Bio217 Week 6: Genome Evolution & Duplication (Bernard)

Front 1

What else is going on between alleles in pops and species tree (except sorting or speciation event)?

Back 1

Allele frequency differences, allele selection differences, allele histories and their persistance differs

Hint 1

what differs between alleles?

Front 2

What is this plot showing us?

Back 2

A comparision of all genes within a genome. The most similar matches are plotted and gives this curve showing frequency of dS (synonymous changes per site). The falling exponential curve indicates that many sites have small differences, few sites have large differences, this is pattern seen in many different organisms/genomes.

Front 3

What creates this pattern of the graph ?

Back 3

GENE DUPLICATION. Genes are copied and then have independant evo.

Patterns:

1. Local, small scale duplication, neighbouring (copied and placed neatby)

2. Ectopic, small scale but not neighbouring (copy placed on other chromosome)

3. Polyploidy

Processes:

1. Unequal recombo

2. Retro element-mediated duplication

3. Unreduced gametes/somatic doubling

Hint 3

Reason + patterns (3 examples) and processes (3 examples) behind this, how it can happen

Front 4

What is tandem duplication and how does it happen? What can facilitate this process?

Back 4

A local duplication of one or few genes via unequal crossing over (due to wrong pairing - misalignment) during meiosis.

Repetetive DNA (e.g retor elements) can facilitate.

Front 5

What kind of duplication has occured in Glycine (soybean)? Has this been good or bad for the plant?

Back 5

Tandem duplication.

Has given clusters of genes that expresses proteins that protect against bacterium infection - this needs a lot of diversity so these duplications has created a good opportunity for more mutations to occur.

Front 6

In what organisms can we see polyploidy?

Back 6

It's quite common in plant genomes, also seen in frogs, salamander and fish

Front 7

Give an example on how ectopic duplication can occur!

What can this kind of duplication cause/create a possibility for?

Back 7

Via retro element insertion. It's a "copy and paste" replication which adds a new copy of sequences to a new genomic location. This process leaves small repeats on either side of the inserted gene.

Since the target site now is changed this gives rise for the possibility of tandem duplication via unequal crossing over.

Front 8

What's special about retro elements?

Back 8

They can induce their own copying and insert somewhere else, anywhere in the genome

Front 9

What is meant by polyploidy?

Back 9

The whole genome has been duplicated

Front 10

What duplications are ongoing vs single events?

Back 10

Ectopic and local (tandem) duplications are ongoing, whilst whole genome duplication occurs at a single event

Front 11

What is autopolyploidy?

Back 11

When polyploidy arises due to failure of segregation during meiosis, creates diploid gametes. Happens within a species.

Via self-fertilization (or mating with other ind that has 2n gametes) a tetraploid individual can occur which is viable & fertile.

Front 12

What is allopolyploidy?

Back 12

When whole genome duplication arise via hybridisation (hybridisation accompanied by genom doubling)

Front 13

What does these graphs illustrate?

Back 13

Whole genome duplication events (polyploidy), for maize it's a young event and for cotton it's an ancient event (which is shared by both cotton species)

Front 14

Which organism family has a history of several polyploid events?

Back 14

The angiosperms, it's an imoportant process. There has even been polyploid events where tetraploids gave hexaploidy (e.g. Brassica)

Front 15

If there has been two events of polyploidy, what will the Ks distribution (graph) look like?

Back 15

Two peaks, the older one a bit smaller than the younger one due to a little bit of loss.

Front 16

What is the meaning of paralogy?

Back 16

The presence of more than 1 homologous gene in the same genome.

Genes that originate from an ancestral gene duplication are paralogous (they descend from the same duplication that occured before speciation)

Front 17

What is the meaning of orthology?

Back 17

The gene copy in different species that arose via speciation, not duplication

Front 18

What's the meaning of homoeology?

Back 18

A subset of paralogy. If the gene duplication giving rise to the genes occured as part of a whole genome duplication event, then the genes are homoeologues.

