Lecture 14 - Molecular Phylogeny- Introduction | Bioinformatics - Botany PDF Download

 Page 1


Molecular Phylogeny- Introduction 
 0 
  
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: Molecular Phylogeny- Introduction 
Lesson Developer: Shailendra Goel 
College/ Department: Department of Botany, University of Delhi 
Page 2


Molecular Phylogeny- Introduction 
 0 
  
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: Molecular Phylogeny- Introduction 
Lesson Developer: Shailendra Goel 
College/ Department: Department of Botany, University of Delhi 
Molecular Phylogeny- Introduction 
 1 
Table of Contents       
 
Chapter: Molecular Phylogeny 
Introduction  
How to generate trees 
Positive and negative selection 
Understanding Trees 
Cladograms vs Phylograms 
Rooted vs Unrooted trees 
Tree Terminology 
Methods of Phylogenetic reconstruction 
Distance Method 
UPGMA distance based method 
Neighbor joining method 
Statistical methods of phylogeny 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
Page 3


Molecular Phylogeny- Introduction 
 0 
  
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: Molecular Phylogeny- Introduction 
Lesson Developer: Shailendra Goel 
College/ Department: Department of Botany, University of Delhi 
Molecular Phylogeny- Introduction 
 1 
Table of Contents       
 
Chapter: Molecular Phylogeny 
Introduction  
How to generate trees 
Positive and negative selection 
Understanding Trees 
Cladograms vs Phylograms 
Rooted vs Unrooted trees 
Tree Terminology 
Methods of Phylogenetic reconstruction 
Distance Method 
UPGMA distance based method 
Neighbor joining method 
Statistical methods of phylogeny 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
Molecular Phylogeny- Introduction 
 2 
 
 
Introduction 
Mutation is the basis of evolution driven by the process of selection. All life forms are 
expected to be part of a tree of life, which should be able to explain their origin and 
evolution. Practically, this may not happen due to extinction of species and further 
complications arising from ways by which organisms can acquire genes (e.g. lateral transfer 
of genes). Phylogenetics exploits available comparative information to generate trees, which 
can explain evolution. Traditionally morphological features were used to compare data and 
generate trees. More recently molecular sequences are used for comparisons among 
species, helping in defining species, families and other taxa, hence named as “Molecular 
Phylogeny”. 
 
How to generate trees 
Trees are generated by comparing traits among organisms. For classical phylogeny these 
traits are morphological traits but for molecular phylogeny we can use DNA, RNA or protein 
sequence data. As a general rule DNA has more phylogenetic information as compared to 
proteins. Proteins are derived through triplet code, in which third bases follow the “wobble 
hypothesis” leading to loss of phylogenetic information. DNA sequences comprise coding 
and non-coding regions that have differing rates of evolution. The rate of evolution also 
depends on the type of organism. 
Comparison of sequences can only be done after aligning them. Without alignment it is very 
difficult to decide which nucleotide/amino acid should be compared with which one 
(homology). Proteins show two types of changes- synonymous and non-synonymous. A 
synonymous change does not result in change in the coded amino acid. 
 
Positive and negative selection 
 
Traditionally, any change which is favored by natural selection is called positive selection. It 
is favored by natural selection because it helps in the survival of organism. Similarly, any 
trait which is not favored by natural selection is normally eliminated and is called negative 
selection. 
Page 4


Molecular Phylogeny- Introduction 
 0 
  
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: Molecular Phylogeny- Introduction 
Lesson Developer: Shailendra Goel 
College/ Department: Department of Botany, University of Delhi 
Molecular Phylogeny- Introduction 
 1 
Table of Contents       
 
Chapter: Molecular Phylogeny 
Introduction  
How to generate trees 
Positive and negative selection 
Understanding Trees 
Cladograms vs Phylograms 
Rooted vs Unrooted trees 
Tree Terminology 
Methods of Phylogenetic reconstruction 
Distance Method 
UPGMA distance based method 
Neighbor joining method 
Statistical methods of phylogeny 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
Molecular Phylogeny- Introduction 
 2 
 
 
Introduction 
Mutation is the basis of evolution driven by the process of selection. All life forms are 
expected to be part of a tree of life, which should be able to explain their origin and 
evolution. Practically, this may not happen due to extinction of species and further 
complications arising from ways by which organisms can acquire genes (e.g. lateral transfer 
of genes). Phylogenetics exploits available comparative information to generate trees, which 
can explain evolution. Traditionally morphological features were used to compare data and 
generate trees. More recently molecular sequences are used for comparisons among 
species, helping in defining species, families and other taxa, hence named as “Molecular 
Phylogeny”. 
 
How to generate trees 
Trees are generated by comparing traits among organisms. For classical phylogeny these 
traits are morphological traits but for molecular phylogeny we can use DNA, RNA or protein 
sequence data. As a general rule DNA has more phylogenetic information as compared to 
proteins. Proteins are derived through triplet code, in which third bases follow the “wobble 
hypothesis” leading to loss of phylogenetic information. DNA sequences comprise coding 
and non-coding regions that have differing rates of evolution. The rate of evolution also 
depends on the type of organism. 
Comparison of sequences can only be done after aligning them. Without alignment it is very 
difficult to decide which nucleotide/amino acid should be compared with which one 
(homology). Proteins show two types of changes- synonymous and non-synonymous. A 
synonymous change does not result in change in the coded amino acid. 
 
