Lecture 22 - Whole Genome Duplication Flashcards
What is the difference between polysomy and polyploidy?
Polysomy - the duplication of a whole chromosome.
Polyploidy - the duplication of a whole genome.
What are the different types of ploidy?
Diploid (2N) - two sets of chromosomes.
Polyploidies - more than two sets of chromosomes.
- Triploid (3N)
- Tetraploid (4N)
- Pentaploid (5N)
- Hexaploid (6N) and so on…
What is a common case of polyploidy observed in nature?
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!!!
What is meant by true polyploidy?
A heritable increase in the genome across all the cells in an organism (and thus a change in ploidy of the gametes).
How do true polyploids arise?
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)
Why is it that odd numbered ploidies are almost always sterile?
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)
What are the most frequently observed of the even numbered ploidies?
Tetraploids (4N).
Where do we see a huge amount of polyploid species?
In plants - due to much more variety and flexibility in their reproductive strategies and sex determination mechanisms.
Although rare, in what animals do we see polyploidy?
- Invertebrates
- Some fish and amphibians
- Asexually reproducing reptiles
What is autopolyploidy?
Doubling of the same set of chromosomes, and of the same origin (within a single species).
What is allopolyploidy?
Involves a hybridisation event, combining genetically distinct (but similar) chromosome sets from two different species.
What kind of chromosomes are involved in autopolyploidy?
Involves two homologous chromosomes.
- Identical, with no preferential pairing during meiosis
What kind of chromosomes are involved in allopolyploidy?
Involves two homoeologous chromosomes.
- Similar, but different enough that chromosomes that originate from the same species will preferentially pair during meiosis
What is the evolutionary survival rate of autopolyploidy?
Low evolutionary survival (i.e., don’t often result in the evolution of new polyploid species).
What is the most commonly known route to hybrid speciation?
Allopolyploidy.
Where is allopolyploidy most commonly observed?
In plants.
What is an example of an animal allopolyploid?
African clawed frog (an allotetraploid).
What is an example of a suspected mammalian allotetraploid?
Red viscacha rats.
Golden viscacha rats.
Give a famous example of hybrid speciation.
The Cabbage Family Triangle.
Give a famous example of hybrid speciation (via allopolyploidy).
- The Cabbage Family Triangle.
- Wheat.
What is a benefit of polyploidisation?
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)
What is a benefit of allopolyploidy in particular?
Hybrid vigour - where allopolyploids show enhancement of parental traits
What do redundant duplicated genes provide opportunity for?
Neofunctionalisation and subfunctionalisation (i.e., opportunity for niche expansion or adaption to environmental change).
What is meant by gene dosage? How is this preserved in polyploids?
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).
What is made possible via the duplication of whole biochemical processes?
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).
What are some disadvantages of polyploidy?
- 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)
What is diploidisation?
The process of converting a polyploid genome back to a diploid one (e.g., tetraploid reverting back to diploid state).
What is the key outcome of diploidisation?
Going from having 4 chromosomes (in tetraploids) that have the potential to pair up during meiosis to having only 2.
What are the two major mechanisms at play in diploidisation?
- Chromosomal rearrangement
- Gene loss
What are chromosomal rearrangements?
Mutations involving long DNA sequences that change location and/or order of gene. These can occur within or between chromosomes.
What type of chromosomal rearrangements can occur WITHIN chromosomes?
- Terminal deletions
- Interstitial deletions
- Duplications
- Pericentric inversions (involving the centromere)
- Paracentric inversions (not involving the centromere)
- Block interchange
What is meant when a chromosomal rearrangement is said to be “balanced”?
When there is no addition or deletion of any genetic information.
- Thus, deletions and duplications are inherently unbalanced!!
What type of chromosomal rearrangements can occur BETWEEN chromosomes?
- Reciprocal translocations
- Nonreciprocal translocations
Give an example of a chromosomal rearrangement in disease.
The Philadelphia Chromosome in leukaemia (resulting from a translocation between chromosomes 22 and 9)
What is synteny?
The physical occurrence of two or more genes on the same chromosome.
What is collinearity?
The arrangement of one sequence in the same linear order as another sequence.
What is the relationship between synteny and gene order with evolutionary distance?
Shared synteny and gene order decreases with evolutionary distance - almost like a molecular clock.
What can shared synteny tell us?
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.
What can conserved synteny and gene order (over long evolutionary time) sometimes indicate?
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.
What is a paleopolyploid?
After diploidisation, a polyploid is called a paleopolyploid.
What is the significance of chromosomal rearrangement in diploidisation?
- 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)
What is the problem for evolutionary geneticists when trying to identify a paleopolyploid?
The longer ago the diploidisation occurred, the harder it is to tell they were a polyploid in the first place (known as cryptopolyploids).
How do we get around the problem of cryptopolyploids?
Look for lots of duplicated regions!
Then…
- Compare phylogenies
- Look for double synteny
Give an example of how patterns of synteny shows tell tale signs of whole genome duplication.
In baker’s yeast.
(See lecture 22 @ 23 mins)
