Evolutionary Analysis Significance

1. APPLIED BIOINFORMATICS
Topic: Evolutionary Analysis Significance

2. What is evolution?
• The gradual development of something
especially from a simple to a more complex
form.
OR
• The process by which different kinds of living
organisms are thought to have developed and
diversified from earlier forms during the history
of the earth.

3. Evolution occurs as a result of
following processes:
• Mutation
• Natural selection
• Genetic drift

4. Mutation Genetic drift

5. What is evolutionary analysis?
• Evolutionary analysis is a set of techniques for
studying long term phenotypical evolution.
• It is also called adaptive dynamics.

6. Phylogenetic analysis has two major
components:
1. Phylogeny inference or “tree building”
The inference of the branching orders, and
ultimately the evolutionary relationships,
between “taxa” (entities such as genes,
populations, species, etc.)
2. Character and rate analysis
Using phylogenies as analytical frameworks
for rigorous understanding of the evolution of
various traits

7. Phylogenetic analysis involves :
• Organismal relationships
• Gene/Protein relationships

8. Organismal relationships
• Improving our understanding of organismal
relationships

9. Gene/Protein relationships
Homolog, ortholog, paralog

10. • Homologs: Have common origins but may or may
not have common activity.
• Orthologs: Homologs produced only by speciation.
They tend to have similar function.
• Paralogs: Homologs produced by gene duplication.
They tend to have differing functions.

11. PHYLOGENETIC DATA ANALYSIS:
A straightforward phylogenetic analysis consists of
four steps:
• 1. Alignment (both building the data model and
extracting a phylogenetic dataset)
• 2. Determining the substitution model
• 3. Tree building
• 4. Tree evaluation

12. 1. Alignment of Sequences
VTISCTGSSSNIGAG-NHVKWYQQLPG
VTISCTGTSSNIGS--ITVNWYQQLPG
LRLSCSSSGFIFSS--YAMYWVRQAPG
LSLTCTVSGTSFDD--YYSTWVRQPPG
PEVTCVVVDVSHEDPQVKFNWYVDG--
ATLVCLISDFYPGA--VTVAWKADS--
AALGCLVKDYFPEP--VTVSWNSG---
VSLTCLVKGFYPSD--IAVEWESNG--
The sole purpose of
multiple sequence
alignments is to
place homologous
positions of
homologous
sequences into the
same column.

13. 2. Determining the substitution model
• Substitution at amino acids and base pairing
level takes place.
• After determining the substitution model tree
building occurs.

14. 3. Tree building

15. 4. Tree Evaluation
• Evaluation of tree helps in understanding the
relationship between organisms.
• In this step we interpret the results by
studying the evolutionary trees.

16. Significance of phylogenetic analysis
• How genes, genomes and species evolve?
• How sequences came to be the way they are
today?
• General principles that enable us to predict
how they will change in the future?

17. Significance in various fields
• Classification
• Forensics
• Identifying the origion of pathogens
• Conservation
• Bioinformatics and computing

18. Phylogenetic Analysis Significance in
Classification
• Phylogenetic analysis based on sequence data
provides us more accurate description of
relatedness than was available before advent of
molecular sequencing.

19. Phylogenetic Analysis Significance in
Forensics
• Phylogenetic analysis is used to access DNA
evidence presented in court cases.

20. Significance in Identifying the origion of
pathogens
• Can be used to learn more about a new
pathogen outbreak.
• This includes finding about which species the
pathogen is related.
• Likely source of transmission.

21. Phylogenetic Analysis Significance in
Conservation
• Phylogenetic analysis can help to inform
conservation policy when conservation
biologists have to make tough decisions about
which species they try to prevent from
becoming extinct.

22. Significance in Bioinformatics and
computing
• Many of the algorithms developed for
phylogenetic analysis have been used to
develop software in other fields.