<commit_before>---
#title: Evolution of Cooperation through Feedback from Niche Construction
#author:
#- <NAME> (UW)

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bibliography: references.bib
csl: nature.csl

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    pdf_document:
        number_sections: yes
        toc: yes
    html_document:
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        fig_width: 5in

...

## Evolution of Cooperation through Feedback from Niche Construction

Cooperative behaviors are common across all branches of the tree of life.
Insects divide labor within their colonies, plants and soil bacteria exchange
required nutrients, birds care for others' young, and the trillions of cells in
the human body restrain their growth and coordinate with others to provide
vital functions. Each instance of cooperation presents an evolutionary
challenge---how can individuals that sacrifice their own well-being to help
others avoid subversion by those that do not? Over time, we would expect these
*defectors* to rise in abundance at the expense of others, eventually driving
cooperators (and perhaps the entire population) to extinction.

A number of factors can defer this potential *tragedy of the commons*
[@hardin1968tragedy; @hamilton1964geneticalboth; @nowak2006five;
@west2007evolutionary]. For example, it has frequently been demonstrated that
close relatives must be more likely to benefit from the cooperative act than
others. This can occur when cooperators are clustered together in
spatially-structured populations [@kudzalfick2011high; @fletcher2009simple;
@nadell2010emergence] or when cooperators use communication [@darch2012density;
@brown2001cooperation] or other cues [@gardner2010greenbeards] to identify and
cooperate conditionally with kin. Interestingly, cooperation can also be
bolstered by genetic association with self-benefitting traits
[@dandekar2012bacterial; @asfahl2015nonsocial; @foster2004pleiotropy], setting
the stage for an "adaptive race" in which cooperators and defectors vie for the
first highly-beneficial non-social adaptation [@waite2012adaptation;
@morgan2012selection]. Using a computational model inspired by corresponding
microbial experiments, we recently showed that cooperators can gain a
substantial leg up on defectors when the cooperative behavior increases
population density, and thus the likelihood of acquiring beneficial mutations
(in prep.). However, this advantage is fleeting (Fig. 1A). Once the
opportunities for adaptation are exhausted, cooperators are once again at a
disadvantage against defectors. As shown in Fig. 1B, however, cooperation can
be maintained indefinitely when environmental change occurs frequently,
providing a stream of adaptive opportunities. While natural organisms typically
find themselves in changing environments, can cooperators bet their success on
these environments providing a steady influx of adaptive opportunities?

Our previous model and others neglected one potentially major determinant of
evolutionary outcomes---environmental change brought about by the organisms
themselves. Through their metabolism, their interactions with others, and even
through their death, organisms constantly modify their environment. These
changes can produce feedback loops in which environmental change alters
selection, which, in turn, alters phenotypes and their corresponding effects on
the environment. **This research aims to reveal how endogenous environmental
change, or *niche construction*, [@odling2003niche] affects the evolution of
cooperation.** First, we will explore how selective feedbacks influence
evolution as populations modify their physical environment. We then expand our
scope to see how this process changes when the environment itself is under
selection, such as when symbiont populations modify their host.


### Phenotype-Driven Niche Construction

As detailed in [Model Overview](#model), we will develop an agent-based model
where evolution occurs in a metapopulation of populations connected by limited
migration. Within each population, growth occurs based on the interaction of
cooperators and defectors. We first consider public goods cooperation, where
the costly production of a public good allows populations to reach greater
densities. For example, many bacterial species produce exoenzymes that digest
large proteins in the environment, making the resulting amino acids an
accessible carbon source for nearby cells. In the model, beneficial non-social
adaptations allow populations to further adapt to their patch. Importantly,
these adaptations alter how populations interact with their environment, which,
in turn, alters selection at that patch. As a result, cooperator populations
may render their environment inhospitable to immigrant defectors. In some
conditions, cooperators may instead construct their own demise, making their
patch *more* hospitable to defectors.

Natural organisms display a great diversity of cooperative behaviors. To
identify more general principles about how niche construction influences the
evolution of cooperation, we will extend our model to study additional forms of
social interaction. For example, bacteria commonly produce toxins that inhibit
or kill competing strains [@riley2002bacteriocins]. These *public bads* are
harmful to others, but benefit the immune cooperator strain by reducing
competition. TODO: model specifics?


### Feedbacks in Host-Symbiont Co-Evolution

As described in the previous aim, the environmental state was implicit,
depending only on the state of the population.

paper [@hamblin2014viral]


#### Model Overview {#model}


Individuals have a length $L+1$ genotype. The first $L$ loci are *stress loci*,
and are each occupied by a $0$ or an integer from the set $A=\{1, \ldots,
a_{max}\}$, where $a_{max}$ is the number of possible alleles. These alleles
represent adaptations to the environment, and the number of loci determine the
number of possible adaptations. All non-zero alleles carry fitness benefit
$\delta$. Although there is no inherent difference between each allele, we
reward genotypes with sequential stress alleles, providing fitness benefit
$\epsilon$ for each allele whose value is 1 greater than the previous allele
(modulo $A$). Because mutations are random, as described below, each population
will evolve sequences that start with different allelic states.  Importantly,
these different sequences represent the unique niches constructed at each
patch.  An additional binary allele at locus $L + 1$ determines whether or not
the individual is a cooperator, which carries cost $c$. Each of the $N$
populations in the metapopulation are initiated with non-adapted individuals
and cooperator proportion $p_0$.

