Lecture 22 - Whole Genome Duplication

Question 1

What is the difference between polysomy and polyploidy?

Answer 1

Polysomy - the duplication of a whole chromosome.
Polyploidy - the duplication of a whole genome.

Question 2

What are the different types of ploidy?

Answer 2

Diploid (2N) - two sets of chromosomes.
Polyploidies - more than two sets of chromosomes.
- Triploid (3N)
- Tetraploid (4N)
- Pentaploid (5N)
- Hexaploid (6N) and so on…

Question 3

What is a common case of polyploidy observed in nature?

Answer 3

Somatic endopolyploidy - found in the tissues of many species (e.g., mammalian liver cells can reach octoploid level).
- However, these cases are very different to heritable or true polyploidy!!!

Question 4

What is meant by true polyploidy?

Answer 4

A heritable increase in the genome across all the cells in an organism (and thus a change in ploidy of the gametes).

Question 5

How do true polyploids arise?

Answer 5

Polyploids arise when a meiotic or mitotic irregularity (e.g., nondisjunction) cause the formation of unreduced gametes with more than one set of chromosomes.
- In other words, diploids giving rise to diploid gametes (instead of haploid)

Question 6

Why is it that odd numbered ploidies are almost always sterile?

Answer 6

Because they cannot undergo meiosis correctly (as they cannot pair up and segregate properly into the gametes).
- This can result in unbalanced gametes that are unviable
- Thus, the best possible way of reproducing is through asexual means (without meiosis)

Question 7

What are the most frequently observed of the even numbered ploidies?

Answer 7

Tetraploids (4N).

Question 8

Where do we see a huge amount of polyploid species?

Answer 8

In plants - due to much more variety and flexibility in their reproductive strategies and sex determination mechanisms.

Question 9

Although rare, in what animals do we see polyploidy?

Answer 9

• Invertebrates
• Some fish and amphibians
• Asexually reproducing reptiles

Question 10

What is autopolyploidy?

Answer 10

Doubling of the same set of chromosomes, and of the same origin (within a single species).

Question 11

What is allopolyploidy?

Answer 11

Involves a hybridisation event, combining genetically distinct (but similar) chromosome sets from two different species.

Question 12

What kind of chromosomes are involved in autopolyploidy?

Answer 12

Involves two homologous chromosomes.
- Identical, with no preferential pairing during meiosis

Question 13

What kind of chromosomes are involved in allopolyploidy?

Answer 13

Involves two homoeologous chromosomes.
- Similar, but different enough that chromosomes that originate from the same species will preferentially pair during meiosis

Question 14

What is the evolutionary survival rate of autopolyploidy?

Answer 14

Low evolutionary survival (i.e., don’t often result in the evolution of new polyploid species).

Question 15

What is the most commonly known route to hybrid speciation?

Answer 15

Allopolyploidy.

Question 16

Where is allopolyploidy most commonly observed?

Answer 16

In plants.

Question 17

What is an example of an animal allopolyploid?

Answer 17

African clawed frog (an allotetraploid).

Question 18

What is an example of a suspected mammalian allotetraploid?

Answer 18

Red viscacha rats.
Golden viscacha rats.

Question 19

Give a famous example of hybrid speciation.

Answer 19

The Cabbage Family Triangle.

Question 20

Give a famous example of hybrid speciation (via allopolyploidy).

Answer 20

• The Cabbage Family Triangle.
• Wheat.

Question 21

What is a benefit of polyploidisation?

Answer 21

Increase in the number of alleles for any given gene.
- Can mask deleterious recessive mutations
- Can maintain more than two alleles per locus
- Higher effective population sizes
2. Can disrupt self-incompatibility mechanisms in plants
- Allows for self-fertilisation (e.g., via the production of diploid gametes)

Question 22

What is a benefit of allopolyploidy in particular?

Answer 22

Hybrid vigour - where allopolyploids show enhancement of parental traits

Question 23

What do redundant duplicated genes provide opportunity for?

Answer 23

Neofunctionalisation and subfunctionalisation (i.e., opportunity for niche expansion or adaption to environmental change).

Question 24

What is meant by gene dosage? How is this preserved in polyploids?

