Phylogenetic Trees Importance of phylogenetic trees What is

Phylogenetic Trees ®Importance of phylogenetic trees ®What is the phylogenetic analysis ®Example of cladistics ®Assumptions in cladistics ®Frequently used terms ®Fundamentals of Phylogenetc models ®Phylogenetic software

Importance of Phylogenetic Tree • • • Classification is important to understand Evolutionary history of an Organism Study of Biological Diversity Organization Progressive Multiple Sequence Alignment

What is Phylogenetic Analysis • • Study of evolutionary relationship Inferring or estimating relationship Usually presented as branching, tree Gene Tree: Inherited relatioships It is also called cladistics clade means branch in Greek Member of group/clade share a common rel.

Example of Cladistics

Assumptions in Cladistics • Any group of oragnisms is related by descent from a common ancestor • Members of a group or clade share common evolutionary history • A group sharing a unique feature, different from other groups • There is bifurrcating pattern of cladogenesis • Change in charterstics occurs in lineages over time

Frequently Used Terms • Clade: A monophyletic taxon. Clades are group of organisms • Taxon: Named group or organisms but not necessarily a clade • Branch Length: In some case it repersent divergence • Node: A bifurcating branch point

Fundamentals of Phylogenetic Models • Sequence alignment (AMPS, Clustal-W) • Substitution model (weight model) – Rates between Bases – Site Substitution(overall compositional change) • Tree building • Tree Evaluation

Tree Building • Distance Based Methods – UPGMA: Unweighted Pair Group Method It is a Clustring algorithm, it cluster tree branches based on greatest similarity among pairs and averages of joined pairs – NJ: Neighbor Joining First, it join nearest pair in start and then continue till one remain • Character-Based – Maximum Parismony (MP) – Maximum Likelihood (ML)

Tree Evaluation • • Randomize Tree Randomize Character Data Bootstrap Likelihood Test

• • • PHYLIP PAUP PUZZLE Tree. Draw MACCLAD Web Based – webphylip, Phylo. Blast