Phylogenetic methods

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Phylogenetic methods

• Phylogeny
• Phylogenetic analysis

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Phylogenetics

• Linnaeuss system systematicist not
  evolutionist
• Darwin using Linnaeuss classification
  hierarchy
• Phylogeny the evolutionary relationship between
  organisms
• Character-based morphological features
  (limitation?)
• Serological reaction (Ab cross-reactivity)
  Nuttall
• Protein electrophoresis similarity in protein
  properties
• DNA-DNA hybridization
• Sequencing protein and DNA

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Advantages of molecular phylogenetics

• Large datasets A, T, C, G for character states,
  every position is one character
• Unambiguous not like shape or length
  (morphology/phenotypes) (convergent evolution)
• No suitable phenotypes to compare, e.g. compare
  among bacteria or between bacteria and flies
• Easy to convert to numerical form for
  mathematical analysis

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Phylogenetic trees

• Distance-based a measure of overall, pairwise
  difference between two data sets, e. g. scores
  from alignments
• Character-based use a well-defined feature that
  exists in a limited number or different states,
  e. g. A, T, C, G anatomical/behavioral
  phenotypes
• character data can be converted to distance data

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• Pheneticist prefer mathematic-based methods,
  emphasize on relationship among data sets
• Cladist prefer biology-based (character)
  methods, emphasize on evolutionary pathways and
  patterns
• unequal weighted characters

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DNA-based phylogenetics

• Higher information content display synonymous
  substitutions
• Variability in non-coding regions also can be
  examined
• Easy sampling and sequencing

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Terminology
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Information inferred from the tree horizontal
gene transfer
xenolog
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ingroups
Assigned by constructor, use other
information/knowledge
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Gene vs. species trees
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Distance matrix methods
Pairwise distance

• UPGMA

Calculate the new matrix d(AB)C1/2(dACdBC) d(AB)
D1/2(dADdBD)
cluster the smallest distance pair
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Cluster first
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• Topology of the tree
• branch pattern relatedness of the taxon
• branch length inferred time of divergence
• cladogram

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Estimation of branch length
x (dAB dAC - dBC )/2 y (dAC dBC - dAB
)/2 z (dBC dAB - dAC )/2
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Tree confidence

• How much confidence for each branch
• How much more likely is one tree to be correct
  than a random alternative tree
• Bootstrapping
• What do bootstrap values mean?
• Bootstrap values for phylogenetic trees do not
  follow standard statistical behaviour.
• Bootstrap value of 95 is actually close to 100
  confidence in that branch.
• Bootstrap value of 75 often close to 95
  confidence.
• Bootstrap value of 60 is much lower confidence.
• Less than 50 bootstrap no confidence in that
  branch over an alternative.

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Procedures of tree reconstruction

• Sequence alignment
• find homologs, not overrepresent or
  underrepresent the sequences
• perform alignment parameter setting
• make a guide tree first, align close related
  sequences first
• place indels at correct positions
• Convert alignment data into a phylogenetic tree
• choose tree methods
• Assess the accuracy of a reconstructed tree
• bootstrap analysis
• Estimate branch length
• calibration with other data

clustalW
clustalW
Use TreeView to view the tree output
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Tree of life

• The deep evolutionary differences in archaea and
  bacteria only can be revealed from molecular data

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Human origins

• Data from mtDNA 0.33 sequences difference
  among ethic groups (5 between orangutan
  subspecies)
• African populations display greatest differences
  Human originate from Africa
• Y-chromosome data also support out-of-Africa
  theory
• Mitochondrial Eve Y-chromosome Adam 200,000
  years ago