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Year 3: Adaptation > QTL mapping > Flashcards

QTL mapping Flashcards

1
Q

Why is QTL mapping used?

A

To test which genes underlie particular quantitative traits, using population genetics to infer selection within a species

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2
Q

Why are QTL studies useful in adaptation?

A

Once you have inferred which genes are involved in producing a trait, you can perform neutrality testing to see what kind of selection the locus is under

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3
Q

Give two examples of neutrality tests?

A

McDonald-Kreitman or Tajima’s D

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4
Q

How does the McDonald-Kreitman test work? What does it focus on specifically?

A

It compares nucleotide substitutions to polymorphisms per gene

Synonymous (silent) and non-synonymous (coding) substitutions/polymorphisms per gene

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5
Q

In the McDonald-Kreitman test, if NI > 1 what kind of selection is a locus under? Why?

A

Negative selection, due to an excess of AA polymorphism

Negative selection removes rare deleterious alleles.

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6
Q

In the McDonald-Kreitman test, if NI

A

Positive selection, due to an excess of AA divergence

Positive selection selects for new advantageous alleles.

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7
Q

What does Tajima’s D test for? What does the D value represent?

A

Deviations from an expected state

D = difference between the number of segregating sites and the average pairwise interaction

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8
Q

Under Tajima’s D, what does it mean if D = 0?

A

There is no selection, as observed = expected

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9
Q

Under Tajima’s D, what does it mean if D

A

There is a selective sweep, as rare alleles are at low frequency

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10
Q

Under Tajima’s D, what does it mean if D > 0?

A

There is balancing selection, as there are multiple alleles with variable frequencies

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11
Q

What is QTL mapping?

A

A basic statistical correlation of alleles that occur at a locus with the phenotypes they produce

Links two types of data, genotype and phenotype

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12
Q

Essentially, what are you doing when you produce a QTL map?

A

A linkage map, as marker loci are linked to traits of interest

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13
Q

What is a QTL?

A

A polygenic trait, multiple loci contribute to the phenotype

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14
Q

What is the purpose of a QTL map?

A

To identify which molecular markers correlate to an observed trait based on linkage.
This allows you to identify candidate genes for a trait of interest.

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15
Q

What is the first step of QTL mapping? Why?

A

Cross two lines that are divergent for the trait of interest. Recombination shuffles the genome, allows you to identify marker loci that are linked to phenotypic variance.

BASICALLY IDENTIFY MARKERS IN THE F1

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16
Q

There are different ways of analysing your marker locus. Give the two most common.

A

ANOVA (for single marker loci)

Interval mapping

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17
Q

In QTL mapping, crossing parental lines to produce an F1 allows you to identify markers. What do you then do with the F1?

A

Cross them to produce an F2, on which you perform the QTL analysis

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18
Q

To produce the F2, you can either perform a backcross or an intercross on the F1.

Why/when is a backcross better? What is a disadvantage of backcrossing?

A

Allows easier identification of QTL as less epistatic effects and linkage.
Better for cases of complete dominance.

Difficult in highly heterozygous or outcrossing species.

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19
Q

To produce the F2, you can either perform a backcross or an intercross on the F1.

Why/when is an intercross better?
What is a disadvantage?

A

Faster and easier than a backcross.
Better in cases of partial dominance as heterozygosity can be identified.

F3 families are still highly heterozygous.

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20
Q

Interval mapping is a more complex way of analysing the F2. How does it work?

A

Calculate a LOD score, assume that locus with the highest LOD score is the locus of interest in the QTL

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21
Q

Interval mapping is a more complex way of analysing the F2. It is more powerful and precise than ANOVA, why is it bad?

A

Bc it needs more computational power and it difficult to include covariates

22
Q

In QTL mapping, if the genome of the organism has been sequenced you can exclude genes of known function as candidate genes. Can QTL mapping still be done on a genome that has not been sequenced?

