Lecture 17 - Molecular Phylogeny

Question 1

What are the advantages to using protein sequences to create species trees (as opposed to DNA sequences)?

Answer 1

• They evolve more slowly than DNA sequences

- Reversals are less common

Question 2

Explain how protein sequences can be used to create species trees.

Answer 2

1) Single copy protein encoding genes are identified
2) Protein sequences are joined together to create a multiple protein sequence for each species
3) Sequences are aligned.

Question 3

Why do protein sequences evolve more slowly than DNA sequences?

Answer 3

Due to redundancy of the genetic code.

Question 4

How many amino acids are there?

Answer 4

20

Question 5

The more proteins you use…

Answer 5

The better resolved the tree is

Question 6

Above what figure is it considered good boot strap support?

Answer 6

Above 70

Question 7

What is TOR?

Answer 7

A protein kinase.

Regulates cell growth in response to nutrient availability and cellular stresses.

Question 8

What do nodes mean in a gene tree?

Answer 8

Either

• speciation event
• gene duplication

Question 9

When are genes said to be homologous?

Answer 9

If they share a common evolutionary ancestor.

Question 10

What are orthologues?

Answer 10

Genes in different species that evolved from a common ancestral gene by speciation.

Question 11

What is a functional orthologue?

Answer 11

A gene that can take the place of another gene.

Question 12

What are paralogous genes?

Answer 12

Genes related by duplication within a genome.

Question 13

What are in-paralogues?

Answer 13

paralogues that were duplicated after a speciation, and are therefore in the same species.

Question 14

What are out-paralogues?

Answer 14

Paralogues that were duplicated before a speciation, and are not necessarily in the same species.

Question 15

What is Whole genome duplication (WGD)?

Answer 15

Complete duplication of the genome, resulting in two copies of every gene.

Question 16

What do phosphoglycerate mutases catalyse the reaction of?

Answer 16

3-phosphoglycerate into 2-phosphoglycerate

Question 17

What are the two types of phosphoglycerate mutase?

Answer 17

• cofactor-dependent PGM

- cofactor-independent PGM

Question 18

What is different about the action of

a) dPGM
b) iPGM

Answer 18

a) dPGM = uses 2,3BPG as a co-factor

b) iPGM = has two bound Mn(II) ions at its active site.

Question 19

Where are the following found

a) dPGM
b) iPGM

Answer 19

a) dPGM = found in yeasts and vertebrates
b) iPGM = found in filamentous fungi, plants and some invertebrates.
Both found in bacteria.

Question 20

Give the four steps to making a phylogenetic tree.

Answer 20

1) Sample sequences from species interested in, using BLAST.
2) Align sequences (e.g. using Clustal)
3) Sample conserved region of alignment, using GBlocks
4) Use these regions to create a phylogenetic tree, using PhyML.