Lecture 15 - hox genes & evolutionary development biology

Question 1

What is a phylogenetic tree made from?

Answer 1

• originally assembled based upon morphological simmilarities
• now we also use molecular sequence data

Question 2

What makes us morphologically different?

Answer 2

changes in expression of a common set of genes (60% the same genes as a banana)

Question 3

What are transcriptional regulatory sequences?

Answer 3

enhancers

Question 4

How do we determine if proteins are similar?

Answer 4

• input the amino acid sequence of the protein in question
• the last program searches huge databases for other proteins which have similar sequences

Question 5

What does a similarity in protein sequence suggest?

Answer 5

• proteins evolved from the same common ancestor and that the proteins have similar molecular functions

Question 6

How many vertebrate FGFs are there?

Answer 6

22 vertebrate FGFs that fall into 4 clusters based upon protein sequence alignment
- Ciona (a chordate) has single representatives in each of the 4 groups. This suggests that the common ancestor of the sea squirt and vertebrates had 4 FGFs

Question 7

How do many FGFs arise?

Answer 7

Gene duplication - changes in ploidy & local duplication

• new copies of genes that arise in the genome are called paralogues
• ploidy = the number of sets of chromosomes in a cell
• there are 22 paralogues in the human genome

Question 8

How does duplication of a chromosome or region of a chromosome occur?

Answer 8

after a duplication, it is likely that the duplicate genes are at first redundant

An extra copy can change by:
1. pattern of expression during development
2. structure of the protein
3. Both small changes caused by point mutations and but changes caused by domain swapping

This is GENE NEOFUNCTIONALISM

Question 9

What is the most common driving force in the morphological evolution of animals?

Answer 9

changes in expression

Question 10

Why are changes in expression patterns of genes thought to play a major role in evolution?

Answer 10

• because regulatory elements can change easily

Question 11

How important is the exact position of the enhancer?

Answer 11

• usually unimportant, and the DNA sequence for transcription factor binding sites is simple
• therefore, it is relatively easy to add or delete sites by rearrangements, insertions, deletions or base pairs substitutions

Question 12

What impact would changing the expression of a gene have on a protein?

Answer 12

changes the effect protein structure would have to be more precise as not to introduce a stop, change the reading frame, interfere with the protein’s folding or disrupt RNA splicing

Question 13

What are HOX genes?

Answer 13

transcription factors that found in clusters in the genome

Question 14

What can be suggested that HOX genes all have quite a similar sequence?

Answer 14

they originated from one gene

Question 15

What is the result of changing Hox gene expression (in the embryo)?

Answer 15

results in changes in segmental identity

Question 16

What are the Hox genes that specify vertebral segmental identity?

Answer 16

• cervical (neck)/Hoxc5
• Thoracic (chest)/Hoxc6

Question 17

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

Answer 17

Expression of the gene C6 starts more posteriorly in chick - this corellates with a longer neck (more cervical vertebrate) and less chest (fewer thoracic vertebrate) than mice

Question 18

How may shifts in HOX gene expression explain the loss of limbs during snake evolution?

Answer 18

• up to 300 somites - mice have 60
• no forelimbs and severely reduced hind limbs
• vertebrae anterior to the hind have ribs and a mixed cervical/thoracic morphology

Question 19

What could be the result of the expansion of HoxC6 & HoxC8?

Answer 19

could confer many of the morphological changes (shift towards thoracic) seen during the evolution of snakes

Question 20

Why do crustaceans have legs on their abdomen but insect don’t?

Answer 20

it turns out that this is because of changes in the protein sequence

Question 21

How may ubx evolution explain why insects don’t have legs on their abdomen?

Answer 21

• in fly larvae, the dlx transcription factor specifies leg precursor cells
• Ubx is expressed in the abdomen where it represses Dlx expression
• crustacean ubx doesn’t act as a repressor of Dlx
• Ubx is expressed in the abodmen of crustacean larvae, but it doesn’t turn off dlx expression
• it is thought that the ubx gene became able to repress dlx expression in an ancestor of Drosophila

Question 22

What is easier - changing regulatory sequences or protein structure?

Answer 22

changing regulatory sequences