MOLECULAR
CLOCK
ANAMIKA R V
MSC ZOOLOGY
MAR IVANIOS COLLEGE
TRIVANDRUM
MOLECULAR CLOCK
Molecular clock is a tool used to analyze the timing
of evolutionary events
The concept of molecular clock was first put
forward by Linus Pauling and Emile Zuckerkandl in
1962 on the basis of empirical observations
It received theoretical backing when Motoo Kimura
developed the neutral theory of evolution
NEUTRAL THEORY
The theory was proposed by Motoo Kimura in 1968
In 1968, Kimura postulated that the majority of molecular changes
in evolution are due to the random fixation of neutral or nearly
neutral mutations .
At the molecular level the majority of evolutionary changes and
much of the variability within species are caused neither by
positive selection of advantageous alleles nor by balancing
selection , but by random genetic drift of mutant alleles that are
selectively neutral (or nearly so).
Neutral mutations are those that does not affect an organism`s
How does the molecular clock work?
A molecular clock works by analyzing biomolecular
data, such as the number of changes or substitutions
in nucleotide sequences of DNA and RNA, or the
amino acid sequence of proteins. Assuming that the
nucleotide or amino acid sequences mutate at a
constant rate, the number of substitutions over time
is equivalent to the evolutionary rate.
The concept of molecular clock suggests that the
steady rate of change in nucleotide sequences in
DNA / gene over time leads to evolutionary
divergence between organisms.
This provides a basis for estimating time of
divergence of their lineages.
The more early in the past an ancestral stock
diverged into present day species, the more
changes get accumulated in the amino acid
sequences of the protein in two contemporary
species.
The greater is the number of mutational difference
It means the number of amino acid modifications
in the line of descent can be used as a measure of
time of the divergence of two species from a
common ancestor.
The molecular clock / evolutionary clock at
molecular level determines the rate at which
many mutations become fixed.
The molecular clock hypothesis(MCH) states that
DNA and Protein sequences evolve at a rate that
is relatively constant over time and among
different organisms
A direct consequence of this constancy is that the
genetic difference between any two species is
proportional to the time since these species last
shared a common ancestor
The clock establishes the time frame for evolution,
and helps to identify the methods of molecular
evolution
The molecular clock ( based on MCH) is a technique
in molecular evolution that uses fossil constraints
and rates of molecular change to deduce the time
in geological history when two species or other
taxa diverged
or
It is a technique that uses the mutation rate of
biomolecules to deduce the time in prehistory
when two or more life forms diverged
The biomolecular data used for such calculations
are usually nucleotide sequences for DNA or amino
acid sequences for proteins
It is sometimes called Gene clock or Evolutionary
EVIDENCES FROM MOLECULAR RECORDS
According to evolutionary theory, every evolutionary
change involves the substitution of a new gene for the
old one and the new allele arises from the old one by
mutation.
Continuous accumulation of change in the DNA coding
for proteins leads to evolutionary differences.
The organism that are more distantly related
accumulate a greater number of evolutionary
differences while two species that are more closely
related share a greater portion of their DNA .
The pattern of divergence is clearly seen in human
Highly conserved protein like heamoglobin and
cytochrome c provide the best example of molecular
clock , determining the rate of evolution and trace of
evoultionary relationship between different groups .
Though all proteins appear to accumulate changes in
the amino acid sequence overtime , the rate of
accumulation of changes / mutations in different
protein is different .
Therefore proteins evolve at very different rates.
The accumulation of molecular changes in proteins at
a constant rate due to changes in the nucleotide
MOLECULAR HOMOLOGY AS SEEN IN MOLECULAR
STRUCTURE OF HEAMOGLOBIN
Heamoglobin is formed of two identical alpha and beta
chains of polypeptide. Each alpha chain is formed of 141
amino acids and each beta chain of 146 amino acids.
Chimpanzees, Gorilla , Orangutans and Macaques that are
closely related to humans , have fewer differences from
humans in amino acids of beta chain of heamoglobin than
from the distantly realted mammals like Dogs .
The heamoglobin of non mammalian vertebrates differs
even more and the non vertebrates heamoglobin has much
more different composition.
molecular evolution of cytochrome c
Cytochrome c is the respiratory pigment in all eukaryotic
cells.
It forms a part of electron transport system and accepts
electrons from H+ ions in all eukaryotes. it is formed of 104
amino acids.
