Download Neutral Theory, Molecular Evolution and Mutation

Neutral Theory, Molecular
Evolution and Mutation Load
Population Genetics
Nic Kooyers
9/21/11
Definitions
• Genetic Polymorphism— “Multiple Forms” –
More than one haplotype at a single locus
within a population
Major Questions in Evolutionary Biology
How much is there?
What are the functional consequences of it?
1
Outline
• How much polymorphism is there?
– Historical Debate
– Rise of technology
• What are the functional consequences?
– Neutral Theory
– Critiques of Neutral Theory
– Current Understanding
• Optimization, Mutation and Genetic Load
The Classical and Balanced School both Arose from a
single laboratory: Thomas Hunt Morgan
Pithecanthropus
A.H.
Sturtevant
H.J.
Muller
1919
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This Debate Was Strongly Influenced By The Techniques
Available for Scoring Genetic Variation: A Recurrent
Theme in Molecular Evolution
Pithecanthropus
A.H.
Sturtevant
H.J.
Muller
1919
Morgan & Muller Scored Variation By
Inbreeding Drosophila To Reveal Single
Locus Variants With Visible
Morphological Effects
3
Inbreeding Wild-Caught Drosophila
Revealed Little Variation In Natural
Populations For Such Single Locus Visible
Variants
Classical School
Natural Populations Have Very Little Polymorphism. Most
Individuals Are Homozygous for a “Wildtype” Allele. Very
Rarely, An Individual Is Heterozygous For A “Mutant” Allele,
Which Is Usually Deleterious.
Rarely, A Beneficial Mutation Arises and Then Goes Rapidly To
Fixation. Therefore, the Phase of Transient Polymorphism Is
Brief.
Therefore, The Population Can Be Characterized By A Single
Homozygous “Wildtype” At Most Loci, With Rare Mutants, And
Occassional Bursts of Evolution Limited By The Input of New,
Beneficial Mutations.
4
The Balanced School
Sturtevant, As An Undergrad, Came
Up With The Idea of A Chromosome
Map.
He Soon Discovered That Different Strains
Had Different Gene Orders: He Had
Discovered Paracentric Inversions By
Mapping.
Polytene Chromosome from Salivary Gland
5
Bringing the field into the lab: Theodosius Dobzhansky
Polytene Chromosome from Salivary Gland
1924
Drosphila melanogaster – “garbage species”
Dobzhansky & Sturtevant (1936): An
Inversion Tree for Drosophila pseudoobscura
(A) and D.persimilis (B)
Olympic (A)
Estes Park (A)
Tree Line (A)
Oaxaca (A)
Mammoth (A)
Santa Cruz (A)
Cuernavaca (A)
Chiricahua I (A)
Hypothetical A ---------- miranda
Pikes Peak (A)
Standard (A & B)
Sequoia I (B)
Arrowhead (A)
Chiricahua II (A)
Klamath (B)
Sequoia II (B)
Cowichan (B)
Wawona (B)
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Olympic (A)
Estes Park (A)
Tree Line (A)
Oaxaca (A)
Mammoth (A)
Santa Cruz (A)
Cuernavaca (A)
Chiricahua I (A)
Much Intraspecific
Polymorphism
Hypothetical A ---------- miranda
Pikes Peak (A)
Standard (A & B)
Sequoia I (B)
Arrowhead (A)
Chiricahua II (A)
Klamath (B)
Sequoia II (B)
Cowichan (B)
Wawona (B)
Olympic (A)
Estes Park (A)
Tree Line (A)
Oaxaca (A)
Mammoth (A)
Santa Cruz (A)
Cuernavaca (A)
Chiricahua I (A)
Hypothetical A ---------- miranda
Pikes Peak (A)
Standard (A & B)
Sequoia I (B)
Each Inversion Mutation Ideally
Occurs Only Once in Tree and
Tree Minimizes Total Number
Of Mutations -Maximum Parsimony
Arrowhead (A)
Chiricahua II (A)
Klamath (B)
Sequoia II (B)
Cowichan (B)
Wawona (B)
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Olympic (A)
Estes Park (A)
Tree Line (A)
Oaxaca (A)
Mammoth (A)
Santa Cruz (A)
Cuernavaca (A)
Chiricahua I (A)
Hypothetical A ---------- miranda
Pikes Peak (A)
Standard (A & B)
Sequoia I (B)
Arrowhead (A)
Maximum
Parsimony (and
other techniques)
allow you to infer
the state of
extinct ancestral
states.
Chiricahua II (A)
Klamath (B)
Sequoia II (B)
Cowichan (B)
Wawona (B)
Olympic (A)
Estes Park (A)
Tree Line (A)
Oaxaca (A)
Mammoth (A)
Santa Cruz (A)
Cuernavaca (A)
Chiricahua I (A)
Hypothetical A ---------- miranda
Pikes Peak (A)
Standard (A & B)
Sequoia I (B)
Arrowhead (A)
Tree Is Rooted By
Looking At a
Closely Related
Species That Is
Known To Be
Phylogenetically
Outside the
Groups of
Interest
Outgroup
Rooting
Chiricahua II (A)
Klamath (B)
Sequoia II (B)
Cowichan (B)
Wawona (B)
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Olympic (A)
