Lecture 19: Mutation, Selection, and Neutral Theory November 2, 2015.
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Transcript of Lecture 19: Mutation, Selection, and Neutral Theory November 2, 2015.
![Page 1: Lecture 19: Mutation, Selection, and Neutral Theory November 2, 2015.](https://reader036.fdocuments.in/reader036/viewer/2022062305/5697bf901a28abf838c8e101/html5/thumbnails/1.jpg)
Lecture 19 : Mutation, Selection, and Neutral Theory
November 2, 2015
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Last Time
Mutation introduction
Mutation-reversion equilibrium
Mutation and drift
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Today
Mutation and selection
Introduction to neutral theory
Exam
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Mutation-Selection Balance
Equilibrium occurs when creation of mutant allele is balanced by selection against that allele
For a recessive mutation:
pqmu
0 smu qq
At equilibrium:
2
2
1 sq
psqp
sqeq
sqeq
2
2
2
1 sq
psqqs
assuming: 1-sq21
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sqeq
What is the equilibrium allele frequency of a recessive lethal with no mutation in a large (but finite) population?
What happens with increased forward mutation rate from wild-type allele?
How about reduced selection?
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Balance Between Mutation and Selection
Recessive lethal allele with s=0.2 and μ=10-5
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Muller’s Ratchet
Deleterious mutations accumulate in haploid or asexual lineages
Driving force for evolution of recombination and sex
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Question:
Do most mutations cause reduced fitness?
Why or why not?
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Relative Abundance of Mutation Types
Most mutations are neutral or ‘Nearly Neutral’
A smaller fraction are lethal or slightly deleterious (reducing fitness)
A small minority are advantageous
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Types of Mutations (Polymorphisms)
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First and second position SNP often changes amino acid
UCA, UCU, UCG, and UCC all code for Serine
Third position SNP often synonymous
Majority of positions are nonsynonymous
Not all amino acid changes affect fitness: allozymes
Synonymous versus Nonsynonymous SNP
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Nuclear Genome Size Size of nuclear genomes varies
tremendously among organisms
Weak association with organismal complexity, especially within kingdoms
Arabidopsis thaliana 120 MbpPoplar 460 MbpRice 450 Mbp Maize 2,500 Mbp Barley 5,000 MbpHexaploid wheat 16,000 MbpFritillaria (lilly family) >87,000 Mbp
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Noncoding DNA accounts for majority of genome in many eukaryotesG
enic
Fra
ction
(%)
Genome Size (x109 bp)
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What is the probability of a mutation hitting a coding region in humans? Assumptions?
Lynch (2007) Origins of Genome
Architecture
Composition of the Human Genome
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Classical-Balance Fisher focused on the dynamics of allelic forms of genes,
importance of selection in determining variation: argued that selection would quickly homogenize populations (Classical view)
Wright focused more on processes of genetic drift and gene flow, argued that diversity was likely to be quite high (Balance view)
Problem: no way to accurately assess level of genetic variation in populations! Morphological traits hide variation, or exaggerate it.
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Molecular Markers Emergence of enzyme electrophoresis in mid 1960’s
revolutionized population genetics
Revealed unexpectedly high levels of genetic variation in natural populations
Classical school was wrong: purifying selection does not predominate
Initially tried to explain with Balancing Selection
Deleterious homozygotes create too much fitness burden
22
211 qspsi
mi for m loci
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The rise of Neutral Theory Abundant genetic variation exists, but perhaps not driven by
balancing or diversifying selection: selectionists find a new foe: Neutralists!
Neutral Theory (1968): most genetic mutations are neutral with respect to each other
Deleterious mutations quickly eliminated
Advantageous mutations extremely rare
Most observed variation is selectively neutral
Drift predominates when s<1/(2N)
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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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Infinite Alleles Model (IAM: Crow and Kimura Model)
Homozygosity will be a function of mutation and probability of fixation of new mutants
21 )1()
2
11(
2
1
t
eet f
NNf
Probability of sampling same allele twice
Probability of sampling two alleles identical by
descent due to inbreeding in ancestors
Probability neither allele mutates
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Expected Heterozygosity with Mutation-Drift Equilibrium under IAM
At equilibrium ft = ft-1=feq
Previous equation reduces to:
214
21
e
eq Nf
Ignoring μ2
14
4
e
ee N
NH
Remembering that H=1-f:4Neμ is called the
population mutation rate
21 )1()
2
11(
2
1
t
eet f
NNf
14
1
eeq Nf
Ignoring 2μ
4Neμ often symbolized by Θ
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Equilibrium Heterozygosity under IAM
Frequencies of individual alleles are constantly changing
Balance between loss and gain is maintained
4Neμ>>1: mutation predominates, new mutants persist, H is high
4Neμ<<1: drift dominates: new mutants quickly eliminated, H is low
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Effects of Population Size on Expected Heterozgyosity Under Infinite Alleles Model (μ=10-5)
Rapid approach to equilibrium in small populations
Higher heterozygosity with less drift
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Stepwise Mutation Model Do all loci conform to Infinite Alleles Model?
Are mutations from one state to another equally probable?
Consider microsatellite loci: small insertions/deletions more likely than large ones?
14
4
e
ee N
NH
IAM:
)18(
11
ee
NH
SMM:
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Which should have higher produce He,the Infinite Alleles Model, or the Stepwise Mutation Model, given equal Ne and μ?
14
4
e
ee N
NH
IAM:
)18(
11
ee
NH
SMM:
Plug numbers into the equations to see how they behave. e.g, for Neμ = 1, He = 0.66 for SMM and 0.8 for IAM
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Expected Heterozygosity Under Neutrality Direct assessment of neutral
theory based on expected heterozygosity if neutrality predominates (based on a given mutation model)
Allozymes show lower heterozygosity than expected under strict neutrality
Why?
Avise 2004
Observed
1
eH
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Neutral Expectations and Microsatellite Evolution
Comparison of Neμ (Θ) for 216 microsatellites on human X chromosome versus 5048 autosomal loci
Only 3 X chromosomes for every 4 autosomes in the population
Ne of X expected to be 25% less than Ne of autosomes:
θX/θA=0.75
AutosomesX
X chromosome
Correct model for microsatellite evolution is a combination of IAM
and StepwiseWhy is Θ higher for autosomes?
Observed ratio of ΘX/ΘA was 0.8 for Infinite Alleles Model and 0.71 for Stepwise model
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Sequence Evolution
DNA or protein sequences in different taxa trace back to a common ancestral sequence
Divergence of neutral loci is a function of the combination of mutation and fixation by genetic drift
Sequence differences are an index of time since divergence
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Molecular Clock If neutrality prevails, nucleotide divergence between two sequences should be
a function entirely of mutation rate
1
t
Expected Time Until Fixation of a New Mutation:
Since μ is number of substitutions per unit time
Time since divergence should therefore be the reciprocal of the estimated mutation rate
Probability of creation of new
alleles
Probability of fixation of new
alleles
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Variation in Molecular Clock If neutrality prevails, nucleotide divergence between two sequences should
be a function entirely of mutation rate
So why are rates of substitution so different for different classes of genes?
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Exam 2 Results: 86.8% Avg, 9.8% Std Dev.