Genome Evolution Flashcards
What did Linnaeus do
What did we find out from genome sequencing
What makes animals different
How much DNA do mice and humans share ?
Made the phylogenic tree of animals based on morphology. Animals were put into groups based on appearance.
Most of the genes are the same in all animals investigated.
Changes in expression of a common set of genes.
85%
For great apes and man the change in nucleotide sequence is about
What can you base a molecular clock on ?
What does the base change clock assume?
How can we estimate the rate of base sequence change ?
1% every 10 million years.
Carbon dating, fossil records or differences in base changes.
That the changes in base pairs is constant over time.
By comparing the fossil records to genomic data.
A model for molecular evolution based upon differences in a protein.
What is parsimony
The amino acid sequences are lined up and all those they have in common are greyed out.
Humans and chimps have a D at amino acid 80 and mice have an E.
It can be said that the common ancestor of humans and chimps had a D at amino acid 80.
This would be parsimony because the simplest model has been assumed.
Although a more complex model would be that the common ancestor has 80E and both the human and chimp undergo change to become 80D by chance.
We can’t go back and see what happened we can only estimate.
How do we get a deep understanding of evolution
Molecular phylogeny
Morphological phylogeny
Fossil records
How many vertebrate FGFs are there and how many clusters do they form.
What are the clusters based on
22 FGFs
Four clusters
Protein sequence alignment
What does each FGF cluster contain
And why is this
How did all the other FGFs arise
What are paralogues
An FGF that is found in ciona (a distant ancestor the sea squirt)
This suggests that sea squirts had four FGFs already before chordates evolved.
Gene duplication. The genome was not segregated properly in meiosis and some gametes have an extra copy of every gene or whole chromosomes.
This would have happened early on when organisms were able to cope with changes in ploidy.
New copies of genes that arise in the genome
What is likely to happen to new duplicate genes ?
How can they change ?
What is the most common driving force in the morphological evolution of animals ?
They are redundant.
But it can change its pattern of expression or change its structure.
Small changes are caused by point mutations.
Big changes are caused by domain swapping.
Changes in expression.
Why are changes in expression patterns of genes thought to play a major role in morphological evolution.
How does this compare to changes in protein structure.
Enhancers can change easily. For example non homologous recombination could bring a new enhancer close to the gene.
The exact position of an enhancer is usually unimportant. The TF binding site is simple. So it is easy to add or delete TF sites by rearrangements.
This means it is easy to change the regulation of the new duplicate gene.
Changes in protein structure would have to be more precise so will be much rarer
An example of how changes in expression have allowed evolution of chick vertebrae
Chicks have 14 cervical vertebrae and they have evolved to have more vertebrae in their neck.
Expression of hox gene C6 results in thoracic vertebrae. And C6 expression starts more posteriorly in chicks so it will have a longer neck and more cervical vertebrae.
What are master regulatory genes
What is ey and what happens if it is expressed on the leg
What is this adaptability called
Genes that are capable of big tasks such as organ formation and can regulate whole gene networks.
In drosophila ey is a master regulatory gene of the eye.
If it is ectopically expressed in the leg the larvae will develop an eye on its leg.
The ectopic eyes are functional.
This adaptability that takes place during development is called evolutionary robustness.
Where do crustaceans and insects have legs.
What causes leg growth in flies
Crustaceans have legs on their abdomen but insects don’t.
In fly embryos dlx is a TF that specifies leg precursor cells.
There are three patches of expression on either side of the thorax to produce six legs.
Dlx is not expressed in the fly abdomen. Ubx is expressed in the abdomen to repress dlx to stop leg growth.
How do crustaceans grow legs
They have ubx expression in their abdomen.
But it must not be repressing dlx like it does in flies because crustaceans can grow legs in the abdomen.
This means ubx must have changed its function during evolution and no longer acts as a represser for dlx in crustaceans.
Crustacean ubx has an anti repression motif that was lost in insects.
How many FGF receptors are there.
What is on the extra cellular structure
Four
Three immunoglobulin repeat domains and the ligand binds to the D2 and 3 domains.
Why do different FGFs binding to the same receptor give very different responses and why
FGF and its receptor form a complex with HSPGs.
HSPGs have three types of protein core.
Transmembrane (syndecan) , tethered (glypican) or secreted (perlecan).
These are attached to long sugar chains called heperans.
These can be modified by sulphation to result in binding sites for specific proteins.
What do these proteins cause
Ras
PI3
PLC
Cell proliferation
Cell survival
Cell motility
