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Molecular Phylogeny Part I

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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Malabika Bhowmick
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83 views10 pages

Molecular Phylogeny Part I

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.

Uploaded by

Malabika Bhowmick
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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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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