Difference between recombination and adaptation, evolution of the Y chromosome Flashcards
Recombination is necessary for adaptive evolution. Why?
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
Define recombination.
Whereby equivalent portions of DNA are exchanged between homologous chromosomes
Define adaptation.
Where an organism evolves in response to a changing environment, becoming better-suited to it
When did homologous evolution evolve? Why was it thought to have evolved?
~3mya
To repairs damaged DNA strands, increasing sequence variance within an individual.
After the evolution of diploidy, what did recombination ensure?
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.
Why do environmental changes causes adaptation?
When the environment changes so do fitness optima, allowing selection to favour different combinations of alleles that are better suited to the environment.
Organisms with advantageous genotypes survive to…
pass on their genes to their offspring, meaning apative traits can spread to fixation
In most vertebrate species sex is determined by…
GSD in the form of sex chromosomes
Which groups display female heterogametey?
Birds; systems are ZZ male and ZW female
Which groups display male heterogametey?
Placental mammals and some insects; systems are XX female and XY male
In XY systems, which is a) the major and b) the minor chromosome?
a) X
b) Y
X and Y have never been homologous. True or false?
False; they evolved from homologous autosomes
What caused divergence between the X and Y?
A series of inversion on the Y
Define an inversion.
When a chromosomal segment is reversed end to end.
The X and Y can no longer recombine at all. True or false?
False; the X and Y can recombine along the pseudo-autosomal region (PAR) that still retains homology.
The majority of genes involved in biological sex are no found on the sex chromosomes. Which major sex-determining locus is and where?
The SRY locus is located on the Y chromosome
What does SRY do?
What happens without SRY activation?
Causes testes differentiation by activating male-specific regulatory networks.
Ovaries develop.
Why does the X still show adaptive potential?
Because the female specific region (FSR) is still able to recombine and generate new allelic combinations between Xs.
The Y has showed considerable degeneration as it cannot recombine. Which two major processes have contributed to this?
- Muller’s ratchet
2. Hill-Robertson effect
Define Muller’s Ratchet.
What effect has this had on the Y?
A lack of recombination causes mutational meltdown as deleterious mutations accumulate without removal.
It is riddled with mutations it cannot lose.
Define the Hill-Robertson effect.
What effect has this had on the Y?
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.
How many functional genes do the X and Y contain?
X = ~1000 Y = a few dozen
How has such a reduction in Y fitness been allowed to persist, surely the Y will erode away and males will become extinct?
Due to sexually antagonistic alleles; in this case a lack of recombination is actually beneficial
What are sexually antagonistic alleles?
Those that are beneficial to one sex but deleterious in the other.
If sexually antagonistic alleles are inherited by the same organism, what happens?
Intragenomic conflict
When is recombination selected against?
When it brings together sexually antagonistic alleles
Why are SAA often linked to sex-determining loci?
Because it guarantees they will end up in the correct sex and so is favoured by selection
Inversions on the Y have allowed the accumulation of…
male-specific genes that have not been broken up by recombination
Linkage of male-specific alleles to SRY means that they only ever end up in males, reducing intragenomic conflict. True or false?
True
Which functional genes have are found on the Y?
Male fitness genes related to sperm production or colour
Y can undergo non-homologous recombination. How?
Who studied this?
Skaletsky et al., 2013:
Large palindromes in its sequences cause DNA exchange between sister chromatids.
Is non-homologous recombination of Y always beneficial?
No, costs can be high too. It can result in infertile males with mutant Ys
How does recombination affect drift?
Recombination reduces drift as it increases Ne, or the number of chromosomes that can contribute to the next generation
Who explained how sex chromosomes evolve? How?
Bachtrog et al., 2014, REVIEW PAPER
Divergence accompanied by the acquisition of a master sex-determining locus, e.g. SRY
Bachtrog et al., 2014:
When did the SRY evolve?
180mya
Bachtrog et al., 2014:
Gene loss from the Y will not stop until the Y is degenerated. True or false, why?
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.
Who looked at mutation accumulation in D. melanogaster? What did they do/find?
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
Rice, 1994:
What was the point of preventing chr2 and 3 from recombining?
How much had fitness decreased after 35 generations?
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
What is hemizygosity?
Where there is only one copy of the gene present, i.e. X-linked genes in males
Recombination must occur in at least one place between each pair of chromosomes. True or false?
True
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?
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
Why is there conflict between PRDM9 and its binding sites?
What does this lead to?
Recombination is mutagenic and alters the binding site sequence
Leads to rapid shifts in recombination hotspots across populations and species
Why are recombination hotspots better off than non-recombining regions? Give 4 reasons.
- They avoid Muller’s Ratchet
- They avoid Hill-Robertson interference, linkage broken up and so selection is more efficient
- Recombination itself can be mutagenic and create new variation
- Larger Ne increases variation
How does small Ne reduce adaptive potential?
There is less diversity and so populations are more susceptible to drift
Why does the Y chromosome have a small Ne? Give 2 reasons.
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.
Recombination hotspots vary between sexes. Why might this be? Give two reasons.
Who said this?
Paigen and Petkov, 2010:
- Selective argument: sexually antagonistic haploid selection selects for sex-specific effects, although this is rare
- Biological argument: arrested meiosis in female vertebrates creates greater chiasmata migration
Izzy’s great quote for ‘why are Y chromosome studies important for understanding recombination and adaptation
‘Y chromosome provides the most compelling evidence that recombination produces adaptation’
Who studied a male genome that hasn’t degenerated? What did they find?
Begero and Charlesworth, 2011:
S. latifolia, male genome still expressed, only 10-20% degeneration in 5-10my