Positive and negative selection 
 
Traditionally, any change which is favored by natural selection is called positive selection. It 
is favored by natural selection because it helps in the survival of organism. Similarly, any 
trait which is not favored by natural selection is normally eliminated and is called negative 
selection. 
Molecular Phylogeny- Introduction 
 3 
Similar kind of selection also operates for molecular sequences. It is common among genes 
to go through duplication. A duplicated copy of gene is free to undergo mutation and create 
variation. This variation goes through positive/negative selection and often leads to 
neofunctionalization, leading to new genes with new functions.   
Understanding Trees 
Cladograms vs Phylograms 
Trees fall under two categories – Cladogram and Phylogram. Cladogram just provide the 
information about relationship between different organisms while phylograms also provide a 
measure of the amount of evolutionary change, as seen in the branch-lengths. Due to this 
fact, branch length has no meaning in cladograms while it has meaning in phylograms. 
 
 
 
Figure: Phylogram    Figure: Cladogram 
 Source: Author                             Source: Author 
 
 
 
 
Rooted vs Unrooted trees 
The root in a tree denotes the ultimate common ancestor and provides direction in time. At 
times, it is not possible to have this information hence there are both types of algorithms 
available- those we do apply a common ancestor hypothesis and those we does not. A 
Page 5


Molecular Phylogeny- Introduction 
 0 
  
 
 
 
 
 
 
 
 
Subject: Bioinformatics 
Lesson: Molecular Phylogeny- Introduction 
Lesson Developer: Shailendra Goel 
College/ Department: Department of Botany, University of Delhi 
Molecular Phylogeny- Introduction 
 1 
Table of Contents       
 
Chapter: Molecular Phylogeny 
Introduction  
How to generate trees 
Positive and negative selection 
Understanding Trees 
Cladograms vs Phylograms 
Rooted vs Unrooted trees 
Tree Terminology 
Methods of Phylogenetic reconstruction 
Distance Method 
UPGMA distance based method 
Neighbor joining method 
Statistical methods of phylogeny 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
Molecular Phylogeny- Introduction 
 2 
 
 
Introduction 
Mutation is the basis of evolution driven by the process of selection. All life forms are 
expected to be part of a tree of life, which should be able to explain their origin and 
evolution. Practically, this may not happen due to extinction of species and further 
complications arising from ways by which organisms can acquire genes (e.g. lateral transfer 
of genes). Phylogenetics exploits available comparative information to generate trees, which 
can explain evolution. Traditionally morphological features were used to compare data and 
generate trees. More recently molecular sequences are used for comparisons among 
species, helping in defining species, families and other taxa, hence named as “Molecular 
Phylogeny”. 
 
How to generate trees 
Trees are generated by comparing traits among organisms. For classical phylogeny these 
traits are morphological traits but for molecular phylogeny we can use DNA, RNA or protein 
sequence data. As a general rule DNA has more phylogenetic information as compared to 
proteins. Proteins are derived through triplet code, in which third bases follow the “wobble 
hypothesis” leading to loss of phylogenetic information. DNA sequences comprise coding 
and non-coding regions that have differing rates of evolution. The rate of evolution also 
depends on the type of organism. 
Comparison of sequences can only be done after aligning them. Without alignment it is very 
difficult to decide which nucleotide/amino acid should be compared with which one 
(homology). Proteins show two types of changes- synonymous and non-synonymous. A 
synonymous change does not result in change in the coded amino acid. 
 
Positive and negative selection 
 
Traditionally, any change which is favored by natural selection is called positive selection. It 
is favored by natural selection because it helps in the survival of organism. Similarly, any 
trait which is not favored by natural selection is normally eliminated and is called negative 
selection. 
Molecular Phylogeny- Introduction 
 3 
Similar kind of selection also operates for molecular sequences. It is common among genes 
to go through duplication. A duplicated copy of gene is free to undergo mutation and create 
variation. This variation goes through positive/negative selection and often leads to 
neofunctionalization, leading to new genes with new functions.   
Understanding Trees 
Cladograms vs Phylograms 
Trees fall under two categories – Cladogram and Phylogram. Cladogram just provide the 
information about relationship between different organisms while phylograms also provide a 
measure of the amount of evolutionary change, as seen in the branch-lengths. Due to this 
fact, branch length has no meaning in cladograms while it has meaning in phylograms. 
 
 
 
Figure: Phylogram    Figure: Cladogram 
 Source: Author                             Source: Author 
 
 
 
 
Rooted vs Unrooted trees 
The root in a tree denotes the ultimate common ancestor and provides direction in time. At 
times, it is not possible to have this information hence there are both types of algorithms 
available- those we do apply a common ancestor hypothesis and those we does not. A 
Molecular Phylogeny- Introduction 
 4 
common way to decide the root of tree is by using an outgroup. An outgroup is a taxon 
from a group closely related to the ingroup, which includes the taxa under study. 
Another way to identify the root is to use midpoint as the rooting point for the longest 
branch. 
 
 
 
 
Figure: Midpoint Rooted Tree    Figure: Outgroup rooted tree 
Source: Author                                                              Source: Author 
 
Tree Terminology 
Trees can be described based on branches and nodes. Terminal branches represent 
Operational Taxonomic Unites (OTU’s). When two branches are connected, it results in 
internal nodes. When two terminal branches are directly connected to each other, they are 
called sister branches.