When two entities interact such that their phenotypic output — as measured variously, e.g., such as in terms of fitness — is greater than it would be were they to not interact, then their interactions can be said to be cooperative. Broadly speaking, these two cooperating entities need not strictly be organisms. For example, in the previous chapter (Genomes) we considered how epistatic interactions between genes can give rise to evolution of linkage between those two genes. The point there is that two or more genes can coevolve such that they are relatively functionless without the presence of these other genes, and thus these two or more genes definitively provide a higher fitness contribution to their harboring organisms when interacting than when not. Without functioning they cannot contribute positively to fitness, so if acquired singly by an organism they would likely be lost. By physically linking together by being adjacent on genomes, however, two or more genes can move together with greater likelihood and thereby are potentially retained following horizontal gene transfer events.

The tie between linkage and cooperation is a strong one. Within the genomes of organisms, for example, one can see that in fact all genes are genetically linked in the sense that they are all found, at least for one generation, within the same organism. Because of this linkage, fates are shared, whether in terms of survival or reproductive success. A gene that does not contribute to the overall fitness of the organism within which it is found can be considered to be not cooperating. Indeed, there are limits to which such so-called selfish genes might evolve given their dependence on other genes within the same genome for their reproductive success.

Alternatively, there can exist circumstances in which the genes found within an individual are capable of transmission in a manner that is independent, at least to some degree, of the organisms in which they reside. Such genes are surprisingly common, and they make up normal flora, pathogens, symbionts (including endosymbionts), infectious genetic elements (e.g., self-transmissible plasmids), viruses, etc. The more these other entities are capable of reproducing independently of their host, the less evolutionary incentive they have to cooperate with that host. That is, their linkage with their host can be relatively slight, and cooperation therefore is less necessary and even less likely. At an extreme, pathogens may reduce host fitness to zero, and do so in ways that serve to increase pathogen fitness.

Table: Cooperation Between Genomes at Many Levels of Biological Organization.
Phenomena	Discussion
Community	Between two different otherwise antonymous species, i.e., within a mutualism.
Population	Cooperation as it occurs between conspecifics. This, as humans, is how we are most familiar with the idea of cooperation.
Organism	Cooperation between clonally related cells but also mutualisms between more than one species, especially between host and symbionts, particularly as between mutualistic normal flora.
Clone	This is cooperation as it occurs between genetically identical entities, particularly the different cells that make up multicellular organisms, less sophisticated colonies of cells, or microcolonies of bacteria making up biofilms.
Cell	Cooperation as it occurs between different genetic entities – different genomes – that can be found with the same cell. This can include different nuclei or multiple otherwise identical copies of genomes but is most striking in terms of the cooperation that occurs between the main genome of a cell and that of endosymbiotic organisms also found within the confines of a single cell.
Genome	This is cooperation as it occurs among the genes and other genetic material that makes up an organism's genome. This cooperation includes that which leads to epistatic relationships and, as for many of the above-noted categories, is a cooperation that can be undermined by parasitic entities.
Gene	For a gene to be functional, then its various parts, e.g., making up protein domains, must coordinate to produce a well-coordinated whole. Though seemingly a trivial idea, in fact for a gene to be retained intact by an organism it must contribute to fitness and this contribution is less likely if its various parts do not 'play nice' together.

There are other scenarios that can give rise to cooperative interactions, such as a number of situations you might experience in everyday life. These other scenarios, however, tend to be less robust motivators toward cooperation than genetic linkage. Since microorganisms, unlike you and I, also are not terribly behaviorally sophisticated, these other mechanisms typically do not apply to microbial evolution of cooperation. Nonetheless, in considering microbial cooperation, it is useful to explore these other means even if ultimately they are rejected as plausible among microorganisms. Such explorations typically if not inevitably will lead to discussions of the game theory of cooperation and defection, which is where we'll start.

Part IV:

Vocabulary

Table: Important Terms and Concepts Pertaining to Cooperation and Defection.
Term	Definition/Discussion
All C	An individual that never defects.
	An All C individual is only able to display behaviors of cooperation. As a consequence they are effectively obligate cooperators and unable, in particular, to display Tit for Tat and perhaps also to display other forms of suppression of the exhibition of defection by others. All C individuals consequently are particularly vulnerable to exploitation by cheaters. In microbial systems, All C individuals, for example, include those that obligately produce extracellular polymeric substances (EPS) as a public good, which other non-producers can then make use of as well, as within bacterial microcolonies making up biofilms.
