L11 Polyploidy

Question 1

C value paradox

Answer 1

the amount of DNA does not correlate with perceived complexity on the phylogenetic tree

Question 2

Complexity

Answer 2

number of cell types
metabolic complexity
behavioural complexity

Question 3

The fraction that is coding vs Intergenic changes

Answer 3

• for prokaryotes and viruses, about 10% of the genome is intergenic
• for animals and plants, less than 10% may encode for proteins

Question 4

What explains genome size variation?

Answer 4

1. Gene duplication
2. blocks of duplication
3. satellites
4. relative rate of insertions and deletions
5. Transposable elements; 40% of human genome is TE
6. Polyploidy

Question 5

Polyploid

Answer 5

Having more than two complete sets of chromosomes e.g. 3n, 4n,5n

Question 6

Euploid

Answer 6

Having a complete complement of chromosomes

Question 7

Aneuploid

Answer 7

Having an incomplete complement of chromosomes e.g. missing/having an extra chromosome, trisomy 21

Question 8

Autopolyploidy

Answer 8

Duplication of the genome with a species e.g. potato, banana

Question 9

Allopolyploidy

Answer 9

Genome duplication deriving from hybridisation between two parental species e.g. wheat, cotton

The gametes are 2n

Distinct from a diploid hybrid

Question 10

Somatic doubling

Answer 10

mitotic doubling then failure of cell division- vegetative propagation in plants

Question 11

Polyspermy

Answer 11

multiple sperm fertilising an egg - 1-3% of human conceptions (not viable)

Question 12

Gametic non-reduction

Answer 12

See OneNote diagram

failure of cell division during meiosis producing 2n gametes - unreduced sperm uncommon in animals, common step in pathway to allopolyploidy in plants

Question 13

How common is polyploidy?

Answer 13

• very common in plants, 70% lineages of angiosperms and led to 15% angiosperm speciation events
• fairly common in fish, amphibians, insects
• rare in mammals

Question 14

Red Vischacha rat

Answer 14

See OneNote

Question 15

Wheat varieties

Answer 15

See OneNote

• hexaploid
• homeologues

Question 16

Homeologues

Answer 16

Homologs derived from polyploidization event

Question 17

Diploidization

Answer 17

• most loci now behaving/segregating like diploids

Question 18

What evidence is there for ancient polyploidy events?

Answer 18

See OneNote

• paleo-polyploidy
  1. evolutionary jumps in c-value e.g. red verschacha rat
  2. evolutionary jumps in chromosome number
  3. Chromosomal pairing- quadrivalents?
  4. Gene number
  5. Gene arrangement
  6. Gene tree topology
  7. Age of gene duplication events (molecular clock)

Question 19

C-value

Answer 19

C-value is the amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism.

Question 20

Ancient genome duplication

Answer 20

See OneNote

- gene loss after duplication

Question 21

Multiple sub-genomic duplications

Answer 21

See OneNote

• not whole genome duplication
• more than 2 copies of some genes

Question 22

Yeast - a paleo-polyploid?

Answer 22

See OneNote

Question 23

Vertebrate 2R hypothesis

Answer 23

See OneNote

• Susumu Ohno proposed that there had been two rounds of polyploidy in the vertebrate lineage
• C-value
• Isozymes
• Identified two pairs of duplicated genes on chromosome 11 and 12 delineating duplicated chromosomal segment

Found consistent data in mice homeobox

Question 24

Evidence for 2R hypothesis

Answer 24

See OneNote

Question 25

2R in seed plants?

Answer 25

See OneNote - point of divergence should match - 2 distinct peaks

Question 26

Proximate causation

Answer 26

- mechanistic explanation e.g. failure of gamete reduction

Question 27

Ultimate causation

Answer 27

- the why question

Question 28

Possible selective advantages

Answer 28

1. increased DNA content 2. increased heterozygosity 3. able to retain genetic diversity even with small census size 4. multiple gene copies 5. higher mutation rate(could also be a cost)

Question 29

Increased DNA content

Answer 29

See OneNote | 4 points

Question 30

Increased heterozygosity

Answer 30

See OneNote | 2 points

Question 31

Able to retain genetic diversity even with small census size

Answer 31

See OneNote | 2 points

Question 32

Multiple gene copies

Answer 32

- neofunctionalisation | - sub-functionalisation

Question 33

Possible costs

Answer 33

1. chromosomal 2. developmental 3. physiological 4. population

Question 34

Chromosomal costs

Answer 34

See OneNote | 2 points

Question 35

Developmental costs

Answer 35

See OneNote | 3 points

Question 36

Physiological costs

Answer 36

See OneNote | 1 point

Question 37

Population costs

Answer 37

See OneNote | 3 points

Question 38

Correlated with asexual reproduction

Answer 38

- in plants asexual reproduction may be a consequence of self-incompatibility systems breaking down - polyploid insects and reptiles probably arose from parthenogenic animals

Question 39

Parthenogenesis

Answer 39

reproduction from an ovum without fertilization, especially as a normal process in some invertebrates and lower plants.

Question 40

Asexual reproduction

Answer 40

Asexual reproduction is a type of reproduction by which offspring arise from a single organism, and inherit the genes of that parent only; it does not involve the fusion of gametes, and almost never changes the number of chromosomes

Question 41

Reconciling costs and benefits

Answer 41

``` Recently formed polyploids have: 1. higher extinction rate than diploids 2. lower speciation rate 3. lower diversification rate YET polyploidy appears associated with major evolutionary diversification events ```