The role of chance and history in the evolution of a novel trait in Pseudomonas fluorescens SBW25 : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Genetics at Massey University, Albany campus, New Zealand
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Date
2013
DOI
Open Access Location
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Journal ISSN
Volume Title
Publisher
Massey University
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Abstract
The
processes
that
lead
to
the
evolution
of
novel
adaptive
traits
are
poorly
understood.
It
is
not
clear
how
the
combination
of
natural
selection
and
random
variation
determine
evolutionary
pathways,
specifically
how
evolutionary
history
affects
the
outcome
of
evolution.
In
a
previous
experiment
in
which
populations
of
the
bacterium
Pseudomonas
fluorescens
were
subjected
to
repeated
evolutionary
reversals
(the
Reverse-‐Evolution
Experiment
(REE))
stochastically
switching
genotypes
evolved
de
novo
in
two
out
of
12
replicate
lineages.
Whole
genome
sequencing
revealed
not
only
causative
mutations
in
carB
(referred
to
as
carB*)
and
rpoD
but
also
the
entire
evolutionary
pathways
comprised
of
eight
additional
mutations.
It
was
hypothesized
that
evolutionary
history
played
a
major
role
in
switcher
evolution.
This
was
tested
by
‘reviving’
four
REE
lineages
and
the
performance
of
‘replay
evolution’
experiments.
Whereas
the
repeated
evolution
of
switcher
genotypes
was
observed
in
three
of
the
four
lineages,
the
likelihood
of
switcher
occurrence
varied
and
depended
on
the
genotype.
By
artificially
introducing
the
original
switcher
mutation
carB*
into
genotypes
from
one
lineage,
potential
fitness
benefits
of
the
switcher
mutation
at
each
point
in
evolutionary
time
were
assessed.
The
introduction
of
carB*
into
the
ancestral
genotype
of
SBW25
created
a
switcher
with
higher
fitness
than
the
ancestor,
indicating
that
evolutionary
history
is
not
necessarily
required
to
give
rise
to
an
evolutionary
successful
switcher.
This
idea
was
tested
further
during
a
real-‐time
evolution
experiment
using
the
same
genotypes
as
founder
populations.
The
capacity
to
evolve
a
switcher,
based
on
the
competitive
fitness
of
carB*,
was
only
partly
reflected
in
the
ability
to
re-‐evolve
switchers,
which
is
most
likely
due
to
the
availability
of
alternative
evolutionary
pathways,
the
number
of
competitors,
and
the
fitness
of
the
founder
genotype.
In
addition,
epistasis
contributed
to
an
increased
capacity
to
produce
a
switcher
based
on
carB*,
resulting
in
an
increased
likelihood
to
evolve
this
novel
trait
in
genotypes
from
the
later
evolutionary
time
points.
Evolutionary
history
plays
an
important
role
in
the
evolution
of
switching.
Even
though
switchers
evolved
repeatedly
from
different
genotypes,
the
likelihood
that
this
path
was
taken
depended
on
genetic
constraints
and
ecological
factors.
These
factors
and
their
contribution
to
the
evolutionary
outcome
were
dependent
on
the
genetic
composition
and
changed
throughout
evolutionary
history.
Description
Keywords
Pseudomonas fluorescens, Pseudomonas fluorescens genetics, Pseudomonas fluorescens evolution, Switcher genotypes, Evolutionary genetics