Transcript Molecular evolution - University of British Columbia

Molecular evolution
Part I: The evolution of macromolecules.
Part II: The reconstruction of the evolutionary
history of genes and organisms.
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Molecular Evolution
AGAMOUS; transcription factor [ Arabidopsis thaliana ]
What information can DNA
sequences give us?
Evaluating the role of
drift/demography vs. selection on
trait divergence.
Identify function. Looking at genes
whose evolutionary history was
shared.
www.ncbi.nlm.nih.gov
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Molecular Evolution
3D Protein Structure of Human
proinsulin
1952: Frederick Sanger
and coworkers determine
the complete amino acid
sequence of insulin.
Munte et al. 2004 FEBS J
MALWMRLLPLLALLALWGPD
PAAAFVNQHLCG
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Molecular Evolution
How and why have molecular sequences
evolved to be the way they are?
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Molecular Evolution
Learning Objectives:
1.
2.
3.
4.
Variability within a population
Subsitution rates
Neutral Theory
Detecting selection at the DNA level.
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Molecular Evolution
REVIEW: NUCLEOTIDE SUBSITUTIONS
Lys
AgAt145
AgAt134
SepAt145
SepAt134
CalAt145
CalAt134
GENE
SPECIES
Ala
Leu
Val
Leu
Leu
AAG GCA CTG GTC CTG TTG
AAA GCA CTG GTC CTC TTG
AGG GCA CTG GTC CTG GTG
AGG GCA CTG GTC CTG GTG
AAG - - - CTG TTC CTG TTG
AAG - - - CTG TTC CTG TTG
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Molecular Evolution
What happens after a mutation arises in
the DNA sequence at a locus?
Polymorphism: mutant allele is one of several present in population.
Substitution: the mutant allele fixes in the
population. (New mutations at other
nucleotides may occur later.)
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Molecular Evolution
L1
Time
(generations)
0
10
20
30
40
L2
L3
aaat aaat aaat
aaat aaat aaat
aaat aaat acat
acat acat acat
acat acat actt
L4
L5
L6
L7
aaat aaat aaat aaat
aaat acat aaat aaat
aaat acat acat acat
acat acat acat acat
acat acat acat acat
Generation 10-29 new mutation
Generation 30 mutation fixed
Generation 40 new mutation
Biol336-12
polymorphism
substitution
polymorphism
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Molecular Evolution
Imagine that five
sequences are
obtained from
each of two
species, and that
the sequences are
related to each
other as shown
here.
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Molecular Evolution
Any mutation that
happens on a red branch
will appear as a
polymorphism within
species 1.
within species
Any mutation that
happens on a blue
branch will appear as a
polymorphism within
species 2.
Any mutation that
happens on the green
branch will appear as a
fixed difference between
the species
between species
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Molecular Evolution
What happens after a mutation arises in
the DNA sequence at a locus?
Polymorphism: mutant allele is one of several present in population.
Substitution: the mutant allele fixes in the
population. (New mutations at other
nucleotides may occur later.)
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Molecular Evolution
Substitution rate: the rate at which
mutant alleles rise to fix within a lineage
By comparing DNA sequences from
different organisms, we can estimate the
rate at which mutations appear and fix,
causing basepair substitutions.
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Molecular Evolution
How many selectively neutral mutants reach
fixation per unit time?
Neutral mutations occur at a rate, μ per locus per generation.
In a diploid population at a particular locus, there are 2N alleles.
The number of mutants arising every generation at a given
locus in a diploid population of size N is 2N*μ
The probability of fixation of selectively neutral allele? 1/2N
Thus, the substitution rate for neutral alleles is
(1/2N)( 2N*μ) = μ
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Molecular Evolution
What is the substitution rate for neutral alleles?
μ
What is the substitution rate for beneficial alleles
(s>0)?
(2Nμ)(2s) = 4Nμs
Fixation probability for a beneficial allele
What is the substitution rate for deleterious
alleles? Close to zero.
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Molecular Evolution
Consider a numerical example:
A new mutant arises in a population of 1000
individuals.
If it is neutral the probability it will fix is 1/2N=1/(2*1000)
If it confers a selective advantage of s=0.01, then
the probability it will fix is, 2*s=0.02 (2%)
If it has a selective disadvantage of s=-0.001? 0.004%
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Molecular Evolution
2s
P( fixation ) 
( 4 Ns )
1 e
If the population size is very large then the
probability of fixation for an advantageous mutation
converges to 2*s
Given s=0.01, N=1000, P(fixation)= 0.02 or 2%,
Given s=0.01, N=100, P(fixation)=0.02037
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Molecular Evolution
2s
P( fixation ) 
( 4 Ns )
1 e
What about slightly deleterious mutations?
s= -0.001, N=1000 P(fixation)=0.000406
s=-0.001, N=100, P(fixation)= 0.0049
s=-0.001, N=10, P(fixation) = 0.0499
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Molecular Evolution
Are most substitutions (fixed changes) due to
drift or natural selection?
vs.
