mating if they do meet (ethological), or from permitting sperm transfer if they get as far as mating (mechanical). Postmating RIMs include embryo mortality, hybrid inviability, and hybrid sterility. A very widespread misunderstanding of this is that “different species cannot interbreed, or if they do their hybrids are sterile” -- but it should be clearly understood is that this is a misunderstanding, and Mayr (1963) devoted two entire chapters of his classic textbook to trying to explain why it is a misunderstanding -- to no avail, it would seem, as far as many people, including all too many that are biologically trained, are concerned!
The BSC works very well if two taxa are sympatric (that is, they occupy the same geographic area), then they are reproductively isolated: they are distinct species, and no further discussion is possible. If they are parapatric (they occupy bordering areas), then equally they have the chance to interbreed, and do not. But what if they are allopatric (they occupy discrete areas)? Several authors have emphasised that the BSC is simply not applicable in cases of allopatry (see, especially, Groves, 2004), and this is perhaps the most cogent reason why the BS cannot be "the" species concept. Another reason is, quite simply, that mtDNA analysis has shown that even widely sympatric species do often interbreed, but looking at phenotypes one would never know it.
Under the Recognition Species Concept (RSC), proposed by Hugh Paterson (Paterson, 1978, 1982), species are recognised by having unique Specific Mate Recognition Systems (SMRSs): one individual emits a signal, to which another responds. A species would be a population (or group of populations) whose members share a common SMRS.
But how to recognise SMRSs in practice? One proposal that has been widely followed, and has proved extremely fruitful, has been to analyse vocalisations. Bushbabies or galagos (Galagidae) were conventionally divided into six species (Napier & Napier, 1967), but throughout the 1980s and 1980s the number was increased, in particular because studies of vocalisations had proved crucial in alerting researchers to the coexistence of sympatric species pairs (Masters, 1991; Nash et al., 1989). As fieldwork progressed, it became evident that allopatric populations within what had previously been deemed unitary species were also, very often, distinguished by unique vocalization types, so that Bearder et al. (1995) felt able to predict the existence of new species. One of these previously undescribed species, first identified by its vocalizations, was indeed subsequently found to be morphologically distinct, and was duly described as such, under the name Galagoides rondoensis (Honess, 1996). Further studies are underway by Simon Bearder's team at Oxford Brookes University to test the reality of other galago species predicted from their vocalizations.
There are several problems with the RSC: would one, in every case, know what actually is a SMRS? Once you have identified them -- vocalizations, splashes of colour, and so on -- how "different" do they have to be in order for one to say that there are two different species involved? And there is always the problem that if two populations happen to have the same apparent SMRS, however different they may be in other respects, some overzealous practitioner of the RSC is going to unite them into a single species!
The Recognition Species Concept has more than proved its value in primatology, yet it has its problems as I have indicated. In particular it may fail, for practical reasons or simply because it does not go far enough, to identify the full range of biological units that we seem to mean when we speak of “species”.
Phylogenetic Species Concept (PSC). This has gone through much discussion, and differing authors have had different views of it, but a good definition is that a species is “an irreducible cluster of sexual organisms within which there is a parental pattern of ancestry and descent and that is diagnosably distinct from other such clusters by a unique combination of fixed characters” Christofferson (1995). Diagnosably distinct means, quite simply, that they are 100% diagnosable (given age/sex variation); they have fixed heritable differences between them; they are genetically isolated, though not necessarily reproductively isolated. The designation "phylogenetic" was given because, under this concept, species are the terminal points on a cladogram, that is to say, they are the least inclusive phylogenetic units -- it has sometimes been misunderstood as implying that species must have a long phylogenetic history, but all that is necessary is in fact that each species is absolutely distinguishable from any other.
Essentially, the BSC can be characterized as a species concept for the lumpers -- it sees the wood, but tends to miss the individual trees. On the contrary, the PSC is a concept for the splitters: it is very concerned at identifying the individual trees, thinking it better to leave the wood for a future state of analysis. It has often been pointed out that the PSC and RSC commonly identify the same units as being species. The PSC has the advantage that it can be used in cases where we do not know anything about SMRSs, hence even can never know anything about them (as in the case of fossils), and that it identifies as species many cases which the RSC will miss because they happen not to differ in features that are known or suspected to act as SMRSs in their relatives. And it is necessary to identify the units of biodiversity: the conservation crisis reminds us of that.
The idea that species ought to be more differentiated genetically than infraspecific groups has a long history goes back to Ayala (1975), who compared values for Genetic Identity and Distance, using various proteins, for various animal groups, showing that species (in invertebrates, fish, salamanders, lizards and rodents) tend to differ more than do subspecies, which in turn differ more than do different local populations. But there are overlaps: one simply cannot say that a certain degree of difference indicates species, a lesser degree indicates subspecies, and so on. In more recent times, the availability of DNA sequencing has provided an enormous amount of data on which to perform similar exercises, but unfortunately what started off as a "rule of thumb" has often been used in a rather rigid way. Curiously, it was not until a key paper by Bradley& Baker (2001) that this idea of species received the name: the Genetic Species Concept (GSC). Bradley & Baker tested the amount of sequence divergence in mtDNA among bats and rodents, finding at least the same amount of overlap between species and subspecies (actually, infra-specific units in general); moreover, different species of rodents seem to be characteristically associated with higher sequence-divergence vales than different species of bats.
