Download Molecular Evolution

Molecular Evolution
Nothing in biology makes sense except in the light of evolution
Dobzhansky, 1973
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Study evolution to make sense of biology
What kind of changes occur at the DNA level during
evolution?
How does the environment influence our genes?
What can our genes tell us about the past
environment?
Can we “read” the evolutionary patterns of our genes
to understand their functions?
The molecule : DNA
actgaatg
||||||||
tgacttac
gene
MALVK
protein
genome
Population …. Speciation
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Advantages:
Highly divergent organisms can be compared
quantitatively without relying on morphological
characters
Changes at the DNA level not presenting phenotypic
effects can be also used as additional information to
compare sequences from different species
Molecular data
•  Protein: biochemical properties
•  Protein: sequence
•  DNA: sequence
–  Coding (makes protein)
–  Non-coding
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•  DNA is both the raw material and the
marker of evolution
–  Genes determine inherited differences, which
is what evolution acts on
–  Genes change and can be used to measure
evolution
A genome (complete DNA of an organism) is a historical
record of evolution. By analysing and comparing the DNA
of related organisms, can learn about their evolutionary
history. … We can also start to classify their relationships
(phylogenetics)
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Complete Genomes
Evolution
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Functional constraint
Abraham Wald
B-29 Bomber
Molecular Evolution
Part 1: Understand patterns and processes of mutation
Part 2: Examine cases where patterns of divergence
differ from patterns of mutation
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Molecular Variation
• 
• 
• 
• 
Nucleotide substitution
Insertions or deletions (indels)
Recombination
Gene duplication and loss
Molecular Variation
Single Nucleotide Polymorphisms (SNPs)
–  One bp difference between “alleles”
–  Human genome
•  Coding DNA – 1 SNP per 1-3 kb (kb = 1000bp)
•  Non-coding DNA – 1 SNP per 0.5-1 kb
DNA sequencing
…ACGTGACTGAGGACCGTG
CGACTGAGACTGACTGGGT
CTAGCTAGACTACGTTTTA
TATATATATACGTCGTCGT
ACTGATGACTAGATTACAG
ACTGATTTAGATACCTGAC
TGATTTTAAAAAAATATT…
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Evolution
• interested in genetic variation - understand generation and
maintenance
• initially (until 1960s) only possible to study indirectly - phenotype
• paucity of data led to controversy on the extent of genetic variation
Classic school - very little genetic
variation due to cost associated
with natural selection
Muller
Balance school - lots of genetic variation
maintained by natural selection
Dobzhansky
• debate settled with advent of molecular approaches (direct) to the
study of genetic variation - electrophoresis, sequencing
•  Zuckerkandel & Pauling – 1960s
•  Electrophoretic gel separation of proteins
•  Proteins travel at different speeds
according biochemical properties or
molecular weight
•  15-50% of genes have 2 or more
electrophoretic alleles
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•  Too much polymorphism to be explained
by mutation and positive selection alone
(NeoDarwinian model)
•  Why so much?
The Neutral Theory of Molecular Evolution
How can we explain the large amounts of variation that
exist in populations?
