From an evolutionary perspective, social behaviours are those which have fitness consequences for both the individual that performs the behaviour, and another individual. Over the last 43 years, a huge theoretical and empirical literature has developed on this topic. However, progress is often hindered by poor communication between scientists, with different people using the same term to mean different things, or different terms to mean the same thing. This can obscure what is biologically important, and what is not. The potential for such semantic confusion is greatest with interdisciplinary research. Our aim here is to address issues of semantic confusion that have arisen with research on the problem of cooperation. In particular, we: (i) discuss confusion over the terms kin selection, mutualism, mutual benefit, cooperation, altruism, reciprocal altruism, weak altruism, altruistic punishment, strong reciprocity, group selection and direct fitness; (ii) emphasize the need to distinguish between proximate (mechanism) and ultimate (survival value) explanations of behaviours. We draw examples from all areas, but especially recent work on humans and microbes.

/pdf/social-semantics-altruism-cooperation-mutualism-strong-3k3ka2y3w8.pdf

Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection.

Antagonistic coevolution between hosts and parasites is believed to play a pivotal role in host and parasite population dynamics, the evolutionary maintenance of sex and the evolution of parasite virulence. Furthermore, antagonistic coevolution is believed to be responsible for rapid differentiation of both hosts and parasites between geographically structured populations. Yet empirical evidence for host-parasite antagonistic coevolution, and its impact on between-population genetic divergence, is limited. Here we demonstrate a long-term arms race between the infectivity of a viral parasite (bacteriophage; phage) and the resistance of its bacterial host. Coevolution was largely driven by directional selection, with hosts becoming resistant to a wider range of parasite genotypes and parasites infective to a wider range of host genotypes. Coevolution followed divergent trajectories between replicate communities despite establishment with isogenic bacteria and phage, and resulted in bacteria adapted to their own, compared with other, phage populations.

/pdf/antagonistic-coevolution-between-a-bacterium-and-a-18rada1pcb.pdf

Antagonistic coevolution between a bacterium and a bacteriophage.

Antagonistic interactions between hosts and parasites are a key structuring force in natural populations, driving coevolution(1,2). However, direct empirical evidence of long-term host-parasite coevolution, in particular `Red Queen' dynamics-in which antagonistic biotic interactions such as host-parasite interactions can lead to reciprocal evolutionary dynamics-is rare(3-5), and current data, although consistent with theories of antagonistic coevolution, do not reveal the temporal dynamics of the process(6). Dormant stages of both the water flea Daphnia and its microparasites are conserved in lake sediments, providing an archive of past gene pools. Here we use this fact to reconstruct rapid coevolutionary dynamics in a natural setting and show that the parasite rapidly adapts to its host over a period of only a few years. A coevolutionary model based on negative frequency-dependent selection, and designed to mimic essential aspects of our host parasite system, corroborated these experimental results. In line with the idea of continuing host-parasite coevolution, temporal variation in parasite infectivity changed little over time. In contrast, from the moment the parasite was first found in the sediments, we observed a steady increase in virulence over time, associated with higher fitness of the parasite.

/pdf/host-parasite-red-queen-dynamics-archived-in-pond-sediment-33omkyse14.pdf

Host–parasite ‘Red Queen’ dynamics archived in pond sediment

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).

https://www.genetics.org/content/genetics/164/4/1635.full.pdf

The Population Genetics of Clonal and Partially Clonal Diploids

Summary Natural selection can adjust the rate of mutation in a population by acting on allelic variation affecting processes of DNA replication and repair Because mutation is the ultimate source of the genetic variation required for adaptation, it can be appealing to suppose that the genomic mutation rate is adjusted to a level that best promotes adaptation Most mutations with phenotypic effects are harmful, however, and thus there is relentless selection within populations for lower genomic mutation rates Selection on beneficial mutations can counter this effect by favoring alleles that raise the mutation rate, but the effect of beneficial mutations on the genomic mutation rate is extremely sensitive to recombination and is unlikely to be important in sexual populations In contrast, high genomic mutation rates can evolve in asexual populations under the influence of beneficial mutations, but this phenomenon is probably of limited adaptive significance and represents, at best, a temporary reprieve from the continual selection pressure to reduce mutation The physiological cost of reducing mutation below the low level observed in most populations may be the most important factor in setting the genomic mutation rate in sexual and asexual systems, regardless of the benefits of mutation in producing new adaptive variation Maintenance of mutation rates higher than the minimum set by this ‘‘cost of fidelity’’ is likely only under special circumstances BioEssays 22:1057‐ 1066, 2000 fl 2000 John Wiley & Sons, Inc

The evolution of mutation rates: separating causes from consequences.