All D   (alt link)	An individual that never cooperates.
	An All D individual is only able to display behaviors of defection. As a consequence they are effectively obligate defectors, a form of cheater, indeed, a potentially extreme form of cheater. Contrast All C, but also behaviors of Tit for Tat. In microbial systems, All D individuals, for example, include those that are obligately unable to produce extracellular polymeric substances (EPS) as a public good within bacterial microcolonies making up biofilms. That is, they (in this case) are able to partake of a public good but do not contribute to the provision of that same public good. You could say that these individuals are obligate stealers of the resources of others, though in fact defection can go beyond mere stealing.
Altruism	Display of cooperation at cost to self.
	Altruism is the performance of a cooperative behavior at direct cost to self. Not all cooperative behaviors are altruistic behaviors, however. For example, in many circumstances it can be possible to be helpful to others with no cost to self (e.g., throwing for-deposit cans out of the window of your car, which are worth money to whomever picks up the cans, but presumably were not worth much of anything to the individual throwing these cans out their window). Often, though, there is some cost to performing a cooperative behavior (e.g., the cost of that can deposit), so the key question in determining whether a behavior is altruistic is whether there is a net cost, that is, whether an individual is not in some manner being compensated for their cooperative actions. If in fact an individual is being sufficiently compensated, then the behavior is not a cooperative one. As performing behaviors for which there is a cost but insufficient payoff is generally not an stable strategy, evolutionarily, in exploring the evolution of cooperation a good place to start is to consider how it is that in fact an individual might have been compensated for their otherwise costly, cooperative behaviors, that is, how it may be that those behaviors are not altruistic. One must keep in mind during these explorations, however, that the compensating rewards for behaviors need not be identical to the results of the behaviors themselves (e.g., shelter can be swapped for food).
Cheater	An individual that displays one or more defection behaviors particularly towards benefit to self.
	A cheater is an individual that, given an opportunity to cooperate, instead does not cooperate. In doing so the cheater avoids paying costs associated with cooperating and/or receives gains associated with defecting. A cheater thus can be an individual that either performs a cheating behavior or alternatively fails to perform a cooperative behavior. In the case of doing nothing and thereby not performing a cheating behavior, the cost is seen in forgoing whatever gain would come from otherwise being a cheater. An alternative perspective is that a cooperative behavior results in another "player" benefiting from that behavior, but while benefits can then be measured in terms of degrees of gain (such as in terms of gains in fitness), benefits also can be measured in terms of a lack of costs. Thus, while cheating may result in costs to others, cooperation can still result in costs to others, just lower costs relative to those resulting from a behavior that otherwise might be described as cheating. A cheater thus imposes some cost on others, and particularly some greater cost versus a lesser or non-cheater, and imposes those costs in order to obtain, in some capacity, some degree of personal gain.
Cheating	Display of one or more defection behaviors especially within the context of unilateral defection.
	Cheating generally is viewed as taking advantage of situations, particularly in which other individuals experience a cost due to another's cheating and/or what otherwise could be a mutually cooperative endeavor does not function as well as it otherwise might. In other words, by cheating one causes others to experience fewer benefits from displaying cooperative behaviors, and explicitly this is because cheating involves some deficit in display of what otherwise could be helpful, cooperative behaviors.
Cooperation	Display by an individual of a behavior that is relatively beneficial to a second or more individual(s) with which an interaction is taking place.
	Cooperation is an act (behavior) from which an associated individual or individuals benefits. Notably, cooperation, as a behavior, is not a description of the joint behavior of two more individuals but instead is a description of the behavior of only a single individual, though others may display cooperative behaviors as well. Joint behaviors of cooperation instead are described as mutual cooperation. Greater display of cheating notably corresponds with reduced display of cooperation. Contrast, as well, cooperation with defection.
Cooperative behavior	Of possible alternatives, the display of a means of interacting that is relatively more versus relatively less beneficial to one or more individuals with which one is interacting.
