Difference between recombination and adaptation, evolution of the Y chromosome

Question 1

Recombination is necessary for adaptive evolution. Why?

Answer 1

Because it generates new combinations of alleles, some of which may be optimum in a changed environment, thus allowing organisms to become better-suited to their surroundings, survive and reproduce

Question 2

Define recombination.

Answer 2

Whereby equivalent portions of DNA are exchanged between homologous chromosomes

Question 3

Define adaptation.

Answer 3

Where an organism evolves in response to a changing environment, becoming better-suited to it

Question 4

When did homologous evolution evolve? Why was it thought to have evolved?

Answer 4

~3mya

To repairs damaged DNA strands, increasing sequence variance within an individual.

Question 5

After the evolution of diploidy, what did recombination ensure?

Answer 5

Recombination of two genomes at meiosis as maternal and paternal chromosomes exchange equivalent portions of DNA before segregating into the gametes.
Recombination ensures offspring differ from their parents.

Question 6

Why do environmental changes causes adaptation?

Answer 6

When the environment changes so do fitness optima, allowing selection to favour different combinations of alleles that are better suited to the environment.

Question 7

Organisms with advantageous genotypes survive to…

Answer 7

pass on their genes to their offspring, meaning apative traits can spread to fixation

Question 8

In most vertebrate species sex is determined by…

Answer 8

GSD in the form of sex chromosomes

Question 9

Which groups display female heterogametey?

Answer 9

Birds; systems are ZZ male and ZW female

Question 10

Which groups display male heterogametey?

Answer 10

Placental mammals and some insects; systems are XX female and XY male

Question 11

In XY systems, which is a) the major and b) the minor chromosome?

Answer 11

a) X

b) Y

Question 12

X and Y have never been homologous. True or false?

Answer 12

False; they evolved from homologous autosomes

Question 13

What caused divergence between the X and Y?

Answer 13

A series of inversion on the Y

Question 14

Define an inversion.

Answer 14

When a chromosomal segment is reversed end to end.

Question 15

The X and Y can no longer recombine at all. True or false?

Answer 15

False; the X and Y can recombine along the pseudo-autosomal region (PAR) that still retains homology.

Question 16

The majority of genes involved in biological sex are no found on the sex chromosomes. Which major sex-determining locus is and where?

Answer 16

The SRY locus is located on the Y chromosome

Question 17

What does SRY do?

What happens without SRY activation?

Answer 17

Causes testes differentiation by activating male-specific regulatory networks.

Ovaries develop.

Question 18

Why does the X still show adaptive potential?

Answer 18

Because the female specific region (FSR) is still able to recombine and generate new allelic combinations between Xs.

Question 19

The Y has showed considerable degeneration as it cannot recombine. Which two major processes have contributed to this?

Answer 19

1. Muller’s ratchet

2. Hill-Robertson effect

Question 20

Define Muller’s Ratchet.

What effect has this had on the Y?

Answer 20

A lack of recombination causes mutational meltdown as deleterious mutations accumulate without removal.

It is riddled with mutations it cannot lose.

Question 21

Define the Hill-Robertson effect.

What effect has this had on the Y?

Answer 21

Linkage between alleles causes selective sweeps, whereby beneficial alleles are selected for but drag along deleterious alleles that are linked to them.

There has been a decay of functional genes as selection cannot act as strongly as it does on each allele independently.

Question 22

How many functional genes do the X and Y contain?

Answer 22

X = ~1000
Y = a few dozen

Question 23

How has such a reduction in Y fitness been allowed to persist, surely the Y will erode away and males will become extinct?

Answer 23

Due to sexually antagonistic alleles; in this case a lack of recombination is actually beneficial

Question 24

What are sexually antagonistic alleles?

Answer 24

Those that are beneficial to one sex but deleterious in the other.

Question 25

If sexually antagonistic alleles are inherited by the same organism, what happens?

Answer 25

Intragenomic conflict

Question 26

When is recombination selected against?

Answer 26

When it brings together sexually antagonistic alleles

Question 27

Why are SAA often linked to sex-determining loci?

Answer 27

Because it guarantees they will end up in the correct sex and so is favoured by selection

Question 28

Inversions on the Y have allowed the accumulation of…

Answer 28

male-specific genes that have not been broken up by recombination

Question 29

Linkage of male-specific alleles to SRY means that they only ever end up in males, reducing intragenomic conflict. True or false?