Agree that:
Most mutations are deleterious and are removed.Some
mutations are favourable and are fixed.
At Dispute:
Are most replacement mutations that fix beneficial or neutral?
Is observed polymorphism due to selection or drift?
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Molecular Evolution
Silent (or synonymous) mutations, where
the amino acid remains unchanged, are
more likely to be neutral.
Replacement (or non-synonymous)
mutations causing an amino acid change
are more likely to experience selection.
–
Form and strength depends on gene and its function
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Molecular Evolution
Mammalian Genes Non-synonymous
substitution rate
(per site per 109
years)
Synonymous
substitution rate
(per site per 109 yrs)
Histone 4
0.00
4.52
Histone 3
0.00
3.94
Myosin
0.10
2.15
Insulin
0.20
3.03
Growth Hormone
1.34
3.79
Immunoglobulin k 2.03
5.56
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Molecular Evolution
Histones seem to have an unusually low
replacement substitution rate.
This suggests that mutations causing basepair
changes in histones are deleterious
WHY?
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Molecular Evolution
Histones are DNA binding proteins around which DNA is coiled
to form chromatin. Many positions within the protein interact
with the DNA or other histones.
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Molecular Evolution
Most amino acid changes
in histone proteins may
have negative or even
lethal consequences.
Histone proteins have
strong functional
constraints.
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Molecular Evolution
Mammalian Genes Non-synonymous
substitution rate
(per site per 109
years)
Synonymous
substitution rate
(per site per 109 yrs)
Histone 4
0.00
4.52
Histone 3
0.00
3.94
Myosin
0.10
2.15
Insulin
0.20
3.03
Growth Hormone
1.34
3.79
Immunoglobulin k 2.03
5.56
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Molecular Evolution
Active sites (antigen
binding sites of
immunoglobins often
have higher
substitution rates
than silent sites
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Molecular Evolution
It could be that
selection favours
mutations in these
regions, thereby
increasing the
diversity among
antibodies produced
by the body and
improving the immune
response
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Molecular Evolution
How and why have molecular sequences
evolved to be the way they are?
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Molecular Evolution
To infer that selection has acted within a genome,
one must reject the null hypothesis that no
selection has acted.
Null hypothesis: describes pattern of sequence
evolution under the forces of mutation and drift.
Remember from neutral theory: The rate at which one
nucleotide is replaced by another nucleotide throughout a
population (substitution) equals the rate of mutation (μ) at that
site.
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Molecular Evolution
How do we detect selection at DNA
sequences?
Comparing intra-species polymorphism to interspecies differences (McDonald-Kreitman test).
Linked/neighbouring neutral markers.
Examine genes for Dn/Ds ratios.
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Molecular Evolution:
The McDonald Kreitman Test
Kreitman and Hudson (1991) sequenced a 4750 basepair
region near the alcohol dehydrogenase (ADH) gene from
11 individuals of D. melanogaster and found higher than
expected levels of polymorphism
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Molecular Evolution:
The McDonald Kreitman Test
There is only one amino acid polymorphism (AdhF/AdhS)
within this region which occurs at site 1490.
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Molecular Evolution:
The McDonald Kreitman Test
Selection may be maintaining this polymorphism at or near
this site.
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Molecular Evolution:
The McDonald Kreitman Test
ADH is an enzyme that breaks
down ethanol.
Flies carrying the ADHF allele
survive better when
their food is spiked with ethanol
than do flies carrying the ADHS
allele (Cavener and Clegg 1981)
Nonetheless, the factor that
maintains ADHF/ADHS
polymorphism remains unknown.
Biol336-12
Alchohol dehydrogenase
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Molecular Evolution:
The McDonald-Kreitman Test
How and why have molecular sequences evolved
to be the way they are?
How do we explain the patterns of variation observed
in ADH DNA sequences?
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Molecular Evolution:
McDonald Kreitman Test
Imagine that five
sequences are
obtained from
each of two
species, and that
the sequences are
related to each
other as shown
here.
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Molecular Evolution:
McDonald Kreitman Test
Any mutation that
happens on a red branch
will appear as a
polymorphism within
species 1.
within species
Any mutation that
happens on a blue
branch will appear as a
polymorphism within
species 2.
