BG23

Question 1

Mapping adaptive traits

Answer 1

if an adaptive trait is polymorphic withn interbreeding population it can be mapped
- if genetic basis is complex, QTL analysis must be used to map it

Question 2

QTL mapping steps

Answer 2

step 1: physical map of polymorphic markers (SNPs etc) can be used.
step 2: make recombinant inbred lines. - easy to make in c. elegans as faultively selfing hermaphrodite
step 3: phenotype RILs
step 4: genotype RILs
step 5: search for association between them

Question 3

results of QTL mapping in c. elegans

Answer 3

bristol and bergerac strains differ in body size and fertility
found that RILS differ in body size and fertility
- several QTLs are identified for each trait
- only the causal region, not the mutation itself is identified.

Question 4

Dog correlations with body size

Answer 4

10K since divergence from wolves

• selected for body size
• also differ in IGF blood titre (causally)

Question 5

Portugese water dog mapping

Answer 5

genetic map constructed using SNPs

- body size (which is variable in PWD) was mapped

Question 6

results of portugese water dog mapping

Answer 6

single qtl found on ch.15 near igf-1 locus

• marker variation around this locus can be reduced two two haplotypes which directly predict size and igf titre level
• clear variant in region influences both

Question 7

scoring of frequency of ch.15 igf-1 haplotype in different breeds

Answer 7

when scored in different breeds in predicts body size based on IGF
(except in rottweilers)

Question 8

IGF- 1 locus in dogs

selection

Answer 8

subject to selective sweep
elevated fst around igf locus
locus is more different among breeds than flanking region

Question 9

Peppered moth forms

and species

Answer 9

B. betlulariac
typica - peppered
carbonaria - melanistic

Question 10

carbonaria locus

Answer 10

mapped to ch17
encodes gene called cortex
carbonaria allele contains a tandemly repeated transriptional element

Question 11

drosophila homolog of cortex

Answer 11

cell cyle gene

Question 12

cortex expression in moths

Answer 12

expressed in splice variants
- differentially expressed in wing imaginal disk
some (CR4) are differentially epxressed between typical and carbonaria genotypes
- transposable elements regulate expression of cortex - or atleast some of its mRNA variants at particular times

Question 13

Carbonaria synteny

Answer 13

pigment patterning loci in other butterflies bigeye and bicyclus and N-P-Yb-Cr/P mimicry locus in Heliconus all map to chromosomal regions syntenic with carbonaria

Question 14

stickleback fresh water invasion

Answer 14

usualyl marine
invaded freshwater >20 times indep.
when they do so they tend to lose the pelvic spines and girdle and armous plating - lack of predation? or lack of Ca?

Question 15

stickleback pelvic bone loss qtl

Answer 15

largest is on ch7

- around TF pitx1 which is known to be important in skeletal formation

Question 16

Sequencing and expression patterns between marine and fresh water sticklebacks of pitx1

Answer 16

1. no difference in coding regions between marine and freshwater morphs
2. difference in expression pattern.

Question 17

marine and freshwater stickleback cross

Answer 17

compared allele specific expression of pitx1 using qtPCR

- marine allele has higher lvels of expression so the different must be due to cis-acting reg elements

Question 18

sequencing of pitx1 reg region

Answer 18

freshwater strains msising 501 bp region upstream of pitx1.

- potentially contains causal reg element

Question 19

how did they show that the cis acting reg element drives expression in the pelvis

Answer 19

take the saltwater sequence of 2.5kn region deleted in freshwater fish adn put it behind a GFP reporter and transfect the fish.
- see it drives expression in pelvis

Question 20

how can it be shownt that Pel-2.5kbSALR contains the causal mutation

Answer 20

put it behind a freshwater pitx1 coding region

• transfect the freshwater fish
• rescues pelvic spine phenotype = prove

Question 21

Pel loss around the world

Answer 21

sequencing shows always lost, lost indep since the precise deletion varies
= convergence at a molecular level.

Question 22

how do we know that loss of pel enhancer is adaptive?

Answer 22

• repeated loss

- signature of selection: loss of heterozgyosity around pel implying a selective sweep.

Question 23

how can we find out if pel is responsible for loss of pelvic structures in two differnet species of stickleback

Answer 23

• complementation test
• F1 hybrid,
  if alelles fail to complement the same locus (pel-pitx1) must be responsible for loss of pelvic structures in freshwater morphs of both species.

Question 24

Lizard pigmentation in white sands of new mexico

Answer 24

independent evolution of pale morphs
due to different mcr-1 mutationswhich regualtes switch between phaeomelanin and eumelanin production which is involved in pigmentation polymorphisms,

Question 25

how can we test the ability of mc1-r mutations of the mexican lizards to transduce a signal

Answer 25

by engineering them in mamamlian cells and challengint them with a ligand and notin the function
- found loss of function

Question 26

what are the 6 steps for identifying adaptive genes

Answer 26

1. examine candidate genes for phenotype
2. if no candidates doa QTL (markers, constructs, physical map, crosses)
3. sequnce QTL region for possible mutation (if find NS coding mutation could be this, if not cis acting).
4. do functional studies - expression studies, in vivo assays, KOs etc to make case for causal roles of a locus
5. examine sequence around putative causal locus for signatures of selection
6. gold standard of proof for causal involvement of locus is phenotype is to rescue by transgenesis or complementation.

Question 27

why might CREs be more important in adaptation

Answer 27

• effects of cre mutations can be more specific that those of coding mutations and are likely to have fewer pleiotropipc effects (more modular), e.g. cre of shh can cause polydactyly or limb loss but null = lethal

Question 28

NS coding mutations are the most known adaptive aleles?

Answer 28

• some studies have shown this

- however there is a bias as coding mutations in general are easier to find

Question 29

is evolution predictable

Answer 29

• no. of cases where indep mutations have occured in the same genes pitx1, mcr1
• other cases ancient mutations are re-used

Question 30

why may the same mutations crop up

Answer 30

many mutations have small phenotypic effects, few have strong ones
when selection is strong those with the largest phenotypic effects will be picked out first
even though they’re the most likely to be deleterious.

Question 31

when might we expect to see complex traits

Answer 31

when selection is weaker may expect many genes will be involved giving rise to adaptive traits controlled by many loci; complex traits