1. Phylogenetic Trees
Jasmin sutkovic

2. What are those?
Phylogenetic trees represent the evolutionary relationships among a set of organisms or groups of organisms
These organisms are called taxa (singular: taxon) that are believed to have a common ancestor

3. To build a phylogenetic tree, biologists collect data about the characters of each organism they are interest in
Characters are heritable traits that can be compared across organisms
Some molecular biologists (like C. Woese) built phylogenetic trees from genetic sequences alone.

4. - The tips (leaves) of the phylogenetic tree represent current day species, groups of descendant taxa.
- The internal nodes represent the common ancestor of those descendants (speciation events)
- The edges connect nodes to nodes and nodes to tips; their lengths may correspond to time estimates - evolutionary time.

6. Sister groups: two descendants that split from the same node:
each one is the closest relative of the other
they have a common ancestor that is unique to them
they have a lot of evolutionary history in common
very little evolutionary history is unique to each one.
Butgroup - a taxon outside the group of interest.
All the members of the group of interest are more closely related to each other than they are to the outgroup.
An outgroup can give a sense of where, on the bigger tree of life, the main group of organisms falls.

7. A clade is a group of organisms that are all descendant from a common ancestor
Thus, a clade includes an ancestor and ALL descendants of that ancestor.

8. Clades can be found in other clades...

9. Trees can be represented differently...

10. Types of trees...
Rooted tree - an internal node corresponding to the most recent common ancestor to ALL species at the tips of the tree
Unrooted tree - no assumption is made about common ancestry

11. Dendogram - any representation of a phylogenetic tree
Cladograms - phylogenetic trees in which the length of the edges DO NOT represent evolutionary time
Phylograms - phylogenetic trees in which the length of the edges DO represent evolutionary time
Tree 1 = Tree 2; Tree 3 ≠ Tree 4

12. Phylogenetic representations are simplified from those in real life

14. Distances...
Length represents the number of changes. U has diverged less than V from their common ancestor.

15. Distances... Red numbers represent a measure of support for the node.
They can be calculated through Bootstrapping (which allows assigning measures of accuracy).
Basically, higher value indicates that there is strong evidence that the sequences to the right of the node cluster together to the exclusion of any other.

19. The branch length is proportional to the number of substitutions per site.

20. Thank you for your attenuation 