Each population grows to capacity $S_{min} + p (S_{max} - S_{min})$, where $p$
is the proportion of cooperators in that population. Mutations alter the
allelic state at stress loci and the cooperation locus with probability
$\mu_{s}$ and $\mu_{p}$, respectively. After growth, individuals migrate to a
randomly chosen neighbor patch at rate $m$. Finally, populations are thinned to
allow for growth in the next cycle. Individuals survive this thinning with
probability $d$.

Environmental changes are triggered either endogenously or exogenously,
depending on the experimental focus, and take one of two forms. The simpler
form reveals an additional stress locus, providing an additional opportunity
for adaptation. Immigrants to less adapted patches will be "pre-adapted" when
change occurs. The more complex form mimics a complete environmental change,
and resets the allelic state of each individual. When representing the onset of
a novel stress, such as the introduction of an antibiotic, individuals survive
this change with probability $\mu_{t}$, which represents the likelihood of
gaining a mutation conferring tolerance.


\newpage

\renewcommand{\figurename}{Fig.}
![(**A**) With "genetic niche hiking", cooperators outrun defectors by association with non-social adaptations that compensate for the cost of cooperation. Once defectors become equally adapted, they drive cooperators from the population. (**B**) When environmental change occurs frequently (here every 1,000 cycles), the continual opportunity for adaptation allows cooperators to persist indefinitely.](figures/Figure1all-scaled.png)

\newpage

## Criterion One: Scientific Strength of the Proposed Project

## Criterion Two: Centrality of Project to BEACON’s Mission

## Criterion Three: Quality of Plan for Obtaining External Funding

## Criterion Four: Degree of Multidisciplinarity of Project

## Criterion Five: Impact on Education and Human Resource Development

## Criterion Six: Knowledge Transfer to Industry

## Criterion Seven: Impact on Achieving the Diversity Goals of BEACON

## Criterion Eight: Multi-Institutionality

## Criterion Nine: Budget Appropriateness

## Criterion Ten: Overall Quality


\newpage

# References
<commit_msg>Updates<commit_after>---
#title: Evolution of Cooperation through Feedback from Niche Construction
#author:
#- <NAME> (UW)

geometry: margin=0.75in
bibliography: references.bib
csl: nature.csl

output:
    pdf_document:
        number_sections: yes
        toc: yes
    html_document:
        number_sections: no
        theme: default
        toc: yes
    word_document:
        fig_height: 5in
        fig_width: 5in

...

## Evolution of Cooperation through Feedback from Niche Construction

Cooperative behaviors are common across all branches of the tree of life.
Insects divide labor within their colonies, plants and soil bacteria exchange
required nutrients, birds care for others' young, and the trillions of cells in
the human body restrain their growth and coordinate with others to provide
vital functions. Each instance of cooperation presents an evolutionary
challenge---how can individuals that sacrifice their own well-being to help
others avoid subversion by those that do not? Over time, we would expect these
*defectors* to rise in abundance at the expense of others, eventually driving
cooperators (and perhaps the entire population) to extinction.

Several factors can defer this potential *tragedy of the commons*
[@hardin1968tragedy; @hamilton1964geneticalboth; @nowak2006five;
@west2007evolutionary]. For example, it has frequently been demonstrated that
close relatives must be more likely to benefit from the cooperative act than
others. This can occur when cooperators are clustered together in
spatially-structured populations [@kudzalfick2011high; @fletcher2009simple;
@nadell2010emergence] or when cooperators use communication [@darch2012density;
@brown2001cooperation] or other cues [@gardner2010greenbeards] to identify and
cooperate conditionally with kin. Interestingly, cooperation can also be
bolstered by genetic association with self-benefitting traits
[@dandekar2012bacterial; @asfahl2015nonsocial; @foster2004pleiotropy], setting
the stage for an "adaptive race" in which cooperators and defectors vie for the
first highly-beneficial non-social adaptation [@waite2012adaptation;
@morgan2012selection]. Using a computational model inspired by corresponding
microbial experiments, we recently showed that cooperators can gain a
substantial leg up on defectors when the cooperative behavior increases
population density, and thus the likelihood of acquiring beneficial mutations
(in prep.). However, this advantage is fleeting (Fig. 1A). Once the
opportunities for adaptation are exhausted, cooperators are once again at a
disadvantage against defectors. As shown in Fig. 1B, however, cooperation can
be maintained indefinitely when frequent environmental changes produce a stream
of adaptive opportunities. While natural organisms typically find themselves in
changing environments, can cooperators bet their success on the environment
providing a sufficient influx of adaptive opportunities?

