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    Week 3c - Phylogenetic - Tree - ConstructionMai PDF

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    Sunil
    This document provides an overview of phylogenetic tree construction. It discusses different types of phylogenetic trees including rooted vs unrooted trees. It also describes common methods for constructing trees, including distance matrix methods like UPGMA and neighbor joining, which calculate evolutionary distances between taxa. The document provides step-by-step examples of constructing a tree using UPGMA. It notes some limitations of UPGMA and advantages of neighbor joining.

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    Week 3c - Phylogenetic - Tree - ConstructionMai PDF

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    Sunil
    163 views19 pages
    This document provides an overview of phylogenetic tree construction. It discusses different types of phylogenetic trees including rooted vs unrooted trees. It also describes common methods for constructing trees, including distance matrix methods like UPGMA and neighbor joining, which calculate evolutionary distances between taxa. The document provides step-by-step examples of constructing a tree using UPGMA. It notes some limitations of UPGMA and advantages of neighbor joining.

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    This document provides an overview of phylogenetic tree construction. It discusses different types of phylogenetic trees including rooted vs unrooted trees. It also describes common methods for constructing trees, including distance matrix methods like UPGMA and neighbor joining, which calculate evolutionary distances between taxa. The document provides step-by-step examples of constructing a tree using UPGMA. It notes some limitations of UPGMA and advantages of neighbor joining.

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    Download as pdf or txt
    163 views19 pages

    Week 3c - Phylogenetic - Tree - ConstructionMai PDF

    Uploaded by

    Sunil
    This document provides an overview of phylogenetic tree construction. It discusses different types of phylogenetic trees including rooted vs unrooted trees. It also describes common methods for constructing trees, including distance matrix methods like UPGMA and neighbor joining, which calculate evolutionary distances between taxa. The document provides step-by-step examples of constructing a tree using UPGMA. It notes some limitations of UPGMA and advantages of neighbor joining.

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    You are on page 1of 19

    Phylogenetic tree construction

    http://libguides.scu.edu/evolution
    Outline
    2

    q Phylogenetic tree types


    q Distance Matrix method
    q UPGMA
    q Neighbor joining
    q Character State method
    q Maximum likelihood
    Phylogenetic tree?
    3

    q A tree represents graphical relation between


    organisms, species, or genomic sequence
    q In Bioinformatics, its based on genomic sequence
    What do they represent?
    4

    q Root: origin of evolution


    q Leaves: current organisms, species, or genomic

    sequence
    q Branches: relationship between organisms, species,

    or genomic sequence
    q Branch length: evolutionary time

    (in cladogram, it doesn't represent time)


    Rooted / Unrooted trees
    5
    q Rooted tree: directed to a unique node
    q (2 * number of leaves) - 1 nodes,

    q (2 * number of leaves) - 2 branches

    q Unrooted tree: shows the relatedness of the leaves


    without assuming ancestry at all
    q (2 * number of leaves) - 2 nodes

    q (2 * number of leaves) - 3 branches

    https://www.nescent.org/wg_EvoViz/Tree
    More tree types used in
    6 bioinformatics (from cohen article)
    q Unrooted tree
    q Rooted tree
    q Cladograms: Branch length have no meaning

    q Phylograms: Branch length represent evolutionary

    change
    q Ultrametric: Branch length represent time, and the length

    from the root to the leaves are the same

    https://www.nescent.org/wg_EvoViz/Tree
    How to construct a phylogenetic tree?
    7

    q Step1:
    Make a multiple alignment from base alignment or
    amino acid sequence (by using MUSCLE, BLAST, or
    other method)
    How to construct a phylogenetic tree?
    8

    q Step 2:
    Check the multiple alignment if it reflects the
    evolutionary process.
    http://genome.cshlp.org/content/17/2/127.full
    How to construct a phylogenetic tree?
    9
    cont
    q Step3:
    Choose what method we are going to use and
    calculate the distance or use the result depending
    on the method

    q Step 4:
    Verify the result statistically.
    Distance Matrix methods
    10

    q Calculate all the distance between leaves (taxa)


    q Based on the distance, construct a tree
    q Good for continuous characters
    q Not very accurate
    q Fastest method
    q UPGMA
    q Neighbor-joining
    UPGMA
    11

    q Abbreviation of Unweighted Pair Group Method


    with Arithmetic Mean
    q Originally developed for numeric taxonomy in
    1958 by Sokal and Michener
    q Simplest algorithm for tree construction, so it's fast!
    How to construct a tree with UPGMA?
    12

    q Prepare a distance matrix


    q Repeat step 1 and step 2 until there are only two
    clusters
    q Step 1:
    Cluster a pair of leaves (taxa) by shortest distance
    q Step 2:
    Recalculate a new average distance with the new
    cluster and other taxa, and make a new distance
    matrix
    Example of UPGMA
    13

    A B C D E
    A 0
    B 20 0
    C 60 50 0
    D 100 90 40 0
    E 90 80 50 30 0
    qNew average distance between AB and C is:
    qC to AB = (60 + 50) / 2 = 55
    qDistance between D to AB is:
    qD to AB = (100 + 90) / 2 = 95
    qDistance between E to AB is:
    qE to AB = (90 + 80) / 2 = 85
    Example of UPGMA cont 1
    14

    AB C D E
    AB 0
    C 55 0
    D 95 40 0
    E 85 50 30 0

    qNew average distance between AB and DE is:


    qAB to DE = (95 + 85) / 2 = 90
    Example of UPGMA cont 2
    15

    AB C DE
    AB 0
    C 55 0
    DE 90 45 0

    qNew Average distance between CDE and AB is:


    qCDE to AB = (90 + 55) / 2 = 72.5
    Example of UPGMA cont 3
    16

    AB CDE

    AB 0

    CDE 72.5 0

    qThere are only two clusters. so this completes the


    calculation!
    Downside of UPGMA
    17

    q Assume molecular clock (assuming the evolutionary


    rate is approximately constant)
    q Clustering works only if the data is ultrametric
    q Doesnt work the following case:
    Neighbor-joining method
    18

    q Developed in 1987 by Saitou and Nei


    q Works in a similar fashion to UPGMA
    q Still fast works great for large dataset
    q Doesnt require the data to be ultrametric
    q Great for largely varying evolutionary rates
    Example Neighbor-Joining Tree for Dogs

    BM vonHoldt et al. Nature 000, 1-5 (2010) doi:10.1038/nature08837

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