Estes Park (A)
Tree Line (A)
Oaxaca (A)
Mammoth (A)
Santa Cruz (A)
Cuernavaca (A)
Chiricahua I (A)
Hypothetical A ---------- miranda
Pikes Peak (A)
Standard (A & B)
Sequoia I (B)
The Inversion Tree Is Not Always
The Same As A Tree of Species Or
Populations, In This Case Because
of:
Transpecific Polymorphism
Arrowhead (A)
Chiricahua II (A)
Klamath (B)
Sequoia II (B)
Cowichan (B)
Wawona (B)
Balanced School
-Lots of polymorphism that persists for long periods
-No “Wild-type”
-Balancing Selection maintains this polymorphism
-Natural Populations can rapidly adapt to changing
conditions using this pool of polymorphism
Problem– No genetic markers equals no new data!
9
Two Types Of Data Became
Widely Available in the 1960’s
• Amino Acid Sequence Data (Primarily
documenting substitutions between
species)
• Protein Electrophoresis Data (Primarily
documenting polymorphisms within
species)
New Field of Molecular Evolution Arises
Amino Acid Sequence Data
Two Central Observations:
• There were two many substitutions to be consistent
with the Classical School
• Divergence in Sequence was not comparable to
divergence in Phenotype!
10
Outline
• How much polymorphism is there?
– Historical Debate
– Rise of technology
• What are the functional consequences?
– Neutral Theory
– Critiques of Neutral Theory
– Current Understanding
• Optimization, Mutation and Genetic Load
Motto Kimura to the Rescue
Neutral Alleles
• Have no effect on any phenotype that
influences reproductive success and
therefore their evolutionary dynamics are
determined by mutation and genetic drift
New class of alleles for the Classical School!!
11
Neutral
Unfavorable
Favorable
Effects of 50 Spontaneous Mutation Lines Derived from a Strain
of Yeast Growing in a Laboratory Environment.
Neutral Alleles
(Kimura 1968)
• Genetic Drift Determines the Rate of Loss = 1/2N
• Mutation Determines the Rate of Input = (2N)μ
• Rate of Evolution = Rate of Input X Rate of Loss =
(2N)μ1/2N = μ
Note: The Rate of Neutral Evolution Does Not
Depend upon Population Size. All populations,
regardless of size, have an innate tendency to
evolve as driven by mutation and drift. Moreover,
if the neutral mutations rates are comparable, this
tendency is just as strong in a large population as
in a small population. GENETIC DRIFT IS
IMPORTANT FOR ALL POPULATIONS!
12
Three Lines of Evidence for Neutral
Theory
• Variation in substitution rates in different
genes (or proteins)
• Variation in nonsynonymous vs. synonymous
substitutions within a locus
• Variation in Pseudogenes
• The molecular clock (disproven)
Evidence for Neutral Alleles
13
Evidence for Neutral Alleles
Evidence for Neutral Alleles
The pseudogene evolves more rapidly than the functional gene
14
Amino Acid Sequence Data– The
Molecular Clock
Human
Mouse
Chicken
Newt
Carp
Shark
Human
M ouse
Chicken
Newt
Carp
Shark
16
35
62
68
79
39
63
68
79
63
72
83
74
84
M ouse
Chicken
Newt
α-Hb Data
Carp
85
(King & Jukes, Sci. 154:788-798,1969)
Homology – Traits (including amino acid or DNA sequences)
found in two or more individuals that have been derived from a
common ancestral form
Molecular Clock -- Change in sequence is constant over time
Data supports Kimura’s theory – Rate of Change is simply μ
Outline
• How much polymorphism is there?
– Historical Debate
– Rise of technology
• What are the functional consequences?
– Neutral Theory
– Critiques of Neutral Theory
– Current Understanding
• Optimization, Mutation and Genetic Load
15
Protein Electrophoresis Data
Protein Electrophoresis Data
• Lewontin & Hubby (Genetics 54: 595-609, 1966),
Johnson et al. (Studies in Genetics. III: 517-532,
1966), and Harris (Proceedings of the Royal Society of
London B 164:298-310. 1966) showed that about 1/3
of all protein coding loci were polymorphic for
electrophoretically detectable alleles in Drosophila
and in humans
•Kimura and Ohta (Nat. 229: 467-489, 1971) could
explain this high level of variation with the Neutral
Theory
16
Kimura & Ohta– Transient Polymorphism
Time Period of Transient Polymorphism
1/(2N) of Neutral Mutations Go To
Fixation and Transiently
Contribute To Polymorphism
Levels
Most Neutral Mutations Are Lost
and Contribute Little to
Polymorphism Levels
Kimura & Ohta
 1 

