Models of Molecular Evolution II

1
Models of Molecular Evolution II

• Level 3 Molecular Evolution and Bioinformatics
• Jim Provan

Page and Holmes Sections 7.3 7.4
2
Isochore structure of vertebrate genomes

• Why do patterns of base composition the
  frequencies of the four bases and of codons used
  to specify amino acids differ between genomes?
• Mean G C content in bacteria ranges from 25 to
  75, but there is little intragenome variation
• Genomes of vertebrates have a much greater range
  of G C values
• Caused by continuous sections (gt 300kb) each of
  which has a uniform G C content (isochores)
• G C content of isochores also varies between
  species

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Properties of vertebrate isochores
4
Theories on the existence of isochores

• Selectionist hypothesis of Bernardi et al.
  suggests that GC-rich isochores predominantly
  found in warm-blooded vertebrates are an
  adaptation to higher body temperature
• Extra hydrogen bond in G-C pair may lessen
  possibility of thermal damage to DNA
• Desert plants also have higher GC contents
• Evidence for independent occurrence of isochores
  since birds and mammals do not share an immediate
  ancestor
• However, some thermophilic bacteria are AT-rich

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Theories on the existence of isochores

• Neutralist explanation for the existence of
  isochores is that they simply reflect variation
  in the process of mutation across the genome
• Studies on argininosuccinate synthetase processed
  pseudogenes from anthropoid primates
• Pseudogenes were derived from same functional
  ancestral gene but then inserted into different
  parts of the genome
• Despite their common ancestry, they now differ in
  base composition
• Because pseudogenes are not subject to selection,
  differences in base composition must have been
  due to regional variation in mutation patterns

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Why should mutation patterns vary across genomes?

• Replication hypothesis suggests that genes which
  replicate earlier in the cell cycle are more
  GC-rich than those which replicate later
• Believed to be due to the fact that G and C
  precursor pools of dNTPs are larger at this time
  errors are more likely to incorporate G or C
• Repair hypothesis is based on assumption that
  efficiency of DNA repair varies across genome
• May be an outcome of transcriptionally active
  areas being repaired more efficiently
• CpG islands are maintained by a special repair
  system efficiency of DNA replication may be
  dependent on location

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Why should mutation patterns vary across genomes?

• Recombination hypothesis claims that isochore
  structure of vertebrate genomes is the outcome of
  differences in the pattern and frequency of
  recombination
• Low GC localities will be associated with regions
  of reduced recombination
• Genes with low rates of recombination have low GC
  values
• The large, non-recombining region of the
  Y-chromosome has a low GC composition
• Fact that recombination plays such a large part
  in the structuring of eukaryote genomes makes
  this an attractive hypothesis
• Although the relative contributions of these
  hypotheses are still unclear, the neutralist
  interpretation seems more likely

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Codon usage
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What determines codon usage?

• Degeneracy of genetic code
• Null hypothesis is that all codons for a
  particular amino acid are used with equal
  frequency
• Refuted when nucleotide sequences became
  available for a wide range of organisms
• Selectionist argument
• Highly expressed genes show most codon bias
  because they require more translational
  efficiency coevolution of tRNAs and codons
• Also supports the neutralist prediction of a
  relationship between functional constraint and
  substitution rate

10
Gene expression and codon bias
Highly expressed genes
Lowly expressed genes
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The molecular clock

• Idea of a molecular clock is central to the
  neutralist theory, since it demonstrates the
  constancy of the underlying neutral mutation rate
• Previous example of a-globin
• Does not imply that all genes and proteins evolve
  at the same rate
• Great variation between proteins (fibrinonectins
  vs. histones)
• Variation in rate among genes and proteins is
  compatible with the neutral theory if the
  underlying cause is changes in selective
  constraint
• Key question concerning the validity of a
  molecular clock is whether rates of substitution
  are constant within genes across evolutionary time

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Neutral theory and the molecular clock

• Rate of nucleotide substitution (fixation) at any
  site per year, k, in a diploid population of size
  2N is equal to the number of new mutations
  (neutral, deleterious or advantageous) arising
  per year, m, multiplied by their probability of
  fixation, u
• k 2N mu
• For a neutral mutation, probability of fixation
  is reciprocal of population size
• u 1/2N
• So substitution rate for a neutral mutation is
• k (2N )(1/2N )m

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Neutral theory and the molecular clock (continued)

• Parameters for population size (2N) cancel out,
  leaving
• k m
• One of the most important formulae in molecular
  evolution means that rate of substitution in
  neutral mutations is dependent only on underlying
  mutation rate and is independent of other factors
  such as population size
• Also holds for mutants with a very weak selective
  advantage e.g. s lt 1/2Ne

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Substitution of selectively advantageous mutations

• Probability of fixation is roughly twice the
  selection coefficient
• u 2sNe/N
• Substituting this into the original equation, we
  get
• k 4Nesm
• In this case, substitution rate for an
  advantageous mutation also depends on population
  size and magnitude of selective advantage
• For natural selection to produce a molecular
  clock, it is necessary for Ne, s and m
  (combination of ecological, mutational and
  selective events) to be the same across
  evolutionary time highly unlikely!

