Substitution Patterns

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Substitution Patterns

• An Introduction to Phylogeny

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Genes and Mutations

• Organism the optimal state for its gene
  products
• Usually
• Mechanisms to prevent harmful errors in DNA
• Proofreading
• Wobble
• DNA repair

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Mutations

• Mutations still occur
• Types of mutations
• Base Substitution
• Missense
• Nonesense
• Silent
• Indel
• Effects on Organism
• Deleterious
• Neutral
• Uncertain which happens more (deleterious or
  neutral)
• Advantageous
• Least often

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Rates of Mutation

• rK/(2T)
• rrate of substitution ( substitutions/site/year)
  
• Knumber of nucleic acid substitutions between 2
  homologous sequences
• Ttime since divergence (multiplied by 2 because
  must account for changes in both sequences)
• Estimated from fossil record
• Rather simplistic
• Doesnt account for back mutations

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An Estimate of Time
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Average Rate of divergence
Mutation/Substitution whats the difference?

• Natural Selection
• Removal of deleterious mutations
• Which changes least often in a DNA sequence?
• Functional Constraint
• Portions responsible for structure and function
• Are they functionally constrained?
• Introns
• Exons
• Downstream of poly A tail (3 flanking region)
• Promoter and regulator regions (5 untranslated
  sequence)
• Upstream of promoter and regulator (5 flanking)
• Sequence immediately following codon region for
  stop codon (3 untranslated)

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• What is the difference between a mutation and a
  substitution?

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Globin substitution rates(/site/109 years)
3.48

• Introns
• Exons
• Downstream of poly A tail (3 flanking region)
• Promoter and regulator regions (5 untranslated
  sequence)
• Upstream of promoter and regulator (5 flanking)
• Sequence immediately following coding region for
  stop codon (3 untranslated)

Rates Different for other genes
1.58
3.60
1.86
3.39
3.00
Functionally Constrained!
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Synonymous VS Non-synonymous

• Synonymous substitutions
• Occur from silent mutation
• Accepted slightly more often than non-synonymous
• Non-synonymous substitutions
• From missense or nonesense mutations
• Nondegenerate position
• 1st or 2nd position usually
• UUU (F), CUU (L), AUU (I), GUU (V)
• Twofold degenerate position
• Third position usually
• GAU and GAC (D), GAA and GAG (E)
• Fourfold degenerate position
• Typically synonymous!
• Third position

Substitution rates 0.56 1.67 2.35
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Indels

• Indels occur 10X less than substitutions
• DNA repair mechanisms

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Variation in substitution rates

• There is a large difference between synonymous
  and nonsynonymous substitution rates in a gene.
  However the two rates should theoretically be the
  same, or similar, since mutations occur random.
• The difference is attributed to the intensity of
  purifying selection. Mutations that result in an
  amino acid substitution have a higher chance of
  causing deleterious effects and be removed from
  the population and never fix.
• Nonsynonymous substitutions may have a chance of
  improving the function of a protein. If
  advantageous (positive) selection plays a major
  role in a particular protein, the rate of
  nonsynonymous substitution should exceed that of
  synonymous substitution in that protein in this
  scenario.
• However, most often, the stronger the functional
  constraint of a protein, the slower the rate of
  evolution (most nonsynonymous substitutions are
  not advantageous).

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Homology

• Paralogous genes
• Gene duplication events
• Tandem copies which evolve independently
• Duplicated genes are paralogous from each other
• Dont necessarily have same function
• Orthologous genes
• Homologous genes that share common ancestry and
  function in the absence of gene duplication

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Orthologs versus paralogs
http//www.ncbi.nlm.nih.gov/Education/BLASTinfo/Or
thology.html
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• Pseudogenes
• Paralogous homology?
• Well before the divergent forms a new function it
  is not transcriptionally active?pseudogene
• 4 substitutions every 109 years
• High substitution frequency
• Actual mutation rate is believed to be fairly
  similar to substitution rates of pseudogenes and
  synonymous substitutions.

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More Evolution Terms

• Chimeric genes
• Some regions of gene are homologous and others
  are not (the whole gene is not homologous)
• Transposition
• Horizontal gene transfer
• Xenologous
• When individual genes do not share same
  evolutionary origin as the organisms overall
  evolutionary origin
• Horizontal gene transfer or symbiosis
• EX) Eukaryotic cell and mitochondrial DNA
• EX) viral transduction
• EX)conjugation
• EX) transformation

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Measuring Substitution Patterns

• Jukes and Cantor Approach (69)
• any nucleotide is just as likely to change into
  any other
• Back mutations are accounted for
• An oversimplification
• Transitions occur 3X more than transversions
• Kimuras 2 parameter model (80)
• Takes different rates of transitions and
  transversions into account
• Account for 2 different rates
• Back mutations accounted for still
• Still an oversimplification

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12 parameter model

• Assume that any nucleotide substitution changes
  at a different rate
• A?T different rate than T?A
• 12 scenarios
• Determine substitution frequencies within an
  alignment and base individuals frequencies on a
  those probabilities
• Problem
• ideally its great
• Realistically
• Different genes result in different substitution
  rates therefore, there is no one reliable
  matrix.
• Two parameter is most reliable of the three, but
  not necessarily the most realistic

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Nucleotide Substitutions in Alu-Y
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Protein Sequence Substitution

• Recall Factors that come into play
• The number of nucleic acid changes influences the
  substitution rate
• Ser?pro (one amino acid change for UCU?CCU)
• Ser?Ile (two amino acid changes for UCU?AUU)
• Conservative changes in aa effect function less
  than radical changes in aa
• Use the PAM or BLOSUM matrix to determine
  frequencies

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Evolutionary Rate Variation

• Histone genes
• Code for proteins that bind DNA in Euks
• Every amino acid associated with DNA binding
• Slowest evolving proteins
• HLA genes
• Code for proteins that help WBCs recognize
  foreign antigens
• Under pressure to diversify
• Better protection from pathogens
• Non-synonymous sub rate is actually greater than
  synonymous sub rate

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Molecular Clocks

• Different proteins have different rates of
  evolutionSURE
• However, amount of change between 2 homologs is
  well correlated with time since divergence
• Can use substitution rates as an evolutionary
  clock
• Molecular phylogeny
• Using molecular comparison of several sequences
  (multiple sequence alignments) to model
  evolutionary changes mathematically.
• Zuckerkandl and Pauling (60s)
• Classical Evolutionists have problems

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Classical Evolutionary Beliefs vs

• Classical Evolutionary models
• Comparison of phenotype only
• Bulk changes
• Cannot account for synonymous changes
• Convergent evolution cannot be deciphered!
• Not all organisms have easily studied phenotypes
• Cant compare unrelated organisms
• Small changes not noticed
• Many missing links in fossil record

• Molecular Evolutionary Models
• Study of substitution rate
• Model changes
• Synonymous
• non-synonymous and neutral
• non-synonymous and advantageous
• Comparison of phenotype
• Molecular changes still correlate well with
  classical speciation models

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Phylogeny

• Rather than bother correlating divergence times
  to fossil record use relative rates
• Divergence dates are questionable
• Phylogenetic trees
• Outgroup (lineage 3)
• Lineage 1 and lineage 2
• Common ancestor A

1
2
3
A