Applications of

Phylogenetic
data analysis

By:
Deivanai.K.P(2022402026)
Harshni. K(2022402028)
Phylogenetics (recap):
• The study of the evolutionary history of living organisms using treelike diagrams to represent pedigrees of these
organisms.

• MOLECULAR PHYLOGENTICS :
• The study of evolutionary relationships of genes and other biological macromolecules by analyzing mutations at
various positions in their sequences and developing hypothesIs about the evolutionary relatedness of the
biomolecules.

• Based on the sequence similarity of the molecules, evolutionary relationships between the organisms can often be
inferred.

• Input data: DNA or protein sequences.

• Output data: Phylogenetic tree.

Why phylogenetics?
Find evolutionary ties between species
Find ancestral relationship between organisms
Estimate time of divergence of a group from its
common ancestor.
WORKFLOW :
• Choosing molecular markers: can be nucleotide / protein sequences .
• Performing multiple sequence alignment: t-coffee, MUSCLE .
• Choosing a model of evolution:
1. For nucleotide sequence - Jukes–cantor model ; Kimura two-parameter
model.,TN93, HKY, and GTR ;
2. For protein sequences –PAM or JTT amino acid substitution matrix.
• Determining a tree building method: Distance based ; Character based
method .
• Assessing tree reliability -bootstrapping and jackknifing
SOFTWARES USED IN PHYLOGENETIC
ANALYSIS:
 Mega - Molecular Evolutionary Genetics Analysis
Integrated program that carries out all four steps in a single environment, with a single user interface eliminating the need for interconverting file

formats.

Input data:
sequence or
distance matrix
 APPLICATIONS
To estimate the relationship among the species represented
by those sequences.
Applications
• Understanding the relationships among the sequences themselves without
regard to the host species, inferring the functions of genes that have not
been studied experimentally, and elucidating mechanisms that lead to
microbial outbreaks.

• Reconstructing the ancestral gene sequences from which extant genes.

• Studying the origin and epidemiology of human diseases.

• Inferring the evolution of ecological and behavioral traits through time

APPLICATIONS :
• Classification: Phylogenetics based on sequence data provides us with more accurate descriptions of patterns of
relatedness than was available before the advent of molecular sequencing. Phylogenetics now informs the Linnaean
classification(based on relatedness in obvious physical traits) of new species.

• Forensics: Phylogenetics is used to assess DNA evidence presented in court cases to inform situations, e.g. where
someone has committed a crime, when food is contaminated, or where the father of a child is unknown.

• Identifying the origin of pathogens: Molecular sequencing technologies and phylogenetic approaches can be used
to learn more about a new pathogen outbreak. This includes finding out about which species the pathogen is related
to and subsequently the likely source of transmission. This can lead to new recommendations for public health policy.

• Conservation: Phylogenetics can help to inform conservation policy when conservation biologists have to make
tough decisions about which species they try to prevent from becoming extinct.
Applications
• Cancer studies

Capture important mutational events among different cancer types. Finding

similarities among breast cancer subtypes based on gene data, helps to map
different pathway to classify cancer subtype acc to their mutations.

• Understanding rapidly mutating virus.

• Predict protein, ligand structure  Drug design.

CASE STUDY

Did a patient’s HIV infection result from

an invasive dental procedure performed by
an HIV+ dentist?
THANK YOU !!!