15
Constancy of the molecular clock

• Neutral theory predicted a molecular clock and
  first protein sequence data appeared to confirm
  this led Kimura to cite this as the best
  evidence for neutrality
• As more comparative sequence data became
  available, particularly from mammals, examples of
  rate variation began to appear
• Debate arose concerning the constancy of the
  molecular clock

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Testing the molecular clock

• Dispersion index R(t) test whether there is more
  rate variation between lineages than expected
  under a Poisson process
• If the data fit a Poisson process, variance in
  number of substitutions between lineages should
  be no greater than the mean number
• If the data fit a Poisson process then R(t)
  1.0, if not then R(t) gt 1.0 and the clock is said
  to be overdispersed
• A star phylogeny should be used, since any
  phylogenetic structure will complicate the
  calculations (e.g. placental mammals)

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Testing the molecular clock

• Mammalian protein data presented a serious
  problem for neutralists
• Problems most likely due to inaccuracies in
  phylogenies
• Outlier in data was guinea pig
• Guinea pig is much more divergent than previously
  thought

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The relative rate test

• The relative rate test compares the difference
  between the numbers of substitutions between two
  closely related taxa in comparison with a third,
  more distantly related outgroup

• If A and B have evolved according to a molecular
  clock, both should be equidistant from C
• dAC dBC
• A and B must be closest relatives and C must not
  be too far removed

19
The relative rate test

• Synonymous sites in nine nuclear genes (3520 bp)
• d12 6.7
• d13 d23 2.3 0.6
• yh-globin pseudogene (1827 bp)
• d12 7.9
• d13 d23 1.5 0.4
• Three introns (3376 bp)
• d12 6.9
• d13 d23 1.0 0.5
• Two flanking regions (936 bp)
• d12 7.9
• d13 d23 3.1 1.1

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Lineage effects and the molecular clock

• Substitution rate varies with underlying neutral
  mutation rate k m
• Three ways for rates to vary between species
• Differences in generation time
• Differences in metabolic rate
• Differences in efficiency of DNA repair
• These are known as lineage effects neutralists
  believe that lineage effects alone can account
  for all variation in molecular clock
• Selectionists believe that genes also show rate
  variation due to other, selection-driven factors
  (residue effects)

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Generation time and the molecular clock
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Generation time and the molecular clock

• At the molecular level, generation time (g) can
  be defined as time it takes for germ-line DNA to
  replicate i.e. from one gamete to the next
• Since most mutations occur at this point, rate
  of substitution under neutral theory is a
  function of both mutation rate and generation
  time
• k m/g
• General conclusion from molecular data is that
  the clock is generation time dependent at silent
  sites and in non-coding DNA
• Silent rates in orang-utan, gorilla and chimp are
  1.3-, 2.2- and 1.2-fold faster than in humans,
  which matches differences in generation times

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The metabolic rate hypothesis

• In sharks, rate of silent change is five- to
  sevenfold lower than in primates and ungulates
  which have similar generation times
• Led to the hypothesis that differences in
  molecular rate are a better explanation for
  differences in mutation rates than differences in
  generation time (metabolic rate hypothesis)
• States that organisms with high metabolic rates
  have higher levels of DNA synthesis
• Two pieces of mitochondrial DNA evidence support
  this
• Small bodied animals, which have higher metabolic
  rates, tend to have higher mutation rates
• Warm-blooded animals also have higher mutation
  rates than cold-blooded animals

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Relationship between body mass and sequence
evolution
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DNA repair and mutation
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DNA repair and mutation

• Repair mechanisms are extremely complex and there
  are many repair pathways
• There is some evidence supporting the hypothesis
  that DNA repair influences mutation rate
• Evidence that highly transcribed genes are more
  efficiently repaired
• Base composition and substitution rates at silent
  sites in mammalian genes tends to be gene- rather
  than species-specific suggests that homologous
  genes are transcribed and repaired in a similar
  manner
• Conversely, closely related species such as
  hominind primates, which share very similar
  repair mechanisms, can exhibit greatly differing
  substitution rates