(last update : 08-11-1999)


1. Purpose of phylogenetics :

2. Disclaimers :

3. Terminology :

Tree terminology

Figure 14 : The tree terminology.

4. Possible ways of drawing a tree :

Trees can be drawn in different ways. There are trees with unscaled branches and with scaled branches. Is is also possible to draw these trees with or without a root. For rooted trees, the root is the common ancestor. For each species, there is a unique path that leads from the root to that species. The direction of each path corresponds to evolutionary time. An unrooted tree specifies the relationships among species and does not define the evolutionary path.

Drawing a tree

Figure 15 : Some possibilities for drawing a tree. (these are just a few examples, there are a lot of variations possible)

5. Methods of phylogenetic analysis :

There are two major groups of analyses to examine phylogenetic relationships between sequences :
  1. Phenetic methods : trees are calculated by similarities of sequences and are based on distance methods. The resulting tree is called a dendrogram and does not necessarily reflect evolutionary relationships. Distance methods compress all of the individual differences between pairs of sequences into a single number.
  2. Cladistic methods : trees are calculated by considering the various possible pathways of evolution and are based on parsimony or likelihood methods. The resulting tree is called a cladogram. Cladistic methods use each alignment position as evolutionary information to build a tree.

5.1. Phenetic methods based on distances :

  1. Starting from an alignment, pairwise distances are calculated between DNA sequences as the sum of all base pair differences between two sequences (the most similar sequences are assumed to be closely related). This creates a distance matrix.
  2. From the obtained distance matrix, a phylogenetic tree is calculated with clustering algorithms. These cluster methods construct a tree by linking the least distant pair of taxa, followed by successively more distant taxa.

5.2. Cladistic methods based on Parsimony :

For each position in the alignment, all possible trees are evaluated and are given a score based on the number of evolutionary changes needed to produce the observed sequence changes. The most parsimonious tree is the one with the fewest evolutionary changes for all sequences to derive from a common ancestor. This is a more time-consuming method than the distance methods.

5.3. Cladistic methods based on Maximum Likelihood :

This method also uses each position in an alignment, evaluates all possible trees, and calculates the likelihood for each tree using an explicit model of evolution (<-> Parsimony just looks for the fewest evolutionary changes). The likelihood's for each aligned position are then multiplied to provide a likelihood for each tree. The tree with the maximum likelihood is the most probable tree. This is the slowest method of all but seems to give the best result and the most information about the tree.

6. Theoretical problems with evolutionary changes between sequences

The next figure shows that there is a chance that many more mutations occur than visible at a certain time. Even the best evolutionary models can't solve this problem...

Possible mutations

Figure : Two homologous DNA sequences which descended from an ancestral sequence and accumulated mutations since their divergence from each other. Note that although 12 mutations have accumulated, differences can be detected at only three nucleotide sites. (from Fundamentals of Molecular Evolution, Wen-Hsiung Li and Dan Graur, 1991)
back to homepage