L17 - Genome Evolution

Question 1

Who created the phylogenetic tree?

Answer 1

Idea created by Carl Linnaeus

Question 2

Phylogenetic tree overview

Answer 2

Most of the genes are the same in all animals investigated
- Mouse and humans have the same genes
Differences morphologically is thought to be caused by changes in expression of a common set of genes

Question 3

How often for apes and man does the change in nucleotide sequence occur?

Answer 3

The change in nucleotide sequence is 1% every 10 million years

Question 4

What are the two ways to use sequence data to assemble molecular phylogeny?

Answer 4

Compare fossil record to genomic data to estimate the rate of sequence change
- Fossil record is used to calibrate the clock
Based upon differences in a protein

Question 5

The highly conserved protein (FOXP2) has differences in the amino acid sequence at which positions?

Answer 5

80, 303 and 325

Question 6

Which nucleotide do humans and chimp have at position 80?

Answer 6

Human and chimp have 80 D - likely that their common ancestor had a 80 D

Question 7

Which nucleotide do mouse and chimp have at position 303?

Answer 7

Mouse and chimp have 303 T - likely that their common ancestor had a 303 T

Question 8

What is parsimony?

Answer 8

Assume the simplest model
Can accomplish this tree with two changes X
Programs consider all of the possible scenarios to come up with the most likely one

Question 9

If we don’t use the simplest model to assemble the tree ?

Answer 9

80 D could have arisen twice by chance
If this happened then this tree below could also explain the data
Called convergent evolution - less likely

Question 10

Molecular phylogeny - FGFs

Answer 10

22 vertebrate FGFs that fall into 4 clusters based upon protein sequence alignment

Question 11

What is the important of Ciona?

Answer 11

Ciona has single FGF representatives in each of the 4 groups

- Suggests that the common ancestor of the sea squirt and vertebrates had 4 FGFs

Question 12

How do so many FGFs arise?

Answer 12

Arise from gene duplication - changes in ploidy and local duplications
New copies of genes that arise in the genome are called paralogues

Question 13

After duplication it is likely that the duplicate gene is at first?

Answer 13

Redundant

Question 14

Duplicate gene can change by?

Answer 14

Pattern of expression 
- Timing
- Position
Structural in the protein
- Small changes caused by point mutations 
- Big changes caused by domain swapping

Question 15

Why do changes in expression patterns of genes play a major role in morphological evolution?

Answer 15

Because enhancers can change easily

E.g. non-homologous recombination could bring new enhancer close to gene

Question 16

Is the exact position of an enhancer important?

Answer 16

No

Question 17

Is the DNA sequence for transcription factor binding sites simple in enhancers?

Answer 17

Yes

Question 18

Why is important that the DNA sequence for transcription factor binding sites is simple and enhancer position is not important?

Answer 18

Easy to add/delete sites by rearrangements, insertions, deletions or base pair substitution

Question 19

Why are changes effecting protein structure more dangerous?

Answer 19

Changes effecting protein structure would have to be more precise to introduce a stop, change the reading frame, interfere with the protein’s folding or disrupt RNA splicing

Question 20

What is the evidence that changes in the expression of single genes has played a role in morphological evolution? - chick

Answer 20

Expression of the gene C6 starts more posteriorly in chick which correlates with

• Longer neck - more cervical vertebrae than in mine
• Less chest - fewer thoracic vertebrae than in mice

Question 21

What is the evidence that changes in the expression of single genes has played a role in morphological evolution? - ectopic organs

Answer 21

By changing expression of a single gene we can create ectopic organs

• Genes capable of such big tasks - master regulatory genes
• Regulate whole gene networks
• Often these organs are functional - this adaptability during development is called evolutionary robustness

Question 22

What is the difference between crustaceans and insects?

Answer 22

Crustaceans have legs on their abdomens but insects don’t

Question 23

What is the theory why flys do not have legs on the abdomen?

Answer 23

Dlx specifies leg precursor cells
Ubx is expressed in the abdomen where it represses Dlx
Legs form only in the thorax

Question 24

What is the theory why crustaceans have legs on the abdomen?

Answer 24

Ubx is not expressed in the abdomen
Dlx is not repressed
Legs grow in the abdomen

Question 25

What was the theory after it was discovered that Dlx and Ubx are both expressed in the abdomen and thorax?

Answer 25

Crustacean Ubx does not act as a repressor
When crustacean Ubx is expressed in the thorax of flies, it does not repress Dlx expression
Crustacean Ubx has an antirepression motif that was lost in insects.