Black
Queen
Gene
Loss
in
a
Structured
Environment
124
125
Spiridon
E.
Papoulis ,
J.
Jeffrey
Morris ,
23
123
12
Benjamin
Kerr ,
Luis
Zaman ,
Richard
E.
Lenski
Michigan
State
University1,
BEACON
Center2,
University
Washington3,
4
5
papoulis@msu.edu ,
jmorris@msu.edu
The
Black
Queen
Hypothesis
(Morris
et
al.
2012):
Removal
of
Environmental
Toxin
in
Avida
1) All
biological
func/ons
have
a
cost.
If
all
things
are
equal,
excluding
a
func/on
causes
a
fitness
advantage
2) Products
of
‘leaky’
biological
func/ons
are
unavoidably
made
available
to
the
community,
thus
providing
“public
goods“.
Examples
of
leaky
func/ons:
1) Detoxifica/on
of
an
environment
2) Cross-‐feeding
3) ‘Cheaters’
are
organisms
that
have
lost
a
vital
leaky
func/on,
but
s/ll
acquire
the
result
of
the
func/on
through
the
environment
by
comple/on
of
this
func/on
by
‘helper’
organisms
4) The
fitness
of
cheaters
and
helpers
is
negaFvely
frequency
dependent,
which
means
each
has
an
advantage
when
rare.
Therefore,
they
can
coexist,
preven/ng
the
loss
of
the
Black
Queen
func/on
in
a
“Tragedy
of
the
Commons”
Black
Queen
Gene
Loss
of
Toxin
Removal
Genes
in
Death
Rate
Each
Avidian’s
chance
of
death
is
calculated
based
on
an
individual
benefit,
which
is
dependent
upon
the
number
of
detoxifying
tasks
completed
by
that
individual,
and
a
global
benefit,
which
is
dependent
upon
the
total
number
of
detoxifying
tasks
completed
in
its
environment.
Avidians
experience
a
fitness
cost
when
comple/ng
the
logical
operator
NOT,
which
is
defined
as
our
detoxifying
task
in
this
experiment.
Liquid
Medium:
C
Propor/on
of
popula/on
mixed
environment
High
weakness,
high
leakiness
Copy
Number
High
toxicity
Low
toxicity
Σtask=
taskpopula/on
or
taskproximity
proximity
of
cell
Calcula/ng
global
benefit
varies
between
mixed
and
structured
environments.
In
a
mixed
environment,
all
cells
in
the
popula/on
are
assumed
to
be
the
same
distance
away
from
every
other
cell
in
the
popula/on
since
posi/on
is
constantly
changing.
In
a
structured
environment,
however,
posi/on
is
fixed,
meaning
that
the
global
benefit
can
only
be
calculated
based
upon
the
surrounding
cells.
Conclusions:
Black
Queen
func/on
loss
is
a
phenomenon
that
can
be
expanded
beyond
biological
evolu/on
Equilibrium
depends
on
leakiness
and
individual
protec/on
of
a
Black
Queen
func/on
in
a
mixed
environment
The
same
parameters
have
very
different
effects
in
a
structured
environment
as
compared
to
a
mixed
environment
Coexistence
is
maintained
in
structured
environments
•
Black
Queen
negaFve
frequency
dependence
avoids
“The
Tragedy
of
the
Commons”
while
allowing
the
persistence
of
cheaters
Invasion
of
cheaters
happens
faster
in
mixed
environments
•
0
1
2
3
Apparent
Equilibrium
•
•
•
Apparent
Equilibrium
Update
Update
•
Propor/on
of
popula/on
B
In
our
laboratory
experiment
(Morris
etal.,
submi]ed),
Escherichia
coli
had
all
oxida/ve
stress
genes
knocked
out,
thus
becoming
vulnerable
to
the
environmental
toxin
H2O2.
Cells
regained
the
ability
to
grow
ajer
being
transformed
with
the
pBADKAT,
a
catalase
producing
plasmid.
Helper
organisms
contained
pBADKAT
and
produced
catalase,
while
cheaters
lacked
the
plasmid.
Evolu/on
experiments
show
coexistence
was
maintained
between
Kat+
(helper)
cell
and
Kat-‐
(cheater)
cells
over
the
1200
genera/ons
(A).
It
was
also
discovered
that
catalase
ac/vity
in
the
helpers
actually
increased
during
this
experiment(B,
gray
points).
