Altruism and social cheating in the social amoeba Dictyostelium discoideum

An evolutionarily significant unicellular strategy in response to starvation in Dictyostelium social amoebae

The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation. Aggregates of up to 10 (6) cells form fruiting bodies containing (i) dormant spores (~80%) that can persist for months in the absence of nutrients, and (ii) dead stalk cells (~20%) that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus affect population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further build a numerical model to test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. Our study highlights the unicellular component of the response of social amoebae to starvation, and thus extends its evolutionary and ecological framework.

An evolutionarily significant unicellular strategy in response to starvation in Dictyostelium social amoebae

The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation. Aggregates of up to 10 (6) cells form fruiting bodies containing (i) dormant spores (~80%) that can persist for months in the absence of nutrients, and (ii) dead stalk cells (~20%) that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus affect population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further build a numerical model to test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. Our study highlights the unicellular component of the response of social amoebae to starvation, and thus extends its evolutionary and ecological framework.

Social amoeba farmers carry defensive symbionts to protect and privatize their crops

Agricultural crops are investments that can be exploited by others. Farmer clones of the social amoeba Dictyostelium discoideum carry bacteria to seed out new food populations but they also carry other non-food bacteria such as Burkholderia spp. Here we demonstrate that these farmer-carried Burkholderia inhibit the growth of non-farmer D. discoideum clones that could exploit the farmers' crops. Using supernatants, we show that inhibition is due to molecules secreted by Burkholderia. When farmer and non-farmer amoebae are mixed together at various frequencies and allowed to complete the social stage, the ability of non-farmers to produce spores falls off rapidly with an increase in the percentage of farmers and their defensive symbionts. Conversely, farmer spore production is unaffected by the frequency of non-farmers. Our results suggest that successful farming is a complex evolutionary adaptation because it requires additional strategies, such as recruiting third parties, to effectively defend and privatize crops.

Collective decision-making in microbes

Microbes are intensely social organisms that routinely cooperate and coordinate their activities to express elaborate population level phenotypes. Such coordination requires a process of collective decision-making, in which individuals detect and collate information not only from their physical environment, but also from their social environment, in order to arrive at an appropriately calibrated response. Here, we present a conceptual overview of collective decision-making as it applies to all group-living organisms; we introduce key concepts and principles developed in the context of animal and human group decisions; and we discuss, with appropriate examples, the applicability of each of these concepts in microbial contexts. In particular, we discuss the roles of information pooling, control skew, speed vs. accuracy trade-offs, local feedbacks, quorum thresholds, conflicts of interest, and the reliability of social information. We conclude that collective decision-making in microbes shares many features with collective decision-making in higher taxa, and we call for greater integration between this fledgling field and other allied areas of research, including in the humanities and the physical sciences.

Social complementation and growth advantages promote socially defective bacterial isolates

Social interactions among diverse individuals that encounter one another in nature have often been studied among animals but rarely among microbes. For example, the evolutionary forces that determine natural frequencies of bacteria that express cooperative behaviours at low levels remain poorly understood. Natural isolates of the soil bacterium Myxococcus xanthus sampled from the same fruiting body often vary in social phenotypes, such as group swarming and multicellular development. Here, we tested whether genotypes highly proficient at swarming or development might promote the persistence of less socially proficient genotypes from the same fruiting body. Fast-swarming strains complemented slower isolates, allowing the latter to keep pace with faster strains in mixed groups. During development, one low-sporulating strain was antagonized by high sporulators, whereas others with severe developmental defects had those defects partially complemented by high-sporulating strains. Despite declining in frequency overall during competition experiments spanning multiple cycles of development, developmentally defective strains exhibited advantages during the growth phases of competitions. These results suggest that microbes with low-sociality phenotypes often benefit from interacting with more socially proficient strains. Such complementation may combine with advantages at other traits to increase equilibrium frequencies of low-sociality genotypes in natural populations.

Numbers count: caste-specific component Allee effects and their interactions

A queen and worker of the Argentine ant Linepithema humile. The numbers of queens and of workers in a colony each have positive relationships with components of fitness. Photo and copyright: Alexander Wild. In Focus: Luque, G., Giraud, T. & Courchamp, F. (2013) Allee effects in ants. Journal of Animal Ecology,. 82, 956-965. Allee effects, positive relationships between fitness and the number or density of conspecifics, are surprisingly widespread and are of profound importance for understanding ecological dynamics. Lucque et al. (2013) provide the first explicit demonstration of Allee effects in a social insect. Using laboratory colonies of the Argentine ant, they show that there are component Allee effects of both workers and queens which interact with negative frequency-dependent effects. Such Allee effects are central to the ecology and evolution of social insects, the societies of which provide a rich, experimentally tractable resource for understanding the mechanisms and impact of Allee effects.

