Can Hamilton’s rule be violated?
 Article
 Figures and data
 Abstract
 Introduction
 The regression method
 The counterfactual method, applied to a general model of assortment in groups of equal size
 Implications for empirical tests of Hamilton’s rule
 Appendix 1
 Data availability
 References
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Abstract
How generally Hamilton’s rule holds is a much debated question. The answer to that question depends on how costs and benefits are defined. When using the regression method to define costs and benefits, there is no scope for violations of Hamilton’s rule. We introduce a general model for assortative group compositions to show that, when using the counterfactual method for computing costs and benefits, there is room for violations. The model also shows that there are limitations to observing violations in equilibrium, as the discrepancies between Hamilton’s rule and the direction of selection may imply that selection will take the population out of the region of disagreement, precluding observations of violations in equilibrium. Given what it takes to create a violation, empirical tests of Hamilton’s rule, both in and out of equilibrium, require the use of statistical models that allow for identifying nonlinearities in the fitness function.
https://doi.org/10.7554/eLife.41901.001Introduction
Hamilton’s rule (Hamilton, 1964a; Hamilton, 1964b) states that prosocial, altruistic behaviour will be selected for if $rb>c$, where $b$ are the benefits to the recipient, $c$ the costs to the donor, and $r$ is the relatedness between them. There is however no consensus concerning how generally this rule applies. Some claim that Hamilton’s rule is completely general (Abbot et al., 2011). Others claim that is almost always wrong (Nowak et al., 2010). Recently it has been suggested that the reason why there is disagreement about the generality of Hamilton’s rule, is that different participants in the debate have different definitions of costs and benefits (Birch, 2014; Birch and Okasha, 2015; van Veelen et al., 2017). Some define costs and benefits using the regression method (Gardner et al., 2011; Marshall, 2011). With this definition, Hamilton’s rule is claimed to always hold, and this version of Hamilton’s rule therefore is also referred to as the general version of Hamilton’s rule, or HRG (Birch, 2014). Others use the counterfactual method to determine costs and benefits (Karlin and Matessi, 1983; Matessi and Karlin, 1984; Matessi and Karlin, 1986; van Veelen et al., 2017). With this definition, Hamilton’s rule is claimed to hold only if the interaction is characterized by ‘generalized equal gains from switching’, or, in other words, if the fitness effects of one individual changing from defection to cooperation are independent of the behaviour of the others, including the recipient (van Veelen et al., 2017).
In what follows, we will consider both definitions, and explore the scope for violations. With the regression method, we will see that there is an identification problem; there are cases in which there are actually multiple linear specifications, leading to multiple Hamilton’s rules, all of which hold. Hamilton’s rule, using the regression method, therefore is not necessarily uniquely defined. For every given specification, however, Hamilton’s rule cannot be violated. This is a short summary of a point made in Section 4 of van Veelen et al., 2017.
In the main part of the paper, we will present a general model of assortative group compositions, which we combine with the counterfactual method for computing costs and benefits. For this model, we define population structure profiles, which reflect the distribution of group compositions that the population structure puts typical mutants in. In combination with the shape of the fitness function, these population structure profiles determine whether invading cooperators, or invading defectors, have a selective advantage. We will find that this allows for violations of Hamilton’s rule. Part of the reason why these violations can occur, is that relatedness $r$ in Hamilton’s rule is a onedimensional measure for population structure, while the population structure profile that is relevant for the direction of selection is a richer description of population structure. Violations in equilibrium, however, may not always be possible, because selection can also take a population out of the region where Hamilton’s rule and the direction of selection disagree. This happens, for instance, in examples with synergies.
In the final section, we discuss implications for empirical tests of Hamilton’s rule. The empirical literature is regularly lacking a precise description of what violations would look like, or how to identify them in the data. Because the regression method does not allow for violations, an empirical test of Hamilton’s rule, using the regression method, is not a meaningful exercise. With the counterfactual method, violations are possible, although observing them either requires studying outofequilibrium dynamics, or studying systems that allow for inequilibrium violations. In both cases nonlinear statistical models should be allowed for.
The regression method
The regression method defines costs and benefits according to an ordinary least squares regression. The fitness of individuals is regressed on two or more variables. One of those variables is their own level of cooperation, which may be a binary value, in case there are only cooperators and defectors. We will denote this variable by ${x}_{se}$ – with $se$ for self – and minus the regression coefficient of that variable is then defined as the cost of cooperation. The other variables are levels of cooperation for different types of interactants – such as, for instance, ${x}_{si}$ for siblings and ${x}_{co}$ for cousins. The benefits of having a cooperative sibling then is the regression coefficient of ${x}_{si}$, and the benefits of having a cooperative cousin is the regression coefficient of ${x}_{co}$. Many models and many empirical studies focus on one type of interaction – such as interactions between siblings only – but here we also want to discuss the issue of model specification, and therefore it will be useful to allow for the possibility that there are different types of interactions happening at the same time – as Hamilton did in the original paper (Hamilton, 1964a; Hamilton, 1964b). This allows us to consider different specifications. In what follows, we will think of an example in which both siblings and cousins may have an effect, where roman numeral I refers to a linear specification that includes siblings only, and II to a linear specification that includes both siblings and cousins.
The relatedness between siblings in this version of Hamilton’s rule is the covariance of ${x}_{se}$ and ${x}_{si}$, divided by the variance of ${x}_{se}$, and the relatedness between cousins is defined in the same way. With this definition of costs, benefits and relatedness, Hamilton’s rule always holds, but it is important to realize that it does so regardless of the linear specification that is chosen (van Veelen et al., 2017). In our example, with siblings and cousins, that means that for any two time periods, be it in a model or in a dataset, the change in average cooperativeness $\mathrm{\Delta}\overline{x}$ equals both
and
The costs and benefits of cooperation carry and index I or II in the subscript, because the value of the regression coefficients may depend on the specification (see Figure 1). Not including cousins in the specification means that ${b}_{co,\text{I}}$ is set to $0$. It is important to realize that Hamilton’s rule holding does not mean that the specification chosen accurately reflects the way in which fitness’s depend on whether one is a cooperator oneself, and on how many siblings and how many cousins are cooperators. Neither specification might represent the true fitness function, and still Hamilton’s rule will hold for both. Relatednesses here do not depend on the model specification (see Section 4 of van Veelen et al., 2017 for a formal derivation).
Hamilton’s rule according to the regression method therefore is not necessarily uniquely defined; only if it happens to be the case that ${b}_{co,\text{II}}=0$ do both versions coincide in this example. To make it uniquely defined, the regression method would need to be combined with a way to choose between specifications – and with data, applying statistical tests seems to be a natural way to do that. Such a way to choose should then also be applied, not just when choosing between linear specifications, but also when choosing between linear and nonlinear ones, and between different nonlinear ones. Hamilton’s rule according to the regression method therefore cannot both be uniquely defined, and fully general, because having it welldefined would imply that in some cases nonlinear specifications would have to be chosen, while Hamilton’s rule being general crucially depends on the specification being linear. But even if Hamilton’s rule is not always uniquely defined, it still holds for any given linear specification. Whichever linear specification is chosen, this should therefore never lead to a violation.
The counterfactual method, applied to a general model of assortment in groups of equal size
With the counterfactual method, the cost of cooperation is defined as the difference between an individual’s fitness if it defects, and its fitness if it cooperates. Similarly, the benefits to another individual are defined as the difference cooperation makes for that other individual’s fitness. In the relatively simple setup considered here, we assume that individuals interact within groups of size $n$, which implies that a model of dyadic interactions would mean $n=2$. Their fitnesses will depend on the number of cooperators in their interaction group, and on whether they are a cooperator or a defector themselves; ${\pi}_{C}\left(i\right)$ is the fitness of a cooperator in a group that contains $i$ cooperators, including the individual itself, and ${\pi}_{D}\left(i\right)$ is the fitness of a defector in a group that contains $i$ cooperators. The cost of cooperation an individual faces, as well as the benefits cooperation confers on the others, thereby may also depend on what the rest of the group it finds itself in consists of.
A population structure here is a function that represents how the composition of the population depends on the overall frequency $p$ of cooperators; ${f}_{i}\left(p\right)$ is the fraction of groups with $i$ cooperators in it, at overall frequency $p$. These have to be defined consistently, so that these frequencies always add up to one (${\sum}_{i=0}^{n}{f}_{i}(p)=1$), and so that $p$ is indeed the overall frequency of cooperators (${\sum}_{i=0}^{n}\frac{i}{n}{f}_{i}(p)=p$). The cost of cooperation in a population is now the average cost, given the distribution of group types, and these may very well vary with $p$.
The counterfactual method dates back to Karlin and Matessi, 1983, Matessi and Karlin, 1984, and Matessi and Karlin, 1986, who in their evaluation of whether or not Hamilton’s rule holds moreover did not allow for costs to vary with $p$. We do allow for costs and benefits to depend on $p$. Section 3 in van Veelen et al., 2017 also discusses some additional differences between the original definition and the one used here.
Selection
In order to answer the question whether or not mutant cooperators will be able to invade a population of defectors, one would have to consider the type of group the average mutant cooperator would find itself in, given the population structure. The probability that a mutant cooperator finds itself in a group with in total $i$ cooperators is
The vector $\underset{\_}{\mathbf{u}}$, with elements as defined above, could be called the “population structure profile” at $p=0$. Its counterpart $\overline{\mathbf{u}}$ at $p=1$ will be defined in the same way:
Cooperators can invade defectors if their average fitness at $p=0$ is larger than the average fitness of defectors, who at $p=0$ only find themselves in groups with defectors only, for any population structure.
Defectors on the other hand can invade cooperators if their average fitness at $p=1$ is larger than the average fitness of cooperators, who at $p=1$ only find themselves in groups with cooperators only.
Hamilton’s rule
Hamilton’s rule says that cooperation will be selected for if $rb>c$. We will rewrite this, at $p=0$ and at $p=1$, so as to get inequalities that look more like Equations 1 and 2. Relatedness $r$ measures how much more likely cooperators are to be matched with other cooperators, compared to how likely defectors are to be matched with cooperators; $r=P\left(C\rightC)P(C\leftD\right)$. In the limit of $p\downarrow 0$, the share of defectors that is matched with cooperators goes to $0$, whatever the population structure. With population structure, the average mutant cooperator however might encounter fellow mutant cooperators. This therefore reduces to $r=P\left(C\rightC)$, which one can rewrite as $r={\sum}_{i=0}^{n1}{\underset{\_}{u}}_{i}\frac{i1}{n1}$. With the counterfactual method, aggregate benefits at $p=0$ are $\left(n1\right)\left[{\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right]$, while costs are ${\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)$. With those, one can rewrite Hamilton’s rule at $p=0$ as follows (see Appendix 1 for more details):
Comparing the equation that indicates when cooperation is selected for (Equation 1) and the one for Hamilton’s rule (Equation 3), we first of all find that they are one and the same equation if the fitness function satisfies ${\pi}_{C}\left(i\right)={\pi}_{C}\left(1\right)+(i1)\left[{\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right]$. In this case, every additional cooperator increases the payoff of a fellow cooperator by just as much as the first cooperator increased the payoff of the defectors in an otherwise alldefector group. Hamilton’s rule will then hold at $p=0$ for any population structure profile $\underset{\_}{\mathbf{u}}$.
If the fitness function satisfies ${\pi}_{C}\left(i\right)\ge {\pi}_{C}\left(1\right)+(i1)\left[{\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right]$ for all $i=1,\mathrm{...},n$, then Hamilton’s rule can be violated at $p=0$. Many cases with synergies would fall under this category. In this case Hamilton’s rule can, however, still not be violated by a population that is in equilibrium at $p=0$. If cooperation is selected against at $p=0$, then that by definition means that Equation 1 does not hold. The left hand side of Equation 3 now is even smaller than the left hand side of Equation 1, so if Equation 1 does not hold, and cooperators are selected against at $p=0$, also Equation 3 does not hold, and $rb<c$. This implies that there is no violation. If, on the other hand, cooperation is selected for at $p=0$, then, by definition, Equation 1 does hold. Now it is possible that Equation 3 does not hold, and $rb<0$, but since cooperation is selected for, the population moves away from $p=0$, and therefore it moves away from where the violation is. Therefore the violation at $p=0$ cannot be observed in equilibrium.
At the other end, where $p=1$, Hamilton’s rule can be rewritten in a similar way. Here, $rb<c$ if
Here, Equation 2 and Equation 4 are one and the same equation if the fitness function satisfies ${\pi}_{D}\left(i\right)={\pi}_{D}(n1)(ni1)\left[{\pi}_{C}\left(n\right){\pi}_{C}(n1)\right]$. In this case, every additional defector decreases the payoff of a fellow defector by just as much as the first defector did to the cooperators in an otherwise allcooperator group. If this is true, then Hamilton’s rule will hold at $p=1$ for any population structure profile $\overline{\mathbf{u}}$.
If the fitness function satisfies ${\pi}_{D}\left(i\right)\ge {\pi}_{D}(n1)(ni1)\left[{\pi}_{C}\left(n\right){\pi}_{C}(n1)\right]$ for all $i=0,\mathrm{...},n1$, then Hamilton’s rule can be violated at $p=1$, but, again, not in equilibrium. If defection is selected against at $p=1$, then Equation 2 by definition does not hold. Under the condition on the fitness function, the left hand side of Equation 4 is now even smaller than the left hand side of Equation 2, so if defectors are selected against at $p=1$, then also Equation 4 does not hold, and $rb\phantom{\rule{thinmathspace}{0ex}}>\phantom{\rule{thinmathspace}{0ex}}c$. This, again, implies that there is no violation. If, on the other hand, defection is selected for at $p=1$, there can be a violation, but this cannot be observed in equilibrium, because defectors being selected for means that the population actually moves away from where the violation is.
So far we have an inequality that prevents violations in equilibrium at $p=0$, and another one that prevents violations at $p=1$. Both concern only the fitness function. If, on top of that, the population structure and the fitness function combined imply that the difference in fitness between cooperators and defectors increases in $p$, then the system does not allow for any violations in equilibrium. The reason is that the latter condition would imply that there simply are no stable interior equilibria. Many systems with synergies will satisfy all three conditions, and therefore preclude inequilibrium violations of Hamilton’s rule. Systems with antisynergies are much more conducive to violations in equilibrium, especially in mixed equilibria, in which cooperators and defectors coexist. Both Figures 2 and 3 illustrate that.