Therefore, although the average species pair differs more (in at least mtDNA) than does the average intraspecific (including subspecies) pair, it is simply not possible to draw a line at some level of sequence divergence and say that above this level they are species, below it they are not. Differences in sampling or in taxonomic practice could account for some of the variation, and high intraspecific genetic distances could be due to retention of ancestral polymorphism and unsual delays in lineage sorting; but we must simply adjust to the fact that even well-differentiated species pairs may show extraordinarily little sequence divergence in a given DNA region.
In a later paper, Baker & Bradley (2006) went on to consider the GSC in more detail. A genetic species, in their definition, is "a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups". This makes it very close to the PSC; indeed, I have maintained (above) that the quality of being genetically isolated is part of the consequences of the PSC. Yet they continue to urge the relevance of genetic distances. This, as I have explained above, is a subjective notion; yet it has a heuristic value, because there are cases where genetic data alone suffice to identify species. There is no doubt that the use of GSC-inspired concepts has been enormously valuable in uncovering cryptic diversity in nocturnal Malagasy lemurs. Yet when all is said and done, species identifications under the GSC, like those under the RSC, fall well within the parameters established for the Phylogenetic Species Concept. Hence I recommend that Primate species be recognised according to the following definition (Eldredge and Cracraft, 198
“A species is a diagnosable cluster of individuals within which there is a parental pattern of ancestry and descent, beyond which there is not, and which exhibits a pattern of phylogenetic ancestry and descent among units of like kind”.
Ayala, F.J. (1975): Genetic differentiation during the speciation process. Evol.Biol. 8, 1-78.
Baker, R.J.; Bradley, R.D.(2006): Speciation in Mammals and the Genetic Species Concept. J.Mamm.87, 643-662.
Bearder, S.K.; Honess, P.E.; Ambrose, L. (1995): Species diversity among galagos with special reference to mate recognition. In: Creatures of the Dark: the Nocturnal Prosimians. Ed. by L.Alterman, G.A.Doyle and M.k.Izard. New York: Plenum Press. Pp 1-22.
Bradley, R.D.; Baker, R.J. (2001): A test of the genetic species concept: cytochrome-b sequences and mammals. J.Mamm. 82, 960-973.
Christofferson, M.L. (1995): Cladistic taxonomy, phylogenetic systematics, and evolutionary ranking. Syst.Biol. 44, 440-454.
Cracraft, J. (1983): Species concepts and speciation analysis. Curr.Ornithol. 1, 159-187.
Dobzhansky, T. (1937): Genetics and the Origin of Species. New York: Columbia University Press.
Groves, C.P. (2001): Primate Taxonomy. Washington, D.C.: Smithsonian Institution Press.
Hey, J. (2001): The mind of the species problem. Trends Ecol.Evol. 16, 1326-329.
Honess, P.E. (1996): Speciation among galagos (Primates, Galagidae) in Tanzanian forests. PhD thesis, Oxford Brookes University, U.K.
Mayden, R.L. (1997): A hierarchy of species concepts: the denouement in the saga of the species problem. In: Species: the Units of Biodiversity. Ed. By M.F.Claridge, H.A.Dawah and M.R.Wilson. New York: Chapman and Hall.
Masters, J.C. (1991): Loud calls of Galago crassicaudatus and G.garnettii and their relation to habitat structure. Primates, 32:153-167.
Mayr, E. (1963): Animal Species and Evolution. Harvard: Belknap Press.
Napier, J.R.; Napier, P.H. (1967). A Handbook of Living Primates. London: Academic Press.
Nash, L.T.; Bearder, S.K.; Olson, T.R. (1989). Synopsis of Galago species characteristics. Int.J.Primatol., 10:57-80.
Paterson, H.E.H. (1978): More evidence against speciation by reinforcement. S.Afr.J.Sci. 74, 369-371.
Paterson, H.E.H. (1982): Perspective on speciation by reinforcement. S.Afr.J.Sci. 78, 53-57.
Rojas, M. (1992): The species problem and conservation: what are we protecting? Conserv.Biol. 6, 170-178.
Simpson, G.G. (1961): Principles of Animal Taxonomy. New York: Columbia University Press.
Colin Groves earned a Ph.D. from London University in 1966, spent two years as a post-doc in the University of California at Berkeley, then took up a fixed term appointment at Cambridge University, and in 1974 came to the School of Archaeology and Anthropology at the Australian National University in Canberra. He has done field work in Kenya, Tanzania, Rwanda, Indonesia and Iran. His specialty is taxonomy and phylogeny of primates, including human evolution. He has also done a great deal of work on ungulates, and some on carnivores, rodents, marsupials and monotremes. For nearly 30 years, he has been a member of the Australian Skeptics, which combats pseudoscience, especially creationism, and those aspects of "traditional medicine" regimes that use animal body parts as supposed cures and which have been so damaging to wildlife. He has published around 200 peer-reviewed scientific papers, and a number of books and monographs including the influential Primate Taxonomy in 2001 and Bones, Stones and Molecules with D.W.Cameron in 2004 and Extended Family: Long Lost Cousins. A Personal Look at the History of Primatology in 2008.