Genome Evolution

Question 1

For great apes and man how frequent were changes in nucleotide sequence?

Answer 1

1% per every 10 million years

Question 2

How can we estimate the rate of sequence change?

Answer 2

By completing the fossil record to genomic data

Question 3

When we assemble the tree which model do we tend to pick?

Answer 3

The simplest one

Question 4

Describe the differences in FOXP2 in mice, chimp and humans and what conclusions can be drawn from this

Answer 4

There are differences in the amino acids at 80 and 303
Since mice and chimp have 303 T it is likely their common ancestors also did (humans = 303 N)
Chimps and humans had 80D so it is likely that their common ancestors also did ( mice = 80E)
This accomplishes a tree with two changes

Question 5

What is parismony?

Answer 5

Assumption of the simplest model

Question 6

What is convergent evolution?

Answer 6

Convergent evolution is the process by which unrelated or distantly related organisms evolve similar body forms, coloration, organs, and adaptations
It is not common but does occur

Question 7

How many vertebrate FGFs are there and how many clusters do they fall in to?

Answer 7

22 which fall unto four clusters based upon their protein sequence alignment

Question 8

What does the organsims ciona suggest about FGFs and why?

Answer 8

It suggests that common ancestor of the sea squirt and vertebrates had four FGFs as it has a representative FGF from each cluster

Question 9

How may have so many FGFs arised?

Answer 9

Gene duplication - changes in ploidy and local duplications

Question 10

What is a paralogue?

Answer 10

A new copy of a gene which arises in the genome

Question 11

What is a syntelog?

Answer 11

a special case of gene homology where sets of genes are derived from the same ancestral genomic region. This may arise from speciation events, or through whole or partial genome duplication events (e.g. polyploidy)

Question 12

An extra copy of a chromosomal region can change in what ways?

Answer 12

1) Pattern of expression

2) Strucural in the protein. Both small changes caused by point mutations and big changes are caused by domain swapping

Question 13

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

Answer 13

Changes in gene expression

Question 14

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

Answer 14

Because enhancers can change easily

Question 15

How could non homologous recombination affect an enhancer?

Answer 15

It could bring a new enhancer closer to a gene

Question 16

Why are changes in enhancers ore likely to affect evolution than changes to a protein?

Answer 16

Enhancers; exact position is not usually important and the DNA for TF binding sights is simple so it is easy to add or delete sites by rearrangements, insertions, deletions or BP substitutions
Proteins; changes have to be precise so as not to introduce stop codons, change the reading frame, interfere with folding or disrupt splicing

Question 17

Changes in reguatory genes can correlate to what type of change?

Answer 17

Morphological

Question 18

Give an example between mice and chicks where regulatory changes affect morphology

Answer 18

C6 - in the chick expression starts more posteriorly correlating with a longer neck and fewer thoracic vertebrae compared to a mouse

Question 19

How can we show that regulatory genes are responsible for large evolutionary changes in model organisms?

Answer 19

By changing gene expression, creating ectopic organs

Question 20

What is a master regulatory gene?

Answer 20

A gene on top of a heirarchy capable of big tasks such as setting up organs. They regulate whole gene networks

Question 21

Why might crustaceans have legs on their abdomen but insects do not?

Answer 21

Changes in the leg master regulatory gene during evolution

Question 22

Ubx evolution can be used to explain what?

Answer 22

Why insects do not have legs on their abdomen

Question 23

Describe the expression of Dlx and Ubx in flies and their roles

Answer 23

Dlx = leg precursor cells
Ubx is expressed in the abdomen where it represses Dlx
As a result legs form only in the thorax of the fly
There are six spots of Dlx expression in the fly

Question 24

Is ubx expressed in the abdomen of crustaceans?

Answer 24

Yes it is

It is also expressed in the thorax so researchers have concluded that crustacean ubx does not act as a repressor

Question 25

How is crustacean and insect Ubx different?

Answer 25

Crustacean has an antirepression motif which has been lost in insects

Question 26

Describe the results of the experiment which shows the difference between crustacean and insect ubx

Answer 26

Crustacean Ubx expressed in the thorax of flies does not repress Dlx, however drosophila Ubx does repress it