This document summarizes phylogenetic trees, which are used to study the evolution of species. Phylogenetic trees depict the evolutionary relationships between species and their most recent common ancestors through branching diagrams. Earlier, morphological traits were used to build trees, but now genetic data like DNA, RNA or protein sequences provide more information. Rooted trees represent evolutionary history with a basal node showing the oldest common ancestor, while unrooted trees only show relationships without directionality. Methods to construct trees include sequence alignment and character-based approaches like maximum parsimony, maximum likelihood, and neighbor joining. The document provides examples of phylogenetic trees analyzing SARS-CoV-2 virus evolution and showing that HIV evolved from SIV multiple times.

1. Phylogenetic Tree
A.Bharath Reddy

2. What is
Phylogenetic Tree
• It is a powerful approach in finding evolution
of current day species.
• Scientists gain a better understanding of how
species have evolved while explaining the
similarities and differences among species.

3. • Earlier, morphological traits
were used for assessing
similarities between species
and building phylogenetic
trees.
• Presently, phylogenetics relies
on information extracted from
genetic material such as
deoxyribonucleic acid (DNA),
ribonucleic acid (RNA) or
protein sequences.

4. Overview of
phylogenetic trees
• The species of interest are shown at the tips of the tree's branches.
• Branches themselves connect in a way that represents the evolutionary
history of the species.
• At each branch point lies the most recent common ancestor shared by
all the species descended from that branch point.
• The lines of the tree represent long series of ancestors that extend
from one species to the next.

5. Rooted
• Represents evolutionary history.
• Has a basal node that represents the common ancestor
• Oldest point in the tree is considered the root.
• The direction of the evolutionary time is shown by a rooted tree.
• The study of the entire group of organisms can be done using a
rooted tree.

6. Unrooted
• Tree that lacks common ancestors or A basal node.
• Does not show the origin of the evolution of the groups of interest.
• Relationship between the organism is only shown without the involvement of
the direction of the evolutionary timeline.
• Unrooted phylogenetic tree can be rooted.
• Unrooted phylogenetic tree can be rooted
• Finding an outgroup

7. Methods of Phylogenetic
Tree Construction
• Sequence Alignment
• Character-Based Methods
1. Maximum parsimony
2. Maximum likelihood
3. Neighbour joining
4. UPGMA.
• Distance-Based Method.

8. Evolutionary analysis of the SARS-CoV-2 genomic sequences from the reinfection case.
A. ML phylogenetic tree of all SARS-CoV-2 whole-genome sequences from Brazil. Branches and tips were colored based on
the lineage and sampling location, respectively, following the legend’s color code. Branch supports (aLRT) are presented at
key nodes.
B. Time-scaled Bayesian MCC tree of SARS-CoV-2 P.1 lineage. Tips are colored according to the sampling location

9. Phylogenetics reveals that HIV has evolved from SIV several times. Tree based
on Frontline and Plantier, J., M. Leoz, J.E. Dickerson, F. De Oliveira, F. Cordonnier, V.
Lemée, … and F. Simon. 2009. A new human immunodeficiency virus derived from
gorillas. Nature Medicine 15:871-872.

10. Thank You
A.Bharath Reddy
Msc., Biotechnology.
AIB – Amity Mumbai