	A cooperative behavior obviously is a behavior of cooperation, though less obviously a cooperative behavior can also entail merely a failure to display a worse behavior of defection. Thus, in contrasting two behaviors, bad versus worse, in terms of their potential impact others, the mere "bad" behavior could be described as relatively cooperative, even though others are not actually net gaining from that behavior in absolute terms, but instead are simply doing better than they might have done were instead the "worse" behavior engaged in. It's as though you were stealing $100 from an individual rather than $200, despite the opportunity to do the latter, perhaps for the sake of hurting this individual less. This forgoing of the extra $100 might therefore be viewed as a cooperative behavior, or even an altruistic behavior, as another benefiting (in relative terms) at the cost to self (in terms of resources acquired). Consider, perhaps equivalently, throwing a party in your parent's home and trying to keep from trashing the place in the process, with the lack of trashing described as a cooperative behaviors because some degree of resistance to displaying even greater levels of cheating was observed. Contrast defection behavior.
Cooperator	Individual that succeeds during an interaction or interactions in question in displaying a behavior that is relatively beneficial to a second or more individual.
	A cooperator is an individual that displays a cooperative behavior. Note, though, that such a description can be limited to a single round of interaction. A cooperator thus can display a cooperative behavior during one moment and a non-cooperative behavior during another, though in that second round the once cooperator may be described as a defector instead. Alternatively, through multiple rounds of interactions, if an individual displays cooperative behaviors sufficiently often that these cooperative behaviors serve to make up for defection behaviors, such that overall the behaviors could be described as cooperative – even if only in relative rather than absolute terms – then such an individual could be described as a cooperator. In yet other words, an individual need not be an All C player to nevertheless be described as a cooperator.
Defection	Failure on the part of an individual to display a behavior that is relatively beneficial to a second or more individual(s) with which an interaction is taking place.
	Defection is the display of a behavior that is not cooperative. More subtlety, defection can involve a failure to display a cooperative behavior or, instead, the display of a behavior that more actively serves to reduce the functionality or fitness of other individuals. Defection thus is not so much the opposite as cooperation as less cooperative than some corresponding cooperative behavior.
Defection behavior	Of possible alternatives, the display of a means of interacting that is relatively less versus relatively more beneficial to one or more individuals with which one is interacting.
	A defection behavior is, obviously, a behavior of defection, though less obviously can entail simply a failure to display or indeed fully display a behavior of cooperation. Over a series of interactions a defection behavior can be ones that supply lower net benefits or instead higher net costs to another individual (or individuals) relative to the behaviors displayed over some alternative series of interactions. Individual that gain from displaying defection behaviors can be described as cheaters. Contrast cooperative behavior.
Defector	Individual that fails during an interaction or interactions in question to display a behavior that is relatively beneficial to a second or more individual.
	A defector is an individual that, minimally, fails to display a cooperative behavior when given an opportunity to do so. This is particularly as during at least a single round of interaction and thus a defector in principle could display a defection behavior during one round of an interaction and then a cooperative behavior during another (and then, as a consequence, be dubbed instead a cooperator). Individuals that are only capable of displaying only defection behaviors we dub instead as All D individuals. "Defector" thus is generally a much shorter-term or alternatively less absolute descriptor than All D, though on the other hand in microbial systems individuals often are genetically predisposed to behaviors of cooperation or defection and thus microbial defectors often are defectors within the context of a longer-term All D behavioral strategy.
Economy	Growth or replication that is efficient in terms of resources used but potentially at the cost of rate of growth or replication.
	Economical growth strategies are ones that tend to emphasize growth yield over growth rate. Economical strategies often are ones of relative cooperation as well as strategies that serve to reduce the tragedy of a Tragedy of the Commons. Contrast economy with expediency.
Expediency	Growth or replication that is inefficient in terms of resources used especially towards increasing rates of growth or replication.
	Expedient growth strategies are ones that tend to emphasize growth rate over growth yield. Expedient strategies often are ones of relative defection as well as strategies that serve to exacerbate the tragedy of a Tragedy of the Commons. Contrast expediency with economy.
Game of Chicken	Interaction between two or more individuals in which mutual defection is associated with a worse outcome for both individuals than unilateral cooperation for the cooperator.
	In Games of Chicken, unilateral defection (T) is preferable to mutual cooperation (R), which is preferable to unilateral cooperation (S), and which in turn is preferable to mutual defection (P). Thus, T > R > S > P. In the classic, car-based Game of Chicken, mutual defection (P) would be a head-on collision. That is, not swerving could be described as defection, swerving as cooperation, and unilateral not swerving (T) brings a reputation of courage whereas swerving brings shame (and head-on collisions, P, can result in death, or at least severe damage to body and vehicle). Contrasting with a Prisoner's Dilemma, in a Game of Chicken a defection behavior does not inevitably result in a better outcome for that player than a cooperative behavior. Instead, whether cooperation is preferable to defection, or vice versa, is dependent on the other player's behavior, with defection on the part of the other player's behavior associated with the distinction between a Prisoner's Dilemma and a Game of Chicken (better for the focus player if they cooperate when their opponent defects rather than defect when their opponent defects). The result, all else held constant, should be stronger selection for cooperation in a Game of Chicken versus in a Prisoner's Dilemma.