The positive replies to our original paper (West et al., 1999) leave us in the pleasurable position of being able to keep our ®nal comments short. Kondrashov (1999) demonstrates what Seger (1999) called `physics envy'. The idea that the Mutational Deterministic hypothesis can be easily validated or rejected, once the minimum rate of deleterious mutations per genome per generation (U) is known, sounds great, especially if the magical number is U > 1. However, quantitative predictions (and assumptions) are almost always model-speci®c, so that there is unlikely to be a single, uncontroversial value, even if we ignore the large con®dence limits that are placed on estimates of U (see West et al., 1999). For instance, with reasonable levels of epistasis, a value of U > 1.5 is required (Charlesworth, 1990). If stochastic effects (which are unavoidable during the early phases of any clonal invasion) or variation in the extent of epistasis are included, then U > 2.0 is required (Howard, 1994; Otto & Feldman, 1997). In addition, irrespective of the value of U, the Mutational Deterministic hypothesis absolutely requires synergistic epistasis between deleterious mutations (Kondrashov, 1982). The idea that a single value of U will resolve the issue seems to us somewhat optimistic. We agree with Kondrashov (1999) that our particular form of pluralist explanation is required for only a small fraction (»0.2 < U < »2.0) of the entire parameter space (0 < U < ¥). However, that `small fraction' is the relevant parameter space: it is where the majority of estimates of the mutation rate in sexual species fall (West et al., 1999). A pressing goal now is to determine the virulence of parasites in the wild, and whether they in fact evolve to infect locally common host genotypes. If the latter is not true, or if parasites are not suf®ciently virulent to drive host gene frequency dynamics, then both the parasite-driven Red Queen and our particular form of pluralism are falsi®ed. We agree with Lenski (1999) that different factors may be responsible for the evolutionary origin and maintenance of sex. As we said, our discussion concerned the maintenance of sex. We also agree that experiments with Escherichia coli offer an exceptional opportunity to test for `a general tendency for genetic structures to exhibit synergistic epistasis among deleterious mutations' (Elena & Lenski, 1997). We note, however, that such experiments cannot test whether synergistic epistasis occurs in a type of organism where sexual reproduction predominates. Do larger, more complex genomes with higher mutation rates lead to synergistic epistasis (Szathmary, 1993; Falush, 1998; Hurst & Smith, 1998)? Do the higher numbers of parasites in larger species help cause truncation selection against individuals with large numbers of mutations? Estimating relevant parameters can be much harder in more complex and sexual species (West et al., 1998), but such results are crucial. We hope eventually to have a range of estimates of the mutation rate and the extent of epistasis from a number of sexual and asexual species, so that a whole slew of more subtle questions can be addressed. Red®eld's (1999) comments give us the opportunity to make the following points, orthogonal to our discussion of plurality. (1) Theoretical models suggest that the rate of crossing over is far more important than chromosome number in determining the effective amount of recombination (Burt, unpublished observations). (2) Variation in recombination rates across species are consistent with Red Queen and mutational models (Burt & Bell, 1987;

Sex may need more than one

One of the greatest challenges for evolutionary biology is explaining the widespread occurrence of sexual reproduction and the associated process of genetic recombination. A large number of theories have been developed that provide a sufficient short-term advantage for sex to offset its two-fold cost. These theories can be broadly classified into environmental (or ecological) and mutation-based models. Traditionally, the different theories have been viewed as competing, and empirical work has attempted to distinguish between them. Here we highlight the advantages that may be gained from considering that multiple mechanisms (environmental and mutational) may be at work, and that interactions between the theories may be very important.

/pdf/a-pluralist-approach-to-sex-and-recombination-vkk9a75prv.pdf

A pluralist approach to sex and recombination

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Sex may need more than one

A pluralist approach to sex and recombination