The fitness function used in panels A and B of Figure 2 is linear in the number of cooperators in the group. This makes Equation 1 and Equation 3 coincide, as well as Equation 2 and Equation 4. With the quadratic fitness function in panel C, both ${\pi}_{C}\left(i\right)\ge {\pi}_{C}\left(1\right)+(i1)\left[{\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right]$ and ${\pi}_{D}\left(i\right)\ge {\pi}_{D}(n1)(ni1)\left[{\pi}_{C}\left(n\right){\pi}_{C}(n1)\right]$ hold, which implies that there can be no violation in equilibrium, either at $p=0$ or at $p=1$. This fitness function would be unambiguously synergistic; benefits from cooperation increase, and costs decrease with $i$. Combined with a simple population structure, elaborated on in Appendix 1, ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$ moreover increases in $p$, precluding any inequilibrium violation. Panel D gives an example of a fitness function with antisynergies, where cooperation is selected for at $p=0$, and selected against at $p=1$, and where there is an equilibrium frequency of cooperators in between $0$ and $1$. At that equilibrium $p$, inclusive fitness is not $0$, which makes Hamilton’s rule disagree with the direction of selection.
Games with 2 players and 2 actions are naturally subsumed under this framework, and they allow for whole trajectories to be depicted (Figure 3). A natural way to define population structures with 2 players and constant relatedness $r$ would be to choose ${f}_{0}\left(p\right)=(1r){(1p)}^{2}+r(1p)$; ${f}_{1}\left(p\right)=(1r)2p(1p)$; and ${f}_{2}\left(p\right)=(1r){p}^{2}+rp$. In this case $\underset{\_}{\mathbf{u}}=\left[0,1r,r\right]$ – implying that a mutant cooperator never finds itself in a group with 2 defectors, obviously; faces a defector with probability $1r$; and another cooperator with probability $r$ – and $\overline{\mathbf{u}}=\left[r,1r,0\right]$. This is combined with two prisoners dilemma’s; one with synergies for panel A:
and one with the opposite for panel B:
In the first one, selection always takes the population out of the region where inclusive fitness disagrees with the direction of selection. In the second one there are mixed equilibria, where neither cooperators or defectors are selected for, while inclusive fitness is not $0$.
A similar point is made with Figures 30 and 31 in van Veelen et al. (2017). The conclusion there – that there is ‘no scope for finding violations in equilibria where either one has gone to fixation’ – is too strong though; with antisynergies, violations at $p=0$ and $p=1$ are possible.
Whether or not Hamilton’s rule will hold, with costs and benefits defined according to the counterfactual method, depends on the combination of fitness function and population structure. How often we should expect Hamilton’s rule to hold therefore depends on what we think the distribution of fitness functions and population structures is. Whether reasonable assumptions concerning these distributions lead to many or not so many violations of Hamilton’s rule is an interesting question for further research that we do not pursue here.
Implications for empirical tests of Hamilton’s rule
There is a number of studies that explicitly set out to test Hamilton’s rule empirically. A recent survey by Bourke (2014) includes Bourke (1997); Emlen and Wrege (1989); Gadagkar (2010); Hogendoorn and Leys (1993); Krakauer (2005); Loeb (2003); Metcalf and Whitt (1977); Nonacs and Reeve (1995); Noonan (1981); Pfennig et al. (1999); Queller and Strassmann (1988); Richards et al. (2005) and Stark (1992). These studies typically consider a behaviour that is present, and therefore presumably selected for, estimate its benefits and costs by linear regression, estimate relatedness, and decide that Hamilton’s rule holds if $rb>c$, and is violated if $rb<0$, where the $r$, $b$ and $c$ now refer to the estimated values of relatedness, costs and benefits. Although intuitively appealing, it is worth realizing that this does not constitute a test of either of the two versions of Hamilton’s rule – where it should be noted that these empirical studies were done before it was even recognized that there are different ways to define costs and benefits to begin with.
If we think of Hamilton’s rule with costs and benefits defined according to the regression method, then we have seen that this version of Hamilton’s rule will hold for any linear specification, applied to any thinkable way in which fitnesses in reality could depend on the behaviour of individuals themselves, and on the behaviour of those they interact with. In other words, if we were to treat Hamilton’s rule being valid as the hypothesis, then the hypothesis covers everything, and the null hypothesis is void, as no true way in which fitness would be determined by the behaviour of self and others would go with Hamilton’s rule not holding (see also Nowak et al., 2017). This would also inevitably hamper a good statistical analysis, because, given that there is no true model for which Hamilton’s rule does not hold, there is no meaningful way to define the distribution of inclusive fitnesses (values of $rbc$) under the null hypothesis, which one then would want to use to test if $rbc$ really is larger than $0$.
On the other hand, if we think of Hamilton’s rule with costs and benefits defined according to the counterfactual method, then estimating costs and benefits in a linear model without considering the possibility of nonlinearities would not allow us to uncover violations, because those, as we have seen, require the fitnesses to be nonlinear. One solid way to decide that Hamilton’s rule is not violated would be to allow for a nonlinear model, and reject all nonlinearities, in favour of a linear model. That, however, is not what these papers do.
Our observations therefore first of all imply that meaningful empirical tests would have to consider the version of Hamilton’s rule that uses the counterfactual method for computing costs and benefits, and that they should use statistical models that allow for nonlinearities. Our observations moreover indicate where to look for violations, and where not to look, as there is a variety of settings in which violations are not expected. First of all, one should look at systems where how much being a cooperator instead of a defector contributes to the fitness of others, and takes away from the fitness of oneself, depends on what the others do. Moreover, if we consider a system that is in equilibrium, we would not observe violations if the three 'synergyconditions’ are satisfied, while systems that (also) have antisynergies do allow for inequilibrium violations (see Figure 4). The presence of polymorphisms, where cooperators and defectors coexist, can be a good indication that such antisynergies are present.
Distinct types
We would also not expect violations in cases where the level of help is a continuous trait, the fitness function is smooth, and where the levels of cooperation across individuals are relatively homogeneous, making fitness effects approximately linear. In models with continuous levels of help, populations can then settle at an equilibrium value of cooperation, where Hamilton’s rule is satisfied, provided that there are no branching events (see Section 6 in van Veelen et al., 2017). What is needed for violations, therefore, is that there are distinct types; cooperators and defectors. Some behaviours or properties are binary by nature; one either jumps into a river in an effort to save someone, or not. Also eating a fellow brood member is an all or nothing trait (Pfennig et al., 1999). When the level of cooperation is a continuous trait, one can however also get distinct types to evolve after a branching event (Doebeli et al., 2004). Notice that also at a singular point where the system branches, Hamilton’s rule, which predicts no change, does not agree with what happens (Doebeli and Hauert, 2006).
Spurious violations
When $b$ and $c$ are estimated linearly, we should not expect violations of Hamilton’s rule. This makes it all the more surprising that 4 out of the 12 explicit tests of Hamilton’s rule, surveyed in (Bourke, 2014), all of which estimate costs and benefits with a linear model, do find apparent violations. A natural question to ask is where those violations come from. One prime candidate has to do with the fact that the result that Hamilton’s rule always holds, if costs and benefits are defined using the regression method, depends on using the cooperativenesses of the individuals involved, not just for computing costs and benefits, but also in the formula for relatedness. The relatedness between siblings, for instance, in this version of Hamilton’s rule, would be $cov({x}_{se},{x}_{si})/var\left({x}_{se}\right)$, where ${x}_{se}$ refers to the cooperativeness of self and ${x}_{si}$ to the cooperativeness of the sibling. Here it is good to notice that if these variables refer to data, this is best described, not as relatedness itself, but as an estimator of relatedness. If a different estimator of relatedness is used, for instance based on gene sequencing, then that would include genes for traits other than cooperative behaviour. The difference between these two estimators can make for a violation. The probability of this happening decreases as sample size increases. For all sample sizes, large and small, Hamilton’s rule, using $cov({x}_{se},{x}_{si})/var\left({x}_{se}\right)$ for relatedness, will hold. With small samples, costs, benefits, and relatedness may all vary quite a bit – although only in concert, because Hamilton’s rule will still have to hold – and with $cov({x}_{se},{x}_{si})/var\left({x}_{se}\right)$ possibly being far away from the true relatedness, the discrepancy between it and another estimator for relatedness might be large enough to create an apparent violation of Hamilton’s rule. Other reasons for finding violations when estimating costs and benefits linearly are also possible (see Section 8 of van Veelen et al., 2017), and all of them are spurious.
Smith et al., 2010
In order to be able to find violations of Hamilton’s rule, with benefits and costs defined according to the counterfactual method, one must allow for a nonlinear statistical model. The study that comes closest to that ideal is Smith et al., 2010 (see also Chuang et al., 2009; Chuang et al., 2010). This experiment does a nonlinear estimation of sporulation efficiency of Myxococcus xanthus, resulting in fitness functions that would imply that, already in a wellmixed population, cooperators can invade defectors, and defectors can invade cooperators. Combined with a range of population structures, this would make a population settle at mixed overall frequencies of cooperators. This study however also has a few conceptual imperfections. Most of the nonlinearity it picks up, results from considering Wrightian fitness’s (numbers of offspring) rather than Malthusian fitness’s (growth rates); see Wu et al. (2013). For small fitness effects that would not matter too much, but the aggregate fitness effects are not small here. Another drawback is that the experiment does not include an independent observation of a population structure. For the experiment, a combination of group compositions is chosen. The growth rates at these different group compositions are used to estimate the fitness function – which it is perfect for. The group compositions themselves, as chosen by the experimenter, are also the sole input for calculations characterizing population structure, which makes it not a proper empirical observation of a population structure. In spite of these drawbacks, this study is the closest to a proper empirical test of Hamilton’s rule.
Polymorphisms
While systems of microorganisms with mixed equilibria seem good candidates, one will have to be careful with identifying the reasons for polymorphisms. In systems where one type can invade the other, and vice versa, already in a wellmixed population (Smith et al., 2010; MacLean and Gudelj, 2006; MacLean et al., 2010; Gore et al., 2009), the reason for stable coexistence may have nothing to do with population structure. If fitness is moreover maximized at intermediate mixtures, it also hard to unambiguously qualify one strain as cooperative and the other as defecting (MacLean et al., 2010). Systems like this might nonetheless point to possible candidates, if there is in fact structure in the population. With microorganisms, one would then naturally want to switch from counting discrete numbers of cooperators to a continuous variable for group compositions, measuring the within group frequency of cooperators. Appendix 1 provides a continuous version that allows for all the equivalent computations needed to establish whether or not Hamilton’s rule is violated empirically.
Wang and Lu, 2018
A study that does look at polymorphisms is Wang and Lu (2018). In this study, players have one of two different roles; there are breeding pairs, which are the potential recipients of help, and potential helpers. This implies that there is no room for the strategic interaction that could create the nonlinearities needed for possible violations; costs and benefits of helping at the nest cannot depend on the recipient type, because the recipient is not facing the same choice. Also in this study, therefore, there is no scope for violations of Hamilton’s rule.
Appendix 1
I. Introduction
If one would want to test the validity of Hamilton’s rule empirically, it would be essential to know if Hamilton’s rule can be violated at all, and if it can, it would be essential to know what violations would look like. Whether or not violations are theoretically possible depends on how costs and benefits are defined. Violations are not possible if the costs and benefits in Hamilton’s rule are defined according to the "regression method". In that case there can only be spurious reasons for finding social behaviour that is selected for, while the data would seem to suggest that $br<c$, or vice versa. The version of Hamilton’s rule that uses the regression method is also referred to as the general version of Hamilton’s rule, or HRG; see Birch (2014).
If costs and benefits are defined according to the "counterfactual method", violations are possible. This is the method we will use here, for a variety of reasons. One is that is seems true to the original idea to define for instance the costs of a social act as the difference between an individual’s fitness if it performs the social act, and its fitness if does not. A reason not to use the regression method is also that this method is incomplete, and as such not welldefined; it ignores the issue of model specification, and therefore there are cases where different specifications would result in different Hamilton’s rules, with different values for costs and benefits; see the main text and Section 4 of van Veelen et al. (2017). While the version of Hamilton’s rule that uses the regression method is also referred to as HRG by Birch, 2014, the version of Hamilton’s rule that uses the counterfactual method is not what Birch, 2014 calls the special version of Hamilton’s rule, of HRS. See Section 9 of van Veelen et al., 2017 for details.
Although the counterfactual method allows for violations, it off course also allows for nonviolations. If the interaction is characterized by ‘equal gains from switching’ then violations should not occur. Equal gains from switching means that the fitness effects (the costs and benefits) of the social behaviour are independent of who else contributes, and also independent of whether or not the recipient performs the behaviour. With equal gains from switching, the costs and benefits therefore are also independent of the current share of cooperators in the population. Violations are only possible if the interaction does not have equal gains from switching, and in that case costs and benefits will vary with the current frequency of cooperators.
The fact that cost and benefits are frequencydependent in those cases can make it harder to derive claims that hold for all frequencies. We will therefore begin by focusing on two specific frequencies: $p=0$ and $p=1$. At, or close to those frequencies, we will compare the direction of selection – which here will indicate whether or not one strategy can invade the other, and vice versa – with the value of $rbc$ at those frequencies. For that, it will be useful to define a "population structure profile" at $p=0$, and one at $p=1$. This will be useful for rewriting both inclusive fitness and the direction of selection, and for comparing these to each other. Later on, when looking at cases with equilibrium mixtures of cooperators and defectors, we will also consider frequencies $p$ in between 0 and 1, and revisit this more generally.
