Cladistics - also called Phylogentic Systematics or Phylogenetic Taxonomy - is a method of classifying organisms by common ancestry, based on the branching of the evolutionary family tree. Cladistics is currently the most popular paradigm of phylogenetic classification in biological taxonomy. Based strictly on determining branching points in the ancestry of organisms, it establishes groups based on their shared, derived features (synapomorphies), while ignoring primitive features (plesiomorphies) inherited from ancestors. Organisms that share common ancestors (and therefore have similar features) are grouped into taxonomic groups called clades. Like Evolutionary Systematics (which it has currently supplanted) Cladism is a method of classification based on the evolutionary history of organisms, dividing organisms into meaningful groups and subgroups. It was developed by Willi Hennig, an entomologist, in 1950, but was not really accepted until the 1980s.
Clades can be represented in terms of a cladogram. A cladogram is a branching diagram that depicts species divergence from common ancestors. They show the distribution and origins of shared characteristics.
Cladistics is based on three principles:
Cladistic Phylogenetic Systematics acknowledges only Monophyletic groupings as valid. Paraphyletic groups (accepted in the Linnean hierarchy and in Evolutionary Systematics) and Polyphyletic groups are rejected as invalid, as is the whole Linenan hierarchy above genus rank (although sometimes taxa such as family etc are used in a more limited context)
Cladistics would seem at first to be more objective then the linnean and linnean-based systems, simply because in getting rid of higher taxa it also does away of the arbitrariness of whether a higher taxon is, say an order or a class.
Cladists believe that cladograms are testable hypotheses of phylogenetic relationships. Cladistic methodlogy can even be used to predict properties of yet-to-be discovered organisms.
A problem with the cladistic definition is that there is no certainty which features are unique to that group (diagnostic in other words) and possesed by the most recent common ancestor and which evolved later.
To give an example. When cladistics first came out there was a huge reaction against palaeontology. The fossil record was considered irrelevant to deducing the history and relationships of organisms. Some bright spark then came upon the idea that because birds and mammals have a number of metabolic and anatomical features in common (these being necessary in order for them to function as endotherms - warm-blooded animals) they must have descended from a single Most Recent Common Ancestor that was unrelated to all other (cold-blooded) reptiles. So the clade Haemothermia ("warm blooded") was coined. This strange concept appeared in some of the respectable scientific literature and was considred quite respectable for some time, although it received a humourous write up in New Scientist (I don't recall the volume number unfortunately).
What this example proves is that depending on which charateristics we use, we have a different common ancestor. If metabolism is used birds and mammals are close cousins and crocodiles unrelated to each (the Haemothermia hypothesis). If skull and heart structure is used birds and crocodiles are close cousins, and mammals unrelated to each. (the standard hypothesis). This proves that despite being an attempt to construct a more "objective" system than the Linnean one, cladistics still has to fall back on the same subjectivity and arbitrariness.
Another illustration of difficulties facing cladistic methodology are given by vertebrate palaeontolgist Philippe Janvier (himself a dedicated cladist) in his book Early Vertebrates.
"Until the 1970s, discussions on interrelationships of major taxa were relatively simple to sum up. Since they were based on the consideration of a small number of characters. Most of them were 'pet characters' of one or another authority, and the 'minor' characters that contradicted them were regarded as homoplasies or simply not considered. With the advent of phylogenetic systematics, or cladistics, an increasingly large number of characters were taken into consideration for phylogeny reconstruction, but it was still possible to compare and discuss contradictory cladograms, since these were few. Since efficient cladistic computer programs came on the scene, the phylogenies, and the characters on which they are based have become so numerous that the task of comparing in detail the merits of respective phylogenies is now virtually impossible at the level of a general book such as this. This method of analysis of the characters, which no doubt will be in general use for a long time, is based on parsimony, and the only point that can be discussed by the average reader is the criterion of choice among a number of equally parsimonious trees. The consensus tree of these equally parsimonious trees produced by the computer is often the only result published by phylogeneticists, and it is generally not very informative. There are even instances of authors who have published only one of the 400 or 500 equally parsimonious trees they obtained, but without telling the reader! Moreover, the options Offered by current cladistic computer programs are numerous and the same data matrix may produce widely different sets of trees, depending on character weights, ordering of character states, etc. Less than ten years after the publication of the first computer-generated phylogenies of the major craniate groups, the discussion of the various competing phylogenies, character by character, has become quite difficult."
One particular illustration of how cladistics can go astray through excessive input of data (and suggestions on how to avoid this happenning) see Toby White's Crocodyliform Notes.
