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    Molecular Phylogeny Part I

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    Malabika Bhowmick
    This document discusses molecular phylogeny and how to construct phylogenetic trees from molecular sequence data. It explains that nucleic acids and proteins can be used to infer evolutionary relationships among microorganisms as they retain evidence of evolutionary history. Computer programs are used to estimate relationships based on sequence homology and closely related organisms have fewer differences. The document provides steps for phylogenetic tree construction, including choosing markers, aligning sequences, selecting an evolutionary model, using tree-building methods like maximum parsimony or likelihood, and statistically testing trees.

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    Molecular Phylogeny Part I

    Uploaded by

    Malabika Bhowmick
    32 views10 pages
    This document discusses molecular phylogeny and how to construct phylogenetic trees from molecular sequence data. It explains that nucleic acids and proteins can be used to infer evolutionary relationships among microorganisms as they retain evidence of evolutionary history. Computer programs are used to estimate relationships based on sequence homology and closely related organisms have fewer differences. The document provides steps for phylogenetic tree construction, including choosing markers, aligning sequences, selecting an evolutionary model, using tree-building methods like maximum parsimony or likelihood, and statistically testing trees.

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    This document discusses molecular phylogeny and how to construct phylogenetic trees from molecular sequence data. It explains that nucleic acids and proteins can be used to infer evolutionary relationships among microorganisms as they retain evidence of evolutionary history. Computer programs are used to estimate relationships based on sequence homology and closely related organisms have fewer differences. The document provides steps for phylogenetic tree construction, including choosing markers, aligning sequences, selecting an evolutionary model, using tree-building methods like maximum parsimony or likelihood, and statistically testing trees.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    32 views10 pages

    Molecular Phylogeny Part I

    Uploaded by

    Malabika Bhowmick
    This document discusses molecular phylogeny and how to construct phylogenetic trees from molecular sequence data. It explains that nucleic acids and proteins can be used to infer evolutionary relationships among microorganisms as they retain evidence of evolutionary history. Computer programs are used to estimate relationships based on sequence homology and closely related organisms have fewer differences. The document provides steps for phylogenetic tree construction, including choosing markers, aligning sequences, selecting an evolutionary model, using tree-building methods like maximum parsimony or likelihood, and statistically testing trees.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 10

    Molecular Phylogeny

    • Phylogenetics is estimating and analysing the


    evolutionary relationships among organisms.
    • We can study morphology, life cycle traits and
    prepare the list of differences and establish
    relationships among organisms.
    • Will we be able to do that while working with
    microbes?
    • We use the ‘information molecules’ to discern
    phylogenetic relationships among
    microorganisms.
    • Nucleic acids and proteins are known as
    ‘information molecules’ as they retain the
    record of evolutionary history of organisms.
    • We compare the nucleic acid or protein
    sequences from different organisms.
    • Computer programs are developed and used
    to estimate the evolutionary relationships
    based on the extent of homology between the
    sequences.
    • Closely related organisms show fewer
    sequence differences than distantly related
    organisms.
    • The sequence of small-subunit of rRNA is
    widely used for this purpose.
    • The sequences from different organism are
    compared and the number of differences can
    be tabulated.
    • The resulting data is finally expressed in the
    form of trees.
    • The position and length of branches can also
    be used to show the relationship between the
    organisms.
    i
    • The trees are mainly of three types

    Image source: google


    Image source: google
    How to proceed for phylogenetic tree construction

    • First, we need to choose the phylogenetic marker. These can be


    gene/ combination of genes or may be DNA region from all the
    organisms we wish to include in the tree.
    • This choice is very crucial. It depends upon how closely or distantly
    related are the organisms we are dealing with.
    • We generally choose conserved DNA region for distantly related
    organisms and exteremely variable regions for closely related
    species.
    • These sequences can be sourced from either the databases or by
    sequencing in the lab.
    • Once we the data, we are ready to do alignment. Hoping you
    remember the various ways to align sequences and multiple
    sequence alignment.
    • Next we need to choose the evolutionary model.
    • This includes parameters like base frequencies, substitution rate
    matrix, gamma distribution.
    • As you know base frequencies are not equal, we cant say each
    base frequency is 25%. Neither can we say its 5% for amino acids.
    • Further, substitution rate is assumed to be equal for each type of
    point mutation. Do you think its logical?
    • Next, we need to choose a method for constructing a
    phylogenetic tree. Maximum Parsimony, Maximum Likelihood
    and Distance Method are some of the most popular methods
    • Finally the tree obtained is tested and evaluated statistically.
    Bootstrap and Jackknife are two most popular methods for this.
    Useful Online Sources
    • https://
    biologia.campusnet.unito.it/didattica/att/313d
    .4334.file.pdf
    • https://www.youtube.com/watch?v=CTrBGyw
    p_nI

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