II. Relatedness at the edges
A. Close to $p=0$
Performing a cooperative act is assumed to be costly. Not all cooperative acts are costly, because there are also mutualistic forms of cooperation, but in this context, we will mostly focus on costly cooperation, hence the assumption. The benefits of being a cooperator – benefits that may or may not outweigh the costs – we assume comes from the structure in the population. This structure might make cooperators also be on the receiving end more often, as they might be matched with cooperators more often than defectors are. This difference is captured by relatedness. Relatedness is defined as the difference in probabilities (between a cooperator and a defector) of being matched with a cooperator: $P\left(C\rightC)P(C\leftD\right)$. Both of these conditional probabilities will typically depend on the current overall frequency of cooperators, denoted by $p$, but for a variety of population structures, the difference between them will not depend on $p$.
In order to compute that difference, we think of a simple chance experiment. First draw an individual from the population, with every individual being equally likely to be drawn. Then randomly select a partner. In our case, we will use a simple setup, where individuals live in groups of equal size. In this case, the second draw simply returns to the group that the first draw happened to come from, and draws a random other group member, with all (other) group members having equal probability of being drawn.
In this setup with groups of equal size, a population structure is defined by functions ${f}_{i}\left(p\right)$, $i=0,\mathrm{...},n$, that specify the frequency of groups with $i$ cooperators and $ni$ defectors in it, at an overall frequency $p$ of cooperators. Using this notation, and Bayes' rule, the difference in conditional probabilities can be written as
Close to $p=0$, the second term on the right hand side goes to 0, because if there are almost no cooperators around, the chance that a random defector runs into a cooperator must go to 0. In other words, the enumerator goes to 0, because
and because ${f}_{0}\left(p\right)$ is multiplied by $\frac{0}{n1}$. These limits for $p\downarrow 0$ follow from the fact that ${\sum}_{i=0}^{n}\text{}\frac{i}{n}{f}_{i}\left(p\right)=p$; this implies that $\frac{i}{n}{f}_{i}\left(p\right)<p$ for each $i>0$, and hence ${f}_{i}\left(p\right)<\frac{n}{i}p$. Therefore ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}\phantom{\rule{thinmathspace}{0ex}}\phantom{\rule{thinmathspace}{0ex}}{f}_{i}\left(p\right)=0$ for $i>0$, and since ${\sum}_{i=0}^{n}\text{}{f}_{i}(p)=1$, moreover ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}\phantom{\rule{thinmathspace}{0ex}}{f}_{0}\left(p\right)=1$.
The denominator goes to 1 because
Therefore we can write
While relatedness is a onedimensional measure that characterizes a population state, or a population structure to some extent, a richer measure will be useful too. This measure captures how likely cooperators are to find themselves in groups of different types at low frequencies $p$.
With this definition, $\underset{\_}{u}}_{i$ is the share of mutant cooperators that find themselves in a group with $i$ cooperators. Relatedness then becomes the inner product of a vector $\underset{\_}{\mathbf{u}}$ with $\underset{\_}{u}}_{i$ as its $i$th element, and a vector with $\frac{i1}{n1}$ as its $i$th element:
The vector $\underset{\_}{\mathbf{u}}$ could be labelled the ‘population structure profile’ in the limit of $p\downarrow 0$, and it is clear that there is typically a variety of profiles $\underset{\_}{\mathbf{u}}$ that produces one and the same relatedness.
B. Close to $p=1$
Close to $p=1$, it is easier to use the equivalent definition of relatedness, reversing the roles of cooperators and defectors:
The second term on the right hand side goes to $0$ again; the enumerator goes to $0$, because
and because ${f}_{n}\left(p\right)$ is multiplied by $\frac{0}{n1}$, while the denominator goes to $1$ because
Therefore we can write
We can furthermore define a measure that captures how likely defectors are to find themselves in groups of different types at low frequencies $1p$ of defectors (which means high frequencies $p$ of cooperators).
Here $\overline{u}}_{i$ is the share of mutant defectors that finds itself in a group with $i$ cooperators. In many models it would be reasonable to assume that mutant defectors face similar numbers of fellow defectors in their group as mutant cooperators face fellow cooperators. If they do, the population structure profiles at $p=0$ and $p=1$ would be each other’s mirror images: $\underset{\_}{u}}_{i}={\overline{u}}_{ni$. Relatedness at $p=1$ again becomes the inner product of a vector $\overline{\mathbf{u}}$ with $\overline{u}}_{i$ as its $i$th element, and a vector with $\frac{ni1}{n1}$ as its $i$th element.
If indeed $\underset{\_}{u}}_{i}={\overline{u}}_{ni$, then ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\uparrow 1}\phantom{\rule{thinmathspace}{0ex}}r\left(p\right)={\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}\phantom{\rule{thinmathspace}{0ex}}r\left(p\right)$.
These population structure profiles, $\underset{\_}{\mathbf{u}}$ at $p=0$ and $\overline{\mathbf{u}}$ at $p=1$, will be useful for rewriting when cooperation can invade defection ($p=0$), and when defection can invade cooperation ($p=1$), as well as when inclusive fitness is positive or negative at these two frequencies.
III. When cooperation/defection can/cannot invade
A. Close to $p=0$
Mutant $C$’s can invade a resident $D$ if they have higher fitness close to $p=0$:
The game between cooperators and defectors is defined by ${\pi}_{C}\left(i\right)$ for cooperators and ${\pi}_{D}\left(i\right)$ for defectors that determine the payoff they get as a function of the number of cooperators in the group they are in (for cooperators: including themselves). We assume a dynamic that linearly translates payoffs into fitness, like the replicator dynamics. This allows us to use payoffs and fitness interchangeably; see van Veelen, 2011.
In the limit of $p\downarrow 0$, all defectors find themselves in groups with other defectors only, whatever the population structure is, which makes ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}\phantom{\rule{thinmathspace}{0ex}}{\overline{\pi}}_{D}={\pi}_{D}\left(0\right)$. The condition for a $C$ invader to do better than a $D$ resident then becomes:
With the shorthand notation introduced in Section II, this can be written as:
where $\underset{\_}{u}}_{i$ is the share of mutant cooperators that find themselves in groups that contain $i$ cooperators.
B. Close to $p=1$
Mutant $D$’s cannot invade a resident $C$ if the resident has higher fitness at $p=1$:
In the limit of $p\uparrow 1$, all cooperators find themselves in groups with only cooperators, which makes ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\uparrow 1}\phantom{\rule{thinmathspace}{0ex}}{\overline{\pi}}_{C}={\pi}_{C}\left(n\right)$. The condition for $C$ to drive out $D$ invaders then becomes:
With the shorthand notation introduced above, this can be written as:
where $\overline{u}}_{i$ is the share of mutant defectors that find themselves in groups that contain $i$ cooperators.
IV. When inclusive fitness is positive/negative
A. Close to $p=0$
At full defection ($p=0$), inclusive fitness is positive if:
The costs of cooperation at $p=0$ – according to the counterfactual method – are ${\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)=\left({\pi}_{C}\right(1){\pi}_{D}(0\left)\right)$. This is minus the difference between the payoff a cooperator gets in a group where everyone else is a defector, and the payoff gets if it were a defector instead. The aggregate benefits are $(n1)\left[{\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right]$, which is $n1$ times how much every defector in that group benefits from the agent being a cooperator instead of a defector. Inclusive fitness being positive at $p=0$ therefore can be rewritten as
With a little rewriting, this inequality becomes
With $\frac{\sum _{i=1}^{n}\text{}i{f}_{i}\left(p\right)}{\sum _{i=1}^{n}\text{}i{f}_{i}\left(p\right)}=1$, this can be rewritten as:
In shorthand notation, inclusive fitness at $p=0$ is positive if:
B. Close to $p=1$
At full cooperation ($p=1$), inclusive fitness is positive if:
The costs of cooperation at $p=1$ – according to the counterfactual method – are ${\pi}_{D}\left(n1\right){\pi}_{C}\left(n\right)=\left({\pi}_{C}\left(n\right){\pi}_{D}\left(n1\right)\right)$. This is minus the difference between the payoff a cooperator gets in a group where everyone else is a cooperator too, and the payoff it gets if it were a defector instead. The aggregate benefits are $\left(n1\right)\left[{\pi}_{C}\left(n\right){\pi}_{C}\left(n1\right)\right]$, which is $n1$ times how much every other cooperator in that group benefits from the agent being a cooperator instead of a defector. Inclusive fitness being positive at $p=0$ therefore can be rewritten as
With a little rewriting, this inequality becomes
With $\frac{\sum _{i=0}^{n1}\text{}\left(ni\right){f}_{i}\left(p\right)}{\sum _{i=0}^{n1}\text{}\left(ni\right){f}_{i}\left(p\right)}=1$, this can be rewritten as:
In shorthand notation, inclusive fitness at $p=1$ is positive if:
V. (Not) observing violations in equilibrium
Now that we have the criteria, both at $p=0$ and at $p=1$, for cooperators to be selected for, as well as for inclusive fitness to be positive, we can compare them to each other, and find out what it takes to observe a violation.
At $p=0$, cooperators can invade if ${\sum}_{i=1}^{n}\text{}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right){\pi}_{D}\left(0\right)$. If we observe a population at $p=0$, and if we assume, or have reason to believe, that this population is in equilibrium, then that means that cooperators can apparently not invade at $p=0$, and the opposite is true:
Inclusive fitness at $p=0$ is negative if
Now there is a variety of ways in which the left hand sides of these two equations can be different from each other, while they are still both smaller than the right hand side that they share. In that case inclusive fitness is not the right criterion, but we would still not observe a violation in equilibrium. This will most certainly be the case if each and every term in the second equation that replaces a ${\pi}_{C}\left(i\right)$–term from the first one is smaller, making the left hand side of the second equation even smaller than the left hand side of the first. In other words, a sufficient condition for the left hand side of the second equation to be lower than, or at most equal to, the left hand side of the first, is that
for all $i\in 1,\mathrm{...},n$. This would then imply that
and therefore that inclusive fitness is certainly negative whenever cooperation is selected against. A ${\pi}_{C}$ and ${\pi}_{D}$ for which this is true thereby precludes observing a violation of Hamilton’s rule in equilibrium at $p=0$.
Observing violations in equilibrium at $p=0$ would require that at least for one $i$,
and that these differences are sufficiently large to make the left hand side of Equation 2 larger than the right hand side, leading to a positive inclusive fitness, while the behaviour is selected against.
This is mirrored at $p=1$, where defectors cannot invade if
Inclusive fitness at $p=1$ is positive if
Again there is a variety of ways in which the right hand sides of these two equations can be different from each other, while they are both smaller than the left hand side that they share. In that case inclusive fitness is not the right criterion, but we would not observe a violation in equilibrium. That will certainly be the case if the game is such that
for all $i\in 0,\mathrm{...},n1$. This would be a sufficient condition for the right hand side of the second equation to be lower than, or at most equal to, the right hand side of the first, so that
For games that satisfy this condition, observing violations in equilibrium at $p=1$ therefore is impossible, because inclusive fitness is certainly positive if cooperation is selected for.
Observing violations in equilibrium at $p=1$ would require that at least for one $i$,
and that these differences are sufficiently large to make the right hand side of Equation 5 larger than the left hand side, leading to a negative inclusive fitness, while the behaviour is selected for.
A. Not observing violations in equilibrium, also in the interior
While inequalities (Equation 3) and (Equation 6) preclude violations of Hamilton’s rule at $p=0$ and $p=1$, respectively, they do not necessarily also preclude violations in the interior. In order to see why in general they do not, we can first look at a simple special case where they do, and that is if $n=2$, and if, moreover, relatedness is constant.
For $n=2$, inequalities (Equation 3) and (Equation 6) are the same; they both require ${\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)$ to be less or equal to ${\pi}_{C}\left(2\right){\pi}_{C}\left(1\right)$. If these two differences would be equal, then that would be the classical ‘equal gains from switching’, so one could perhaps call it ‘increasing gains from switching’ if the latter is larger.
A population structure with constant relatedness and $n=2$ can only be
We can compute and rewrite the average payoffs of cooperators and defectors for $n=2$ as follows:
and
Since the terms between square brackets in the second line of both are the ‘gains from switching’, increasing gains from switching here implies that the difference in average fitness between cooperators and defectors ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$ is increasing in the frequency of cooperators $p$. Therefore, at $n=2$, inequality (Equation 3) and/or (Equation 6), combined with constant relatedness, implies that if cooperators are selected for at $p=0$, they will be selected all the way to $p=1$, and if they are selected against at $p=1$, they will be selected against all the way to $p=0$. This implies that there are no stable interior equilibria, and therefore are there not only no inequilibrium violations possible at $p=0$ and $p=1$, but also not in between. This is illustrated in Figure 3a in the main text.
If we go to group sizes $n$ larger than $2$, there are many degrees of freedom that make things much more complicated. First of all, conditions (Equation 3) and (Equation 6) do not imply increased gains from switching in some more general, across the board sense. Inequality (Equation 3) only puts limitations on how ${\pi}_{C}\left(i\right){\pi}_{C}\left(1\right)$ relates to ${\pi}_{D}\left(1\right){\pi}_{C}\left(0\right)$, but not, for instance, on how ${\pi}_{C}\left(i\right){\pi}_{C}(i1)$ relates to ${\pi}_{C}(i1){\pi}_{C}(i2)$ or to ${\pi}_{D}(i1){\pi}_{D}(i2)$. One can therefore construct payoff functions that satisfy both inequalities, and yet have gains from switching that sometimes increase and sometimes decrease, depending on how many cooperators there currently are.
Second, one can also tinker with the population structure to create internal stable equilibria. While the grey lines in Figure 3a in the main text represent population structures with fixed $r$, it is clear that if $r$ is allowed to vary with $p$, one can create grey lines (population structures) that have multiple intersections with the green line that separates the region where cooperators are selected for and selected against, thereby creating stable and unstable equilibria. This can happen, in spite of the fact that, for $n=2$, inequalities (Equation 3) and (Equation 6) are as global as it gets. Moreover, with $n>2$ there are enough degrees of freedom in the notion of a population structure to expect that, when combined with almost any fitness function, one might be able to cook up populations structures that result in stable interior equilibria, even with constant $r$. In any case it is clear that conditions on the fitness function alone are not enough to preclude violations of Hamilton’s rule in stable interior equilibria.