Answer 24

Gene dosage is the amount of gene product being produced.

Polyploidies preserve stoichiometry between gene products (unlike in polysomies, where deleterious gene dosage imbalances can occur).

Question 25

What is made possible via the duplication of whole biochemical processes?

Answer 25

Combination of redundancy and preserved gene dosage of many interacting genes may aid the development of novel pathways and functions (that could never arise via single duplication events).

Question 26

What are some disadvantages of polyploidy?

Answer 26

• Prolongation of cell division
• Unbalanced changes in genome size, nucleus volume and cell volume
• Increase in chromosome disjunctions at meiosis
• Genetic imbalance
• Interference with sex differentiation (e.g., in bees, whose sex determination is based around ploidy - with haploid males and diploid females)

Question 27

What is diploidisation?

Answer 27

The process of converting a polyploid genome back to a diploid one (e.g., tetraploid reverting back to diploid state).

Question 28

What is the key outcome of diploidisation?

Answer 28

Going from having 4 chromosomes (in tetraploids) that have the potential to pair up during meiosis to having only 2.

Question 29

What are the two major mechanisms at play in diploidisation?

Answer 29

1. Chromosomal rearrangement
2. Gene loss

Question 30

What are chromosomal rearrangements?

Answer 30

Mutations involving long DNA sequences that change location and/or order of gene. These can occur within or between chromosomes.

Question 31

What type of chromosomal rearrangements can occur WITHIN chromosomes?

Answer 31

• Terminal deletions
• Interstitial deletions
• Duplications
• Pericentric inversions (involving the centromere)
• Paracentric inversions (not involving the centromere)
• Block interchange

Question 32

What is meant when a chromosomal rearrangement is said to be “balanced”?

Answer 32

When there is no addition or deletion of any genetic information.
- Thus, deletions and duplications are inherently unbalanced!!

Question 33

What type of chromosomal rearrangements can occur BETWEEN chromosomes?

Answer 33

• Reciprocal translocations
• Nonreciprocal translocations

Question 34

Give an example of a chromosomal rearrangement in disease.

Answer 34

The Philadelphia Chromosome in leukaemia (resulting from a translocation between chromosomes 22 and 9)

Question 35

What is synteny?

Answer 35

The physical occurrence of two or more genes on the same chromosome.

Question 36

What is collinearity?

Answer 36

The arrangement of one sequence in the same linear order as another sequence.

Question 37

What is the relationship between synteny and gene order with evolutionary distance?

Answer 37

Shared synteny and gene order decreases with evolutionary distance - almost like a molecular clock.

Question 38

What can shared synteny tell us?

Answer 38

By comparing synteny, it can tell us about the evolutionary genome rearrangements on two closely related lineages since they split - and using this information we can try to reconstruct what the ancestral genome might have looked like.

Question 39

What can conserved synteny and gene order (over long evolutionary time) sometimes indicate?

Answer 39

Can sometimes indicate some type of functional constraint.
- Conservation indicates that it may be detrimental to change the order or location of these particular genes.

Question 40

What is a paleopolyploid?

Answer 40

After diploidisation, a polyploid is called a paleopolyploid.

Question 41

What is the significance of chromosomal rearrangement in diploidisation?

Answer 41

• Over time, the tetraploid (or other polyploids) will build up chromosomal rearrangements over time.
• These will eventually prevent pairing of all 4 chromosomes (i.e., the rearrangements become fixed differences)
• In other words, they make the two pairs of chromosomes less similar such that they can no longer match up together in different combinations
• Gradually leads to diploidisation (each chromosome only has 1 matching homolog and not 3)

Question 42

What is the problem for evolutionary geneticists when trying to identify a paleopolyploid?

Answer 42

The longer ago the diploidisation occurred, the harder it is to tell they were a polyploid in the first place (known as cryptopolyploids).

Question 43

How do we get around the problem of cryptopolyploids?

Answer 43

Look for lots of duplicated regions!
Then…
- Compare phylogenies
- Look for double synteny

Question 44

Give an example of how patterns of synteny shows tell tale signs of whole genome duplication.

Answer 44

In baker’s yeast.
(See lecture 22 @ 23 mins)