Our previous study and others have neglected one potentially major determinant
of evolutionary outcomes---environmental change brought about by the organisms
themselves. Through their metabolism, their interactions with others, and even
through their death, organisms constantly modify their environment. These
changes can produce evolutionary feedback loops in which environmental change
alters selection, which, in turn, alters phenotypes and their corresponding
effects on the environment. **This research aims to reveal how endogenous
environmental change, or *niche construction*, [@odling2003niche] affects the
evolution of cooperation.** First, we will explore how selective feedbacks
influence evolution as populations modify their environment. We then expand our
scope to see how this process changes when the environment itself is also a
target of selection, such as when symbiont populations modify their host.
**[TODO: add big picture questions here? applications?]**


### Phenotype-Driven Niche Construction

As detailed in the [Model Overview](#model), we will develop an agent-based
model to observe evolution in a metapopulation where populations are connected
by limited migration. Within each population, growth occurs based on the
interaction of cooperators and defectors. We first consider public goods
cooperation, where the costly production of a public good allows populations to
reach greater densities. For example, many bacterial species produce exoenzymes
that digest large proteins in the environment, unlocking the resulting amino
acids as a carbon source for nearby cells. In the model, beneficial non-social
adaptations allow populations to further adapt to their patch.  Importantly,
these adaptations alter how populations interact with their environment, which,
in turn, alters selection at that patch. As a result, cooperator populations
may ensure survival by rendering their environment inhospitable to immigrant
defectors. However, in some conditions, cooperators may instead construct their
own demise by making their patch *more* hospitable to defectors.

Natural organisms display a great diversity of cooperative behaviors. To
identify more general principles about how niche construction influences the
evolution of cooperation, we will extend our model to study additional forms of
social interaction. For example, bacteria commonly produce toxins that inhibit
or kill competing strains [@riley2002bacteriocins]. These *public bads* are
harmful to others, but benefit the immune cooperator strain by reducing
competition. TODO: model specifics?


### Feedbacks in Host-Symbiont Co-Evolution

As described in the previous aim, the environmental state was implicit,
depending only on the state of the population...

viral nc paper [@hamblin2014viral]


#### Model Overview {#model}


Individuals have a length $L+1$ genotype. The first $L$ loci are *stress loci*,
and are each occupied by a $0$ or an integer from the set $A=\{1, \ldots,
a_{max}\}$, where $a_{max}$ is the number of possible alleles. These alleles
represent adaptations to the environment, and the number of loci determine the
number of possible adaptations. All non-zero alleles carry fitness benefit
$\delta$. Although there is no inherent difference between each allele, we
reward genotypes with sequential stress alleles, providing fitness benefit
$\epsilon$ for each allele whose value is 1 greater than the previous allele
(modulo $A$). Because mutations are random, as described below, each population
will evolve sequences that start with different allelic states.  Importantly,
these different sequences represent the unique niches constructed at each
patch.  An additional binary allele at locus $L + 1$ determines whether or not
the individual is a cooperator, which carries cost $c$. Each of the $N$
populations in the metapopulation are initiated with non-adapted individuals
and cooperator proportion $p_0$.

Each population grows to capacity $S_{min} + p (S_{max} - S_{min})$, where $p$
is the proportion of cooperators in that population. Mutations alter the
allelic state at stress loci and the cooperation locus with probability
$\mu_{s}$ and $\mu_{p}$, respectively. After growth, individuals migrate to a
randomly chosen neighbor patch at rate $m$. Finally, populations are thinned to
allow for growth in the next cycle. Individuals survive this thinning with
probability $d$.

Environmental changes are triggered either endogenously or exogenously,
depending on the experimental focus, and take one of two forms. The simpler
form reveals an additional stress locus, providing an additional opportunity
for adaptation. Immigrants to less adapted patches will be "pre-adapted" when
change occurs. The more complex form mimics a complete environmental change,
and resets the allelic state of each individual. When representing the onset of
a novel stress, such as the introduction of an antibiotic, individuals survive
this change with probability $\mu_{t}$, which represents the likelihood of
gaining a mutation conferring tolerance.


\newpage

\renewcommand{\figurename}{Fig.}
![(**A**) Through "genetic niche hiking", cooperators outrun defectors by association with non-social adaptations that compensate for the cost of cooperation. Once defectors become equally adapted, however, they quickly drive cooperators to extinction. (**B**) When environmental change is frequent (here every 1,000 cycles), the continual potential for adaptation allows cooperators to persist indefinitely.](figures/Figure1all-scaled.png)

\newpage

## Criterion One: Scientific Strength of the Proposed Project

## Criterion Two: Centrality of Project to BEACON’s Mission

## Criterion Three: Quality of Plan for Obtaining External Funding

## Criterion Four: Degree of Multidisciplinarity of Project

## Criterion Five: Impact on Education and Human Resource Development

## Criterion Six: Knowledge Transfer to Industry

## Criterion Seven: Impact on Achieving the Diversity Goals of BEACON

## Criterion Eight: Multi-Institutionality

## Criterion Nine: Budget Appropriateness

## Criterion Ten: Overall Quality


\newpage

# References

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