Phylogenetic Analysis

Proteins evolve at different rates because of intrinsic factors (repair mechanisms) and extrinsic factors (environmental mutagens). Highly conserved proteins apparently have only been able to tolerate a few minor changes, whereas some other proteins have been able to absorb many mutations without loss of function. Mutations that occur outside a region involved with normal function of the molecule may be tolerated as a selectively neutral mutation. Over geological time, these neutral mutations tend to accumulate within a geneological lineage. If it is assumed that such neutral mutations accumulate at a fairly constant rate for a highly conserved protein, it is possible to establish the branching pattern of a phylogenetic tree (also called a cladogram or an evolutionary tree).

The principle of parsimony is commonly used to determine the minimum number of genetic changes required to account for the amino or nucleotide sequence differences between organisms sharing a common ancestor. The evolutionary distances separating organisms in a phylogenetic tree are usually expressed in units of nucleotide mutations or amino acid substitutions along each arm of the tree between branch points (see Figure 12-1).

Notes
Some evolution rates (point mutations per 100 million years):
Triose phosphate isomerase = 3
Hemoglobin = 21
Nonfunctional pseudogenes = 400