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Module 6 - Session - 1

This document provides an introduction to molecular evolution and phylogenetics as part of an online bioinformatics course. It discusses the history of molecular evolution, mechanisms of evolutionary change including mutation, genetic drift, gene flow and natural selection. It also covers the neutral theory of molecular evolution, the molecular clock hypothesis, and how new species arise through the process of speciation. The overall goal is to understand molecular evolution at the sequence level and use molecular data to study evolutionary relationships between organisms.

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Mohamed Ali Abdi
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© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
20 views

Module 6 - Session - 1

This document provides an introduction to molecular evolution and phylogenetics as part of an online bioinformatics course. It discusses the history of molecular evolution, mechanisms of evolutionary change including mutation, genetic drift, gene flow and natural selection. It also covers the neutral theory of molecular evolution, the molecular clock hypothesis, and how new species arise through the process of speciation. The overall goal is to understand molecular evolution at the sequence level and use molecular data to study evolutionary relationships between organisms.

Uploaded by

Mohamed Ali Abdi
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Introduction to Bioinformatics Online Course : IBT

Molecular Evolution &


phylogenetics
Introduction, History, Mechanism of evolution, Neutral
theory, Molecular clock and Speciation

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Learning Objectives

● Know about the history of molecular evolution thoughts


● Understand the mechanism of evolution
● Understand the concept of molecular evolution
● Understand the neutral theory of evolution
● Understand molecular clock
● Learn how species result from speciation

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
What is Molecular evolution

● Is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and
proteins across generations.
● The field of molecular evolution uses evolutionary biology and population genetics principles to explain
patterns in these changes.
● Evolution at a molecular level is observable at the base (nucleotide) level changes in the DNA and amino
acid changes in proteins
● Molecular evolution addresses two broad range of questions:
1) Use DNA to study the evolution of organisms, e.g population structure, geographic variation and
phylogeny
2) Use different organisms to study the evolution of the process of DNA

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
History of molecular evolution
● The history of molecular starts in the early 20th century with “comparative biochemistry”, but the field of
molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology.

● The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence
comparison, and to use the differences between homologous sequences as a molecular clock to
estimate the time since the last common ancestor.

● In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular
clock.

● After the 1070s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly
conserved ribosomal RNA sequences, the foundation of reconceptualization of the early history of life.

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Mechanism of Evolutional change
The forces that drive evolution changes are as follows

● Mutation

● Genetic drift

● Gene flow

● Natural selection

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Mutation
● A mutation is any change in a gene sequence that can be passed on to offspring.

● Mutations are stochastic and typically occur randomly across genes.

● Most mutations are deleterious, or neutral; i.e. they can neither harm nor benefit, but can also be
beneficial sometimes.

● Not all mutations matter to evolution e.g. somatic mutations.

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Genetic Drift

● Genetic drift is the change of allele frequencies from one generation to the next due to stochastic
effects of random sampling in finite populations.

● They happen by chance in nature

● some alleles are completely lost within the population

● Effect of genetic drift is larger in small populations and smaller in larger populations

● Two examples of random drift are population bottleneck and founder effect which can have
significant effects in a small population

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Population Bottleneck
● This occurs when a sudden sharp decline in a population’s size is typically due to environmental factors from
natural disasters to disease to geographic isolation.
● A random event where genes are extinguished from a population.
● It results in a drastic reduction of the total genetic diversity of the original gene pool

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Founder effect
● The loss of genetic variation occurs when a new population is established by a small number of
individuals cleaved from a larger population.
● It leads to a loss of genetic variability.

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Gene flow
● Geen flow is any movement of individuals, and/or the genetic material they carry, from one
population to another.
● It may change frequency and /or the range of alleles in the populations.

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Natural selection
● Natural selection leads to an evolutionary change when some individuals with certain traits in the
population have higher survival and reproductive rate than others and pass on these inheritable
genetic features to their offspring.

● It has often been called a "self-evident" mechanism because it necessarily follows from three simple
facts:
Heritable variation exists within populations of organisms.
Organisms produce more offspring than can survive.
These offspring vary in their ability to survive and reproduce.

● The cumulative effects of natural selection operate by differential reproductive success (fitness) of
individuals.

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
The Darwin’s Finches diagram illustrates the way the finch has adapted to take advantage
of feeding in different ecological niches

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Neutral Theory of Molecular Evolution
● Motoo Kimura (1968)

The vast majority of molecular differences are selectively neutral

Most evolutionary change is the result of genetic drift acting on neutral alleles

● 1968-69

The Neutral theory states that evolution is at the level of the DNA and proteins, but not at the level of adaption or natural selection.

The neutral theory of Motoo Kimura states that many mutations have such a small effect on the fitness of an organism that they can be

considered “neutral”

● Most of the genetic variation in populations is the result of mutation and genetic drift and not selection.

● Many amino acids in protein can be exchanged for other amino acids with similar biochemical properties, with negligible impact

on the overall function or structure.

● The rate of genetic change per generation is a result of species with shorter generations that tend to evolve more quickly per unit

time.
Introduction to Bioinformatics Online Course: IBT:
Molecular evolution & Phylogenetics
Molecular clock Hypothesis
● Molecular clock is proposed in year 1960s by Zuckerkandl and Pauling

● Molecular clock hypothesis states that DNA and protein sequences evolve at a rate
that is relatively constant over time and among different organisms.

● It estimates evolutionary rates and time scales using data from DNA or protein.

● Genetic difference between any two species is proportional to the time since they
shared a common ancestor.

● Traditionally such inferences were made from the fossil record, coupled with
radiometric dating.

● It is used in phylogenetic analyses, which aim to reconstruct evolutionary trees that


show the relationships among species of interest.

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
Speciation
● Species: A group of similar organisms that can breed with each other and produce fertile offspring. New species
can arise as a result of genetic variation, natural selection and speciation.

● Speciation: The formation of new species from a common ancestor. It is a lineage-splitting event that produces two or
more separate species

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics
How does speciation occur?

Introduction to Bioinformatics Online Course: IBT:


Molecular evolution & Phylogenetics

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