Lecture 18: Mutation October 30, 2015. Last Time uExam to be returned Monday. Answer key is posted...
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Transcript of Lecture 18: Mutation October 30, 2015. Last Time uExam to be returned Monday. Answer key is posted...
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Lecture 18 : Mutation
October 30, 2015
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Last Time Exam to be returned Monday. Answer
key is posted
Effects of population structure, admixture, selection, and mutation on LD
Admixture calculation
Selective sweeps
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Today
Mutation introduction
Mutation-reversion equilibrium
Mutation and selection
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What Controls Genetic Diversity Within Populations?
4 major evolutionary forces
Diversity
Mutation+
Drift-
Selection
+/-
Migration
+
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Mutation
Primary driver of genetic diversity
Main source of new variants within a reproductively isolated species
Mutation often ignored because rates assumed to be extremely low relative to magnitude of other effects
Accumulation of mutations in population primarily a function of drift and selection PLUS rate of back-mutation
Mutation rates are tough to estimate!
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Spontaneous mutation rates Schlager and Dickie (1967) tracked
spontaneous mutation at 5 loci controlling coat color in 17 million house mice
Forward > Backward mutation
http://www.gsc.riken.go.jphttp://jaxmice.jax.org
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Mutation Rates can Vary Tremendously Among Loci
Length mutations occur much more frequently than point mutations in repetitive regions
Microsatellite mutation rates as high as 10-2
Source: SilkSatDB
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Reverse Mutations Most mutations are “reversible” such that original allele can
be reconstituted
Probability of reversion is generally lower than probability of mutation to a new state
Possible States for Second Mutation at a Locus
Thr Tyr Leu LeuThr Tyr Leu LeuACC TACC TAAT TTG CTGT TTG CTG
ReversionACC TACC TGGT TTG T TTG CTG Thr CTG Thr PhePhe Leu Leu Leu LeuC GC GACC TACC TCCT TTG CTG Thr T TTG CTG Thr
SerSer Leu Leu Leu Leu
A CA C
ACC TACC TTTT TTG CTG Thr T TTG CTG Thr CysCys Leu Leu Leu Leu
C TC T
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Allele Frequency Change Through Time
001 ppp
With no back-mutation:
0)1( p
0)1( pp tt
How long would it take to reduce A1 allele frequency by 50% if μ=10-5?
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Two-Allele System with Forward and Reverse Mutation
where μ is forward mutation rate, and ν is reverse mutation rate
A1 A2 µ
ν
qpq Expected change in mutant allele:
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Allele Frequency Change Driven By Mutation
Equilibrium between forward and reverse mutations:
)(
eq )(
ep
qpq
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Allele Frequency Change Through Time with Reverse mutation
Forward Mutation (µ)
Reverse Mutation (ν)
Allele Frequency (p)
Mutant Alleles (q)
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Equilibrium Occurs between Forward and Reverse Mutation
Forward mutation 10-5
Lower rate of reverse mutation means higher qeq
)(
eqIs this equilibrium stable or unstable?
μ=10-5
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Mutation-Reversion Equilibrium
)(
ep
where µ=forward mutation rate (0.00001)and ν is reverse mutation rate (0.000005)
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What if the population is not infinite?
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Fate of Alleles in Mutation-Drift Balance
Time to fixation of a new mutation is much longer than time to loss
Npu
21)(
Nqu
211)(
u(p) is probability of fixationu(q) is probability of loss
An equilibrium occurs between creation of new mutants, and loss by drift
p=frequency of new mutant allele in small
population
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Infinite Alleles Model (Crow and Kimura Model)
Each mutation creates a completely new allele
Alleles are lost by drift and gained by mutation: a balance occurs
Is this realistic?
Average human protein contains about 300 amino acids (900 nucleotides)
Number of possible mutant forms of a gene:
542900 1014.74 xn If all mutations are equally probable, what is the chance
of getting same mutation twice?
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Fate of Alleles in Mutation-Drift Balance
Time to fixation of a new mutation is much longer than time to loss
Npu
21)(
Nqu
211)(
u(p) is probability of fixationu(q) is probability of loss
An equilibrium occurs between creation of new mutants, and loss by drift
p=frequency of new mutant allele in small
population
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Mutation & Mating Simulation1. Select two gametes from the gamete
pool (brown is wild=type, green=mutant
2. Find a mate using the Excel sheet (e.g., see below)
3. Pass a random allele down to each of 2 offspring. One of these offspring will become you for the next generation.
4. Mutate an offspring allele if indicated by the Excel sheet by choosing a new random allele from the pool (cup of candy) (rate = 1x10-2)
5. Repeat for the next generation.
xApoorva Margo
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Results of Mutation & Mating Simulation
The forward mutation rate was quite high (1x10-2), and the reverse mutation rate was at least an order of magnitude lower (based on the freqency of brown M&M’s in the mutant pool), so the frequency of mutant alleles increased fairly dramatically even with substantial potential for genetic drift.