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C-value (amount of DNA) paradox:

- The amount of DNA does not correlate with perceived complexity of position of the phylogenetic tree
- Complexity = number of ell types, metabolic complexity, behavioural complexity


What explained genome size variation?

- Gene duplication
- Satellites (often heterochromatic
- Relative rate of insertions and deletions
- Transposable elements
- Polyploidy (whole genome duplication)



- Having a complete complement of chromosomes



- Having an incomplete complement of chromosomes



- Whole genome is duplicated within a species
- (self duplication)
- Banana's, peanut, potato



- Genome duplication deriving from hybridisation between two parental species
- Eg) wheat, cotton, apples, sugar cane


The mechanics:

- Somatic doubling
- Polyspermy
- Gemetic non-reduction


Somatic doubling:

Mitotic double then failure of cell division



Multiple sperm fertilise the same egg


Gemetic non-reduction

- Failur of cell division during meiosis (2n gametes)
- Doesn't happen much in animals, but does in plants
- Can occur from sterile hybrids


How common is polyploidy?

- Very common in plants! (70% of angiosperms)
- 15% of speciation events in angiosperms
- Fairy common in fish (asexual reproduction), amphibians and insects
- Rare in mammals


What varieties and polyploidy:

- AA (einkorn) crossed with BB (goat grass)
- AABB (durum wheat, used for pasta) crossed with DD (goat grass)
- Bread wheat today is AABBDD
- Happened about half a million years ago


Red viscacha rat:

- 4N! it has double the amount of DNA of related species
- Genomic in situ hybridisation (label with fluorescent DNA and wash away, so only the fluorescent label is left where there is a good match)
- Showed that allopolyploidy is likely


What evidence is there for ancient polyploidy events?

- Evolutionary jumps in C-value
- Chromosome pairing patterns
- Gene number
- Gene arrangement
- Gene tree topology
- Age of gene duplication events (molecular clock)


Is yeast a peleo-polyploid?

- No evidence that duplicated gene blocks are duplicated again
- All blocks have the same centromere-telomere orientation (some should show an inversion if it were multiple-sub)
- Synonymous site divergence is about the same of all pairs of blocks (suggests duplication at the same time)


Vertebrate '2R' hypothesis:

- 2 rounds of poly-ploidy in the vertebrate lineage
- Based on evidence from C-value (amount of nuclear DNA), isozymes, and two pairs of duplicated genes on chromosome 11 and 12 delineating duplicated chromosomes
- This was confirmed


In order to determine if duplication events were close together using the molecular clock method we need:

- Enough species to cover before/after putative duplication events
- Enough genes to five statistical power
- Whole genomes are ideal


'2R' in the seed plants:

- Species tree for plants is well known, a gene tree is also well known
- There have been two whole genome duplication events, this was proved by comparing eudicots, monodictos and plotting them on a species tree


Possible selective advantages (some are also disadvantages) for polyploidy:

- Increased DNA content
- Increased heterozygosity (able to retain sufficient genet diversity even with small census size, potential for subfunctionalization and differential expression, higher mutation rate)


Possible costs of polyploidy:

- Chromosomal pairing errors and sex determination
- Developmental: orchestration of gene expression called a 'genomic shock', and timing of DNA replication, dosage compensation
- Physiological: higher DNA content requires more phosphorus
- Population: initially rare, loss due to drift. Competition with locally adapted progenitor species


How do benefits and costs compare evolutionarily?

- Recently formed polyploids have a higher extinction rate, lower speciation rates and lower diversification rates
- But polyploidy seems to be able to drive longer timer evolutionary success