Introduction to Phylogenetic Trees

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Introduction to Phylogenetic Trees

• Jana Sperschneider
• Institute for Computer Science
• Albert-Ludwigs-Universität, Freiburg

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Contents

• Introduction
• Biological foundations
• Terminology
• Applications of phylogenetic trees
• Construction of phylogenetic trees
• Molecular phylogenetic analysis
• Advantages
• Procedure
• Distance Based Methods
• Example UPGMA algorithm
• Neighbor Joining

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Biological Foundations

• Evolution is driven by
• Inheritance
• Variation
• Mutations
• Recombination
• Selection
• All organisms share a common ancestry

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Terminology

• Phylogeny
• The evolutionary relationships among organisms,
  based on a common ancestor
• Phylogenetics
• Area of research concerned with finding the
  genetic relationships between species
• (Greek phylon race and genetic birth)

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Terminology

• Phylogenetic tree Visual representation of
  evolutionary distances between species

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Terminology
Rooted tree Unrooted tree
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Applications of phylogenetic trees

• Evolution studies
• Systematic biology
• Medical research and epidemiology
• Ecology
• Others like grouping languages, medieval
  manuscripts

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Contents

• Introduction
• Biological foundations
• Terminology
• Applications of phylogenetic trees
• Construction of phylogenetic trees
• Molecular phylogenetic analysis
• Advantages
• Procedure
• Distance Based Methods
• Example UPGMA algorithm
• Neighbor Joining

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Definitions

• Classic phylogenetic analysis uses morphological
  features
• Anatomy, size, number of legs, beak shape
• Modern phylogenetic analysis uses molecular
  information
• Genetic material (DNA and protein sequences)

Molecular phylogenetic analysis
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Advantages of molecular phylogenetic analysis

• Analogous features (share common function, but
  NOT common ancestry) can be misleading
• DNA sequences more simple to model, we only have
  the four states A, C, G, T
• DNA samples for sequence analysis easy to prepare

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Procedure Steps of a molecular phylogenetic
analysis

• Decide what sequences to examine
• Determine the evolutionary distances between the
  sequences and build distance matrix
• Phylogenetic tree construction

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1. Decide what to examine

• Choose homologous sequences in different species
• Homologous sequences must, by definition, be
  derived from a common ancestral sequence
• Homology is not similarity

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2. Determine the evolutionary distances and build
distance matrix

• For molecular data, evolutionary distances can be
  the observed number of nucleotide differences
  between the pairs of species.
• Distance matrix simply a table showing the
  evolutionary distances between all pairs of
  sequences in the dataset

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2. Determine the evolutionary distances and build
distance matrix - A simple example

• AGGCCATGAATTAAGAATAA
• AGCCCATGGATAAAGAGTAA
• AGGACATGAATTAAGAATAA
• AAGCCAAGAATTACGAATAA
• Distance Matrix
• In this example the evolutionary
  distance is expressed as the number of
  nucleotide differences for each sequence
  pair. For example, sequences 1 and 2 are
  20 nucleotides in length and have four
  differences, corresponding to an
  evolutionary difference of 4/20 0.2.

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3. Phylogenetic Tree Construction example (UPGMA
algorithm)
UPMGA (Michener Sokal 1957)
Bear Raccoon 0.13
0.13

• 1. Pick smallest entry Dij
• 2. Join the two intersecting species and assign
  branch lengths Dij/2 to each of the nodes

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3. Phylogenetic Tree Construction example (UPGMA
algorithm)
Bear Raccoon 0.13
0.13
3. Compute new distances to the other species
using arithmetic means
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3. Phylogenetic Tree Construction example (UPGMA
algorithm)
Bear Raccoon Seal
0.13 0.1825 0.1825
1. Pick smallest entry Dij 2. Join the two
intersecting species and assign branch lengths
Dij/2 to each of the nodes
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3. Phylogenetic Tree Construction example (UPGMA
algorithm)
Bear Raccoon Seal
0.13 0.1825 0.1825

• Compute new distances to the other species using
  arithmetic means

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3. Phylogenetic Tree Construction example (UPGMA
algorithm)
Bear Raccoon Seal Weasel
0.13 0.1825 0.2
0.2

• Pick smallest entry Dij.
• Join the two intersecting species and assign
  branch lengths Dij/2 to each of the nodes.
• Done!

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Weakness of UPGMA

• UPGMA assumes a constant molecular clock (i.e.
  accumulate mutations at the same rate)
• All leaves in the same level
• Only constructs rooted trees

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Neighbor Joining (Saitou and Nei, 1987)

• Most widely used distance-based method
• UPGMA showed that it is not enough to just pick
  closest neighbors
• Neighbor Joining
• Principle Join nodes that are close to each
  other and far from everything else
• Produces an unrooted tree

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In the next talk

• How to construct a tree from incomplete distance
  matrices
• Maximum-likelihood methods
• Under a model of sequence evolution, find the
  tree which gives the highest likelihood of
  observed data
• Parsimony methods
• Choose tree that minimizes number of changes
  required to explain data

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References

• Mona Singh, Phylogenetics,
• http//www.cs.princeton.edu/mona/Lecture/phyloge
  ny-slides.pdf
• T. A. Brown, Genomes, http//www.ncbi.nlm.nih.gov/
  books/bv.fcgi?ridgenomes
• Joe Felsenstein, Phylogeny methods,
  http//evolution.gs.washington.edu/gs541/2005/lect
  ure26.pdf
• Microbial diversity lecture, http//www.mbio.ncsu.
  edu/JWB/MB409/home.htm
• Michener, C.D. and Sokal, R.R. (1957) A
  quantitative approach to a problem in
  classification. Evolution, 11, 130-162.

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Thanks for listening!

• Any questions?