1 
2
F (t )  
 1 
 F (t  1)(1   )
 2N  2N 

Average Probability
of Identity by Decent
at generation t
Probability of
Identity by Decent
due to Genetic Drift
Probability of Identity
by Decent due to
Mutation
At Equilibrium: F(t) =F(t-1)
17
Kimura & Ohta
Feq 
2N
Let  = 4Nef

1
1
(1  )2

1  1

1
4N  1
for  small
Commonly Reported

1

1 Feq  H eq  1

 1  1
Expected Heterozygosity!

Critique of the Neutral Theory
Most
Observations
Below This
Threshold
This Implies A Small Range of
Population Sizes, and That Almost
All Species Have N < 5,000
(Including Insects & Bacteria).
18
Ohta (1973-1976) Created The Nearly
Neutral Theory To Explain The
Heterozygosity Observations
•In small populations- slightly deleterious mutations act like neutral mutations
•Neutral Mutation rate not total mutation rate
•Showed That Genetic Drift Determines Evolutionary Dynamics For Any Mutation With
|s|<1/(2Nev)
•Let μ(s) describe the probability of a mutation having selection coefficient s, then
1
•The neutral mutation rate=μneutral=
2N ev
 (s)ds
0
•This explains why Heterozygosity levels off and has a narrow range (recall θ=4Nμneutral)
•Unfortunately, this also means you lose the molecular clock because the rate of
 of Nev
substitution is now a function
Neutral & Nearly
Neutral
Effects of 50 Spontaneous Mutation Lines Derived from a Strain
of Yeast Growing in a Laboratory Environment.
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Difficulties with Molecular Clock
Human
Mouse
Chicken
Newt
Carp
Shark
-Mutation rate is calculated in rate
per generation – Not in rate per
absolute time
Z
Y
-Artifact of Calculation
X
Shark-Human: X+Y
Shark- Carp: X+Z
Pairwise differences appear similar
even with changes to X and Z
Outline
• How much polymorphism is there?
– Historical Debate
– Rise of technology
• What are the functional consequences?
– Neutral Theory
– Critiques of Neutral Theory
– Current Understanding
• Optimization, Mutation and Genetic Load
20
Molecular Evolution
Is No Longer Dominated
By the Neutral Theory
•
•
•
•
•
Much of the good fit of the clock was an artifact; More rigorous tests show
frequent violations of Kimura’s Poisson Clock
Still Cannot Simultaneously Explain Substitution Rates and Heterozygosity
Now Have Better Tests of Selection: E.g., Fay et al (Nature 415:1024-1026)
Found evidence for positive and balancing selection in 60% of the protein
coding genes in D. melanogaster, “far higher than permitted by the neutral
theory of molecular evolution.”
The neutral theory is still a widely used null hypothesis in molecular evolution
Recent models blur the distinction between neutral and selected mutations
(Wagner, Nat. Rev. Genetics 9: 965-974, 2008)
Molecular Evolution
Now Focuses On Problem Areas
Without A Single Dogma Dominating
the Field
1)
2)
3)
4)
5)
Gene and Genome Evolution – What kinds of evolutionary changes occur
in various genes and genome types and what evolutionary forces are
involved?
Organismal Evolution – Use the results of studies on genes and genomes
to study and test hypotheses about organismal micro- and macroevolution
Population Genetics & Intraspecific Phylogeography – Describe the
amount and distribution of molecular variation within a species and test
and detect the evolutionary forces responsible
Quantitative Genetics – Use molecular genetics to understand the genetic
basis of phenotypic variation
Phylogenetics – Reconstruct the evolutionary history of species, and help
determine species status
21
Molecular Evolution :
A lesson from the past that is
relevant today
1)
2)
3)
4)
The origins and initial research focus of the area of Molecular
Evolution was strongly influenced by the development of and
ability to practically apply protein electrophoresis and amino acid
sequencing in the 1960’s
Techniques for surveying genetic variation at the molecular level
are constantly changing.
These changes in molecular screening techniques sometimes, but
not always, resolve the questions that had been debated in the
field, but inevitably new questions and issues arise with the
development of novel scoring techniques
As a consequence, the field of Molecular Evoution is a highly
dynamic one, with a constantly shifting and evolving research
focus.
Relevance of Neutral Theory
Measures how similar
populations are
Selection? --Compare Neutral Markers to Functional Genes
22
Outline
• How much polymorphism is there?
– Historical Debate
– Rise of technology
• What are the functional consequences?
– Neutral Theory
– Critiques of Neutral Theory
– Current Understanding
• Optimization, Mutation and Genetic Load
Optimization is a rare word in
Evolutionary Biology
• Ideal (highest possible fitness) is impossible to
define
• Ideal is constrained by decent and context
Load  L 
Wmax  W
Wmax
Muller- 1950-- “Our Load of Mutations”
23
Muller’s Model
• Mutation: From Wildtype A to Deleterious
Mutant a: Aa at rate μ
• Fitness Model: AA
Aa
aa
»
1
1
1-s
• Assuming Random Mating, Input Rate of a is μ,
and Output Rate Is sq2
• At Equilibrium, Input = Output, so μ = sq2
qeq=√μ/s
• W=p2(1)+2pq(1)+q2(1-s)=1-q2s=1- μ at Equil.
Muller’s Model
Load  L 
W max  W
W max
At Equilibrium, The M utational Load Is :
L
1 (1  )