During
colony
counts
(C),
helpers
exhibited
“sectored”
colonies.
These
colonies
originated
from
plasmid
containing
clones,
and
during
colony
growth,
some
cells
mutated
and
lost
the
plasmid.
Brown
regions
are
plasmid
containing
cells
while
white
regions
are
cell
that
lack
the
plasmid
.This
suggests
that
Black
Queen
gene
loss
may
be
possible
even
in
a
structured
environment,
despite
the
fact
that
structure
is
ojen
though
of
as
a
protec/on
against
cheaters
(Chao
and
Levin,
1981).
Low
weakness,
low
leakiness
Structured
environment*
A
Structured
environment
Effect
of
Structure
on
Coexistence
of
Helpers
and
Cheaters
in
Avida
Propor/on
of
popula/on
4)
Toxicity
and
cells
evenly
distributed
Death
Rate=𝑡𝑜𝑥𝑖𝑛/𝑡𝑜𝑥𝑖𝑛+𝑡𝑎𝑠𝑘/𝑤𝑒𝑎𝑘𝑛𝑒𝑠𝑠 ∗exp(−𝑙𝑒𝑎𝑘𝑖𝑛𝑒𝑠𝑠∗Σ𝑡𝑎𝑠𝑘)
Future
Work:
Propor/on
of
popula/on
3)
Number
of
task
copies
Digital
organisms
(Avidians)
compete
for
processor
cycles
and
memory
in
a
digital
environment
Avidians
are
not
meant
to
represent
biological
organisms,
rather
en//es
that
are
able
to
change
over
/me
due
to
muta/on.
This
implies
Avida
is
not
a
simula/on
of
life
Genomes
are
composed
of
instruc/ons
that,
upon
replica/on,
are
subject
to
change
due
to
muta/on,
allowing
evolu/on
1)
Logical
operators,
such
as
NAND,
NOR,
and
EQU,
are
mathema/cally
calculated
by
instruc/ons
2)
There
are
an
infinite
number
of
ways
to
calculate
logical
operators
In
the
environment
file,
logical
operators
are
defined
as
tasks,
where
an
organism
can
receive
a
fitness
benefit
or
cost
depending
on
how
the
task
is
defined
Mixed
environment
Weakness
Leakiness
Avida:
A
PlaKorm
for
Digital
EvoluFon
1)
2)
Individual
Benefit
Total
tasks
in
the
environment
Global
Benefit
Update
• A
larger
parameter
range
to
inves/gate
how
this
effects
structure
• Manipula/ng
the
environment
file
• Inves/ga/ng
differences
between
using
different
logical
operators
in
our
detoxifying
task
• Adding
the
ability
to
control
the
radius
of
proximity
in
structured
experiments
• Structure
will
be
thoroughly
tested
to
ensure
results
are
valid
Update
*parameters
had
no
effect
on
structured
experiments
on
given
values
Propor/on
of
subpopula/ons
in
Avida
for
each
respec/ve
set
of
parameters.
Simula/ons
were
ini/ated
by
injec/ng
helpers
containing
3
copies
of
the
detoxifying
task,
and
cheaters
containing
zero
copies
of
the
detoxifying
task.
All
variables
were
consistent
between
structured
and
mixed
simula/ons,
except
for
how
global
benefit
was
calculated
and
how
toxin
flows
into
the
environment.
Acknowledgements:
We
would
like
the
Ins/tute
for
Cyber-‐Enable
Research
at
Michigan
State
University
for
gran/ng
us
access
to
their
high
performance
computer
center
and
to
fellow
Beacon
members
for
the
assistance
in
trouble
shoo/ng
problems.
We
would
also
like
to
thank
ASM
for
providing
a
travel
grant
to
a]end
ASM
2014
and
BEACON
for
addi/onal
funds.
We
would
also
like
to
thank
Neerja
Hajela,
Jamie
Johnson,
and
Rafeal
Mar/nez
for
maintain
all
lab
supplies.
References:
Morris
JJ,
Lenski
RE,
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ER.
2012.
The
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Queen
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of
dependencies
through
adap/ve
gene
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mBio
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10.1128/mBio.0003612
Nahum
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Harding
BN,
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B.
2011.
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restraint
in
a
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rock-‐paper-‐scissors
community.
PNAS108:10831-‐10838
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L,
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BR
1981.
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JJ,
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Submi]ed.
Coexistence
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RE,
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RT,
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C.
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avida.devosoj.org
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