23 - Phylogenetic trees - building trees

Question 1

What are the leaves of a phylogenetic tree?

Answer 1

the tip nodes

Question 2

What are the root nodes of a phylogenetic tree?

Answer 2

most recent common ancestors

Question 3

What is a clade on a phylogenetic tree?

Answer 3

everything that is down from a particular node

Question 4

How are phylogenies constructed?

Answer 4

trait data
- morphological or molecular data

Question 5

How do you use the UPGMA method?

Answer 5

1) find the lowest value (closest relation)
2) combine these taxa
3) find lowest value again
4) this becomes the next node
5) repeat until you have a full tree

Question 6

What does it mean if a tree is most parsimonious?

Answer 6

when there is the fewest evolutionary steps

Question 7

What is the problem with parsimony reconstructions?

Answer 7

• not all changes are equally likely
• different mutation rates - transitions are more frequent than transversions (A-G or C-T most common)
• different substitution rates - changes at 3rd codon more likely to be synonymous
• massive amount of trees to see best one

Question 8

What are solutions to the issues with parsimony reconstructions?

Answer 8

mutation rate
- substitution model - different substitutions at different rates

• only look at plausible trees, not all possible
• use algorithms - subtree prune and regraft

Question 9

What are trees without branch length information called?

Answer 9

cladograms