The positive side of things though is that this method of considering character-state distributions prevents - to some extent - writers from falling in the pitfall of 'pet characters'. Second, the rapidity of such character analyses enables a large number of research workers to propose phylogenies based on various sets of characters. Over a period of less than ten years, it appears that the trees produced for the same (mainly recent) taxa are more and more stable, that is, better and better corroborated [Ibid]. Of course we have to remmeber that a consensus is not necessarily the truth. Science can indeed be seen as a progression of more and more useful metaphors, but as Thomas Kuhn has shown it is not an inexoerable march from ignorance to truth.
illustration from Philippe Janvier Early Vertebrates
(Clarendon Press, Oxford, 1996), p.286
One of the big weaknesses of the cladistic system is it's disregard of the sequence of fossils in the stratigraphic record. This is based on the fact that cladists seem to assume it is enough simply to know all the charcateristics of the representative members of a group in order to work out their precise phylogentic relationships. If the resulting cladogram agrees with the fossil record for the group (the "basal" (= primitive) taxa appearing first, the most "derived" (=advanced) taxa last, well and good. If it doesnt the fossil sequence is rejected. The reasoning seems to be that since the fossil record is so incomplete in any case the missing taxa smply werent preserved, but lived elsewhere. The result is a series of hidden or "ghost" lineages that are base don absolutely no evidence other than assumptions drawn from (possibly unreliable) cladograms.
A good illustration of the vagaries of (either on or both) the cladistic method and the fossil record is shown in the diagrams to the left, from Philippe Janvier's book Early Vertebrates. At the top are cladograms of two families of closely related early Devonian Ostracoderms (armoured jawless fish - in this case Osteostraci), the Kiaeraspididae (A) and the the Boreaspididae (B). Both groups of organisms are found in the same locality (the Wood Bay Formation of Spitzberg) and the animals when alive presumably lived in a very similiar environment and had similiar habits (lagoonal bottom-dwelling filter-feeders). At the bottom is shown the stratigraphic range of each of these taxa. These creatures were geographically localised (endemic) and lived in conditions that favoured preservation. In addition their hard exoskeletons (head shields) were easily preserved. So we have pretty optimal conditions here.
Now, here is something interesting. The Kiaeraspidid (A1) cladistic analysis matches their stratigraphic occurances (A2). The most basal or primitive species (a) also appears earliest (at the bottom of the stratigraphic chart). And the most advanced or specialised ("derived") species (g) and (h) occur last (top of time range diagram).
But the exact same cladistic analysis appled to the Boreaspidids (B1) does not match their stratigraphic occurances (B2). Although the basal taxon (i) is also among the earliest, some of the most advanced types (r) are equally ancient.
So we have a situation where apparent "ancestors" (well, the grand-uncles rather than the grand-fathers, because cladistics is all about the descendents of the common ancestor, never the common ancestor at the base of the node) appear after their "descendents"
The cladistic assumption is simply that the fossil record is incomplete. These creatures evolved elsewhere, or if they evolved in that locality they were not preserved. However, it is possible to reconstruct the "ghost lineages" - e.g. the dotted line in the Sigurdfjellet formation leading to the j/k/l/m cluster that appears on the next formation up (more recent).
I would offer an alternative and I believe much simpler (though obviously equally one-sided) explanation. The cladistic analysis of the Boreaspidids may simply not be as accurate as the Kiaeraspidid analysis. The j/k/l/m cluster, rather than being a basal group, may actually be an advanced one, like the s/t grouping, and it only appears primitive (perhaps through degeneration or loss of characteristics).
It is of course impossible to tell which of these two alternatives is the correct one. Lacking a functioning time machine, one cannot travel back and actually observe these creatures evolving, making stopover observations at, say, 50,000 year intervals, while hopefully avoidng the grandfather paradox! ;-) In that way phylogenetics is not and cannot be a hard science in the way chemistry, physics, or even neontological (study of extant species) biology is. Between science and metaphysics there is not such a gap after all, a sobering realisation that nevertheless gives a perceptive insight into the way our understanding of the world works.
Proceedings of a Mini-Symposium on Biological Nomenclature in the 21st Century - suggests replacing the Linnean system with a cladistic phylogenetic systm of nomenclature.
Systematic Zoology - basic intro to Cladistics
Introductory Glossary of Cladistic Terms - Michael D. Crisp
Cladistics - notes and glossary
The Compleat Cladist: A Primer of Phylogenetic Procedures by E.O. Wiley, D. Siegel-Causey, D.R. Brooks, and V.A. Funk - first edition - available free for download in Adobe Acrobat format. (648 kb)
Willi Hennig Society Homepage
Glossary of Phylogenetic Systematics with a critic of mainstream cladism - Günter Bechly - best coverage
Crocodyliform Notes - Toby White - a somewhat technical essay (at least for the non-specialist) that is worth persevering with, as it gives a useful illustration regarding the strengths and weaknesses of the Cladistic system.
Re: Quick cladistics question - Adam Yates makes some pertinant observations on difficulties arising in cladism through the use of Linnean terms. From the Dinosaur mailing group archives
Much ado about species (and genus) level taxonomy - how the species concept fits in with cladism. A distinction is made "between lineages (a series of entities forming a single line of direct ancestry and descent; [e.g. a species]) and clades, clans, and clones (all paths or lines of descent from a given ancestor). Clades, clans, and clones are monophyletic, whereas lineages may be paraphyletic." by Thomas R. Holtz; from the Dinosaur mailing group archives
Why Do Biologists Need Cladistics? - short entry