Interspecies and intraspecies interactions in social amoebae

The stable co-existence of individuals of different genotypes and reproductive division of labour within heterogeneous groups are issues of fundamental interest from the viewpoint of evolution. Cellular slime moulds are convenient organisms in which to address both issues. Strains of a species co-occur, as do different species; social groups are often genetically heterogeneous. Intra- and interspecies 1 : 1 mixes of wild isolates of Dictyostelium giganteum and D. purpureum form chimaeric aggregates, following which they segregate to varying extents. Intraspecies aggregates develop in concert and give rise to chimaeric fruiting bodies that usually contain more spores (reproductives) of one component than the other. Reproductive skew and variance in the proportion of reproductives are positively correlated. Interspecies aggregates exhibit almost complete sorting; most spores in a fruiting body come from a single species. Between strains, somatic compatibility correlates weakly with sexual compatibility. It is highest within clones, lower between strains of a species and lowest between strains of different species. Trade-offs among fitness-related traits (between compatible strains), sorting out (between incompatible strains) and avoidance (between species) appear to lie behind coexistence.

Nonadaptive processes can create the appearance of facultative cheating in microbes

Adaptations to social life may take the form of facultative cheating, in which organisms cooperate with genetically similar individuals but exploit others. Consistent with this possibility, many strains of social microbes like Myxococcus bacteria and Dictyostelium amoebae have equal fitness in single-genotype social groups but outcompete other strains in mixed-genotype groups. Here we show that these observations are also consistent with an alternative, nonadaptive scenario: kin selection-mutation balance under local competition. Using simple mathematical models, we show that deleterious mutations that reduce competitiveness within social groups (growth rate, e.g.) without affecting group productivity can create fitness effects that are only expressed in the presence of other strains. In Myxococcus, mutations that delay sporulation may strongly reduce developmental competitiveness. Deleterious mutations are expected to accumulate when high levels of kin selection relatedness relax selection within groups. Interestingly, local resource competition can create nonzero "cost" and "benefit" terms in Hamilton's rule even in the absence of any cooperative trait. Our results show how deleterious mutations can play a significant role even in organisms with large populations and highlight the need to test evolutionary causes of social competition among microbes.

Spatial self-organization favors heterotypic cooperation over cheating

Heterotypic cooperation—two populations exchanging distinct benefits that are costly to produce—is widespread. Cheaters, exploiting benefits while evading contribution, can undermine cooperation. Two mechanisms can stabilize heterotypic cooperation. In ‘partner choice’, cooperators recognize and choose cooperating over cheating partners; in ‘partner fidelity feedback’, fitness-feedback from repeated interactions ensures that aiding your partner helps yourself. How might a spatial environment, which facilitates repeated interactions, promote fitness-feedback? We examined this process through mathematical models and engineered Saccharomyces cerevisiae strains incapable of recognition. Here, cooperators and their heterotypic cooperative partners (partners) exchanged distinct essential metabolites. Cheaters exploited partner-produced metabolites without reciprocating, and were competitively superior to cooperators. Despite initially random spatial distributions, cooperators gained more partner neighbors than cheaters did. The less a cheater contributed, the more it was excluded and disfavored. This self-organization, driven by asymmetric fitness effects of cooperators and cheaters on partners during cell growth into open space, achieves assortment.

DOI:http://dx.doi.org/10.7554/eLife.00960.001

Cooperation between individuals of the same species, and also between different species, is known to be important in evolution. Large fish, for example, rely on small cleaner fish to remove parasites, while the small fish benefit from the nutrients in these parasites. However, cooperation can be undermined by other individuals or species who “cheat” by taking advantage of those who cooperate, without providing any benefits in return. For example, some cleaner fish cheat by biting off healthy tissue from their host, in addition to parasites.

Genetically-related individuals who cooperate by sharing identical benefits can combat cheaters by giving preferential treatment to their relatives (a process known as kin discrimination) or by staying close to the relatives to form clusters (kin fidelity). However, two genetically-unrelated populations that mutually cooperate by sharing different benefits cannot employ these methods to overcome cheaters. Instead they rely on either partner choice or partner fidelity feedback.

Partner choice – the approach adopted by cleaner fish and their hosts – relies on one population recognizing a signal from the other population and responding accordingly: for example, large fish observe cleaner fish and approach those that cooperate with their current host and avoid those that cheat. Partner fidelity feedback, on the other hand, relies on repeated interactions between the two populations providing an advantage in terms of evolutionary fitness to both: for example, organelles called mitochondria and chloroplasts live inside cells, helping the cells to harvest energy and providing energy for themselves and the host cells in the process. In some cases – such as the cooperation between figs and fig wasps, or between certain plants and the bacteria that fix nitrogen in their roots – researchers cannot agree if the populations are relying on partner choice or partner fidelity feedback.

Now Momeni et al. have used a combination of experiments on yeast and mathematical modeling to explore partner fidelity feedback in greater detail. They started by using genetic engineering techniques to produce two species of yeast that mutually cooperate, each providing a metabolite that is essential to the other, but are not able to recognize each other: this means that these populations cannot rely on partner choice to combat cheaters. Momeni et al. then observed how these two species interacted with each other and a third species of yeast that cheated by consuming one of the metabolites without releasing any metabolite of its own.

