Introduction to Bioinformatics Online Course : IBT

Molecular Evolution &

Phylogenetic

Introduction: Phylogeny, aspect of phylogenies,

interpreting tree and pattern of relatedness

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
 Learning Objectives

● Understand a basic introduction to the field of phylogenetics, with an

emphasis on how to read and interpret phylogenetic trees.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Introduction to Phylogenetics

● Phylogenetics is the study of evolutionary relationships.

● Relationships are illustrated by Phylogenetic tree and phylogeny inference
● Phylogenetic trees are reconstructed by looking at the nucleotide or protein sequences and combining
this with our understanding of sequence evolution, which is described using an evolutionary model.
● This enables to infer evolutionary events that happened in the past and also provides more
information about the evolutionary processes operating on sequences.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Phylogeny
● A phylogeny, also known as a tree, is an explanation of how sequences evolved, their
genealogical relationships, and how they came to be the way they are today.

● One of the first sketches of a phylogenetic tree was made by Charles Darwin. This famous diagram
is one of his earlier sketches from a series of notes that he used to develop the idea.

Figure 3 Sketch by Charles Darwin using the metaphor of a tree to

represent evolutionary
Introductionrelationships.
to Bioinformatics Online Course: IBT:
Molecular evolution & Phylogenetics
A true tree

● The case of a family tree is a rare example where we typically know part of the true biological tree; it
has a complete explanation of the genealogical relationships among family members. This is
because,
1) all of the ancestors and descendants who are or ere recently living;
2) the identities of the biological parents of each child

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Family Tree

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Aspects of phylogenies

• Topology
• Branches
• Nodes
• Tips
• Internal nodes
• Root

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Topology
● The topology is the branching structure of the tree.
● It indicates patterns of relatedness among taxa,

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
 Branches
● Branches show the path of transmission of genetic information from one generation to the next.

● Branch lengths indicate genetic change i.e. the longer the branch, the more genetic change (or
divergence) has occurred.

● The extent of genetic change are measured by estimating the average number of nucleotide or protein
substitutions per site.

● Informative branch lengths are typically drawn to scale and indicate the number of substitutions per site

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Nodes
● Nodes are the points at the ends of branches that represent sequences or hypothetical sequences at
various points in evolutionary history.

● The tips or external nodes: The sequences that are sampled and used to construct phylogeny occur
on single terminal branches, known as the tips or external nodes.

● Internal nodes: Internal nodes occur at the points where more than one branch meets and represent
the (usually inferred) ancestral sequences.

● The root: The root is a very important internal node representing the most recent common ancestor
of all sequences in the phylogeny.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Root

● The root is the most recent common ancestor of all of the taxa in the tree.
● It’s the oldest part of the tree and tells the direction of evolution, with the flow of genetic information
moving from the root, towards the tips with each successive generation.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Tree terminology

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Rooted vs unrooted trees
● Rooted tree. Has a root that denotes common ancestry
● Unrooted tree. Only positions the individual taxa relative to each other without indicating the

direction of the evolutionary process.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
How to estimate genetic change

Human A T G T T G A C T C
Rat A T G C T G A C T C

there is one site that is different between the two sequences, and we could say that based on this tiny sample
there are 1/10 = 0.1 substitutions per site.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Understanding phylogenetic tree
● The root of tree represents an ancestral lineage
● Tips of the branches represent the descendants of that ancestor
● Time moves upward direction from Root to tips

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
● Lineage splits (speciation) represented as branching
● When speciation occurs, ancestral lineage gives rise to two or more daughter lineages

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
● Phylogenies trace patterns of shared ancestry between lineages.
● Each lineage has part of its history, unique to it alone and part are shared with other
lineages.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
● Each lineage has ancestors unique to that lineage and ancestors that are shared with other lineages
–common ancestors

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
● A clade is grouping a common ancestor and all the descendants (living and extinct) of that ancestor.

● Clades are nested within one another: they form a nested hierarchy

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
Relating distance, Rate and Time
● Evolutionary rate and time are confounded
● The genetic change is calculated by a combination of the rate of substitution and the time that has
elapsed

Genetic change = Evolutionary rate x Divergence time

(substitutions/site) (substitutions/site/year) (years)

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics
 Interpreting patterns of relatedness
● The key is tracing back to the point in the tree where taxa shared their most recent common ancestor
(MRCA).
● It relies on a tree being rooted because it defines the direction of evolution and therefore what is the
more recent in evolutionary time
● If branches are rotated to change the topology of the tree, then the tree has the same biological
meaning and evolutionary relationships.

Introduction to Bioinformatics Online Course: IBT:

Molecular evolution & Phylogenetics