Game theory	Use of rule-based scenarios as well as mathematics to characterize strategies of organism behavior such as in terms of their impact on Darwinian fitness.
	Examples of games considered by game theory include the Prisoner's Dilemma and the Game of Chicken. Indeed, these two games are examples of what can be describes as two-by-two or 2×2 games (two players with two possible behaviors, each). The evolution of cooperation, or cooperation generally, often is studied using game theory since the whole point of cooperation, or defection, is that some individuals, or behaviors, gain more while other individuals, or behaviors, gain less. It is the taking of the behaviors of individuals, the behaviors or more than one interacting individual, and the costs and benefits associated with these interactions (payoffs) that together give rise to the "rules" underlying these "games" and which, as a consequence, allows cooperation and defection to be considered within a game theory context.
Growth rate	Degree of increase in body or population size as a function of time.
	Higher growth rates correspond to faster rates of increase in population sizes, densities, and/or biomass. Organisms that are expedient in their growth strategies tend to emphasis growth rates over growth yields. Organisms that are economical in their growth strategies tend to emphasize growth yields over growth rates. Emphasis of growth rates over growth yields can exacerbate the tragedy of the Tragedy of the Commons. Emphasis of growth rates over growth yields also can be described, in various scenarios, as defection behaviors whereas emphasis of growth yields over growth rates can be described equivalently as cooperation behaviors.
Growth yield	Overall, end-point, or steady-state extent of increase in body or population size.
	Growth yield is best measured at the point of population or environmental maturation whether that is an end point, such as during batch growth (e.g., final number of organisms present), or a steady state, such as in the case chemostats (i.e., organism density that balances organism growth with organism washout). Organisms that are economical in their growth strategies tend to emphasize growth yield over growth rate. Organisms that are expedient in their growth strategies tend to emphasis growth rate over growth yield. Emphasis of growth yields over growth rates can serve to reduce or at least delay the tragedy of the Tragedy of the Commons. Emphasis of growth rates over growth yields also can be described, in various scenarios, as defection behaviors whereas emphasis of growth yields over growth rates can be described equivalently as cooperation behaviors.
Mutual cooperation	Display on the part of two or more interacting individuals of a behavior that is relatively beneficial to the other individual(s).
	Mutual cooperation is when more than one interacting individual displays a behavior of cooperation. In its simplest case, two individuals over a single round of interaction both display a behavior of cooperation. Mutual cooperation gives rise to a payoff of R. Importantly, a cooperative behavior is not automatically mutual cooperation, since cooperative behavior describes only the actions of a single individual. Also of importance, "Cooperation" does not inevitably imply "Mutual cooperation", since one individual within an interaction could display cooperation, but mutual cooperation occurs only if both (or more) individuals both (or all) display cooperation. Things become ambiguous, however, in a situation with numerous interacting individuals (an n-player game) in which most but not all individuals display cooperative behaviors. Is that then a case of mutual cooperation but with some cheating?
Mutual defection	Failure on the part of two or more interacting individuals to each display a behavior that is relatively beneficial to the other individual(s).
	Mutual defection is when two or more interacting individuals fail to display behaviors of cooperation. Mutual defection gives rise to a payoff of P. In a Game of Chicken mutual defection provides the worst possible payoff whereas in a Prisoner's Dilemma unilateral cooperation provides a worse payoff than mutual defection.
P	Abbreviation of payoff for mutual defection.
	P stands for Punishment for mutual defection. It is a description of a payoff associated with a specific combination of behaviors displayed by two interacting individuals, as experienced by the focus individual, in this case which defects while the other defects. In a Game of Chicken P provides the worst possible payoff whereas in a Prisoner's Dilemma S provides a worse payoff than P.
Policing	Behaviors that serve to suppress tendencies towards defection by individuals that otherwise are found in one's midst.
