Phylogenetic Tre es - I

1. Phylogenetic Trees - I

2. Phylogenetic Tree • - phylogenetic relationships are normally displayed in a tree-like diagram (phylogenetic tree/cladogram) • a cladogram is a branching diagram describing the phylogenetic relationships of the taxa under investigation. • a phylogenetic tree graphically represents a hypothetical evolutionary process. • phylogenetic trees are subjected to revision as additional data becomes available. • evolutionary tree is used synonymously as phylogenetic tree.

3. Phylogenetic Tree - a cladogram consists of two major elements: nodes and branches. - a node represents a taxon; a branch represents evolutionary event(s). - the branching pattern of a cladogram is called the topology.

4. Phylogenetic Trees Cladogram

5. Clade • a clade is an ancestor species with all its descendants. • a monophyletic group is a clade. • There are three ways to define a clade for use in a cladistic taxonomy • i) Node based • ii) Stem based • iii) Apomorphy based

6. Clade Node-based the most recent common ancestor of A and B along with all of its descendants Stem-based all descendants of the oldest common ancestor of A and B that is not also an ancestor of Z Apomorphy-based the most recent common ancestor of A and B, along with all of its descendants, possessing a certain derived character. This definition is generally discouraged by most cladists

7. Cladogram / Phylogram / Phenogram - A cladogram/phylogram displays branching information to explain the evolutionary relationships. - A phylogram has additional information: the length of branches according to the amount of changes (evolutionary process).

8. Cladogram / Phylogram Cladogram Phylogram

9. Cladogram / Phylogram / Phenogram - A phenogram is generated from phenetic analysis (numerical taxonomy). It does not necessary explain the ancestor-descendant relationships of the taxa in the investigation.

10. Gene trees and species trees A a Species tree Gene tree B b C c We often assume that gene trees give us species trees

11. Characters and Character States • Organisms comprise sets of features • When organisms/taxa differ with respect to a feature (e.g. its presence or absence or different nucleotide bases at specific sites in a sequence) the different conditions are called character states • The collection of character states with respect to a feature constitute a character

12. Homoplasy • Homoplasy is similarity that is not homologous (not due to common ancestry) • It is the result of independent evolution (convergence, parallelism, reversal) • Homoplasy can provide misleading evidence of phylogenetic relationships (if mistakenly interpreted as homology) • homoplasy can be common in DNA data • There are a limited number of alternative character states (e.g. Only A, G, C and T in DNA) • Rates of evolution are sometimes high