Question

How do phenetic (distance) analyses differ from cladistic (character state) analyses in the types of data that they use, the kinds of trees they build and what types of inference you can make about evolutionary history from each?

Answer 1

Phenetic based analysis involves studying the relationship among the organism groups based on the degree of similarity between them. The similarity can be in terms of the phenotype, or anatomy. they simply takes into account the number of differences between two sequences.

The tree representing the network and this distance based relation is called Phenogram.

Phenetic analysis rely on UPGMA method (Unweighted pair group method with arithmetic mean) clustering algorithm that produces trees by joining branches based on highest similarity among pairs involved and taking average of the joined pairs.. IT can generate accurate tree topology with correct tree branch lengths when the divergence is proportional to the molecular clock.

NJ(neighbour joining method )in which the tree which is fully resolved is further decomposed from an unresolved tree by insertion of branches between closed neighbour pairs and inserting remaining terminals.

Cladistics works on grouping organism based on their ancestors and descendents,or the branching sequence.

Tree generated showing relationship between the ancestors and the descendents is called cladogram(Branching diagram).

Maximum parsimony approach in which the phylogenetic tree generated based on the minimum number of character changes are taken into consideration among all possible trees. This approach is based on the principle of parsimony which says that the simplest observation which is sufficient to explain more number of observations should be preferred over the complex . MP tress is the shortest tree.

ML (maximum likelihood) wherein the likelihood having highest likelihood is considered, it is derived from each of the base positions in the alignment. likelihood becomes the sum of probabilities of each possible substitution.

One cana infer differently from each type of method the tree generated will give us the information about the mutation rate between two sequences by looking at the site of substitutions ( frequency of trasitions and transversions)and the divergence pattern betwen two sequences and the evolutionary history. HOMOLOGY, ORTHOLOGY BETWEEN POLYPEPTIDE SEQUENCES