For many examples, however, it is more straightforward to directly check the key property that would be relevant to preclude stable interior equilibria, and that is that population structure and fitness function combine in a way that makes ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$ nondecreasing in $p$ – as we did for the case of $n=2$ and fixed relatedness. If inequalities (Equation 3) and (Equation 6) are satisfied, and this ‘relative synergies’ property also holds, then all inequilibrium violations of Hamilton’s rule are ruled out. Just to make sure: this relative synergies property is symmetric, in the sense that ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$ is nondecreasing in $p$ if and only if ${\overline{\pi}}_{D}\left(p\right){\overline{\pi}}_{C}\left(p\right)$ is nondecreasing in $1p$.
VI. Examples
The two conditions from Section V, one for $p=0$, one for $p=1$, allow us to easily make examples of strategic interactions that do not allow for any observations that violate Hamilton’s rule, as long as the population is in equilibrium. Take for instance payoff functions of the following form:
This can be interpreted as a situation where cooperators can produce a public good. How much is produced depends on how many individuals contribute, and that is reflected by $g\left(i\right)$. Besides affecting the payoffs through the public good, contributing always lowers the payoff of an agent by a fixed amount $K$, which is why cooperators always get a payoff that is $K$ below what their defecting fellow group members get. (The costs, according to the counterfactual method, are typically of the form ${\pi}_{D}\left(i\right){\pi}_{C}(i+1)=K+\left(g\right(i)g(i+1\left)\right)$. These also take the difference in payoffs due to the public good production into account, of which the agent itself also benefits, and those are not assumed to be constant.)
A sufficient condition on $g\left(i\right)$ to prevent violations of Hamilton’s rule in equilibrium at $p=0$ and $p=1$ is that there should be synergies – or at least no dissynergies – in the production of the public good:
for $i=1,\mathrm{...},n$. This implies that
for $i=1,\mathrm{...},n$. In Section V we saw that this prevents violations of Hamilton’s rule at $p=0$. Moreover,
for $i=0,\mathrm{...},n1$, which we saw prevents violations of Hamilton’s rule at $p=1$.
A few specific choices for $g\left(i\right)$ can also help illustrate a few possible situations.
Equal gains
If $g\left(i\right)=2\left(\frac{i}{n}\right)$ and $K=0.4$, then
Combined with a population structure elaborated on in Section IX, this results in ${\overline{\pi}}_{C}{\overline{\pi}}_{D}=0.16$, both at $p=0$ and at $p=1$. Inclusive fitness is also $r\left(p\right)b\left(p\right)c\left(p\right)=\frac{1}{4}\frac{48}{25}\frac{32}{100}=0.16$, also both at $p=0$ and at $p=1$. Cooperation therefore will be selected for at both extremes (and everywhere in between) and inclusive fitness agrees with the direction of selection. This is always the case with equal gains from switching. Details about the computations can be found in Section IX.
Synergies
If $g\left(i\right)=2{\left(\frac{i}{n}\right)}^{2}$ and $K=0.5$, then
Combined with the same population structure elaborated on in Section IX, this results in ${\overline{\pi}}_{C}{\overline{\pi}}_{D}=0.33$ at $p=0$ and ${\overline{\pi}}_{C}{\overline{\pi}}_{D}=0.45$ at $p=1$. Cooperation therefore will be selected against at $p=0$, and selected for at $p=1$, which makes both $p=0$ and $p=1$ stable equilibria. Inclusive fitness is $0.48$ at $p=0$ and $0.6$ at $p=1$. Inclusive fitness therefore is more negative than $\overline{\pi}}_{C}{\overline{\pi}}_{D$ at $p=0$, and more positive at $p=1$, which prevents observing violations at equilibrium. Details of the computations, as well as the computation of costs and benefits for the regression method, can be found in Section IX.
Antisynergies
If $g\left(i\right)=2{\left(\frac{i}{n}\right)}^{\frac{1}{2}}$ and $K=0.5$, then
Combined with the same population structure elaborated on in Section IX, this results in ${\overline{\pi}}_{C}{\overline{\pi}}_{D}=0.55$ at $p=0$ and ${\overline{\pi}}_{C}{\overline{\pi}}_{D}=0.19$ at $p=1$. Cooperation therefore will be selected for at $p=0$, and selected against at $p=1$, which makes neither $p=0$ nor $p=1$ an equilibrium. Inclusive fitness is $2.3$ at $p=0$ and $0.22$ at $p=1$. Inclusive fitness therefore is more positive than $\overline{\pi}}_{C}{\overline{\pi}}_{D$ at $p=0$, and more negative than $\overline{\pi}}_{C}{\overline{\pi}}_{D$ at $p=1$. This particular combination of a payoff function and a population structure would not lead to observations of violations in equilibrium at $p=0$ or $p=1$, but if we simply increase $K$, or choose a population structure with less assortment, we could make $\overline{\pi}}_{C}{\overline{\pi}}_{D$ drop below $0$ at $p=0$, while inclusive fitness is still positive. At the other end, we could decrease $K$, or increase assortment, to make $\overline{\pi}}_{C}{\overline{\pi}}_{D$ positive, while inclusive fitness is still below 0, also creating a violation in equilibrium. Moreover, and more importantly, since cooperators invade defectors and defectors invade cooperators, we can expect violations at a mixed equilibrium, which is what Section VII is about. Details of the computations, as well as the computation of costs and benefits for the regression method, can be found in Section IX.
VII. Mixed equilibria
When cooperators can invade defectors and defectors can invade cooperators, there for sure must be at least one equilibrium mixture of cooperators and defectors. Also other games without equal gains from switching may have stable frequencies $p$ at which cooperators and defectors coexist. At those frequencies, we can compare the direction of selection with inclusive fitness. In Sections III, IV and V we did this comparison at $p=0$ and $p=1$ only, now we will need to also do it at the equilibrium frequency, which may be anywhere between 0 and 1.
A. Population structure profiles and relatedness
Similar to before, we can define the probability that a randomly chosen cooperator finds itself in a group in which there are $i$ cooperators:
and the probability that a randomly chosen defector finds itself in a group in which there are $i$ cooperators:
This makes ${\underset{\_}{u}}_{i}={\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}\phantom{\rule{thinmathspace}{0ex}}{u}_{i,C}\left(p\right)$ and ${\overline{u}}_{i}={\mathrm{l}\mathrm{i}\mathrm{m}}_{p\uparrow 1}\phantom{\rule{thinmathspace}{0ex}}{u}_{i,D}\left(p\right)$. Relatedness now becomes
B. Equilibrium
An interior equilibrium is a frequency ${p}^{\ast}\in \left(0,1\right)$ such that the average payoff of cooperators and the average payoff of defectors are equal:
This can be written as
Here we assume that it is clear that average payoffs ${\overline{\pi}}_{C}\left(p\right)$ and ${\overline{\pi}}_{D}\left(p\right)$ depend on the frequency $p$ of cooperators in the overall population, whereas game payoffs ${\pi}_{C}\left(i\right)$ and ${\pi}_{D}\left(i\right)$ depend on the number of cooperators in the group. An equilibrium is stable, if cooperators have a higher average payoff than defectors do for $p<{p}^{\ast}$, and defectors have a higher payoff than cooperators for $p>{p}^{\ast}$.
At $p=0$, all defectors find themselves in groups with no cooperators, and cooperators cannot invade if their average payoff is lower than that of defectors. This gave us the criterion that we used before:
At $p=1$, all cooperators find themselves in groups with no defectors, and defectors cannot invade if their average payoff is lower than that of cooperators. This gave us the criterion that we used before:
C. Costs and benefits
The costs and benefits an individual faces may depend on the type of group an individual finds itself in. The composition of the population ${f}_{i}\left(p\right)$, indicating what the frequencies of the different types of groups will be, depends on the overall frequency $p$ of cooperators. The average costs and benefits therefore may also depend on this frequency $p$. The counterfactual method, as originally suggested by Karlin and Matessi (1983), Matessi and Karlin (1984) and Matessi and Karlin (1986) only considers the costs actually bore by cooperators, and the benefits actually conferred by them onto others. In Section 3 of van Veelen et al. (2017) we show that the costs and benefits of cooperation (compared to defection) then are not necessarily minus the costs and benefits of defection (compared to cooperation). We therefore suggested to include all individuals that faced the opportunity to cooperate, whether they ended up cooperating or defecting. This definition is consistent, and this is also the definition we use here. The cost for a cooperator – comparing its payoffs when it cooperates to its payoffs had it defected – then is ${\pi}_{D}(i1){\pi}_{C}\left(i\right)$; the cost for a defector is ${\pi}_{D}\left(i\right){\pi}_{C}(i+1)$. Average costs then become
Aggregate average benefits similarly become
D. Comparison
Previously, in Section V, we have seen that inclusive fitness $r\left(p\right)b\left(p\right)c\left(p\right)$ may have a sign that is different from the sign of ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$, at $p=0$ and/or at $p=1$, even though that may not always be observable in equilibrium. In a mixed equilibrium ${p}^{\ast}$, where ${\overline{\pi}}_{C}\left({p}^{\ast}\right){\overline{\pi}}_{D}\left({p}^{\ast}\right)=0$, there is also no reason why $r\left({p}^{\ast}\right)b\left({p}^{\ast}\right)c\left({p}^{\ast}\right)$ would be 0 too – unless there is equal gains from switching. Here this discrepancy would be observable (see Appendix 1—figure 5). Note that equal gains would be at odds with there being a stable mixed equilibrium at $0<p\ast <1$. Details of the computations, as well as the computation of costs and benefits for the regression method, can be found in Section IX. With equal gains, ${\pi}_{C}\left(i\right){\pi}_{C}(i1))={\pi}_{D}(j){\pi}_{D}(j1\left)\right)$ for all $i,j\in \{1,\mathrm{...},n\}$ and ${\pi}_{D}(i1){\pi}_{C}\left(i\right))={\pi}_{D}(j1){\pi}_{C}(j\left)\right)$ for all $i,j\in \{1,\mathrm{...},n\}$. If we denote these constants by $\mathbf{b}$ and $\mathbf{c}$, then inclusive fitness becomes $r\left(p\right)\left(n1\right)\mathbf{b}\mathbf{c}$ – where $\left(n1\right)\mathbf{b}$ is the aggregate benefits. This is found by filling in the constants in the formulas at subsection C above.
E. If ${\pi}_{D}$ and ${\pi}_{C}$ are linear, but not parallel, they still violate ‘equal gains from switching’
Equal gains from switching means that the effect of any given individual changing from defection to cooperation on the fitness of other individuals and on her own fitness is independent of what these other individuals choose. The examples of violations above, depicted in Appendix 1—figures 3–7, all have nonlinear ${\pi}_{D}$ and ${\pi}_{C}$. Violations can also occur when ${\pi}_{D}$ and ${\pi}_{C}$ are linear, but not parallel – in which case the fitness effects depend on whether the recipient is a cooperator or defector itself.
An example would be $\pi}_{D}=1+3\frac{i}{n$ and $\pi}_{C}=2+\frac{i}{n$. Both of these are linear in the number of cooperators, but they are not equally steep. Switching to cooperation benefits the other more if the other is a defector, compared to if the other is a cooperator. The total benefit one can confer to others therefore is higher in a group in which most of the others are defectors, and it is lower in a group in which most of the other group members are cooperators. If we choose the same population structure as for Appendix 1—figures 2–5, then there is a mixed equilibrium – at $p=\frac{8}{9}$ – at which Hamilton’s rule is violated; $\frac{1}{4}\left(\frac{88}{75}\right)\left(\frac{2}{3}\right)\approx 0.373\ne 0$.
F. An aside about the regression method
It might also be good to illustrate how the regression method would have treated this fitness function. The regression method chooses $\alpha $, $\beta $ and $\gamma $ so as to minimize
where $\alpha $ is the intercept, $\beta $ is interpreted as $n1$ times the benefit of being matched with one additional cooperator and $\gamma $ is interpreted as the cost of being a cooperator oneself. It is easier to illustrate this without population structure, so the figures on the next page show what this would result in for the fitness function of the last example, combined with the well mixed population, and a group size of $n=25$. In Section IX we will also consider a case with population structure.
The $\alpha $, $\beta $ and $\gamma $ are computed in the limit of $p\downarrow 0$ (top panel), at $p=\frac{1}{2}$ (middle panel), and in the limit of $p\uparrow 1$ (bottom panel). For the well mixed population, it is not too hard to compute these in general at $p\downarrow 0$ and $p\uparrow 1$. In the limit of $p\downarrow 0$, the regression method always results in $\alpha ={\pi}_{D}\left(0\right)$. The reason is that ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}{f}_{0}\left(p\right)=1$, and ${\mathrm{l}\mathrm{i}\mathrm{m}}_{p\downarrow 0}{f}_{i}\left(p\right)=0$ for all $i>0$. Therefore, in the limit, for sure $\left({\pi}_{D}\left(0\right)\alpha \right)}^{2$ must be minimized. Because ${f}_{1}\left(p\right)$ is of the order $p$, while ${f}_{i}\left(p\right)$ is of the order ${p}^{2}$ or higher, for $i>1$, $\beta $ and $\gamma $ must, in the limit, also minimize $\frac{1}{n}{\left({\pi}_{C}\left(1\right)\left(\alpha \gamma \right)\right)}^{2}+\frac{n1}{n}{\left({\pi}_{D}\left(1\right)\left(\alpha +\beta \frac{1}{n1}\right)\right)}^{2}$. This can be done here by simply choosing $\gamma =\alpha {\pi}_{C}\left(1\right)={\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)$, and $\beta =\left(n1\right)\left({\pi}_{D}\left(1\right)\alpha \right)=\left(n1\right)\left({\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right)$. The ‘estimated’ ${\pi}_{D}$ at $p\downarrow 0$ therefore is always a straight line, the steepness of which derives from the first step, from $i=0$ to $i=1$, in ${\pi}_{D}\left(i\right)$. The ‘estimated’ ${\pi}_{C}$ is a line parallel to ${\pi}_{D}$, but then shifted up by ${\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)$, and to the right by $\frac{1}{n1}$.
