|Evolutionary systematics||Molecular phylogeny|
Phylogeny and Systematics
A modern cladogram. Strict consensus of 20 minimum length trees for the equally-weighted parsimony analysis of the combined data set (57,269 steps). The contents of 12 taxonomic groups, including the total clades Cetaceamorpha and Cetancodontamorpha are delimited by different colored boxes ('Hippo' = Hippopotamidamorpha). Lineages that connect extant taxa in the tree are represented by thick gray branches, and wholly extinct lineages are shown as thin black branches. Estimates of branch support scores are above internodes; given the complexity of the data set, these should be interpreted as maximum estimates.
A cladogram is a phylogenetic tree made up of dichotomous branches, with groups of organisms or individual species represented as terminals (the ends of each branch). Each branching point, or node represents divergence from a hypothetical common ancestor, and is defined in terms of shared characteristics inhereted from that ancestor. A cladogram is not a literal evolutionary tree, but a way of representing phylogenetic hypothesis, regarding the way living organisms are related to each other. Each branch derived from that node is considered a natural grouping, and called a clade. Every clade has to be monophyletic, that is, it has to derive from a single ancetsor, and must include every descendent. Nodes do not represent actual ancestral taxa. Were an actual ancestor to be included it would ideally appear (if the cladogram is correct in this regard) as the sister taxon of the sub-clade that includes all its descendants.
Originally, cladograms used Hennigian methodology, and were based on immediately apparent synapomorphies and the simplest branching order (called parsimony). Although easy to draw they were difficult to quantify, as distinguishing a synapomorphy unique to that clade from a shared primitive state or an evolutionary convergence may be problematic.
From the 1990s onwards, cladograms have tended to become bigger and more complex, as powerful computers make it possible to run cladistic analyses using hundreds of traits and taxa, plotted in supermatrixes. Emphasis shifts from a few easily recognised synapomorphies to large arrays of quantifiable data, statistically analysed in terms of parsimony or likelihood (which may not be the same). A lot depends on how statistically robust the actual branches are. Although some clades are robust, others may not be, for example, including or deleting a few taxa or character states can change the shape (topology) of the entire cladogram. The current trend in cladistics is to incorporate data from molecular sequencing; these total evidence cladograms are important in phylogenetics
As a result of the cladistic and phylogenetic revolutions, cladograms have almost entirely replaced Haeckelian and Evolutionary trees in textbooks and popular science books. A distinction should be mnade however between the three superficially similar dichotomous branching diagrams: the chronogram, the cladogram, the dendrogram, the phenogram, and the phylogram.
Cladograms give information about branching order, but not about the amount of evolutionary change or stratigraphic range, or even superficial similarity. Cladograms can be drawn in any direction; it doesn't matter, all that matters is the sequence of branching, the topology or shape of the tree (which taxa are related to which). Several types of cladograms are used, depending on the methodology; these are referred to by somewhat unofficial terms:
Computational cladograms statistically, and should show (using small superscripts and subscriptts) how robust - how strongly or weakly supported - each branch is, depending on the algorithm used; there is the tendency for them to only have individual species in each terminal. Because there rae many possible trees (phylospace), computational cladograms are phylogenetic hypothesis, which are used in phylogenetics
Supertrees are cladograms of cladograms; they are constructed through using individual cladograms as if they were taxa and avoid the problem of excessive number crunching when using large numbers of taxa. These impressive diagrams have a lot of appeal, especially as regards the goal of large scale tree of life phylogeny, although as with anything they are not without their difficulties; for example they were only as good as the data that generated the component cladograms.
Phylograms are statistical diagrams used in molecular phylogeny. They not only show the branching sequence, exactly as in cladograms, but also the degree of evolutionary change or difference of each species, as shown by the length of the branch; the longer the branch, the motre change. They can be rooted or unrooted; rooted trees show the ancestors, whereas unrooted ones don't.
Phenograms are statistically generated trees used in phenetics. They look like cladograms but aren't. They only give information about overall similarity. While they may be useful for identifying species, they are now rarely uised
Chronograms are like cladograms, but use the contrast of thin/unshaded and thick/shaded branches to show the stratigraphic range of the taxon represented by each branch. They are widely used and have replaced spindle diagrams in books and scientific papers
Dendrograms as we use the term here, are informal cladograms. They are not intended as hypotheses but as speculative phylogeny, and are informal supertrees and phylogenies. They are popular on paleo discussion mail list, and on some projects like the Tree of Life web project. Here at Palaeos we use dendrograms to organise the taxonomic pages.