Phylogenetic Analysis

Traditional phylogenetic trees - historical relationships of groups organisms.

Each group is called a taxon. The relationships of groups were based on primarily on morphological character data from extant taxa and the fossil record.

Molecular biologists are interested in the relationships of the sequences (nucleotide, protein). The word “taxa” and “sequences” are used interchangeably in the modern phylogentic analysis.

A phylogenetic tree is a simple object consisting of nodes and branches.

A branch: is a line that connects two nodes.

Nodes:

External node: which are the tips of the tree that are the taxa being considered.

That exist today and that we can actually examine.

Internal nodes: which are points that represent a common ancestor of two or more other nodes.

That we can only infer from the existing data.

Clade: All of the descendants of a common ancestor represented by a node belong to the same clade.

Distance is the number of changes that have taken place along a branch, usually expressed as the number of substitutions per site.

Methods for constructing phylogenies:

1. Neighbor joining (NJ)

Distance methods, convert the aligned sequences into a distance matrix of pairwise differences (distances) between the sequences. The matrix is much like the tables of “5” homology” that often appear when only a few sequences are being compaired.

Character-based methods

2. Maximum parsimony (MP)

3. Maximum likelihood (ML)

4. Bayesian (BAY)

Use the multiple alignment directly by comparing characters within each column (each site) in the alignment.