In this particular case, the squared difference at $p=\frac{1}{2}$ is minimized by choosing $\gamma =0$, making the ‘estimated’ $\pi}_{C$ and $\pi}_{D$ coincide. With population structure, this will all be a bit different, but what remains true is that the ‘estimated’ $\pi}_{C$ and $\pi}_{D$ will always be parallel straight lines, whether the true $\pi}_{C$ and $\pi}_{D$ are straight and parallel or not. The slope and positions of these straight parallel lines typically changes with $p$. The reason why this particular choice for (mis)specifying $\pi}_{C$ and $\pi}_{D$ would lead to Hamilton’s rule always holding, is given in Section 4 of van Veelen et al. (2017).
VIII. Continuous frequencies
For proper large group sizes it can be easier, and more natural, to work with continuous distributions of withingroup frequencies, instead of functions ${f}_{i}\left(p\right)$, which are only defined for $i=0,\mathrm{...},n$. In this section we will therefore introduce the continuous counterparts of definitions from previous sections.
A. Relatedness at the edges
Let ${\left\{{F}_{p}\right\}}_{p\in [0,1]}$ be a set of cumulative distribution functions ${F}_{p}:[0,1]\to [0,1]$, one for every frequency $p$ of cooperators in the population as a whole. ${F}_{p}\left(x\right)$ is the probability, at frequency $p$, that the share of cooperators in a randomly chosen group is smaller than or equal to $x$. Consistency requires that ${\int}_{0}^{1}xd{F}_{p}(x)=p$, and therefore that ${F}_{p}$ converges weakly to the Dirac measure at $0$ for $p\downarrow 0$, and to the Dirac measure at $1$ as $p\uparrow 1$. If ${F}_{p}$ has a density, then one can write ${\int}_{0}^{1}g(x)d{F}_{p}(x)$ as ${\int}_{0}^{1}g(x){f}_{p}(x)dx$.
To relate this to the setting in previous sections, with discrete withingroup frequencies, one would normalize those group types to be values in $[0,1]$, and let them be $\left\{0,\frac{1}{n},...,1\right\}$ instead of $\{0,\mathrm{...},n\}$. Furthermore, one would turn a population structure characterized by functions ${f}_{i}\left(p\right)$, $i=0,\mathrm{...},n$, into one characterized by a cumulative distributions by choosing ${F}_{p}(x)={\sum}_{j=0}^{i}{f}_{j}(p)$ if $\frac{i1}{n}<x\le \frac{i}{n}$. For cumulative distributions ${F}_{p}$ with a density ${f}_{p}$, this density is the natural counterpart of the vector with ${f}_{i}\left(p\right)$ as its $i$th element. The notation is a bit different, though; the overall frequency $p$ is a subscript in the one, and an argument in the other case, while group composition $x$ is an argument in the one, and its counterpart $i$ is a subscript in the other.
Now define cumulative distribution functions $\underset{\_}{U}$ and $\overline{U}$ as follows:
and
and assume that these limits exist.
Again, this one could relate to earlier sections; we can get the vectors $\underset{\_}{\mathbf{u}}$ and $\overline{u}$ back by simply ‘uncumulating’ $\underset{\_}{U}$ and $\overline{U}$; define ${\underset{\_}{u}}_{i}=\underset{\_}{U}\left(\frac{i}{n}\right)\underset{\_}{U}\left(\frac{i1}{n}\right)$ and ${\overline{u}}_{i}=\overline{U}\left(\frac{i}{n}\right)\overline{U}\left(\frac{i1}{n}\right)$.
The fitness functions here will also be defined on $[0,1]$. They will be denoted by ${\pi}_{C}\left(x\right)$ for the fitness of a cooperator in a group with frequency of cooperators $x$, and ${\pi}_{D}\left(x\right)$ for its defector counterpart. Analogous to the derivation in Section II, relatedness at $p=0$ is ${\int}_{0}^{1}\text{}xd\underset{\_}{U}\left(x\right)$, and at $p=1$ it is ${\int}_{0}^{1}\text{}\left(1x\right)d\overline{U}\left(x\right)$. Moreover, it would be natural to assume that $\overline{U}\left(x\right)=\underset{\_}{U}\left(1x\right)$, and therefore that relatedness at $0$ and $1$ are equal.
B. Invasions and inclusive fitness
At $p=0$
The more general version of Equation 1 is that cooperation cannot invade at $p=0$ if their average payoff is less than that of defectors:
Aggregate benefits according to the counterfactual method are defined analogously to Section IV. There they were defined at $p=0$ as $n1$ times the difference between the payoff of a defector that finds itself in a group with one cooperator and defector that finds itself in a group with zero cooperators. In normalized terms, that would be $b\left(0\right)=\left(n1\right)\left[{\pi}_{D}\left(\frac{1}{n}\right){\pi}_{D}\left(0\right)\right]$, which, if $n$ were to go to infinity, would amount to $b\left(0\right)=\frac{{d}_{+}{\pi}_{D}}{dx}\left(0\right)$, where $\frac{{d}_{+}{\pi}_{D}}{dx}\left(0\right)$ is the right derivative of ${\pi}_{D}$ at $0$. Similarly at $p=1$, where aggregate benefits are $b\left(1\right)=\frac{{d}_{}{\pi}_{C}}{dx}\left(1\right)$, which is the left derivative of ${\pi}_{C}$ at $1$. (Discrete population structures, with finite group size, are subsumed under the more general case with distribution functions. Computation of costs and benefits there, however, do differ from how they are computed here, because here one individual changing strategies has no effect on within group frequency $x$, while in the finite case that is not true.)
With those benefits, we can write the continuous version of Equation 2. At $p=0$ inclusive fitness is negative if
which can be rewritten as
If ${\pi}_{C}\left(0\right)+x\frac{{d}_{+}{\pi}_{D}}{dx}\left(0\right)={\pi}_{C}\left(x\right)$, then the left hand sides of Equations 7 and 8 are the same, and inclusive fitness will always agree with the direction of selection at $p=0$. If ${\pi}_{C}\left(0\right)+x\frac{{d}_{+}{\pi}_{D}}{dx}\left(0\right)<{\pi}_{C}\left(x\right)$ the left hand sides of Equations 7 and 8 will not be the same, but a violation in equilibrium at $p=0$ will not be observed; if inequality Equation 7 holds, and cooperators cannot invade, then certainly Equation 8 will hold, making inclusive fitness negative, as its left hand side is even smaller than the left hand side of Equation 7.
At $p=1$
Similarly, defection cannot invade at $p=1$ if
while inclusive fitness at $p=1$ is positive if
which can be rewritten as
If ${\pi}_{D}\left(1\right)\left(1x\right)\frac{{d}_{}{\pi}_{C}}{dx}\left(1\right)={\pi}_{D}\left(x\right)$, then the left hand sides of Equations 9 and 10 are the same. If ${\pi}_{D}\left(1\right)\left(1x\right)\frac{{d}_{}{\pi}_{C}}{dx}\left(1\right)<{\pi}_{D}\left(x\right)$, the left hand sides of Equations 9 and 10 will not be the same, but a violation in equilibrium at $p=1$ will not be observed; if inequality Equation 9 holds, and defectors cannot invade, then certainly Equation 10 will hold, making inclusive fitness positive, as its left hand side is even smaller than the left hand side of Equation 9.
C. Mixed equilibria
Again, when cooperators can invade defectors and defectors can invade cooperators, then for sure there must be at least one equilibrium mixture of cooperators and defectors. Also other games without equal gains from switching may have stable frequencies $p$ at which cooperators and defectors coexist. At those frequencies, we can again compare the direction of selection with inclusive fitness. Here we will assume that at the equilibrium frequency ${p}^{\ast}$, ${F}_{{p}^{\ast}}\left(x\right)$ has a density ${f}_{p}^{\ast}\left(x\right)$, which allows us to write ${f}_{{p}^{\ast}}\left(x\right)dx$ for $d{F}_{{p}^{\ast}}\left(x\right)$.
Equilibrium
An equilibrium is a frequency ${p}^{\ast}$ for which the average payoff of cooperators and defectors are equal; ${\overline{\pi}}_{C}\left({p}^{\ast}\right)={\overline{\pi}}_{D}\left({p}^{\ast}\right)$, that is,
Inclusive Fitness
Relatedness, benefits and costs are computed as before, in Section VII, but now with a continuous ${f}_{p}$.
Again, there is no reason why in equilibrium, where ${\overline{\pi}}_{C}\left({p}^{\ast}\right){\overline{\pi}}_{D}\left({p}^{\ast}\right)=0$, also $r\left({p}^{\ast}\right)b\left({p}^{\ast}\right)c\left({p}^{\ast}\right)$ would be equal to 0.
Example
Consider the following payoff function
Then ${p}^{\ast}$ is an equilibrium frequency if
Inclusive fitness is
and unless $\alpha =1$, the last expression is typically not $0$ for $p={p}^{\ast}$.
IX. Discrete population structures
The population structure used in the examples is not meant to be realistic or reflect any particular real population structure; it is just a convenient vehicle to generate a variety of structures. Imagine a parent group that is assembled by randomly drawing $m$ parents from a large population, a share $p$ of which are cooperators. A parent group consisting of $k$ cooperators and $mk$ defectors is drawn with probability
Then an offspring group is made by drawing – with replacement – $n$ times a parent who reproduces. The probability that a parent group with $k$ cooperators reproduces an offspring group with $i$ cooperators is
This then implies the following population structure, with
for $i=0,\mathrm{...},n$. This is a consistent population structure. Firstly, the frequencies of different group types add up to one.
Here we use twice that the probabilities of the binomial distribution add up to $1$. Also, the frequency of cooperators in the offspring population is consistent with $p$.
Again we twice use that the probabilities of the binomial distribution add up to $1$.
Relatedness is
We first compute $P\left(C\rightC)$ in a straightforward, but somewhat elaborate way.
Here we used twice that the probabilities in the binomial distribution add up to $1$, again, and once that the expectation of the binomial distribution, with $m1$ trials and probability $p$, is $(m1)p$.
This answer makes perfect sense, because if an individual is a $C$ itself, then its parent is one too, while the other $m1$ individuals in the parent group are random draws, with probability $p$ of also being a $C$. The probability that a randomly drawn other offspring is also a $C$ therefore is $\frac{1}{m}+\left(1\frac{1}{m}\right)p$. Similarly, one can compute $P\left(C\rightD)$ to be $\left(1\frac{1}{m}\right)p$, which makes $r\left(p\right)=P\left(CC\right)P\left(CD\right)=\frac{1}{m}$, which is actually independent of $p$.
The population structure profile at $p=0$ for a population structure from this family is ${\underset{\_}{u}}_{0}=0$ and
This can be found by simply evaluating the limits. The easier intuition is that in the limit of $p\downarrow 0$, all cooperator parents find themselves in parent groups in which they are the only one, and all others are defector parents. This means that, conditional on being a cooperator offspring, the composition of the remainder of its offspring group follows a binomial distribution, with the probability of any draw being a cooperator equal to $\frac{1}{m}$.
Similarly, the population structure profile at $p=1$ for a population structure from this family is ${\underset{\_}{u}}_{n}=0$ and
Now, conditional on being a defector offspring, the composition of the remainder of the offspring group it is in follows a binomial distribution, with the probability of any draw being a cooperator equal to $\frac{m1}{m}$.
The population structures used for Appendix 1—figures 1–5 all have $n=25$ for the size of the offspring group. Appendix 1—figures 1a has $m=10$ for the size of the parent group, and hence relatedness $\frac{1}{10}$, as does Figure 2a in the main text. Appendix 1—figures 1b through 5 here, and their corresponding figures in the main text, feature a parent group size of $m=4$, and hence relatedness $\frac{1}{4}$. All computations of ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$ and all computations of inclusive fitness are done by combining these population structures with the different payoff functions from Sections III, IV and V, as described below. Mathematica files with further computational details can be obtained from the author.
Figure 2a in the main text
At $p=0$, and with $m=10$, ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right)=$ ${\sum}_{i=1}^{25}\left(\begin{array}{c}251\\ i1\end{array}\right){\left(\frac{1}{m}\right)}^{i1}{\left(\frac{m1}{m}\right)}^{25i}\cdot \left(0.6+2\left(\frac{i}{25}\right)\right)$ $=0.872$, while ${\pi}_{D}\left(0\right)=1+2\left(\frac{0}{25}\right)=1$, and therefore ${\sum}_{i=1}^{25}\text{}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right){\pi}_{D}\left(0\right)=0.128$. According to the counterfactual method, benefits are $\left(n1\right)\left({\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right)=$ $24\left(1+2\left(\frac{1}{25}\right)\left(1+2\left(\frac{0}{25}\right)\right)\right)$ $=\frac{48}{25}$, costs are ${\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)=$$1+2\left(\frac{0}{25}\right)\left(0.6+2\left(\frac{1}{25}\right)\right)$ $=\frac{8}{25}$ and inclusive fitness is $\frac{1}{10}\frac{48}{25}\frac{8}{25}=0.128$.
At $p=1$, and with $m=10$, ${\pi}_{C}\left(25\right)=0.6+2\left(\frac{25}{25}\right)=2.6$, while ${\sum}_{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=$ ${\sum}_{i=0}^{251}\text{}\left(\begin{array}{c}251\\ i\end{array}\right){\left(\frac{m1}{m}\right)}^{i}{\left(\frac{1}{m}\right)}^{25i1}\cdot \left(1+2\left(\frac{i}{25}\right)\right)$ $=2.728$, and therefore ${\pi}_{C}\left(25\right){\sum}_{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=0.128$. According to the counterfactual method, benefits are $\left(n1\right)\left({\pi}_{C}\left(25\right){\pi}_{C}\left(24\right)\right)=$ $24\left(0.6+2\left(\frac{25}{25}\right)\left(0.6+2\left(\frac{24}{25}\right)\right)\right)$ $=\frac{48}{25}$, costs are ${\pi}_{D}\left(24\right){\pi}_{C}\left(25\right)=$ $1+2\left(\frac{24}{25}\right)\left(0.6+2\left(\frac{25}{25}\right)\right)$ $=\frac{8}{25}$, and inclusive fitness is $\frac{1}{10}\frac{48}{25}\frac{8}{25}=\frac{4}{25}=0.128$.