Answer 29

True

Question 30

Which functional genes have are found on the Y?

Answer 30

Male fitness genes related to sperm production or colour

Question 31

Y can undergo non-homologous recombination. How?

Who studied this?

Answer 31

Skaletsky et al., 2013:

Large palindromes in its sequences cause DNA exchange between sister chromatids.

Question 32

Is non-homologous recombination of Y always beneficial?

Answer 32

No, costs can be high too. It can result in infertile males with mutant Ys

Question 33

How does recombination affect drift?

Answer 33

Recombination reduces drift as it increases Ne, or the number of chromosomes that can contribute to the next generation

Question 34

Who explained how sex chromosomes evolve? How?

Answer 34

Bachtrog et al., 2014, REVIEW PAPER

Divergence accompanied by the acquisition of a master sex-determining locus, e.g. SRY

Question 35

Bachtrog et al., 2014:

When did the SRY evolve?

Answer 35

180mya

Question 36

Bachtrog et al., 2014:

Gene loss from the Y will not stop until the Y is degenerated. True or false, why?

Answer 36

False: this assumes a constant rate of gene loss, yet loss will slow as the Y becomes more gene-poor. There an equilibrium content will be reached whereby further loss is v. unlikely.

Question 37

Who looked at mutation accumulation in D. melanogaster? What did they do/find?

Answer 37

Rice, 1994

Chromosome 2 and 3 prevented from recombining.
After 35 generations male fitness was reduced.
Adult male fitness measured by counting the number of males that emerged 2 days post-eclosion

Question 38

Rice, 1994:

What was the point of preventing chr2 and 3 from recombining?

How much had fitness decreased after 35 generations?

Answer 38

To assess mutation accumulation on a Y, so chr2 and 3 were made to co-segregate ‘as if they were one large, non-recombining Y chromosome’.

Therefore this experiment provides explanation as to why mutation load might accumulate on a Y

25% fitness reduction in 35 gens

Question 39

What is hemizygosity?

Answer 39

Where there is only one copy of the gene present, i.e. X-linked genes in males

Question 40

Recombination must occur in at least one place between each pair of chromosomes. True or false?

Answer 40

True

Question 41

Recombination is far from random. Which gene controls recombination in humans? Give a reference.

What percentage of recombination does it control?

How big is it?

How does it control recombination?

Answer 41

Paigen and Petkov, 2010

PRDM9

41%

It is a 13bp motif

It encodes a zinc-finger protein that binds to specific DNA motifs to initiate chiasmata formation, a trans-acting factor

Question 42

Why is there conflict between PRDM9 and its binding sites?

What does this lead to?

Answer 42

Recombination is mutagenic and alters the binding site sequence

Leads to rapid shifts in recombination hotspots across populations and species

Question 43

Why are recombination hotspots better off than non-recombining regions? Give 4 reasons.

Answer 43

1. They avoid Muller’s Ratchet
2. They avoid Hill-Robertson interference, linkage broken up and so selection is more efficient
3. Recombination itself can be mutagenic and create new variation
4. Larger Ne increases variation

Question 44

How does small Ne reduce adaptive potential?

Answer 44

There is less diversity and so populations are more susceptible to drift

Question 45

Why does the Y chromosome have a small Ne? Give 2 reasons.

Answer 45

Because of mate choice, only some males get to mate. This already selects a subset of Ys from the entire population, thus reducing Ne.

In XY systems, at reproduction when XX females and XY males come together, there are 4 autosomes for every 3 major and 1 minor chromosomes. The Ne of Y is inferior to the autosomes and to X.

Y suffers a twofold reduction in Ne before it even gets to the recombination stage.

Question 46

Recombination hotspots vary between sexes. Why might this be? Give two reasons.

Who said this?

Answer 46

Paigen and Petkov, 2010:

1. Selective argument: sexually antagonistic haploid selection selects for sex-specific effects, although this is rare
2. Biological argument: arrested meiosis in female vertebrates creates greater chiasmata migration

Question 47

Izzy’s great quote for ‘why are Y chromosome studies important for understanding recombination and adaptation

Answer 47

‘Y chromosome provides the most compelling evidence that recombination produces adaptation’

Question 48

Who studied a male genome that hasn’t degenerated? What did they find?

Answer 48

Begero and Charlesworth, 2011:

S. latifolia, male genome still expressed, only 10-20% degeneration in 5-10my