Lecture 21 - Concerted Evolution

Question 1

What are “tandem duplicates”?

Answer 1

Duplicated sequences that are positioned beside one another in the genome (can also be called gene amplification - multiple copies of a gene in the same locus).

Question 2

How are tandem repeats classified?

Answer 2

Based on the degree of differentiation we see between the different repeats.
1. Invariant repeats - identical or near identical.
2. Variant repeats - still homologous, but differ in their sequences to a lesser or greater extent.

Question 3

In variant repeats, what does the level of amino acid sequence divergence depend on?

Answer 3

Depends on time since duplication and selective pressures (nonfunctionalisation and sub/neofunctionalisation).

Question 4

What is nonfunctionalisation?

Answer 4

A neutral evolutionary process (i.e., a loss of purifying selection) that leads to a faster rate of evolution.
- Substitution rate is equal to mutation rate

Question 5

What is subfunctionalisation or neofunctionalisation?

Answer 5

Where two sequences diverge through positive/adaptive selection (i.e., can speed up mutation rates via positive selection).

Question 6

How do invariant repeats occur initially?

Answer 6

They are an initial product of any gene amplification, but these copies are expected to diverge over time.

Question 7

How are some invariant repeats maintained over long periods of time? And why does this happen?

Answer 7

1. Can be maintained through strong purifying selection to preserve dosage of specific gene products (i.e., they are conserved sites, for example, structures of rRNAs tRNAs and histones are highly conserved).
2. Concerted evolution!

Question 8

What was observed when comparing rRNA tandem repeat sequencing between frog species?

Answer 8

Expected observation:
- Sequences under high functional constraint were conserved between species.
- Non-transcribed intergenic sequences (IGS) were very different between species
Unexpected observation:
- IGS regions were very similar within the same species

Question 9

What would we expect to see in sequences under little functional constraint?

Answer 9

Under classical divergent evolution, the similarity between two units within a species should be the same as that between species.

Question 10

What is concerted evolution? How does this model of evolution compare to what we would expect under classical divergent evolution?

Answer 10

It is the non-independent evolution of genes, with mutations spreading horizontally to all members of a multi-gene family.
- Repeats seem to be evolving dependent on one another (i.e., they seem to be accumulating the exact same set of changes)

Question 11

What two mechanisms have been described that allow concerted evolution to occur?

Answer 11

1. Unequal crossing-over
2. Gene conversion

Question 12

What is an unequal crossing-over?

Answer 12

A crossing-over event that results in a sequence duplication in one chromatid or chromosome and a corresponding deletion in the other.
- It is a homogenising process

Question 13

How does unequal crossing over lead to concerted evolution?

Answer 13

Over time, it can lead to preferential duplication of one repeat and deletion of others (i.e., one repeat becomes dominant in the array).

Question 14

What does concerted evolution through unequal crossing-over events require?

Answer 14

1. Mutation events (deletions, duplications)
2. Fixation events (through drift or selection for/against different arrays)

Question 15

What is gene conversion?

Answer 15

Conversion is a non-reciprocal recombination process in which two sequences interact so that one is converted to the other.
- In other words, one sequence replaces another homologous sequence in such a way they become identical!
- There is no deletion or duplication of material

Question 16

How does gene conversion work?

Answer 16

It occurs as one of the possible consequences of homologous recombination typically initiated by double-stranded break repair.

Question 17

What is the synthesis-dependent strand annealing pathway that can result in a gene conversion following a dsDNA break?

Answer 17

• Information exchange but no physical exchange (invading strand released from donor DNA and anneals to its initial strand).
• Donor molecule remains unchanged while both repaired sequences contain donor DNA information.

Question 18

What is meant by conversion by heteroduplex formation?

Answer 18

A heteroduplex is a region where one strand matches the original sequence while the other strand matches the donor sequence, which can result in base mismatches.

Question 19

What is the Double Holliday junction model that can result in a gene conversion following a dsDNA break?

Answer 19

• A physical exchange between two DNA molecules occurs.
• Where one 3’ end anneals to the donor sequence, but the other 3’ end anneals to the other strand of the donor sequence
• The loose strands are then ligated together and this results in a Double Holliday junction
• Can result in a chromosomal crossover depending on where the junctions are cut and ligated (see lecture 21 @ 26 mins)
• In the case of gene conversion, we are interested in NON-crossover resolutions

Question 20

Why do we see a bias in heteroduplex mismatch repair? How often do we therefore expect gene conversion to occur via heteroduplex mismatch repair?

Answer 20

Because one sequence will have a conversional advantage (e.g., G and C nucleotides favoured over A and T).
- Thus, gene conversions do not occur 50% of the time as we might expect without bias!

Question 21

What are some important differences between unequal crossing-over (UC) and gene conversion (GC)?

Answer 21

UC - changes gene copy number.
GC - does not change gene copy number.

UC is more efficient than GC for concerted evolution of tandem duplicates as it can include many repeats in a single event (whereas GC acts on a few kb at most).

GC can act on dispersed repeats because it does not involve crossing-over (i.e., the homologous sequences do not need to be near each other on the chromosome).

GC is also biased - thus more likely to reach fixation.

Question 22

Give two examples of concerted evolution in action.

Answer 22

1. Globin genes in the Great Apes.
2. Resurrection of a ribonuclease pseudogene in bovines.
   (See lecture 21 for discussion on both examples @ 33 mins)