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Evolutionary and Population Genetics (GEU33075) > Lecture 22 - Whole Genome Duplication > Flashcards

Lecture 22 - Whole Genome Duplication Flashcards

1
Q

What is the difference between polysomy and polyploidy?

A

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

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2
Q

What are the different types of ploidy?

A

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

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3
Q

What is a common case of polyploidy observed in nature?

A

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!!!

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4
Q

What is meant by true polyploidy?

A

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

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5
Q

How do true polyploids arise?

A

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)

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6
Q

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

A

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)

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7
Q

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

A

Tetraploids (4N).

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8
Q

Where do we see a huge amount of polyploid species?

A

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

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9
Q

Although rare, in what animals do we see polyploidy?

A
  • Invertebrates
  • Some fish and amphibians
  • Asexually reproducing reptiles
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10
Q

What is autopolyploidy?

A

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

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11
Q

What is allopolyploidy?

A

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

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12
Q

What kind of chromosomes are involved in autopolyploidy?

A

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

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13
Q

What kind of chromosomes are involved in allopolyploidy?

A

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

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14
Q

What is the evolutionary survival rate of autopolyploidy?

A

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

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15
Q

What is the most commonly known route to hybrid speciation?

A

Allopolyploidy.

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16
Q

Where is allopolyploidy most commonly observed?

A

In plants.

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17
Q

What is an example of an animal allopolyploid?

A

African clawed frog (an allotetraploid).

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18
Q

What is an example of a suspected mammalian allotetraploid?

A

Red viscacha rats.
Golden viscacha rats.

19
Q

Give a famous example of hybrid speciation.

A

The Cabbage Family Triangle.

20
Q

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

A
  • The Cabbage Family Triangle.
  • Wheat.
21
Q

What is a benefit of polyploidisation?

A

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)

22
Q

What is a benefit of allopolyploidy in particular?

A

Hybrid vigour - where allopolyploids show enhancement of parental traits

23
Q

What do redundant duplicated genes provide opportunity for?

A

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

24
Q

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

A

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).

25
Q

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

A

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).

26
Q

What are some disadvantages of polyploidy?

A
  • 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)
27
Q

What is diploidisation?

A

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

28
Q

What is the key outcome of diploidisation?

A

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

29
Q

What are the two major mechanisms at play in diploidisation?

A
  1. Chromosomal rearrangement
  2. Gene loss
30
Q

What are chromosomal rearrangements?

A

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

31
Q

What type of chromosomal rearrangements can occur WITHIN chromosomes?

A
  • Terminal deletions
  • Interstitial deletions
  • Duplications
  • Pericentric inversions (involving the centromere)
  • Paracentric inversions (not involving the centromere)
  • Block interchange
32
Q

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

A

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

33
Q

What type of chromosomal rearrangements can occur BETWEEN chromosomes?

A
  • Reciprocal translocations
  • Nonreciprocal translocations
34
Q

Give an example of a chromosomal rearrangement in disease.

A

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

35
Q

What is synteny?

A

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

36
Q

What is collinearity?

A

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

37
Q

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

A

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

38
Q

What can shared synteny tell us?

A

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.

39
Q

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

A

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.

40
Q

What is a paleopolyploid?

A

After diploidisation, a polyploid is called a paleopolyploid.

41
Q

What is the significance of chromosomal rearrangement in diploidisation?

A
  • 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)
42
Q

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

A

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

43
Q

How do we get around the problem of cryptopolyploids?

A

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

44
Q

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

A

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

Evolutionary and Population Genetics (GEU33075) (10 decks)

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