Front 19

In the gene tree shown: at least how many gene duplications have taken place?

Back 19

At least 3

Front 20

In the gene tree shown: at least how many gene losses has taken place?

Back 20

At least 3. Compare the trees, find speciation events in the gene tree and sort out duplication events. From each duplication event there should be branches, we then see that there's at least 3 branches missing.

Front 21

In the gene tree shown: which of these comparisions are between orthologs (copies that arose through speciation)?

Alternatives:

1. D2 & E1

2. A1 &B1

3. D1 & D2

4. C1 & E1

Back 21

Alternative 1. D2 & E1

They are orthologous since they arose through speciation

Front 22

How is the selection pressure on the two copies of genes after a duplication?

Back 22

It's relaxed since two copies are initially redundant when they are both fully functional

Front 23

What happens if one gene copy from a duplication event gets deleterious mutations?

Back 23

Since the gene's function needs to be maintained, the selection pressure on the still functional copy is restored - it gets under purifying selection.

Front 24

What happens if one gene copy from a duplication gets a mutation that is advantageous? What is this process called?

Back 24

The advantageous mutation gives rise to a new function, and still keeps the original function.

This is called neofunctionalisation and the modified copy is put under positive selection, we can expect rapid evolution in this copy (which then can be seen in a phylogram)

Front 25

What is Ohno's dilemma and subfunctionalisation? Give an example of observation of subfunct!

Back 25

Ohno proposed that neofunct. is the main mechanism to get new functions, but then the dilemma arose: the model doesn't explain the retention of duplicated copies, how can both copies be kept over a long time?

A possible solution is subfunctionalisation (DDC-model): both copies are required to maintain the entire complement of functions (they complement eachother). Duplication-Degeneration-Complementation: the copied gene has multipel, important functions so neither of the copies are redundant since they can loose one function - the other one is then needed to retain full function of the gene.

In the Zebrafish, hoxb1 genes were duplicated, both are present but they have each lost one function at a part of the gene - both copies are needed to maintain full function (they complement eachother through diff timing of expression)

Front 26

How can subfunctionalisation be expected to look in a phylogram?

Back 26

Expect similar rates of evo between the copies (relaxed selection on both), but somewhat faster than a single copy in another species

Front 27

What is pseudogenisation?

Back 27

Another solution to Ohno's dilemma. It says that both copies are NOT kept, one is lost. This could happen in a way of one copy getting more and more mutations which causes loss of function, then the copy with original function is put under purifying selection and is less of a target for mutations.

One copy can also be lost due to uneven crossing over.

Front 28

How would pseudogenisation look in a phylogram?

Back 28

Front 29

What does the solution "specialisation" to Ohno's dilemma indicate?

Back 29

There's an escape from adaptive conflict (EAC model):

single copy gene develops second function but is constrained from improving either the ancestral or new function (can't specialize, conflict between the two functions).

After duplication each gene copy can be driven by positive selection to specialize => after the change, both copies are better than one another in diff functions.

Front 30

How might the EAC model work?

Back 30

Pleiotropy (when one gene influences many traits) is an example of when two original functions can't be independently improved. If a change in one direction is favoured by selection for one trait, but in a conflicting direction for another trait, then change might be kept on hold.

After duplication each gene copy can be driven by pos selection to specialize, developing new or improved functions.

NOTE: specialisation starts before the gene duplication (unlike neofunct where it occurs after)

Hint 30

What could block Specialization?

Front 31

How would specialisation look in a phylogram?

Back 31

Front 32

Are the different solutions to Ohno's dilemma enough to solve it?

Back 32

No, more models are needed to explain why duplicated genes stick around.

Front 33

Which model for a solution to Ohno's dilemma allows the genes to retain the same function, how?

Back 33

The subfunctionalisation model, the genes can retain the same function IF they diverge in expression:

in time

or

in space

Front 34

As a summary, name all the different evolutionary fates of duplicated genes, with phylograms to explain!

Back 34