Because the true fitness function is linear, the regression method would give the same costs and benefits, both at $p=0$ and at $p=1$.
Appendix 1—figure 2 (Figure 2b in the main text)
At $p=0$, and with $m=4$, ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right)=$ ${\sum}_{i=1}^{25}\left(\begin{array}{c}251\\ i1\end{array}\right){\left(\frac{1}{m}\right)}^{i1}{\left(\frac{m1}{m}\right)}^{25i}\cdot \left(0.6+2\left(\frac{i}{25}\right)\right)$ $=1.16$, while ${\pi}_{D}\left(0\right)=1+2\left(\frac{0}{25}\right)=1$, and therefore ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right){\pi}_{D}\left(0\right)=0.16$. Benefits and costs according to the counterfactual method are the same as in Figure 2a in the main text, which makes inclusive fitness equal to $\frac{1}{4}\frac{48}{25}\frac{8}{25}=\frac{4}{25}=0.16$.
At $p=1$, and with $m=4$, ${\pi}_{C}\left(25\right)=0.6+2\left(\frac{25}{25}\right)=2.6$, while ${\sum}_{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=$ ${\sum}_{i=0}^{251}\text{}\left(\begin{array}{c}251\\ i\end{array}\right){\left(\frac{m1}{m}\right)}^{i}{\left(\frac{1}{m}\right)}^{25i1}\cdot \left(1+2\left(\frac{i}{25}\right)\right)$ $=2.44$, and therefore ${\pi}_{C}\left(25\right){\sum}_{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=0.16$. Benefits and costs according to the counterfactual method are the same as in Figure 2a in the main text, which makes inclusive fitness equal to $\frac{1}{4}\frac{48}{25}\frac{8}{25}=\frac{4}{25}=0.16$.
Because the true fitness function is linear, the regression method would give the same costs and benefits, both at $p=0$ and at $p=1$.
Appendix 1—figure 3 (Figure 2c in the main text)
At $p=0$, ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right)=$ ${\sum}_{i=1}^{25}\text{}\left(\begin{array}{c}251\\ i1\end{array}\right){\left(\frac{1}{m}\right)}^{i1}{\left(\frac{m1}{m}\right)}^{25i}\cdot \left(0.5+2{\left(\frac{i}{25}\right)}^{2}\right)$ $=0.6712$, while ${\pi}_{D}\left(0\right)=1+2{\left(\frac{0}{25}\right)}^{2}=1$, and therefore ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right){\pi}_{D}\left(0\right)=0.3288$.
According to the counterfactual method, benefits at $p=0$ are $\left(n1\right)\left({\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right)=$ $24\left(1+2{\left(\frac{1}{25}\right)}^{2}\left(1+2{\left(\frac{0}{25}\right)}^{2}\right)\right)$ $=\frac{48}{625}$. Costs at $p=0$ are ${\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)=$ $1+2{\left(\frac{0}{25}\right)}^{2}\left(0.5+2{\left(\frac{1}{25}\right)}^{2}\right)$ $=\frac{1}{2}\frac{2}{625}$ and inclusive fitness is $\frac{1}{4}\frac{48}{625}\frac{1}{2}+\frac{2}{625}=0.4776$.
In the limit of $p\downarrow 0$, all groups are groups with defectors only. The regression method therefore would imply that $\alpha ={\pi}_{D}\left(0\right)=1$ (see also Section VII F). Furthermore, minimizing the squared difference between true fitness’s and the fitness’s according to a linear model, given the relative weights of all frequencies of groups with $i$ cooperators, with $i\ge 1$, would then amount to
resulting in $b={\beta}^{\ast}=0.586971$, and $c={\gamma}^{\ast}=0.475543$. This makes inclusive fitness $rbc=0.3288$.
At $p=1$, ${\pi}_{C}\left(25\right)=0.5+2{\left(\frac{25}{25}\right)}^{2}=2.5$, while ${\sum}_{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=$ ${\sum}_{i=0}^{251}\text{}\left(\begin{array}{c}251\\ i\end{array}\right){\left(\frac{m1}{m}\right)}^{i}{\left(\frac{1}{m}\right)}^{25i1}\cdot \left(1+2{\left(\frac{i}{25}\right)}^{2}\right)$ $=2.0512$, and therefore ${\pi}_{C}\left(25\right){\sum}_{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=0.4488$.
According to the counterfactual method, benefits at $p=1$ are $\left(n1\right)\left({\pi}_{C}\left(25\right){\pi}_{C}\left(24\right)\right)=$ $24\left(0.5+2{\left(\frac{25}{25}\right)}^{2}\left(0.5+2{\left(\frac{24}{25}\right)}^{2}\right)\right)$ $=\frac{2352}{625}=3.7632$. Costs at $p=1$ are ${\pi}_{D}\left(24\right){\pi}_{C}\left(25\right)=$ $1+2{\left(\frac{24}{25}\right)}^{2}\left(0.5+2{\left(\frac{25}{25}\right)}^{2}\right)$ $=\frac{1}{2}\frac{98}{625}$, and inclusive fitness is $\frac{1}{4}\frac{2352}{625}\frac{1}{2}+\frac{98}{625}=0.5976$.
Because in the limit of $p\uparrow 1$, all groups are groups with cooperators only, the regression method would imply that $\alpha +\beta \gamma ={\pi}_{C}\left(25\right)=2.5$ (see also Section VII F). Minimizing the squared difference between true fitness’s and the fitness’s according to a linear model, considering all frequencies of groups with less than $n$ cooperators, would then amount to
resulting in $b={\beta}^{\ast}=3.25303$, and $c={\gamma}^{\ast}=0.364457$. This makes inclusive fitness $rbc=0.4488$.
Appendix 1—figure 4
At $p=0$, ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right)=$ ${\sum}_{i=1}^{25}\text{}\left(\begin{array}{c}251\\ i1\end{array}\right){\left(\frac{1}{m}\right)}^{i1}{\left(\frac{m1}{m}\right)}^{25i}\cdot \left(0.5+2{\left(\frac{i}{25}\right)}^{0.5}\right)$ $=1.54546$, while ${\pi}_{D}\left(0\right)=1+2{\left(\frac{0}{25}\right)}^{0.5}=1$, and therefore ${\sum}_{i=1}^{25}{\underset{\_}{u}}_{i}{\pi}_{C}\left(i\right){\pi}_{D}\left(0\right)=0.54546$. According to the counterfactual method, benefits are $\left(n1\right)\left({\pi}_{D}\left(1\right){\pi}_{D}\left(0\right)\right)=$ $24\left(1+2{\left(\frac{1}{25}\right)}^{0.5}\left(1+2{\left(\frac{0}{25}\right)}^{0.5}\right)\right)$ $=\frac{48}{5}$, costs are ${\pi}_{D}\left(0\right){\pi}_{C}\left(1\right)=$ $1+2{\left(\frac{0}{25}\right)}^{0.5}\left(0.5+2{\left(\frac{1}{25}\right)}^{0.5}\right)$ $=\frac{1}{2}\frac{2}{5}$ and inclusive fitness is $\frac{1}{4}\frac{48}{5}\frac{1}{2}+\frac{2}{5}=2.3$. According to the regression method, as for Figure 3, but now with the fitness function of Figure 4, costs are $0.350649$, benefits are $3.58443$, and inclusive fitness is $0.54546$.
At $p=1$, ${\pi}_{C}\left(25\right)=0.5+2{\left(\frac{25}{25}\right)}^{0.5}=2.5$, while $\sum _{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=$ $\sum _{i=0}^{251}\text{}\left(\begin{array}{c}251\\ i\end{array}\right){\left(\frac{m1}{m}\right)}^{i}{\left(\frac{1}{m}\right)}^{25i1}\cdot \left(1+2{\left(\frac{i}{25}\right)}^{0.5}\right)$ $=2.69403$, and therefore ${\pi}_{C}\left(25\right)\sum _{i=0}^{251}\text{}{\overline{u}}_{i}{\pi}_{D}\left(i\right)=0.19403$. According to the counterfactual method, benefits are $\left(n1\right)\left({\pi}_{C}\left(25\right){\pi}_{C}\left(24\right)\right)=$ $24\left(0.5+2{\left(\frac{25}{25}\right)}^{0.5}\left(0.5+2{\left(\frac{24}{25}\right)}^{0.5}\right)\right)$ $\approx 0.9698$, costs are ${\pi}_{D}\left(24\right){\pi}_{C}\left(25\right)=$ $1+2{\left(\frac{24}{25}\right)}^{0.5}\left(0.5+2{\left(\frac{25}{25}\right)}^{0.5}\right)$ $\approx 0.4596$, and inclusive fitness is $\frac{1}{4}0.96980.4596\approx 0.217$. According to the regression method, as for Figure 3, but now with the fitness function of Figure 4, costs are $0.45629$, benefits are $1.04905$, and inclusive fitness is $0.19403$.
Appendix 1—figure 5 (Figure 2d in the main text)
At $p=0.473$ and $n=25$,
and
which, with 3digit precision in the solution variable, makes ${p}^{\ast}=0.473$ the equilibrium frequency.
According to the counterfactual method, aggregate average benefits, at ${p}^{\ast}=0.473$ and $n=25$ are
Average costs, similarly computed, are
This makes inclusive fitness at ${p}^{\ast}=0.473$ and $n=25$ equal to $rb\left({p}^{\ast}\right)c\left({p}^{\ast}\right)=$ $\frac{1}{4}\left(2.10255\right)0.412394=0.1129435$
According to the regression method, aggregate benefits as well as costs, at ${p}^{\ast}=0.473$ and $n=25$, follow from the following minimization
which results in ${\alpha}^{\ast}=1.43807$, $b={\beta}^{\ast}=1.71421$, and $c={\gamma}^{\ast}=0.428575$. This makes $rbc=0$.
Mathematica files with further computational details can be obtained from the author.
Notice that in these examples, the costs and benefits according to the regression method are uniquely defined, because – unlike the example in the main text – there is only one type of interactant here. Any specification that includes it, will therefore result in the same regression coefficients. In Appendix 1—figures 3, 4 and 5 it does however still misspecify the shape of the payoff function, in the sense that it replaces a nonlinear function by a linear one.
X. Continuous population structures
Also the continuous population structure we use for the examples is meant to be convenient rather than realistic. Here we use the Beta distribution with parameters $ap$ and $a(1p)$:
This is a consistent population structure. Firstly, the frequencies of different group types, by definition of the Gamma function, integrate to one.
Also, the frequency of cooperators – which is just the first moment of the Beta distribution – is consistent with $p$.
Relatedness is
This makes $P\left(C\rightC)$ the second moment of the Beta distribution, over $p$, while $P\left(C\rightD)$ is the first minus the second moment, over $1p$. Relatedness therefore is
This is independent of $p$. The population structure used for Appendix 1—figure 6 has $a=3$, and hence relatedness $\frac{1}{4}$. The computations of ${\overline{\pi}}_{C}\left(p\right){\overline{\pi}}_{D}\left(p\right)$ and of inclusive fitness are done by combining this population structure with the payoff function from the example, in the way suggested in Section VIII.
Data availability
This is a theoretical paper and all relevant information is provided in the manuscript and supporting files.
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Decision letter

Michael DoebeliReviewing Editor; University of British Columbia, Canada

Diethard TautzSenior Editor; MaxPlanck Institute for Evolutionary Biology, Germany

Burt SimonReviewer; University of Colorado, Denver, United States
In the interests of transparency, eLife includes the editorial decision letter and accompanying author responses. A lightly edited version of the letter sent to the authors after peer review is shown, indicating the most substantive concerns; minor comments are not usually included.
[Editors’ note: a previous version of this study was rejected after peer review, but the authors submitted for reconsideration. The first decision letter after peer review is shown below.]
Thank you for submitting your work entitled "How to test Hamilton's rule empirically" for consideration by eLife. Your article has been reviewed by a Senior Editor, a Reviewing Editor and three peer reviewers. The following individuals involved in review of your submission have agreed to reveal their identity: Burt Simon (Reviewer #1); Eörs Szathmáry (Reviewer #2).
As you can see from the reviewer reports, opinions are divided about the merits of the paper. Based on these reports, your paper is unfortunately not publishable in eLife in its current form. However, we encourage you to resubmit a new version of your manuscript, as we think that it contains an important and useful message.
I strongly encourage you to consider the following points in case you decide to submit a new version of the paper.
1) Two reviewers mentioned that the paper should have a different title, and one report goes into some details explaining the reasons for this. I concur with those explanations. Essentially, your paper contains a nice mathematical model that allows you to apply the counterfactual method for calculating HR and to classify situations in which HR predicts the directions of evolution, and situations in which it does not. After explaining that HR always trivially makes the right predictions when HR is calculated using the regression method, I think the model and the classification of different cases should take central stage. I concur with reviewer 1 that putting the question of empirical tests of HR in the centre misses the mark, and that the empirical perspective should be scaled back and only discussed after the model is explained. I encourage you to take the comments of reviewer 1 into consideration in this regard. Putting the experimental perspective upfront, and in particular putting it in the title, slants the paper in wrong direction in our view. (My suggestion for a title would e.g. contain something like "testing HR with a mathematical model…".)
2) One of the reviewers suggest that your results are not new. I agree with this to some extent, e.g. with regard to the tautological nature of the regression method. I do not share the reviewer's view with regard to the counterfactual model. The reviewer points to two figures in one of your 2017 papers, however, despite those figures being similar to Figure 4 in the current paper, the model used here is quite different, and more general, and I therefore think that its publication is warranted. However, I would urge you to explain in some detail what is different from previous publications, and in that regard, it would again seem advantageous to put the model at central stage (rather than the empirical question).
3) It would be good to present some results as to the overall "likelihood" that HR fails in the model presented. There are a few places where the argumentation is vague, and it would be good if it were made more quantitative. For example, the paper states that when the system moves away from (unstable) equilibria at which HR fails, it then moves into regions where HR holds again (e.g. subsection “Hamilton’s rule”). But as far as I can tell, the claim that HR holds in the regions into which the systems moves is not substantiated. Also, the first paragraph of the Discussion section seems to imply that HR always holds with continuous traits, but the logic there is not clear. E.g. it says that "Alternatively,…", but then does not go into whether HR holds or not in the case of branching, but only states that rather obvious fact that branching leads to conclusion. In fact, I would say that HR does not hold at a branching point, because at such a point HR predicts that there is no evolution (HR=0), even though in fact all (nearby) types can invade! Perhaps this should be discussed in more detail.
