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IMPRS workshop
Comparative Genomics
18th-21st of February 2013
Lecture 4
Positive selection
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What is positive selection?
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Positive selection is selection on a particular trait
- and the increased frequency of an allele in a population
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Woolhouse et al, 2002. Nat. Genet
Directional selection
Balancing selection
Population levelPositive selection can drive the changes in frequencies of two alleles
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Species B Species CSpecies A
Diversifying positive selection
Interspecific levelPositive selection driving divergence
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Why is it interesting to identify traits which
have undergone or are under positive selection?
FunctionEvolution
Environment……
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How can we detect positive selection?
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Changes in a protein sequence….
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Come from changes in the
nucleotide sequence
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Quantifying non-synonymous variation
- an estimate of positive selection
Synonymous mutations: neutral mutationsNon-synonymous mutations: non-neutral mutations
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Rate of synonymous mutations
Rate of non-synonymous mutations
To measure positive selection:
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Positive selection between species
Neutral evolution
Purifying selection
Positive selection
f.ex. effector genes
f.ex. housekeeping genes
f.ex. pseudogenes
Ks or dS
Ka or dN
KA or dN: rate of non-synonymous divergence
KS or dS: rate of synonymous divergenceEvolution between species
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Positive selection in a population
Neutral evolution
Purifying selection
Positive selection
f.ex. housekeeping genes
f.ex. pseudogenes
PS
PN: rate of non-synonymous polymorphisms
PS: rate of synonymous polymorphismsEvolution within species
PN
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Species A Species B Species C
d N /
d S
PN / Ps
Estimates of non-synonymous and synonymous polymorphisms and substitutions provide insight into the evolutionary processes
Analysing divergence and polymorphism:
• KA / KS ratios > 1 indicate positive selection
• KA / KS ratios < 1 indicate negative selection
• KA / KS ratios = 1 indicates neutral evolution
KA and dN: rate of non-synonymous substitutions
KS and dS: rate of synonymous substitutions
PN: Amount of non-synonymous polymorphisms
PS: Amount of synonymous polymorphisms
Ka/Ks
branch-specific estimate
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Species A Species B Species C
d N /
d S
PN / Ps
Estimates of non-synonymous and synonymous polymorphisms and substitutions provide insight into the evolutionary processes
Contrasting divergence and polymorphism:
Ka/Ks
• The branch specific dN / dS ratios
are measures of adaptive evolution
particular to one branch
• Ratios of PN / PS provide insight
into the strength of purifying
selection in the species
• Ratios of KA / KS provide insight
into the amount of non-
synonymous divergence
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Nei and Gojobori, 1986
- Counts of non-synonymous mutations for each gene (Nd)
- Counts of synonymous mutations for each gene (Sd)
- Counts of potential non-synonymous sites for each gene (N)
- Counts of potential synonymous sites for each gene (S)
Non-synonymous substitution rate: KA = Nd / N
Synonymous substitution rate: KS = Sd / S
Ratio KA/KS as an inidicator of evolutionary
mode in each gene
Basic analyses of the proportion of non-synonymous to synonymous divergence KA/KS
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Calculate potential synonymous sites (S) for each codon A fourfold degenerate site counts as S = 1 (N = 0)A non-degenerate site counts as S = 0 (N = 1)A two fold degenerate site counts as S = 1/3 (N = 2/3) 1. Proline S = 0 + 0 + 1 = 12. Phenylalanine S = 0 + 0 + 1/3 = 1/33. For Glycine S = 0 + 0 + 1 = 1, for Alanine S = 0 + 0 + 1 =
Take the average: S=14. Leucine for UUA, S = 1/3 + 0 + 1/3 = 2/3 for CUA, S = 1/3 + 0 + 1 = 4/3 Take the average of these: S = 1 for codon 45 Phenylalanine for UUU, S = 1/3 for guanine, S = 1 Take average: S = 2/3 For whole sequence, S = 1 + 1/3 + 1 + 1 + 2/3 = 4 N = total number of sites: S = 15 - 4 = 11
Counts of possible synonymous sites for each gene (S) 1 2 3
4 5Pro Phe Gly
Leu PheSeq 1 CCC UUU GGG UUA UUUSeq 2 CCC UUC GAG CUA GUA
Pro Phe Ala Leu Val
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Calculate Sd and Nd for each codon. 1. Sd = 0, Nd = 02. Sd = 1, Nd = 03. Sd = 0, Nd = 14. Sd = 1, Nd = 05. this could happen in two ways
UUU --> GUU --> GUANd = 1 Sd = 1 Route 1: Sd = 1, Nd
= 1
UUU --> UUA --> GUANd = 1 Nd = 1 Route 2: Sd = 0, Nd = 2
Take average of these two:
Sd = 0.5, Nd = 1.5 Total Sd = 2.5
Total Nd = 2.5 Sd / S = 2.5/4 = 0.625 Nd / N = 2.5/11 = 0.227
dN/dS = 0.363
1 2 3 4 5
Pro Phe Gly Leu PheSeq 1 CCC UUU GGG UUA UUUSeq 2 CCC UUC GAG CUA GUA
Pro Phe Ala Leu Val
Counts of synonymous changes
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Positive selection between species
Neutral evolution
Purifying selection
Positive selection
f.ex. effector genes
f.ex. housekeeping genes
f.ex. pseudogenes
ds
dN
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Species A Species B Species C
PN / Ps
When positive selection is related to species divergence
Contrasting divergence and polymorphism:
Ka/Ks
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McDonald Kreitman (MK) test to contrast within and between species variation
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Repl: Nonsynonymous, Syn: SynonymousFixed: Substitution, Poly: Polymorphisms
Drosophila dataset alcohol dehydrogenase
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The proportion of non-synonymous fixed differences between species much higher than the proportion of non-synonymous polymorphisms
MK test contrasts within and between species synonymous and non-synonymous differences
Contingency table can be tested by a G-test
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Conclusion from MK-test:
Adh locus in Drosophila has accumulated
adaptive mutations (been under positive
selection) when the Drosophila species
diverged
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One problem with the “counting methods”
Sometimes the signal of selection is not very strong
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Positive selection on one or few particular codonsor in one particular branch
Evolutionary model to detect selection in particular codons or branches