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
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