4) Finally, I would recommend to think about whether it would be a good idea to comment on the possibility of HR failing in other "general" models, e.g. the one by Lehmann et al., 2016 (Please note that including such material is not a requirement for a resubmission, I would simply recommend considering this.)
When resubmitting your paper, please address the above points, as well as all the points raised by the reviews whenever possible.
Reviewer #1:
I think the population model in the appendix is worthy of publication on its own. it contains enough parameters and flexibility to study the evolution of cooperation in a wide variety of idealized structured populations. The mathematics is both nontrivial and aesthetically pleasing, and there are a number of important aspects of the model that can be analyzed exactly. It's a very nice model that is (literally) tailor made for studying Hamilton's rule.
I'm not nearly as enthusiastic about some of the other aspects of the paper. To start, I don't think the title is a good description of the contents. From the title I was expecting the paper to describe an experiment designed to test Hamilton's rule that a scientist could perform with (say) microbes, and/or an informative review/critique of previous attempts to test HR empirically. The review of previous experiments in the last section of the main text assumes the reader is already familiar with those experiments. I was not familiar with them, and after reading the present paper, I still don't know how those experiments were designed or why the results did or didn't support HR.
So the paper is not really about empirical experiments for testing HR. What it seems to really be about is being specific about what it means for Hamilton's rule to fail in a mathematical model, and in which scenarios this is even possible. So, a better title might be "How to test Hamilton's rule with a mathematical model".
A scientist could (perhaps) read this paper and then design a proper experiment to test HR. If this is the intended purpose of the paper, then it has mostly succeeded. The reason the paper doesn't fully succeed (in my view) is that as nice as the mathematical model is, it may not really apply to any biological experiment that could actually be performed. In order for the mathematics to be relevant, the microbes would need to be cooperators or defectors with an unambiguous way to tell which is which, and groups would need to be carefully placed into separate containers so the desired population structure is in place. It would also need to be true that reproduction in the population is synchronized. It may be possible to do all these things. But (in my view) the experiment wouldn't really be necessary anyway. If someone can find parameter settings for the model where HR fails, where the parameters at least loosely align with a real biological system, then the case is closed: HR does not always hold. Why isn't this enough? If the author can make the (philosophical) argument that to show HR doesn't always hold, it is sufficient to consider mathematical models, I think that would be an important contribution.
My suggestion is that the paper should be rearranged so the model and its analysis (the Appendix) is center stage. It would be nice to then see an example worked out where (of course) the regression method yields {r,b,c} that is consistent with HR, but the counterfactual method yields a different {r,b,c} that is not. Perhaps parameter settings could be chosen randomly (repeatedly) and statistics gathered to get at the interesting question of how often HR holds in the model.
Reviewer #2:
This is very valuable paper. It contributes a lot of clarity to a field that traditionally has been shaped substantially by belief and/of tautology. There are stronger philosophical contributions to be drawn later  but that is another (scary) matter.
The paper can be published as it is.
Reviewer #3:
This paper is titled "How to test Hamilton's rule empirically." From this title, one might expect a series of instructions or guidelines on what to measure to test Hamilton's Rule in the real world, or at least a discussion and critique of how existing empirical tests have gone about doing this. But instead, the paper is almost entirely a disquisition on when different versions of Hamilton's rule may or may not hold at the equilibrium of a discrete, twotrait model.
There are two arguments in the paper, one for the regression definition of HR and one for the HR defined by what the author calls the "counterfactual" method. The summary of the two arguments are below:
1) Linear regression definition of HR always holds by construction, so no data is required, but the regression coefficients will depend on model specification.
2) The "counterfactual" HR always holds with additive fitness, and with positive nonadditivity at the two edge equilibria, but with negative nonadditivity, it may not hold at the interior equilibrium.
Before moving on to the content of these arguments (which I think is weak), I should say that both points have been both made, in a substantively identical way, in a previous paper by Van Veelen et al.,(2017). Point 1 is found in their section 4 and point 2 is essentially a rearranged version of the argument in their Sections 3 and 8. In fact, one of the figures in this manuscript, Figure 4, is essentially a replication of Figure 30 and Figure 31 in Van Veelen et al. As far as I can see, the only technically new addition here might be an extension of the argument for nonadditive games to Nplayers but that is a relatively minor technical extension (the mathematical machinery of this is also present in Van Veelen et al.,). I would therefore say this manuscript essentially reproduces previously published material, with no new points being made. Thus, on novelty grounds I don't see why this is publishable in eLife.
1) It is trivially true that the model specification will of course change the regression coefficients inferred from a given statistical model. Does that mean any statistical fitting exercise is just futile? No, because the model fit (or the likelihood of data) given different specifications is informative about potential causal effects. This is of course the purpose of the timehonored theory of quantitative genetics which the author makes not even a passing reference to (e.g., reading McGlothlin et al., 2014, Phil Trans can give the author some idea of how one might use regression and allied statistical methods productively).
But the author isn't even technically correct when he asserts HR regression cannot fail: *of course* it can: in the sense that RBC can be positive, but the trait might be going down in frequency due to environmental effects, correlated selection and genetic constraints, etc. The world is not identical to our models which is why we go out and test then.
2) The "failure" of the counterfactual method (at the mixed equilibrium of a game with negative synergy) essentially stems from trying to pretend nonadditive model can be used to describe an additive system. So, this is not a surprise here (quite apart from the fact that the same author has already made the point), and I think this simple fact is much less useful than the author seems to think. I do believe that empirical researchers tend to use too simplistic versions of HR without thinking carefully about the structure of the interaction in their model system (e.g., see Akcay and Van Cleve, 2016), but there is nothing in the current treatment that provides any positive insight beyond essentially a rehashing of the nonadditivity issue in a vaguely hostile way.
In short, I don't see why this manuscript adds to the literature on empirical testing, certainly beyond other recent papers by the same author. Therefore, I cannot recommend publication.
https://doi.org/10.7554/eLife.41901.016Author response
[Editors’ note: The authors submitted a new version of their paper for consideration and what now follows is the authors’ response to the first round of peer review.]
As you can see from the reviewer reports, opinions are divided about the merits of the paper. Based on these reports, your paper is unfortunately not publishable in eLife in its current form. However, we encourage you to resubmit a new version of your manuscript, as we think that it contains an important and useful message.
I strongly encourage you to consider the following points in case you decide to submit a new version of the paper.
1) Two reviewers mentioned that the paper should have a different title, and one report goes into some details explaining the reasons for this. I concur with those explanations. Essentially, your paper contains a nice mathematical model that allows you to apply the counterfactual method for calculating HR and to classify situations in which HR predicts the directions of evolution, and situations in which it does not. After explaining that HR always trivially makes the right predictions when HR is calculated using the regression method, I think the model and the classification of different cases should take central stage. I concur with reviewer 1 that putting the question of empirical tests of HR in the centre misses the mark, and that the empirical perspective should be scaled back and only discussed after the model is explained. I encourage you to take the comments of reviewer 1 into consideration in this regard. Putting the experimental perspective upfront, and in particular putting it in the title, slants the paper in wrong direction in our view. (My suggestion for a title would e.g. contain something like "testing HR with a mathematical model…".)
Title. All reviewers indeed found the old title not representative of the content. Reviewer 1 moreover prefers the focus of the paper to shift away from empirical testing, and towards the implications of the population model, and the new title should reflect that change. Reviewer 2 also suggests a title in question form that is a better teaser. I have changed it to “Can Hamilton's rule be violated?”, which I hope accommodates both wishes.
Organization and focus of the paper. I think I have reorganized the paper as suggested, taking the primary focus away from the empirical testing, and only discussing empirical implications at the end.
2) One of the reviewers suggest that your results are not new. I agree with this to some extent, e.g. with regard to the tautological nature of the regression method. I do not share the reviewer's view with regard to the counterfactual model. The reviewer points to two figures in one of your 2017 papers, however, despite those figures being similar to Figure 4 in the current paper, the model used here is quite different, and more general, and I therefore think that its publication is warranted. However, I would urge you to explain in some detail what is different from previous publications, and in that regard, it would again seem advantageous to put the model at central stage (rather than the empirical question).
It is true that there is overlap, and I am very happy that the Editor and reviewers 1 and 2 recognized the added value and elegance of the more general model. I also hope that it is clear that in the old version, I made no effort to hide the overlap, as I referred in detail to different sections in the 2017 paper, but I totally understand that it is helpful to indicate better what is new and what is not, and also to make the (new) general model more central. Pointing to the overlap for Figure 3 also allowed me to point to a mistake in our 2017 paper (which was entirely my mistake, and not of my coauthors).
3) It would be good to present some results as to the overall "likelihood" that HR fails in the model presented.
I agree that this would be interesting, but I don’t really know what to assume as a prior for the distributions of fitness functions and population structures. Also, I imagine that this could be such a broad question, that it would warrant a whole paper on its own. I therefore hope it is OK that I leave this question unanswered here.
There are a few places where the argumentation is vague, and it would be good if it were made more quantitative. For example, the paper states that when the system moves away from (unstable) equilibria at which HR fails, it then moves into regions where HR holds again (e.g. subsection “Hamilton’s rule”). But as far as I can tell, the claim that HR holds in the regions into which the systems moves is not substantiated.
This point is totally correct. The whole reason to focus on the extremes, where cooperators invade defectors or vice versa, was that in the interior, things are much more complicated. Therefore, I was wrong to suggest that the conditions that prevent violations at 𝑝 = 0 and 𝑝 = 1 also preclude violations in the interior. The new subsection “Not observing violations in equilibrium, also in the interior” of the Appendix hopefully solves this, by exploring possible claims about the absence of inequilibrium violations in the interior much more precisely.
This has also led to a new version of a paragraph in the main text (subsection “Hamilton’s rule”).
Besides this, I now elaborate on the computations that went into Figure 2 of the main text (section IX "Discrete population structures" of the Appendix), including new computations of inclusive fitness for the regression method, as suggested by reviewer #1. I am also happy to make the Mathematica files available, so that readers can play around with the computations for themselves.
Also, the first paragraph of the Discussion section seems to imply that HR always holds with continuous traits, but the logic there is not clear. E.g. it says that "Alternatively,…", but then does not go into whether HR holds or not in the case of branching, but only states that rather obvious fact that branching leads to conclusion. In fact, I would say that HR does not hold at a branching point, because at such a point HR predicts that there is no evolution (HR=0), even though in fact all (nearby) types can invade! Perhaps this should be discussed in more detail.
I have rephrased the description there, which now is in subsection “Implications for empirical tests of Hamilton’s rule”. The mismatch between the prediction of HR and what happens at a branching point is now mentioned separately. I hope though that, besides those smaller changes, I can keep this discussion of continuous traits short, in hope to seduce the readers to read Section 6 of the 2017 paper, which is more precise, because it is more extensive.
4) Finally, I would recommend to think about whether it would be a good idea to comment on the possibility of HR failing in other "general" models, e.g. the one by Lehmann et al., 2016 (Please note that including such material is not a requirement for a resubmission, I would simply recommend considering this.)
I have chosen to not also consider other general models, to keep this paper from growing too much in size.
When resubmitting your paper, please address the above points, as well as all the points raised by the reviews whenever possible.
Reviewer #1:
I think the population model in the appendix is worthy of publication on its own. it contains enough parameters and flexibility to study the evolution of cooperation in a wide variety of idealized structured populations. The mathematics is both nontrivial and aesthetically pleasing, and there are a number of important aspects of the model that can be analyzed exactly. It's a very nice model that is (literally) tailor made for studying Hamilton's rule.
I am very glad that the model is appreciated! I am also very glad that the reviewer likes the Appendix, and I hope that, even more than before, I can seduce the readers in the main text to also read the details in the Appendix, which I hold dear.
I'm not nearly as enthusiastic about some of the other aspects of the paper. To start, I don't think the title is a good description of the contents. From the title I was expecting the paper to describe an experiment designed to test Hamilton's rule that a scientist could perform with (say) microbes, and/or an informative review/critique of previous attempts to test HR empirically. The review of previous experiments in the last section of the main text assumes the reader is already familiar with those experiments. I was not familiar with them, and after reading the present paper, I still don't know how those experiments were designed or why the results did or didn't support HR.
So the paper is not really about empirical experiments for testing HR. What it seems to really be about is being specific about what it means for Hamilton's rule to fail in a mathematical model, and in which scenarios this is even possible. So, a better title might be "How to test Hamilton's rule with a mathematical model".
Title. I have changed the title in response to these remarks, as well as the remarks of reviewers #2 and #3 and the editor.
Description of the empirical literature. I hope I also improved the parts that describe the current empirical literature. Also, the reorganization – putting it after the theory part – might help already. I hope I can be excused not to go into all the details of the current empirical tests – besides Smith et al., (2010) – and focus only on the fact that none of these other papers use nonlinear statistics to analyze their data, which is a necessity if the statistics is to be able to capture meaningful violations at all.
A scientist could (perhaps) read this paper and then design a proper experiment to test HR. If this is the intended purpose of the paper, then it has mostly succeeded.
This is indeed the purpose; I hope that this paper would force anyone that sets out to test Hamilton’s rule to reflect on what violations look like, where not to expect them, and to treat the data so that they can capture violations properly – that is, by allowing for nonlinearities in their statistical models.
The reason the paper doesn't fully succeed (in my view) is that as nice as the mathematical model is, it may not really apply to any biological experiment that could actually be performed. In order for the mathematics to be relevant, the microbes would need to be cooperators or defectors with an unambiguous way to tell which is which, and groups would need to be carefully placed into separate containers so the desired population structure is in place. It would also need to be true that reproduction in the population is synchronized. It may be possible to do all these things.
I agree that it will be very difficult to get observations, both of a fitness function, and of a population structure. Papers like Smith et al. (2010) and Chuang et al., (2009, 2010) are examples that good empiricists can achieve at least the measuring of the fitness as a function of (local) shares of cooperators, as the reviewer suggests, but it is true that more remains to be done, including capturing the population structure.
