Coalescence, genetic diversity in sexual populations under selection

In sexual populations, selection operates neither on the whole genome, which is repeatedly taken apart and reassembled by recombination, nor on individual alleles that are tightly linked to the chromosomal neighborhood. The resulting interference between linked alleles reduces the efficiency of selection and distorts patterns of genetic diversity. Inference of evolutionary history from diversity shaped by linked selection requires an understanding of these patterns. Here, we present a simple but powerful scaling analysis identifying the unit of selection as the genomic "linkage block" with a characteristic length determined in a self-consistent manner by the condition that the rate of recombination within the block is comparable to the fitness differences between different alleles of the block. We find that an asexual model with the strength of selection tuned to that of the linkage block provides an excellent description of genetic diversity and the site frequency spectra when compared to computer simulations. This linkage block approximation is accurate for the entire spectrum of strength of selection and is particularly powerful in scenarios with many weakly selected loci. The latter limit allows us to characterize coalescence, genetic diversity, and the speed of adaptation in the infinitesimal model of quantitative genetics

Inferring HIV escape rates from multi-locus genotype data

Cytotoxic T-lymphocytes (CTLs) recognize viral protein fragments displayed by major histocompatibility complex (MHC) molecules on the surface of virally infected cells and generate an anti-viral response that can kill the infected cells. Virus variants whose protein fragments are not efficiently presented on infected cells or whose fragments are presented but not recognized by CTLs therefore have a competitive advantage and spread rapidly through the population. We present a method that allows a more robust estimation of these escape rates from serially sampled sequence data. The proposed method accounts for competition between multiple escapes by explicitly modeling the accumulation of escape mutations and the stochastic effects of rare multiple mutants. Applying our method to serially sampled HIV sequence data, we estimate rates of HIV escape that are substantially larger than those previously reported. The method can be extended to complex escapes that require compensatory mutations. We expect our method to be applicable in other contexts such as cancer evolution where time series data is also available

Adherence to public institutions that foster cooperation

Here, the authors examine how altruism can emerge as people come to trust a public institution of moral assessment, which broadcasts whether individuals have good or bad reputations for reciprocity

Model parameters and variables.

Social reputations provide a powerful mechanism to stimulate human cooperation, but observing individual reputations can be cognitively costly. To ease this burden, people may rely on proxies such as stereotypes, or generalized reputations assigned to groups. Such stereotypes are less accurate than individual reputations, and so they could disrupt the positive feedback between altruistic behavior and social standing, undermining cooperation. How do stereotypes impact cooperation by indirect reciprocity? We develop a theoretical model of group-structured populations in which individuals are assigned either individual reputations based on their own actions or stereotyped reputations based on their groups’ behavior. We find that using stereotypes can produce either more or less cooperation than using individual reputations, depending on how widely reputations are shared. Deleterious outcomes can arise when individuals adapt their propensity to stereotype. Stereotyping behavior can spread and can be difficult to displace, even when it compromises collective cooperation and even though it makes a population vulnerable to invasion by defectors. We discuss the implications of our results for the prevalence of stereotyping and for reputation-based cooperation in structured populations.</div

Supplementary analysis.

Social reputations provide a powerful mechanism to stimulate human cooperation, but observing individual reputations can be cognitively costly. To ease this burden, people may rely on proxies such as stereotypes, or generalized reputations assigned to groups. Such stereotypes are less accurate than individual reputations, and so they could disrupt the positive feedback between altruistic behavior and social standing, undermining cooperation. How do stereotypes impact cooperation by indirect reciprocity? We develop a theoretical model of group-structured populations in which individuals are assigned either individual reputations based on their own actions or stereotyped reputations based on their groups’ behavior. We find that using stereotypes can produce either more or less cooperation than using individual reputations, depending on how widely reputations are shared. Deleterious outcomes can arise when individuals adapt their propensity to stereotype. Stereotyping behavior can spread and can be difficult to displace, even when it compromises collective cooperation and even though it makes a population vulnerable to invasion by defectors. We discuss the implications of our results for the prevalence of stereotyping and for reputation-based cooperation in structured populations.</div

Competition among discriminators who stereotype (1DISC), discriminators who do not stereotype (0DISC), and players who cooperate only with the in-group (TAG).

Arrows indicate the dynamical flow within the simplex of three competing strategies. All reputations are public information assessed according to the Stern Judging norm. Individuals are distributed across two groups of equal size (K = 2, ν1 = ν2 = 0.5). TAG exhibits behavior qualitatively similar to ALLD when competing with 0DISC and 1DISC (A–D versus Fig 4E–4H). The basin of attraction towards the 0DISC vertex, which produces high levels of cooperation (Fig 2), is largest when individual reputations are inexpensive (low η; A), but it quickly shrinks with increasing η (B–D). For sufficiently high access cost (D), 0DISC can be invaded not only by TAG but also by 1DISC, which, in turn, can be invaded by TAG—so that pure tribalism (TAG) is the only stable outcome. Parameters: b = 3, c = 1, ue = ua = 0.02. (PDF)</p

Cooperation levels in monomorphic populations of <i>p</i>DISC (Scoring).

Cooperation levels in monomorphic populations of pDISC (Scoring).</p

Fitness in monomorphic populations.

We analyzed individual fitness levels under the Stern Judging norm among pDISC strategists with a uniform stereotype-use propensity p. As in Fig 2, individuals are in two groups of equal size (K = 2, ν1 = ν2 = 0.5). Each panel shows a combination of monitoring systems for individual (row) and stereotyped (column) reputations. Color indicates access cost η. Parameters: b = 3, c = 1, ua = ue = 0.02. (PDF)</p

Stereotyping can produce high or low levels of cooperation depending on the scale of information sharing.

A-I: We analyzed the equilibrium level of cooperation among pDISC strategists under the Stern Judging norm, as a function of the propensity p to use stereotypes instead of individual reputations. The population consists of two groups of equal size (K = 2, ν1 = ν2 = 0.5). Each panel shows a combination of monitoring systems for individual (row) and stereotyped (column) reputations. Solid lines show the average cooperation levels across the entire population; dashed lines show average cooperation levels within (dark blue) and between (light blue) groups. The gap between in- and out-group cooperation is most pronounced when individuals use only individual reputations (p = 0; B, E, and F) or only stereotypes (p = 1; D, E, and H). Error rates are ua = ue = 0.02. Analogous results for the Scoring, Shunning, and Simple Standing norms are shown in S1–S3 Figs. Analytical results corresponding to the case in panel A are provided in Section 3.2 of S1 Text.</p

The use of stereotypes can destabilize cooperation (group-wise monitoring).

As in Fig 4, but with group-wise monitoring for both individual and stereotyped reputations. The outcomes for both sets of strategies (A–D: ALLD, ALLC and in pDISC; E–H: ALLD, 0DISC, and 1DISC) are qualitatively similar to the corresponding results under public monitoring (Fig 4). Results are shown for the Stern Judging norm, as in Fig 4. (PDF)</p