• Most mutations are selectively neutral (not advantageous or
disadvantageous) … generate new neutral alleles
• These will be fixed (= present at 100% frequency) in the population by
Genetic Drift
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Random Genetic Drift
Selection
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Allele frequency
advantageous
disadvantageous
0
time
time
The Neutral Theory of Molecular Evolution
• The rate of neutral evolution is equal to the rate of neutral mutation
Kimura reasoned that the majority of both polymorphism (allelic
frequencies within populations) and substitution (fixed differences between
populations) result from fixation of selectively neutral variants by random
genetic drift
- the main role of natural selection is elimination of deleterious variants
(maintenance of the status quo) - molecular evolution is conservative
- adaptively favorable mutations fixed by natural selection are a small
minority of all nucleotide substitutions
Huge debate between selectionists (variation is a product of natural
selection) and neutralists (variation is a product of random fixation of
neutral variants)
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Molecular Clock
•  MOLECULAR CLOCK
# differences
•  Rate of substitution = rate of mutation
time
•  Number of changes is proportional to time
•  Use number of changes to estimate
relative divergence of species or genes
• Neutral Theory makes explicit quantitative
predictions about levels of genetic variation - null
hypothesis of molecular evolution
•  functionally important parts of a molecule will change
slower than non-functional parts (Molecular Clock
does not always hold)
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Evolution of protein coding
sequences
Rates and patterns of nucleotide
substitution in protein-coding seqs
•  Controlled by three things
–  Functional constraint (negative selection)
–  Positive selection
–  Mutation rate
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Standard Genetic Code
Phe
Leu
Leu
Ile
UUU
Ser
UCU
Tyr
UAU
Cys
UCC
UUA
UCA
ter
UAA
ter
UGA
UUG
UCG
ter
UAG
Trp
UGG
CCU
His
CAU
Arg
CGU
CUU
Pro
CUC
CCC
CUA
CCA
CUG
CCG
AUU
Thr
ACU
AUC
ACC
AUA
ACA
Met
AUG
ACG
Val
GUU
Ala
GCU
GUC
GCC
GUA
GCA
GUG
GCG
UAC
UGU
UUC
Gln
Asn
UGC
CAC
CGC
CAA
CGA
CAG
CGG
AAU
Ser
AAC
Lys
AAA
AGC
Arg
AAG
Asp
Glu
GAU
AGU
AGA
AGG
Gly
GGU
GAC
GGC
GAA
GGA
GAG
GGG
synonymous subs - do not change encoded amino acid
nonsynoymous subs - do change encoded amino acid
GAT AAC ATC CAA GGA ATA ACT GCA ATC
GAC AAC ATC CAA GGT ATC ACG GCT ATC
Asp Asn Ile Gln Gly Ile Thr Ala Ile
•  in virtually every gene ever studied synonymous sites
change at a higher rate than nonsynonymous sites
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Evolution of protein-coding
sequences
•  The Genetic Code is redundant
•  Some nucleotide changes do not change
the amino acid coded for
–  3rd codon position often synonymous
–  2nd position never
–  1st position sometimes
Synonymous
Consensus
Seq1
Seq2
Seq3
Consensus: AAT GGC TCT TTT GAA AAA ...
N
Seq4
Seq5
Seq6
G
F
F
N
K
.
Seq2: AAC GGA TGT TTC GAG AAA...
N
Seq7
Seq8
Seq9
Seq10
Seq11
G
C
F
E
K
.
Non-synonymous
Number of
individuals
Positive
selection
Neutrally
fixed
Purifying
selection
E
Number of mutations
AAT GGC TGT TTT GAA AAA ...
N
G
C
F
N
K
.
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rates
•  In general, the rates of nucleotide
substitution are lowest at nondegenerate
sites (0.78 x 10-9 per site per year)
•  Intermediate at two-fold degenerate sites
(2.24 x 10-9)
•  Highest at fourfold degenerate sites (3.71
x 10-9)
Effect of amino acid substitutions
•  Deleterious
•  Neutral
•  Advantgageous
86%
14%
0.0% ? (very low)
•  In protein coding sequences, selection is often
acting to remove changes
•  Less common outcome is drift of neutral
changes
•  Rarely see positive selection for advantageous
changes
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Functional constraint
Abraham Wald
B-29 Bomber
Functional Constraint
•  Proteins often have some functional constraint
•  This may involve
•  a few amino acids in a critical site
–  Haeme pocket of Haemoglobin is constrained
–  The rest just needs to be hydrophillic
•  Or almost the whole protein
–  Histone 4
–  Almost all in contact with DNA or other proteins
•  Or hardly be present at all
–  Fibrinopeptide amino acid sequence is not important
•  The stronger the functional constraint, the slower the rate
of evolution
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Rates and Patterns
•  Patterns of change can be informative of
the function of a protein
•  Different genes evolve at different rates
•  Amino acids that are always conserved
are likely to be critical to the function
synonymous substitutions - little or no
effect on the fitness of the organism.
non-synonymous substitutions always
change the protein. Since most changes
are deleterious, we expect these
changes to be removed by selection.
rate of evolution at synonymous sites is
greater than at non-synonymous sites.
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• The differences in the rates of evolution are usually due
to functional constraints
•  mutations that remove or reduce the function of a gene
are removed by negative selection
•  very important genes tend to evolve slowly
•  proteins (gene products) that interact with other
proteins etc. also evolve slowly at interacting interfaces –
mutations may disturb the interaction and be
consequently deleterious
•  if there is low or no functional constraint, then the
proteins will fix new mutations by random drift and so
evolve faster
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