Cytochrome c is a protein that has evolved at a constant
rate.
When a graph is plotted between the time since each pair of
The molecular clock shows a
linear relationship.
The x axis shows evolutionary
time since the species
diverged.
The y axis show the number of
change in nucleotide
sequences between
homologous chromosomes
between two species.
The diagram shows that longer is the time of
seperation of two groups, the larger is the number
of nucleotide substitutions in their genes for
cytochrome c. for example
In chimpanzees and human , cytochrome c genes
are identical
In human and kangaroo, there is substitution of
nucleotide in a period.
In human and cow , the substitution is about 75
nucleotides during the period of 120 million years
Molecular clocks are typically used in phylogenetic
analysis, which aim to reconstruct evolutionary trees
that shows the relationships among species of
interest
When estimating evolutionary timescales, the
molecular clock needs to be calibrated
Calibration done by assigning an absolute age to one
or more nodes in the phylogeny, which can then act
as a reference point for estimating the ages of the
remaining nodes (nodes in the tree represent
evolutionary divergent events)
MOLECULAR CLOCK CALIBRATION
Rate of nucleotide changes between species is
determined with
a. When the ancestor diverged into two species.
b. Fossil records
Following equation is then used
The amount of differences in nucleotides divided by
the years since the two species emerged from the
common ancestor.
For example, let us assume that
the rate of substitution for the
alpha chain of hemoglobin is
0.56 x 10-9 substitutions per site
per year, and that alpha- globins
from rat and human differ by
0.093 substitutions per site.
Then, under the molecular clock
hypothesis, the divergence time
between the human and rat
lineages is estimated to be
approximately
0.093/(2 x 0.56 x 10-9) = 80
Molecular clock is useful for obtaining
evolutionary information when you have little or
no fossil record.
For example: fungi, which are soft and squishy,
don’t make fossil well.
But we can take the rate of change of genes from
vertebrates or plants, which have a decent fossil
record, and apply it to the unknown group
ASSUMPTIONS OF MOLECULAR CLOCK
1. The mutations at molecular level are incorporated at
fixed or regular rates over a time.
2. The fixation of molecular mutations does not occur on
their adaptive or selective value but on a fixed rate.
3. The proportional rate of fixation of mutation in one gene
relative to the rates of fixation of mutation in other genes
remain same throughout any line of descent
4. The lines of descent leading from a common ancestor to
all its descendants have similar rates of fixed mutation
FACTORS AFFECTING
Changing generation times (if the rate of
new mutations depends at least partly on
the number of generations rather than the
number of years)
Population size(Genetic drift is stronger in
small populations, and so more mutations
are effectively neutral)
Species-specific differences(due to differing
metabolism, ecology, evolutionary
history.......)
Change in function of the protein studied
SIGNIFICANCE
Molecular clock is an important tool in molecular
systematics
It uses the information from molecular genetics to
determine the correct scientific classification of organisms
It is used to estimate the time of occurrence of events
called speciation or radiation
Establishing the dates of phylogenetic events such as
diverging of living taxa
Helpful in those taxon where no fossil records available
Formation of the phylogenetic tree
The use of multiple genes may improve estimates
PROBLEMS WITH MOLECULAR CLOCK
The molecular clock does not run as smoothly as
neutral theory predicts
Irregularities result from natural selection in which
some DNA changes are favoured over others
Estimates of evolutionary divergences older than the
fossil records have a high degree of uncertainty
Using molecular clock , it was estimated that two
species A & B must have diverged from their
common ancestor about 9 * 10^6 years ago . If
the rate of divergence per base pair is estimated
to be 0.0015 per million years , what is the
proportion of base pairs that differ between the
two species now ?
a. 0.0270
b. 0.0135
c. 0.00017
d. 0.0035
REFERENCE
EVOLUTIONARY GENETICS AND CASE STUDIES
CHARLES W.FOX,JASON .B.WOLF
OXFORD UNIVERSITY PRESS,2006
FUNDAMENTALS OF MOLECULAR EVOLUTION
DAN GRAUR AND WEN HSIUNG LI
SINAUER ASSOCIATES,SECOND EDITION
EVOLUTION AN INTRODUCTION
STEPHEN C.STEARNS AND ROLF F.HOEKSTRA
OXFORD UNIVERSITY PRESS,2000
ORGANIC EVOLUTION
VEERBALA RASTOGI
MED TECH SCIENTIFIC PRESS,14 th EDITION
