Lecture 20 - Gene Duplication Flashcards
Where do new genes come from?
Gene duplication.
Who made the argument of “evolution by gene duplication”?
Susumu Ohno - proposed that each new gene must have arisen from an existing gene.
What are the different types of DNA duplication?
- Partial gene duplication
- Whole gene duplication
- Segmental duplication
- Polysomy (whole chromosomal duplication)
What is a tandem repeat?
A repeat that is found beside the original gene.
What are the two major mechanisms of duplication?
- Unequal crossing over
- Transposition
What are the two types of crossing over that we see?
- Homologous unequal crossing over
- Non-homologous unequal crossing over
When an unequal crossing over occurs and produces tandem duplicates in the DNA strand, what do these duplicated sequences allow?
More opportunity for unequal crossovers (i.e., duplication encourages further duplication)!
What is homology?
Similarity due to shared common descent.
What is paralogy?
Homology due to DNA duplication.
What are paralogs?
Paralogs are genes that started diverging due to duplication
What is orthology?
Homology due to shared vertical descent.
What are orthologs?
Orthologs are genes that started diverging due to a speciation event.
What is a gene family?
A group of orthologous and/or paralogous genes that share a common ancestral gene.
What is a gene superfamily?
Implies a more distant relationship between the gene members (might carry out very different functions).
What is an orphan gene?
A gene with no homologs in other evolutionary lineages.
What is the biggest gene family in mammals?
Olfactory receptors (ORs) gene superfamily.
At what rate do duplications arise?
They arise spontaneously at high rates.
In general, do gene duplications have an effect on the organisms fitness?
No, most of them are viable (with no change in the organisms fitness).
BUT a small fraction of duplicates are retained and even fewer evolve new functions!
What are the potential fates of a duplicated gene?
- Nonfunctionalisation (loss of function)
- Conservation
- Subfunctionalisation (partial loss of function)
- Neofunctionalisation (novel function)
What is nonfunctionalisation?
Gene loss, resulting in a non-processed pseudogene (i.e., does not undergo RNA processing).
- The most likely fate of a duplicated gene
- Duplicated gene becomes “redundant”
What is neofunctionalisation?
Where over time, the duplicated gene accumulates mutations that allows it to acquire a novel function.
What is neofunctionalisation?
Where over time, the duplicated gene accumulates mutations that allows it to acquire a novel function.
Give an example of neofunctionalisation in humans.
GLUD2 gene (a duplicate of GLUD1) - which encodes the enzyme that helps us recycle glutamate (a hugely important neurotransmitter in the brain).
What is subfunctionalisation?
Genes that are multifunctional (i.e., encode several products) can divide up these functions after duplication.
Can involve…
- Complementary loss of sub-function
- Specialisation of different copies in different tissues/developmental stages
- Escape from adaptive conflict
Why might duplicates be conserved (i.e., retain the same function as the original)?
Often caused by selection for gene dosage (the more gene product the better, thus having more copies of the gene is advantageous).
- E.g., Esterase B which confers insecticide resistance, strong selection for more copies of this gene (i.e., esterase repeats evolve)
How can we date duplication events directly?
Can be done by estimating the rate of substitution (r) for duplicate genes.
What do we need in order to estimate the rate of substitution (r) for specific duplicated genes?
We need a calibration point. Thus we can use…
1. Time of speciation (Ts, of a known speciation event)
2. Number of substitutions per site between the species (K)
From this, we can get the average rate.
(SEE LECTURE 20 (part 2) @ 6:30 FOR FORMULA)
How are our olfactory receptor (OR) genes evolving?
Through an extremely rapid process of birth-and-death evolution - with high rates of duplication, neofunctionalisation, and gene loss.
What differentiation can we make by looking at the abundance of OR sequences in aquatic and terrestrial vertebrates?
Huge number of alpha- and gamma-subfamilies in terrestrial animals but little or none in aquatic animals.
- Tells us that these subfamilies have specialised to detect airborne odours.
The other 5 OR subfamilies are found in great numbers in aquatic vertebrates but little or none in terrestrials.
- Tells us that these subfamilies have specialised to detect water-soluble odours.
