Molecular Phylogenetics Tutorial

by Sophia Kossida

Summary of BioMOO tutorial held 27.3.96

IndexIndex to Course Material IndexIndex to Section 4

Molecular Phylogenetics

If Dobzhansky's (1973) famous dictum is correct that:

Nothing in biology makes sense except in the light of evolution

then it might be appended that "much in evolution makes sense in the light of phylogeny".

Molecular evolution encompasses roughly two areas of study:
1) the evolution of macromolecules, where attempts are focussed on figuring out the rates and patterns of change occuring in them (macromolecules mean DNA and proteins) and
2) the reconstruction of the evolutionary history of genes and organisms (molecular phylogeny).
The two disciplines are intimately interrelated and progress in one area facilitates studies in the other.

The study of molecular phylogeny, in the sense of the reconstruction of the evolutionary history of genes and organisms, began at the turn of this century. The most commonly used visual representation of phylogenetic relationships are the phylogenetic trees. The objectives of phylogenetic studies are:
(i) to reconstruct the correct genealogical ties between organisms and
(ii) to estimate the time of divergence between organisms since they last shared a common ancestor.

In phylogenetic studies, the evolutionary relationships among a group of organisms are illustrated by means of a phylogenetic tree. A phylogenetic tree is a graph composed of nodes and branches, in which only one branch connects any two adjacent nodes. The nodes represent the taxonomic units and the branches define the relationships among the units in terms of descent and ancestry. The branching pattern of a tree is called the topology. The branch length usually represents the number of changes that have occurred in that branch. The taxonomic units represented by the nodes can be species, populations, individuals or genes.

Phylogenetic trees can be either rooted or unrooted. In a rooted tree there exists a particular node, called the root, from which a unique path leads to any other node. An unrooted tree is a tree that only specifies the relationships among the OTUs and does not define the evolutionary path. In the distance matrix methods evolutionary distances (usually the number of nucleotide or amino acid substitutions separating two taxonomic units) are computed for all pairs of taxa, and a phylogenetic tree is constructed by using an algorithm based on some functional relationships among the distance values. In maximum parsimony methods character states (e.g. the nucleotide or amino acid at a site) are used, and the shortest pathway leading to these character states is used as the phylogenetic tree. Maximum likelihood is a method of statistical inference. The principle of the method is is to find the tree which best explains the observed sequence data given an explicit stochastic model of molecular evolution (i.e. a probabilistic description of evolutionary change between nucleotides).

Last updated 2nd April '96