A

Yes; it is free of assumptions, simply shows you where the linkage is

23
Q

How might you discern the function of an unknown gene?

A

Compare its sequence to known genes, can be done with BLAST

24
Q

Give 4 advantages of QTL mapping in adaptation studies.

A
  1. Genome does not need to be known, free from assumption
  2. By finding genes that underlie a trait you can perform neutrality tests to see what kind of selection a locus has been exposed to and make inferences
  3. Good for large effect mutations
  4. You can get multiple data from QTLM, like number of loci/effect size/overlap and epistatic effects
25
Q

Name four example studies in which QTL has been used to show adaptive evolution (give references).

A
  1. Coat colour in beach mice (Steiner et al., 2007)
  2. Pelvic structure in sticklebacks (Shapiro et al., 2004)
  3. Armour in sticklebacks (Colosimo et al., 2004)
  4. Mate calling in crickets (Shaw et al., 2007)
26
Q

Steiner et al., 2007:

What species was studied?

Why was coat colour thought to be adaptive?

A

Peromyscus polionotus (the oldfield mouse)

Mainland morph is brown, beahc morph is sandy/white

Thought that crypsis provided by reflective pelage (white) allows predator evasion (foxes and owls)

27
Q

What must you do with each phenotype produced in the F2 in crosses in QTL mapping?

A

Score each phenotype

28
Q

Steiner et al., 2007:

During QTL mapping, how did the authors score the phenotype?

A

By using 7 locations on the mouse body that show most divergence in pigmentation

29
Q

Steiner et al., 2007:

What genes did the authors find to be implicated? How?

A

mc1r and agouti signalling protein

Beach mice had a mutation in coding region of mcr1
Beach mice had an increase in agouti expression (no change to coding region)

30
Q

Steiner et al., 2007:

What kinds of mutation did the authors find to be responsible for changes to coat colour in beach mice?

A

Causative (in the coding region of mc1r) and regulatory (due to expression changes in agouti)

31
Q

Steiner et al., 2007:

In which body regions did mc1r produce the biggest variation?
What about agouti?

A 
mc1r = cheek, eyebrow, tail
agouti = rostrum and ear
both = dorsal and rump
32
Q

Steiner et al., 2007:

The results show that a large number of genes had a small effect on mouse coat colour. True or false?

A

False: a small number of genes (two) had a large effect on coat colour

33
Q

Further experiments supported Steiner et al.’s (2007) work that coat colour is adaptive. Who did further work with plasticine models?

A

Vignieri et al., 2010

Plasticine mice made, either light or dark morph, dark morphs attacked more frequently

34
Q

Who described how mc1r and agouti work? What are their functions?

A

Nachmann et al., 2003

mc1r = g-protein coupled recptor, highly expressed in melanocytes, activation by alpha-MSH produces cAMP and eumelanin (dark)

agouti signalling protein = mc1r antagonist, binds mc1r and reduces cAMP formation, produces phaeomelanin (light)

35
Q

What is mouse wildtype colour and why?

A

Agouti-banded black hairs due to a pulse of agouti expression during the middle of the hair cycle

36
Q

Shapiro et al., 2004:

Which species was studied?

Why was pelvic size thought to be adaptive? Give 3 reasons.

A

Gasterosteus aculeatus (threespine stickleback)

Marine morph is heavily armoured and spined, whilst freshwater morph is not.
Thought that spines evolved in marine environments as
1. Predator defences
2. Increased Ca2+ in saltwater makes calcification of spines less costly.
3. In freshwater systems lack of spines allows faster growth and accumulation of winter reserves.

37
Q

Shapiro et al., 2004:

How many chromosomes did QTL mapping implicate in spine formation?

Where is the Pitx1 gene and what does it do?

A

1 major and 4 minor chromosomes.

On the major chromosome, controls pelvic size

38
Q

Shapiro et al., 2004:

What did the authors do in QTL mapping?

What did they find in the F1?

What did they find in the F2?

