Download Lect 11: Inbreeding, evolution at multiple loci Exam 1, Monday, 2

Lect 11: Inbreeding, evolution at
multiple loci
• Non-random mating-Inbreeding
Exam 1, Monday, 2 October
• Lectures 1-10, plus first part of today
• Labs week 2-5
– evolutionary consequences
• Synthesis:
• Readings Ch 1-6
– drift-migration: population
structure
– Population genetics of prairie
chickens
• On the web page
• Evolution at multiple loci
– Lecture notes
– Linkage disequilibrium
– Study guide
– Selection, selective sweeps
Consequences of Inbreeding:
Genotype frequencies
Consequences of Inbreeding:
Genotype frequencies
Selfing F = 0.5
Fr(AA) = p2 + pqF
AA
Aa
aa
Fr(Aa) = 2pq - 2pqF
Fr(aa) =
q2
+ pqF
AA
Aa
aa
• Inbreeding leads to a deficiency of
heterozygotes and an excess of homozygotes
• Inbreeding does not affect allele frequencies
Evolutionary Consequences of
Inbreeding?
• Inbreeding depression
! = 1 - ws/wo
ws = fitness of selfer
wo = fitness of outcrosser
• Dudash 1990
– Sabatia angularis
Fr(AA) = p2 + pqF
Fr(Aa) = 2pq - 2pqF
Fr(aa) = q2 + pqF
F = 0
F = 1
p2
p
2pq
0
q2
q
Evolutionary Consequences of
Inbreeding?
• Inbreeding depression
! = 1 - ws/wo
• Field:
! = 1 - 0.25/0.66
! = 0.62
Evolutionary Consequences of
Inbreeding?
In Humans: Fig 6.28
Fig. 6.28
Causes of Inbreeding depression?
Fr(AA) = p2 + pqF
Fr(Aa) = 2pq - 2pqF
Fr(aa) = q2 + pqF
• Increased
homozygosity
• Decreased
heterozygosity
• Inbreeding important
when:
– selection on rare
recessive alleles as
homozygotes:
“unmasked”
– overdominance
Drift
Drift
Drift
• Populations drift to different
allele frequencies
• H within pops decreases
• Fst increases:
FST
Synthesis: Drift-Migration
– divergence in allele frequencies among
populations
Time
Migration
Migration
Strong gene flow
Fst?
Smaller
H w/in pops? Larger
Drift-migration
FST
low gene flow
Synthesis: Greater
Prairie Chickens
Figure 6.2
high gene flow
25,000
2,000
Time
Opposite effect on H
Greater Prairie Chickens
Why decline
despite more
habitat?
Why rebound?
Figure 6.3
50
Extinction vortex, genetic rescue
Decline: Small populations,
drift, absence of
migration, inbreeding
depression
Evolution at multiple loci
• Fitness affected by more than one genetic locus?
• Two loci: A, B
• Many loci: Quantitative genetics (polygenic inheritance)
• Two loci, two alleles
Rebound: Migration
restored
polymorphism, reduces
inbreeding
A
b
A
B
A
B
a
b
a
b
a
B
Parent
Gametes
Linkage Equilibrium
Linkage Disequilibrium
Definition: Random association of alleles at different loci
Definition: Non-random association of alleles at different loci
Gamete types
Locus 1
A (fr = p)
a (fr = q)
AB (fr = ps)
Locus 2
B (fr = s)
b (fr = t)
aB (fr = qs)
Ab (fr = pt)
ab (fr = qt)
What if selection
favors A allele?
Prob. that B allele
associated with A = s
Prob. that B allele
associated with a = s
No effect on B allele
Coefficient of linkage
disequilibrium (D)
Gamete types
AB (fr = gAB)
Ab (fr = gAb)
aB (fr = gaB)
ab (fr = gab)
D = gABgab - gAbgaB
D ranges -0.25 to 0.25
D = 0 Linkage equilibrium
When D ! 0, non-random
associations
Gene pool
Gamete types
Locus 1
A (fr = p)
a (fr = q)
AB (fr ! ps)
Locus 2
B (fr = s)
b (fr = t)
aB (fr ! qs)
What if selection
favors A allele?
Prob. that B allele
associated with A ! s
Ab (fr ! pt)
Selection on A allele
causes change in
frequency of B allele
ab (fr ! qt)
Linkage Disequilibrium
What eliminates it?
Recombination
reduces D over time*
D’ = D(1 - r)
r = recombination
rate
*IF no force acts
to maintain D
0.25
Linkage Disequilibrium
Gene pool
0.00
r = 0.0
r = 0.1
r = 0.5
5
10
15
20
generation
25
Linkage Disequilibrium
What creates it?
1. Selection
Linkage Disequilibrium
What creates it?
1. Selection on
both loci
Locus 2:
Locus 1:
Habitat
choice
color
2. Genetic drift
3. Pop’n admixture
GG, Gg
rr
4. Non-random mating
“coadapted gene complex” gg
RR, Rr
Survivors will tend to have g and r alleles
Selective Sweeps
Linkage Disequilibrium
What creates it?
A
b
A
b
Positive
selection
(A only)
2. Selective sweeps: hitch-hiking by
closely linked allele
A
b
Positive
selection
(A only)
Linkage Disequilibrium
Review
Linkage Disequilibrium:
Ab gametes more
common than by chance
b hitchhikes
to high
frequency
• Inbreeding (Non-random mating) increases homozygosity,
decreases heterozygosity
– Affect evolution through inbreeding depression
• Disequilibrium created by selection,
drift, admixture & non-random mating
• Disequilibrium broken down by
recombination (unless maintained by
selection, etc.)
• When D ! 0, selection on one locus
causes evolutionary change at another
• Unmasking deleterious recessives
• The absence of heterozygotes under overdominance
• Synthesis:
– Drift-migration: outcome for polymorphism within populations
and divergence between populations depends on the relative
strength of these two forces
– Forces acting on Greater Prairie Chicken: strong drift,
inbreeding depression, weak migration.
• Evolutionary consequences reversed with migration
• Evolution at two loci: linkage disequilibrium caused by
selection, selective sweeps