Genome evolution Flashcards
Who created the phylogenic tree of animals?
Carl Linnaeus
What did genome sequencing of different animals show?
Many genes in different animals are the same with similar functions
Indicates that during evolution, many genes and proteins are generated early on, before becoming multicellular
What makes organisms morphologically different?
Changes in expression of a COMMON SET of genes
What question does sequencing data answer?
How do we estimate the timing and position of branchpoints of the phylogenetic tree
What are humans related to? (in order of distance)
Chimpanzee
Gorilla
Orangutan
How can we estimate the rate of sequence change in?
By comparing fossil record to genomic data
What is the rate of change in nucleotide sequence for great apes and man?
What does this suggest?
1% ever 10 million years
Suggests base changes are relatively constant over time
Which great ape has the fewest differences in its genome when compared to man?
What is the reason for this?
Chimpanzee
Due to short time that has been available for the accumulation of mutations in the 2 diverging lineages
What is used to calibrate the molecular clock?
Fossil records
What is FOXP2?
A highly conserved protein which has different amino acids at sequences 80, 303 and 325 (between human, chimp and mouse)
In the FOXP2, which position has the same amino acid between chimp and human?
What does this show?
Position 80 - both have D
Shows that their common ancestor is also likely to have a D at position 80
In the FOXP2, which position has the same amino acid between chimp and mouse?
What does this show?
Position 303 - both have T
Shows that their common ancestor is also likely to have a T at position 303
What is a parsimony tree?
Shows the relationship between different organisms in the SIMPLEST way
How is a parsimony tree created?
Using programmes related to blast - consider all the possibilities and come up with the most likely one
What is the ‘most likely’ scenario with a parsimony tree?
The one with the least amount of changes
What is convergent evolution?
Is this likely?
The process of the same amino acid in the same position arising by chance
Organisms INDEPENDANTLY evolve to have similar sequence with some identical AA in identical places
HIGHLY unlikely
What is the difference between morphological phylogeny and molecular phylogeny?
Morphological phylogeny is producing a tree of how related species are to each other based upon physical characteristics
Molecular phylogeny is a tree of relationships based upon differences in the genetic sequence
What 3 things are used together to give us an idea of evolution?
1) Molecular phylogeny
2) Morphological phylogeny
3) Fossil records
How many vertebrate FGFs are there?
22
How can the vertebrate FGFs be clustered?
What type of phylogeny is this?
Based upon protein sequence alignment (how similar the amino acid sequence is)
Molecular phylogeny
How many families do human FGFs fall into?
4
What does comparison between humans and Ciona (sea squirt) show?
What does this show?
Ci has single representatives in each of the 4 groups of human FGFs
Shows that the common ancestor of humans and sea squirt already had 4 FGFs before it begun to evolve
What are paralogues
New copies of genes that arise in the genome
Why do so many FGFs arise?
Due to accidental duplications in genes over evolution
What are 2 types of gene duplication?
Changes in ploidy (duplication of a whole chromosome)
Local duplications (duplication of region of a chromosome)
How does whole genome duplication occur?
Mistakes in meiosis, causing whole chromosomes to be inherited in the next generation
Whole genome or extra chromosomes can be inherited at once
Are duplicate genes active at first?
No, they are most likely redundant
What are 2 ways that the extra copy of a chromosome be modified?
1) Pattern of expression (timing and position)
2) Structural in the protein
How can small changes in the structure of the protein occur?
By point mutations
How can large changes in the structure of the protein occur?
By domain swapping
What is the largest driving force in the morphological evolution of animals?
Why?
Changes in the expression pattern of genes
Because enhancers can change easily
What can non-homologous recombination between 2 chromosomes cause?
A NEW enhancer to be close to the gene
This gene now gets a DIFFERENT type of regulation
Is the exact position of an enhancer important?
Why?
No
Enhancers regulate many genes in ‘reach’
Why is it important that the binding site for a transcription factor is very simple?
- Can easily gain a new binding site
- Easy to ADD/DELETE transcription factor binding sites by REARRANGEMENTS, insertions, deletions or base pair substitutions
Which modifications to the extra chromosome have to be more precise and why?
What does this mean for this type of modification?
Changes that effect protein structure as to not:
- Introduce a stop codon
- Change the reading frame
- Interfere with protein folding
- Disrupt RNA splicing
As these will result in proteins that are not functional
- Means that these types of mutations are much rarer
What is the evidence that shows changes in the expression of single genes to play a major role in morphological evolution?
(regarding Hox genes)
- Hox genes confer identity to vertebrae
- Chick has 14 cervical vertebrae, mice have 7
- Chick has Hox C5 extending very far, in mice = shorter
- Hox C6 is characteristic of thoratic vertebrae
- Border between C5 and C6 - transition from cervical to throratic
Can change the expression - correlates to morphological changes:
- Change borders between expression of Hox genes
- Can add/subtract vertebrae
When is changing the expression domain of genes easy?
In evolution, where there is a selection pressure
How can ectopic organs be created?
By experimentally changing the expression of a single gene
What plays a major role in morphological evolution?
What are the 2 pieces of evidence for this?
Changes in the expression of a single gene
Evidence:
- Create ectopic organs by changing expression
- Can add/subtract vertebrae by changing expression domain of Hox genes
What are the single genes that can create ectopic organs called?
Master regulatory genes
What do master regulatory genes do?
Regulate WHOLE GENE networks that specify an ENTIRE organ
What is the master regulator for the eye?
ey
Why do some organisms have more eyes/legs than others?
More expression of the master regulators
If ectopically express master regulator of the eye- get another eye forming
What is evolutionary robustness?
The ability of the organism to cope with changes
Ectopic organs are usually functional
What is the difference between crustaceans and insects?
What 2 questions does this pose?
Crustaceans have legs on the abdomen, whereas insects don’t
Questions:
1) Is this because the expression of the leg master regulatory gene has changed during evolution?
2) Or because of evolution of a protein sequence?
What MAY explain why insects dont have legs on their abdomen?
ubx expression
What specifies leg precursor cells in the fly embryo?
What type of molecule is this?
dlx
A transcription factor - master regulator
Where is dlx expressed in the fly?
In the thorax
Not in the abdomen
Where is ubx expressed in the fly and what does it do?
What does this cause
In the abdomen
Represses dlx expression - legs cannot form here
Where is dlx and ubx expressed in crustaceans?
How is this different to what is expected? Why?
BOTH expressed in the thorax and abdomen (ubx doesn’t repress dlx function)
Expected that ubx to be expressed in the thorax and dlx to be expressed in the abdomen
Because in the fly, ubx represses dlx expression (which specifies legs)
What do studies between ubx expression in insects an crustaceans show?
- Ubx repressor function has changed function over evolution
- In crustaceans, has an anti-repression motif which is lost in insects
Insects evolved from crustaceans