A

Crossed a marine female and a freshwater male

F1 all had pelvic spines, showing spine loss to be recessive

F2 had a range of spine sizes

39
Q

Shapiro et al., 2004:

The authors found numerous linkage groups interacting to produce pelvic size, what does this imply?

What did they conclude about the mutations involved in pelvic variation?

A

Additive variance and epistasis

Relatively few loci produce a large effect

40
Q

Shapiro et al., 2004:

What is Pitx1? Therefore what kind of mutation controls pelvic variance?

A

A transcription factor

A regulatory mutation

‘Authors conclude a cis-acting regulatory mutation in Pitx1 is the major cause of pelvic reduction’

41
Q

Shapiro et al., 2004:

The authors performed complementation crosses. What was the point of this? What did they find?

A

To see whether pelvic morphology could be restored in gene knockouts to see if multiple loci were involved.

Complementation crosses did not restore morphology, implying a single gene (Pitx1) was responsible.

42
Q

Shapiro et al., 2004:

How was the regulatory mutation in Pitx1 seen to be adaptive?

A

There is parallel fixation of Pitx1 across separate freshwater groups, convergent evolution, must be an adaptive advantage

43
Q

Who studied armour in sticklebacks, G. aculeatus?

Why do sticklebacks need armour?

A

Colosimo et al., 2004

Marine = predator defence
Freshwater = do not need for predator defence, can grow larger and accumulate more fat reserves for overwinter storage, can reach sexual maturity younger
44
Q

Colosimo et al., 2004

What did they do?

What did they find?

A

QTL mapping and complementation experiments

A major QTL and several minor; major QTL contained the gene EDA

45
Q

Colosimo et al., 2004

What does EDA do?

What kind of mutation was it and what did it produce?

A

Ectodysplasin; important in teeth, hair, bone development

A structural mutation, produced 2 alleles of EDA; C (complete plate) and L (low plate)

46
Q

Who proved that the low-plate allele in sticklebacks was adaptive?

What did they do?

What did they find? How was the L allele found to be adaptive?

A

Barrett et al., 2008

Put 182 marine sticklebacks with armour that were heterozygous at the EDA locus (CL) in 4 artificial freshwater ponds. Thus the allele frequency at the start was known.

Allele frequency of L increased over time. This was initially due to higher overwinter survival, adaptive

47
Q

Barrett et al., 2008

What 4 qualities did L individuals display?

A

Were larger
Were heavier
Had higher fecundity
Grew more quickly on the same amount of food

48
Q

Who studied mate calling in crickets?

A

Shaw et al., 2007

49
Q

Shaw et al., 2007:

Which species did they look at?

Why did they look at mate calling? What does this suggest?

What did they find? What does this show?

A

2 species of the genus Laupala; L. paranigra and L. kohalensis

These species are morphologically and ecologically cryptic, yet they exhibit vastly different male calls and female acoustic preferences. Suggests directional selection favours divergence, leading to reproductive isolation and speciation.

8 QTLs in one replicate, with at least 4 of these mapping onto the same region in the second replicate. Mate calling is controlled by many genes of moderate to little effect.

50
Q

Why might mate calling be adaptive? Reference the sensory bias hypothesis, give 2 examples.

A

Dawkins and Guilford, 1996

  1. Sensory bias might be adaptive as it increases male detectability so females can find mates more quickly
  2. Sensory bias avoids heterospecific mating which can lead to sterile/inviable hybrids

This favours more exaggerated signals as it makes the disparity between species more obvious, may be a reason why cricket calls are so divergent

51
Q

What is the formula for the null hypothesis in the McDonald-Kreitman test?

A

Dn/Ds = Pn/Ps

52
Q

Give 2 disadvantages of using QTL in adaptation studies.

A
  1. Assumes genetic variation is additive

2. Not good for detecting complex or weak effect loci, does not reveal hidden heritability

Year 3: Adaptation (10 decks)

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