But (in my view) the experiment wouldn't really be necessary anyway. If someone can find parameter settings for the model where HR fails, where the parameters at least loosely align with a real biological system, then the case is closed: HR does not always hold. Why isn't this enough? If the author can make the (philosophical) argument that to show HR doesn't always hold, it is sufficient to consider mathematical models, I think that would be an important contribution.
I very much agree that it is already interesting in and of itself to see how Hamilton’s rule, in theory, can be violated. I do however think that in this case it is also worth pointing to the remarkable state of the empirical literature, which is mostly guided by what I think is a naïve idea of what violations of Hamilton’s rule would look like. If theory can finally make a link to help do better empirics, I think it is worth discussing empirical implications. I hope that it is OK that, although the main focus of the paper is now on the general model itself, it still ends with implications for empirical tests.
My suggestion is that the paper should be rearranged so the model and its analysis (the Appendix) is center stage. It would be nice to then see an example worked out where (of course) the regression method yields {r,b,c} that is consistent with HR, but the counterfactual method yields a different {r,b,c} that is not. Perhaps parameter settings could be chosen randomly (repeatedly) and statistics gathered to get at the interesting question of how often HR holds in the model.
I have rearranged the paper, also following similar suggestions by the editor. In the Appendix, I now elaborate (section IX) on the computations that went into Figure 2 of the main text, and, in response to this comment, I have also added computations of costs and benefits, and thereby inclusive fitness, according the regression method, for the different panels of Figure 2 (which are mostly also separate figures in the Appendix).
Reviewer #2:
This is very valuable paper. It contributes a lot of clarity to a field that traditionally has been shaped substantially by belief and/of tautology. There are stronger philosophical contributions to be drawn later  but that is another (scary) matter.
The paper can be published as it is.
I am very glad to hear this!
Reviewer #3:
This paper is titled "How to test Hamilton's rule empirically." From this title, one might expect a series of instructions or guidelines on what to measure to test Hamilton's Rule in the real world, or at least a discussion and critique of how existing empirical tests have gone about doing this. But instead, the paper is almost entirely a disquisition on when different versions of Hamilton's rule may or may not hold at the equilibrium of a discrete, twotrait model.
Since all reviewers found that the title did not match the content well enough, it has been changed.
There are two arguments in the paper, one for the regression definition of HR and one for the HR defined by what the author calls the "counterfactual" method. The summary of the two arguments are below:
1) Linear regression definition of HR always holds by construction, so no data is required, but the regression coefficients will depend on model specification.
2) The "counterfactual" HR always holds with additive fitness, and with positive nonadditivity at the two edge equilibria, but with negative nonadditivity, it may not hold at the interior equilibrium.
This is an almostcomplete summary of the results. There are two possible elements of increased precision, both at point 2.
a) There is a difference between HR not holding – which in fact happens at 𝑝 = 0 and 𝑝 = 1 for any deviation of additivity – and not holding in equilibrium – which in some cases (see Figure 3A) can indeed not happen at the corners.
b) For other cases, it can actually even in equilibrium be violated at 𝑝 = 0 and 𝑝 = 1 (see Figure 3B). This is also a point where our JTB paper was incorrect, so I of course cannot blame the reviewer for overlooking this possibility here too. I now point out that our 2017 paper did not draw the right conclusion in subsection “Hamilton’s rule” of the manuscript (this mistake was entirely mine, and not of my coauthors).
Before moving on to the content of these arguments (which I think is weak), I should say that both points have been both made, in a substantively identical way, in a previous paper by Van Veelen et al., (2017). Point 1 is found in their section 4 and point 2 is essentially a rearranged version of the argument in their Sections 3 and 8. In fact, one of the figures in this manuscript, Figure 4, is essentially a replication of Figure 30 and Figure 31 in Van Veelen et al. As far as I can see, the only technically new addition here might be an extension of the argument for nonadditive games to Nplayers but that is a relatively minor technical extension (the mathematical machinery of this is also present in Van Veelen et al.,). I would therefore say this manuscript essentially reproduces previously published material, with no new points being made. Thus, on novelty grounds I don't see why this is publishable in eLife.
I agree that some of the points are made previously in our 2017 paper. (Just to be sure: I think I have also made no effort to hide the overlap, as I referred, also before, in detail to different sections in the 2017 paper). I do however disagree that there is not enough value added – although I see that this is perhaps a matter of taste. The new model I think is much more general, and certainly not all of the mathematical machinery is already present in the 2017 paper; for instance, the quite central idea of a population structure profile is entirely absent in the 2017 paper.
1) It is trivially true that the model specification will of course change the regression coefficients inferred from a given statistical model. Does that mean any statistical fitting exercise is just futile? No, because the model fit (or the likelihood of data) given different specifications is informative about potential causal effects. This is of course the purpose of the timehonored theory of quantitative genetics which the author makes not even a passing reference to (e.g., reading McGlothlin et al., 2014, Phil Trans can give the author some idea of how one might use regression and allied statistical methods productively).
This remark does not match with what it is that the paper claims, and ‘refutes’ things that I am not saying.
1) I do not claim that it is deep or nontrivial that regression coefficients change with model specifications. Quite the contrary: I hope that the familiarity of those that do statistics with this straightforward observation, will actually help bring the point across. All I claim is that estimators of regression coefficients vary with specification. Nothing more, nothing less. This is the core ingredient for observing that costs and benefits in Hamilton’s rule are not necessarily uniquely defined, when using the regression method. The paper I think was and is quite clear that this (Hamilton’s rule not being uniquely defined with the regression method) is the point.
2) I do not claim that statistical fitting exercises are futile. There is really nothing in the text to suggest that. What I would say actually goes in the opposite direction. For making a good fit, it is not productive to do the fitting exercise within an a priori restricted set of linear models only – which is what the regression method does – especially when the data would suggest otherwise. And for fit, it is an even worse (actually an absurd) idea in modelling exercises, in which the postulated model is explicitly not linear, and you could get perfect fit by just taking the postulated model itself, and not replacing it with something linear. The linear model then produces Hamilton’s rule, according to the regression method, but that goes at the expense of the fit, in a case where we moreover know for sure there is a mismatch. So in fact I care very much – and not very little – for good fit!
But the author isn't even technically correct when he asserts HR regression cannot fail: *of course* it can: in the sense that RBC can be positive, but the trait might be going down in frequency due to environmental effects, correlated selection and genetic constraints, etc. The world is not identical to our models which is why we go out and test then.
Again, this is a comment that disagrees with something I am not claiming, and that overlooks what it is that I am claiming.
Here it will be helpful to separate “models of how the world works” on the one hand from Hamilton’s rule on the other. Hamilton’s rule is not a model. It is a rule, that one can define (in different ways, depending on the definition of costs and benefits) for any given model. The generality of Hamilton’s rule with the regression method is that, whichever model of the world one chooses, Hamilton’s rule will always agree with the direction of selection. So, while any given model of the world could (indeed, of course) be rejected, the fact that for any conceivable way in which the world could work (including the way the world really works), Hamilton’s rule, with costs and benefits according to the regression method, holds, means that this version of Hamilton’s rule cannot fail.
I have rephrased one small part of the paper to stress this point a bit more (now subsection “Implications for empirical tests of Hamilton’s rule”).
2) The "failure" of the counterfactual method (at the mixed equilibrium of a game with negative synergy) essentially stems from trying to pretend nonadditive model can be used to describe an additive system. So, this is not a surprise here (quite apart from the fact that the same author has already made the point), and I think this simple fact is much less useful than the author seems to think. I do believe that empirical researchers tend to use too simplistic versions of HR without thinking carefully about the structure of the interaction in their model system (e.g., see Akcay and Van Cleve, 2016), but there is nothing in the current treatment that provides any positive insight beyond essentially a rehashing of the nonadditivity issue in a vaguely hostile way.
This remark is upside down in an almost dazzling way. It is not the counterfactual method that, as the reviewer writes, is “trying to pretend a nonadditive model can be used to describe an additive system”. That would be weird, because additive models are nested in the larger set of nonadditive ones, so if that were the case – which it is not, because the counterfactual method just is not doing that – then that could never even be a problem. The point that I make, is the double contrary of what the reviewer writes. It is the regression method that is trying to describe a nonadditive system with an additive model. That is where a real difference between the two methods can arise, since nonadditive models are not a subset of additive ones. Again, it is remarkable that the reviewer reads this into the paper, because both the theory and the examples all clearly point towards the issues at hand arising when the real world is not additive, and the different methods for computing costs and benefits diverge, and not when the real world is additive, in which case both methods (with the “right” specification for the regression method) just find the same costs and benefits, and Hamilton’s rule for both agrees with the direction of selection.
The fact that the reviewer seems to shrug his or her shoulders about empirical researchers tending to use simplistic versions without thinking carefully about the structure of the interaction in their model, I also find strange. I think it would be of obvious importance for empirical researchers to think carefully about this, because for explicit tests of Hamilton’s rule, this makes the difference between a test that is meaningless, because it by design does not allow for nonspurious violations, and a test that is meaningful, because it can, if the real world happens to be nonlinear, in principle reject Hamilton’s rule.
Finally, I think the paper is not vaguely hostile at all. I do not really know how to respond to this accusation, but I do find it very unpleasant that bringing up factual points about limitations of inclusive fitness, here and in other instances, apparently cannot be done without being accused of hostility, in spite of the fact that I appreciate the value of Hamilton’s rule very much, and have expressed that appreciation regularly.
In short, I don't see why this manuscript adds to the literature on empirical testing, certainly beyond other recent papers by the same author. Therefore, I cannot recommend publication.
The (sometimes creative) misreading of the manuscript, and the fact that this happens more often, to me indicates that there is a relatively general unwillingness to seriously consider the possibility that there can be limitations of Hamilton’s rule. Although being defensive about something as valuable as Hamilton’s rule is understandable, this unwillingness is not rooted in scientific considerations only, and therefore this report to me only underscores the importance of publishing a balanced demarcation of when Hamilton’s rule can, and when it cannot be violated.
https://doi.org/10.7554/eLife.41901.017Article and author information
Author details
Funding
The authors declare that there was no funding for this work.
Acknowledgements
I would like to thank Peter Spreij, Ben Allen, Carl Veller, and the reviewers.
Senior Editor
 Diethard Tautz, MaxPlanck Institute for Evolutionary Biology, Germany
Reviewing Editor
 Michael Doebeli, University of British Columbia, Canada
Reviewer
 Burt Simon, University of Colorado, Denver, United States
Publication history
 Received: September 10, 2018
 Accepted: October 10, 2018
 Accepted Manuscript published: October 15, 2018 (version 1)
 Version of Record published: November 22, 2018 (version 2)
Copyright
© 2018, van Veelen et al.
This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
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 Developmental Biology
 Evolutionary Biology
We have focused on the mushroom bodies (MB) of Drosophila to determine how the larval circuits are formed and then transformed into those of the adult at metamorphosis. The adult MB has a core of thousands of Kenyon neurons; axons of the earlyborn g class form a medial lobe and those from laterborn a'b' and ab classes form both medial and vertical lobes. The larva, however, hatches with only g neurons and forms a vertical lobe 'facsimile' using larvalspecific axon branches from its g neurons. Computations by the MB involves MB input (MBINs) and output (MBONs) neurons that divide the lobes into discrete compartments. The larva has 10 such compartments while the adult MB has 16. We determined the fates of 28 of the 32 types of MBONs and MBINs that define the 10 larval compartments. Seven larval compartments are eventually incorporated into the adult MB; four of their larval MBINs die, while 12 MBINs/MBONs continue into the adult MB although with some compartment shifting. The remaining three larval compartments are larval specific, and their MBIN/MBONs transdifferentiate at metamorphosis, leaving the MB and joining other adult brain circuits. With the loss of the larval vertical lobe facsimile, the adult vertical lobes, are made de novo at metamorphosis, and their MBONs/MBINs are recruited from the pool of adultspecific cells. The combination of cell death, compartment shifting, transdifferentiation, and recruitment of new neurons result in no larval MBINMBON connections persisting through metamorphosis. At this simple level, then, we find no anatomical substrate for a memory trace persisting from larva to adult. For the neurons that transdifferentiate, our data suggest that their adult phenotypes are in line with their evolutionarily ancestral roles while their larval phenotypes are derived adaptations for the larval stage. These cells arise primarily within lineages that also produce permanent MBINs and MBONs, suggesting that larval specifying factors may allow information related to birthorder or sibling identity to be interpreted in a modified manner in these neurons to cause them to adopt a modified, larval phenotype. The loss of such factors at metamorphosis, though, would then allow these cells to adopt their ancestral phenotype in the adult system.

 Evolutionary Biology
 Genetics and Genomics
Causal lossoffunction (LOF) variants for Mendelian and severe complex diseases are enriched in 'mutation intolerant' genes. We show how such observations can be interpreted in light of a model of mutationselection balance, and use the model to relate the pathogenic consequences of LOF mutations at presentday to their evolutionary fitness effects. To this end, we first infer posterior distributions for the fitness costs of LOF mutations in 17,318 autosomal and 679 Xlinked genes from exome sequences in 56,855 individuals. Estimated fitness costs for the loss of a gene copy are typically above 1%; they tend to be largest for Xlinked genes, whether or not they have a Y homolog, followed by autosomal genes and genes in the pseudoautosomal region. We then compare inferred fitness effects for all possible de novo LOF mutations to those of de novo mutations identified in individuals diagnosed with one of six severe, complex diseases or developmental disorders. Probands carry an excess of mutations with estimated fitness effects above 10%; as we show by simulation, when sampled in the population, such highly deleterious mutations are typically only a couple of generations old. Moreover, the proportion of highly deleterious mutations carried by probands reflects the typical age of onset of the disease. The study design also has a discernible influence: a greater proportion of highly deleterious mutations is detected in pedigree than casecontrol studies, and for autism, in simplex than multiplex families and in female versus male probands. Thus, anchoring observations in human genetics to a population genetic model allows us to learn about the fitness effects of mutations identified by different mapping strategies and for different traits.