Evolution

Gareth2.Robinson@uwe.ac.uk

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Introduction
• Current views on microbial
evolution.
• The universal phylogenetic
tree – what is it and how is
it constructed?
• What makes a good
evolutionary chronometer?

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Origin of life
• Radio-dating – Earth est. 4.6 thousand million years
old.
• Conditions too harsh for ~100 million years.
• Bombardment by meteorites decreased; liquid water
appeared.
• Geological activity released gases to form the atmosphere.
• First life on Earth - fossils of prokaryotic cells
dated at 3.5 to 3.8 thousand million years old
• Were likely to be anaerobic and thermophilic.
• Fossil record from Swartkoppie chert and Archaeon
Apex chert.

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Life over geological
time

Eukaryotic expansion

Aerobic bacteria and

Nitrifying/denitrifying bacteria (2.4 bn)
Oxygenic cyanobacteria
(2.8 bn)

Anoxygenic photosynthetic
Bacteria (3.4 bn)
Anaerobic prokaryotes
(3.8 bn)
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The RNA world

• In modern cells, three molecules fulfil the roles of catalysts,

structural molecules and hereditary molecules.
• Proteins (enzymes) are catalytic.
• Other proteins are structural.
• DNA stores hereditary information to be passed to the next generation.
• RNA converts the information stored in DNA into protein.
• Any evolutionary hypothesis must account for the evolution of
DNA, RNA and protein.

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The modern cell
• Proteins do cellular work.
• Their synthesis depends on
DNA, RNA and other protein.
• DNA stores information but
can’t do cellular work.
• RNA is synthesised from a
DNA template using proteins
as catalysts.

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RNA: The first self-replicating entity

• Proteins perform cellular work but can’t

replicate.
• The opposite is true for DNA.
• In 1981 a self-splicing RNA molecule was
discovered in the protozoan Tetrahymena.
• 3 years later an RNA molecule was discovered in
E. coli that cleaves phosphodiester bonds
(RNaseP).
• RNA molecules with catalytic activity are
called ribozymes.
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The evolution of metabolism

• Early earth was hot and anoxygenic.

• Cells that arose must have been able to use the available resources.
• Archaea living today are tolerant if high temperature and use FeS as an
energy source.
• Oxygenic photosynthesis thought to have arisen in cyanobacteria
~2.5 bn years ago.
• Evolution of life video.

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Oxygen accumulation
• Oxygenic photosynthesis
evolved in cyanobacteria.
• Accumulation of oxygen in
environment gradually built up
to 20% (oxidising
environment).
• Formation of ozone layer.
• Lead to evolution of eukaryotic
microorganisms.
• Endosymbiont evolution of
mitochondria and chloroplasts.
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Endosymbiosis

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Microbial Phylogeny
• Phylogeny = evolutionary
history.
• Prokaryotes have been
evolving for thousands of
millions of years.
• Vast number of different
species.
• How can you sort out
evolutionary relationships?
• What can you use as an
evolutionary chronometer?
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Choosing the right chronometer

• Molecule used must be universally present in all organisms.

• Must be functionally homologous in all organisms (identical

function).

• Must be able to align molecules from different organisms (for

direct comparison).

• Must change sequence very slowly and be independent of

selection.
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Carl Woese

• Pioneered use of 16S rRNA as a phylogenetic tool.

• Revolution in bacterial phylogenetic classification.
• 70S ribosome has 3 rRNA molecules.
• Ancient molecules, functionally constant, universally
distributed, well conserved.
• 16S rRNA has approx 1500 nucleotides.
• Many sequences involved in ‘scaffolding’, so
conserved.
• In between, the sequence will change slowly (no
selection).
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rRNA from different organisms

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Constructing a phylogenetic tree 1

• Easy to isolate and sequence

rRNA molecules.

• Give ‘signature sequences’ -

retained by a closely related
group.

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Constructing a
phylogenetic tree 2

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Major discovery using 16S rRNA - Universal tree of life shows 3
domains

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Universal Phylogenetic Tree
• Bacteria (prokaryotic)
• Archaea (prokaryotic)
• Eukarya (eukaryotic: 18S
rRNA)
• Tree generated by distance
matrix method
• Two rRNA sequences aligned
and evolutionary distance (ED)
calculated.

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An alternative model
• The Norman Pace model of
the Universal Phylogenetic
Tree.
• Root close to the centre.
• The data suggests that the
LUCA should be placed at the
root.

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The Root of the Universal Phylogenetic Tree

• Root of tree is on earliest region of bacterial branch.

• Root is considered to be the Last Universal Common Ancestor
(LUCA).
• Archaea and Eukarya probably evolved independently of Bacteria.
• Bacteria and Archaea aren’t phylogenetically linked.
• They do share similar cellular construction.
• Archaea and Eukarya probably descended from same ancestor
but diverged to give separate domains.

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Eukaryotic Evolutionary
Hypotheses: 1
• An archaeon and bacterium
living in close association
fused.
• Archaeal genes involved in
metabolism were lost.
• Bacterial genes involved in
information processing were
degraded over time.

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Eukaryotic Evolutionary
Hypotheses: 2
• A series of endosymbioses:
• Archaeal cell engulfs bacterial
cell.
• Bacterial cell donates genes by
horizontal gene transfer.

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Eukaryotic Evolutionary
Hypotheses: 3
• Others argue for a series of
horizontal gene transfer
events.
• Alternatively, that the
eukaryotes evolved from
early Gram negative
bacteria.

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• Comparison of Bacteria,
Archaea and Eukarya.

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Norman Pace
• Pace has argued that the
term "prokarya" should be
dropped from biology since
it defines organisms by the
fact that they don’t have
nuclei. The correct terms are
Bacteria and Archaea.

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The Open Tree of Life
• Recently a project has been
published attempting to link
every known life form.
• Based on automatically
assembling other published
trees.
• Can be accessed at
Tree of Life.

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Summary

• Life on Earth is microbial in origin.

• Quite how that life evolved remains the subject of debate.
• The Universal Phylogenetic Tree shows how all organisms are
interrelated and linked to a common ancestor.
• This depends of a useful evolutionary chronometer.

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