Molecular Clock

• The molecular clock (based on the molecular

clock hypothesis (MCH)) is a technique in
molecular evolution that uses fossil constraints
and rates of molecular change to deduce the
time in geologic history when two species or
other taxa diverged. It is used to estimate the
time of occurrence of events called speciation or
radiation. The molecular data used for such
calculations is usually nucleotide sequences for
DNA or amino acid sequences for proteins. It is
sometimes called a gene clock or evolutionary
clock.
 According to Ayala's 1999 study, 5 factors
combine to limit the application of
molecular clock models:
• 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 (can be avoided
in closely related species by utilizing non-coding DNA
sequences or emphasizing silent mutations)
• Changes in the intensity of natural selection
• Molecular evolution is the process of
evolution at the scale of DNA, RNA, and
proteins.
 Principles of molecular evolution
• Mutations are permanent, transmissible
changes to the genetic material (usually DNA
or RNA) of a cell. Mutations can be caused by
copying errors in the genetic material during
cell division and by exposure to radiation,
chemicals, or viruses, or can occur
deliberately under cellular control during the
processes such as meiosis or hypermutation.
• Mutations are considered the driving force of
evolution, where less favorable (or deleterious)
mutations are removed from the gene pool by
natural selection, while more favorable (or
beneficial) ones tend to accumulate.
Neutral mutations do not affect the organism's
chances of survival in its natural environment and
can accumulate over time, which might result in
what is known as punctuated equilibrium; the
modern interpretation of classic evolutionary
theory.
 Causes of change in allele frequency
• Genetic drift describes changes in gene
frequency that cannot be ascribed to selective
pressures, but are due instead to events that
are unrelated to inherited traits. This is
especially important in small mating
populations, which simply cannot have
enough offspring to maintain the same gene
distribution as the parental generation.
• Gene flow or Migration: or gene admixture is
the only one of the agents that makes
populations closer genetically while building
larger gene pools.
• Selection, in particular natural selection produced by
differential mortality and fertility. Differential mortality
is the survival rate of individuals before their
reproductive age. If they survive, they are then
selected further by differential fertility – that is, their
total genetic contribution to the next generation. In
this way, the alleles that these surviving individuals
contribute to the gene pool will increase the frequency
of those alleles. Sexual selection, the attraction
between mates that results from two genes, one for a
feature and the other determining a preference for
that feature, is also very important.
• Molecular systematics is a product of the
traditional field of systematics and
molecular genetics. It is the process of using
data on the molecular constitution of
biological organisms' DNA, RNA, or both, in
order to resolve questions in systematics, i.e.
about their correct scientific classification or
taxonomy from the point of view of
evolutionary biology.
• Molecular systematics has been made possible
by the availability of techniques for
DNA sequencing, which allow the determination
of the exact sequence of nucleotides or bases in
either DNA or RNA. At present it is still a long and
expensive process to sequence the entire
genome of an organism, and this has been done
for only a few species. However, it is quite
feasible to determine the sequence of a defined
area of a particular chromosome. Typical
molecular systematic analyses require the
sequencing of around 1000 base pairs.
 The driving forces of evolution
• While recognizing the importance of random
drift for silent mutations,[2] selectionists
hypotheses argue that balancing and positive
selection are the driving forces of molecular
evolution. Those hypotheses are often based
on the broader view called panselectionism,
the idea that selection is the only force strong
enough to explain evolution, relaying random
drift and mutations to minor roles.[1]
• Neutralists hypotheses emphasize the
importance of mutation, purifying selection
and random genetic drift.[3] The introduction
of the neutral theory by Kimura,[4] quickly
followed by King and Jukes' own findings,[5] led
to a fierce debate about the relevance of
neodarwinism at the molecular level.
• The Neutral theory of molecular evolution
states that most mutations are deleterious
and quickly removed by natural selection, but
of the remaining ones, the vast majority are
neutral with respect to fitness while the
amount of advantageous mutations is
vanishingly small. The fate of neutral
mutations are governed by genetic drift, and
contribute to both nucleotide polymorphism
and fixed differences between species.[6][7][8]
• Mutationists hypotheses emphasize random
drift and biases in mutation patterns.[9] Sueoka
was the first to propose a modern mutationist
view. He proposed that the variation in GC
content was not the result of positive
selection, but a consequence of the GC
mutational pressure.[10
 Genome Evolution
• Genomic evolution is a set of phenomena
involved in the changing of the structure of a
genome through evolution.
• The study of genome evolution involves
multiple fields such as structural analysis of
the genome, the study of genomic parasites,
gene and ancient genome duplications,
polypoidy, and comparative genomics.
Evolutionary biologists are interested
in five specific questions in regards to
evolution of the genome[13], these are:
• How did the genome evolve into its current size?
• What is the content within the genome, is it
mostly junk or not?
• What is the distribution of genes within a
genome?
• What is the composition of the nucleotides
within the genome?
• How does translation of the genetic code evolve?
 Genome Size
• Genome size is all the DNA that makes the
genome [13]. A genome can consists of genetic
regions and noncoding regions. Genetic
regions are those that encode proteins while
noncoding regions refer to promoters and
junk DNA. The C-value is another term for the
genome size. Within a species the C-value
does not show much variation, but there is a
significant difference in the C-value between
species[13].
 Prokaryotic Genome
• Prokaryotes are unicellular organisms that do
not have membrane-bound organelles and
lack a structurally distinct nucleus. Research
on prokaryotic genomes shows that there is a
significant positive correlation between the C-
value of prokaryotes and the amount of genes
that compose the genome. This indicates that
gene size is the main factor influencing the
size of the genome [1
 Eukaryotic Genome
• In eukaryotic organisms, there is a paradox
observed, namely that the number of genes
that make up the genome does not correlate
with genome size. In other words, the genome
size is much larger than would be expected
given the total number of protein coding
genes.
 Molecular systematics or molecular
phylogenetics.
• An important area within the study of
molecular evolution is the use of molecular
data to determine the correct
biological classification of organisms.
• Tools and concepts developed in the study of
molecular evolution are now commonly used
for comparative genomics and molecular
genetics, while the influx of new data from
these fields has been spurring advancement in
molecular evolution.
 Key researchers in molecular
evolution
• Motoo Kimura — Neutral theory
• Masatoshi Nei — Adaptive evolution
• Walter M. Fitch — Phylogenetic reconstruction
• Walter Gilbert — RNA world
• Joe Felsenstein — Phylogenetic methods
• Susumu Ohno — Gene duplication
• John H. Gillespie — Mathematics of adaptation
• Dan Graur - Neutral models of molecular evolution
• Wen-Hsiung Li - Neutral models of molecular evolution
 Journals
• Journals dedicated to molecular evolution
include Molecular Biology and Evolution,
Journal of Molecular Evolution, and Molecular
Phylogenetics and Evolution. Research in
molecular evolution is also published in
journals of genetics, molecular biology,
genomics, systematics, or evolutionary
biology.
• The Society for Molecular Biology and
Evolution publishes the journal "Molecular
Biology and Evolution" and holds an annual
international meeting.