	The object of policing is to make it more costly in some manner for others to display defection behaviors, typically as implemented either during or following the cheating behavior rather than prior to the display by a specific individual of a specific behavior. This can include via a behavioral strategy that is known as Tit for Tat, but is not limited to Tit for Tat. The idea regardless is that suppression of tendencies to cheat occur for the sake of avoiding the increased cost that is imposed on cheating by policing, either in behavioral terms or instead in evolutionary terms. Thus, if you defectors are identified and killed (or some significant but nonetheless less extreme punishment), then there will be selection against defectors, or if you are hit on top of the head every time you perform a specific behavior, then you will be less tempted to perform that behavior. Policing can include removal of defectors from one's local environment. Policing, however, is not necessarily equivalent to preventing potential cheaters from entering one's local environment to begin with. Policing can be costly to implement and can require relatively high levels of behavioral sophistication since policing can require recognition of cheating behavior as well as acting on that recognition. Policing can be described as 'mutual' if carried out by normal players versus specialized individuals such as immune-system cells as found within multicellular organisms.
Prisoner's Dilemma	Game of cooperation and defection between two or more individuals in which especially unilateral cooperation provides a worse payoff than mutual defection.
	In a Prisoner's Dilemma, generally abbreviated as PD, unilateral defection is preferable to mutual cooperation which is preferable to mutual defection, which in turn is preferable to unilateral cooperation. With PDs the reward is always greater for behaviors of defection than for behaviors of cooperation. Thus, T > R > P > S. Compare with Game of Chicken where S > P rather than P > S.
R	Abbreviation of payoff for mutual cooperation.
	R stands for Reward for mutual cooperation. It is a description of a payoff associated with a specific combination of behaviors displayed by two interacting individuals, as experienced by the focus individual, in this case which cooperates while the other also cooperates.
Reciprocal altruism	Mutual cooperation that is stabilized especially by motivation on the part of all players to avoid mutual defection.
	Reciprocal altruism is literally "I'll scratch your back if you'll scratch mine", that is, the doing of cooperative favors to specific others in the hope that specific others will do cooperative favors in return.
S	Abbreviation of payoff for unilateral cooperation.
	S stands for Sucker's payoff. It is a description of a payoff associated with a specific combination of behaviors displayed by two interacting individuals, as experienced by the focus individual, which in this case cooperates while the other defects.
T	Abbreviation of payoff for unilateral defection.
	T stands for Temptation to defect. It is a description of a payoff associated with a specific combination of behaviors displayed by two interacting individuals, as experienced by the focus individual, in this case which defects while the other cooperates.
Tit for Tat	Game strategy in which a player displays whatever behavior was displayed by an opponent during a previous round of interaction.
	Tit for Tat can be viewed as a means of punishing defectors, that is, with behaviors of defection returned with behaviors of defection. Though potentially stabilizing of mutually cooperative interactions, Tit for Tat also can stabilize ongoing mutual defection. Note that the punishing reply associated with Tit for Tat need not be identical to whatever defection behavior was observed during the previous round of interaction. Note too that Tit for Tat can require a relative degree of behavioral sophistication to accomplish since at a minimum a player must be aware of the behavior of an opponent during a previous round of interaction and then act on that awareness.
Tragedy of the Commons	Multiplayer game in which cheating behavior has the effect of reducing the ability of an environment to support the well being of all players.
	Here the commons is the environment and the tragedy is the environment's degradation. The problem is that when goods are shared then there can be incentive to take more than one's share, but at the cost of how many goods are available to all and, crucially, at the cost of how many goods are available even to the cheater over the long term. In some ways the Tragedy of the Commons can be viewed as equivalent to what can be described as an n-player Prisoner's Dilemma, that is, consisting of n players (not necessarily just 2) rather than just 2.
Unilateral cooperation	Display by only a single of two or more interacting individuals of a behavior that is relatively beneficial to the other individual(s).
	Unilateral cooperation is when an individual displays a behavior of cooperation while interacting with one or more individuals who display instead behaviors of defection. Note that All C individuals can be prone to displaying unilateral cooperation if they cannot otherwise avoid associating with would-be defectors. Unilateral cooperation gives rise to a payoff of S to the cooperator, which is the lowest payoff in a Prisoner's Dilemma.
Unilateral defection	Failure by only a single of two or more interacting individuals to display a behavior that is relatively beneficial to the other individual(s).
	Unilateral defection occurs when an individual displays a behavior of defection while interacting with one or more individuals who display instead behaviors of cooperation. Unilateral defection gives rise to a payoff of T to the defector, which is the highest payoff in a Prisoner's Dilemma as well as a Game of Chicken.