1
Load Is Independent of s and Is A Function Only Of μ

24
Other Models-- Loads
• Substitution load- Haldane– The “Cost of Natural
Selection” must limit beneficial mutations
State of Transient Polymorphism
Haldane concludes that very few loci can have a beneficial mutation at one time
Genetic Load has been largely
discredited
• Much of the theory was an artifact of using
relative fitness and ridiculous Wmax’s
• More realistic fitness models have no load at
all
Current Renditions of Genetic Load
1.) Muller’s Ratchet --- Assexual populations
2.) Mutational Meltdown --- Small populations
3.) Current Human Literature
25
Muller’s Ratchet
Are selfing species evolutionary dead-ends?
Accumulate mutations without the ability to purge via recombination
Growth and decline of populations can
facilitate increases in mutation load
N0 > N1> N2….
--In a declining population (death exceeds birth) selection does not act
as efficiently at eliminating deleterious mutations (“drift load”)
-- This in turn promotes further decline within an environment as
average fitness decreases
-- Decrease in average fitness is due to both deleterious mutations and
to impacts of increasing inbreeding (both F and f)
--This cyclical process is known as Mutational Meltdown
-- Never empirically shown (Gilligan et al., 1997)
26
Growth and decline of populations can
facilitate increases in mutation load
N0 < N1<< N2….
--Growth should have the opposite effect as decline in that the population
should be more efficient at weeding out deleterious mutations
-- (Super) Exponential growth may relax purifying selection and contribute to
a mutation load
Mutation Load in Homo sapiens
r = -0.3, therefore explains 9% of the variance in phenotype
(RA Yeo et al. PLOS One 6,1)
27
Mutation Load Conclusions
• Although optimization remains a untouchable
concept in evolution, mutation load has
recently enjoyed a renaissance
• Genomic data and interest in asexual systems
provide future motivation in a completely data
depauperate field
General Conclusions
• Neither the classical or balanced schools were
correct in understanding polymorphism
• Conclusions are only as good as data…
• Polymorphisms are widespread and can be
maintained through both neutral and selective
mechanisms (not mutually exclusive)
• Neutral Theory is now a null hypothesis
• There are situations where deleterious
mutations are maintained but evidence is rare
28