Any mutation that
happens on the green
branch will appear as a
fixed difference between
the species
between species
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Molecular Evolution:
McDonald Kreitman Test
Some abbreviations:
Within species
Ps=numbers of synonymous polymorphisms
Pn=numbers of non-synonymous polymorphisms
Between species
Ds=numbers of synonymous substitutions
Dn=numbers of non-synonymous substitutions
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Molecular Evolution:
McDonald Kreitman Test
If mutations occur
randomly over time
and if the chance that
a mutation does or
does not cause an
amino acid change
remains constant,
then the ratio of
replacement to
silent changes
should be the same
along any of these
branches
Between species
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Molecular Evolution:
McDonald Kreitman Test
If mutations are neutral
any of these mutations
has an equal chance of
persisting.
Pn/Ps
Dn/Ds
So the ratio of
replacement to silent
polymorphisms within a
species (Pn/Ps) should be
the same as the ratio of
replacement to silent
differences fixed between
species (Dn/Ds)
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Molecular Evolution
The McDonald-Kreitman Test:
Ho: If all changes are neutral, the ratio of
replacement to silent changes at polymorphic sites
(within species) should equal the ratio among fixed
differences (between species).
H1: If replacement mutations are advantageous,
they fix rapidly, causing a higher replacement to
silent ratio between species and a lower
replacement to silent ratio within species.
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Molecular Evolution
The McDonald-Kreitman Test:
H2: If replacement mutations are deleterious, they
rarely fix. Thus there will be a lower ratio of
replacement to silent changes between species and
a higher replacement to silent ratio within species.
H3: If replacement mutations are subject to
heterozygote advantage or frequency dependent
selection, they rarely fix, causing a lower
replacement to silent ratio between species and a
higher replacement to silent ratio within species.
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Molecular Evolution
Pn Dn

Ps Ds
Null: all changes are neutral : drift
Pn Dn

Ps Ds
H1: changes are advantageous, positive
selection
Pn Dn

Ps Ds
H2: changes are deleterious, purifying
selection
H3: replacement changes never fix
because of heterozygote advantage.
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Molecular Evolution:
McDonald Kreitman Test
ADH gene
Fixed differences
Between species
Polymorphisms
Within species
Replacement
7
2
Silent
17
42
Btwn species: Ratio of replacement to silent = 7/17 =0.41
Wn species: Ratio of replacement to silent = 2/42 =0.05
FIXED>POLYMORPHISM
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Molecular Evolution:
McDonald Kreitman Test
Using a X2 test, the null hypothesis that
selection is absent is statistically rejected for
ADH.
The excess of replacement differences
between species suggests that mutations
have been postively favoured.
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Molecular Evolution:
McDonald Kreitman Test
Assumes:
All synonymous mutations are neutral (codon bias).
All non-synonymous mutations are either strongly deleterious, neutral or
strongly advantageous.
Levels of polymorphism are governed by the neutral mutation rate.
Within a species, advantageous mutations contribute little to
polymorphism but can contribute to divergence between species.
A problem with this test is that:
A failure to reject the null hypothesis could be
because both purifying and directional selection have
taken place.
Not all synonymous changes are in fact neutral. In
some organisms, some codons are preferentially
used.
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Molecular Evolution
How else might you detect selection in the
genome, in particular the presence of selective
sweeps?
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Molecular Evolution:
Neighbouring marker sites
If a beneficial mutation appears and sweeps
through a population, what will happen to the
level of polymorphism present at neighbouring
DNA sites?
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Molecular Evolution:
Neighbouring marker sites
If a beneficial mutation appears and sweeps through
a population, what will happen to the level of
polymorphism present at neighbouring DNA sites?
Genetic hitchhiking will decrease variation.
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Molecular Evolution:
Neighbouring marker sites
In the case of Plasmodium falciparum,
diversity at neighbouring marker loci
decreased.
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Molecular Evolution:
Neighbouring marker sites
Wootton et al.(2002) Nature
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Molecular Evolution:
Neighbouring marker sites
If there is overdominance at a nucleotide site,
what will happen to the level of polymorphism
at neighbouring sites?
Variation at linked sites is more likely to
be maintained.
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Molecular Evolution:
Neighbouring marker sites
If there is directional selection to remove a
particular mutant allele (purifying selection),
what will happen to the marker allele that
happens to be on the same chromosome?
It will decrease in frequency as a result of this
association. This is called background selection.
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Molecular Evolution
So what is the evidence for natural selection shaping
DNA sequences?
Nielsen et al.(2005) PloS Biology
H0: neutral
Dn
1
Ds
H1: positive
Dn
1
Ds
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Molecular Evolution
Nielsen et al.(2005) PloS Biology
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Molecular Evolution
How can you detect the signature of selection?
Comparing intra-species polymorphism to interspecies differences (McDonald-Kreitman test).
Linked/neighbouring neutral markers.
Examine genes for Dn/Ds ratios.
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Molecular Evolution
Zayed and Whitfield (2008) PNAS
If drift and demography are important then the effects will be seen
on the whole genome.
If selection is important, then the effects will be seen in specific
regions of the genome.
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