Momeni et al. found that as long as there was space for the yeast cells to grow into, the two species that cooperated self-organized into mixed clusters, with the cheating species being excluded from these clusters. The self-organization was driven by a positive feedback loop involving the two species that cooperated, with each species helping to increase the fitness of the other. The results of Momeni et al. demonstrate that it is possible for two genetically unrelated populations to cooperate and combat cheaters without the use of partner choice.

DOI:http://dx.doi.org/10.7554/eLife.00960.002

Toward an evolutionary definition of cheating

The term "cheating" is used in the evolutionary and ecological literature to describe a wide range of exploitative or deceitful traits. Although many find this a useful short hand, others have suggested that it implies cognitive intent in a misleading way, and is used inconsistently. We provide a formal justification of the use of the term "cheat" from the perspective of an individual as a maximizing agent. We provide a definition for cheating that can be applied widely, and show that cheats can be broadly classified on the basis of four distinctions: (i) whether cooperation is an option; (ii) whether deception is involved; (iii) whether members of the same or different species are cheated; and (iv) whether the cheat is facultative or obligate. Our formal definition and classification provide a framework that allow us to resolve and clarify a number of issues, regarding the detection and evolutionary consequences of cheating, as well as illuminating common principles and similarities in the underlying selection pressures.

Crozier's paradox revisited: maintenance of genetic recognition systems by disassortative mating

Background

Organisms are predicted to behave more favourably towards relatives, and kin-biased cooperation has been found in all domains of life from bacteria to vertebrates. Cooperation based on genetic recognition cues is paradoxical because it disproportionately benefits individuals with common phenotypes, which should erode the required cue polymorphism. Theoretical models suggest that many recognition loci likely have some secondary function that is subject to diversifying selection, keeping them variable.

Results

Here, we use individual-based simulations to investigate the hypothesis that the dual use of recognition cues to facilitate social behaviour and disassortative mating (e.g. for inbreeding avoidance) can maintain cue diversity over evolutionary time. Our model shows that when organisms mate disassortatively with respect to their recognition cues, cooperation and recognition locus diversity can persist at high values, especially when outcrossed matings produce more surviving offspring. Mating system affects cue diversity via at least four distinct mechanisms, and its effects interact with other parameters such as population structure. Also, the attrition of cue diversity is less rapid when cooperation does not require an exact cue match. Using a literature review, we show that there is abundant empirical evidence that heritable recognition cues are simultaneously used in social and sexual behaviour.

Conclusions

Our models show that mate choice is one possible resolution of the paradox of genetic kin recognition, and the literature review suggests that genetic recognition cues simultaneously inform assortative cooperation and disassortative mating in a large range of taxa. However, direct evidence is scant and there is substantial scope for future work.

Multilevel selection analysis of a microbial social trait

The study of microbial communities often leads to arguments for the evolution of cooperation due to group benefits. However, multilevel selection models caution against the uncritical assumption that group benefits will lead to the evolution of cooperation. We analyze a microbial social trait to precisely define the conditions favoring cooperation. We combine the multilevel partition of the Price equation with a laboratory model system: swarming in Pseudomonas aeruginosa. We parameterize a population dynamics model using competition experiments where we manipulate expression, and therefore the cost-to-benefit ratio of swarming cooperation. Our analysis shows that multilevel selection can favor costly swarming cooperation because it causes population expansion. However, due to high costs and diminishing returns constitutive cooperation can only be favored by natural selection when relatedness is high. Regulated expression of cooperative genes is a more robust strategy because it provides the benefits of swarming expansion without the high cost or the diminishing returns. Our analysis supports the key prediction that strong group selection does not necessarily mean that microbial cooperation will always emerge.

Kin recognition protects cooperators against cheaters

The evolution of sociality and altruism is enigmatic because cooperators are constantly threatened by cheaters who benefit from cooperation without incurring its full cost [1, 2]. Kin recognition is the ability to recognize and cooperate with genetically close relatives. It has also been proposed as a potential mechanism that limits cheating [3, 4], but there has been no direct experimental support for that possibility. Here we show that kin recognition protects cooperators against cheaters. The social amoebae Dictyostelium discoideum cooperate by forming multicellular aggregates that develop into fruiting bodies of viable spores and dead stalk cells. Cheaters preferentially differentiate into spores while their victims die as stalk cells in chimeric aggregates. We engineered syngeneic cheaters and victims that differed only in their kin-recognition genes, tgrB1 and tgrC1, and in a single cheater allele and found that the victims escaped exploitation by different types of nonkin cheaters. This protection depends on kin-recognition-mediated segregation because it is compromised when we disrupt strain segregation. These findings provide direct evidence for the role of kin recognition in cheater control and suggest a mechanism for the maintenance of stable cooperative systems.

The rate and effects of spontaneous mutation on fitness traits in the social amoeba, Dictyostelium discoideum

We performed a mutation accumulation (MA) experiment in the social amoeba Dictyostelium discoideum to estimate the rate and distribution of effects of spontaneous mutations affecting eight putative fitness traits. We found that the per-generation mutation rate for most fitness components is 0.0019 mutations per haploid genome per generation or larger. This rate is an order of magnitude higher than estimates for fitness components in the unicellular eukaryote Saccharomyces cerevisiae, even though the base-pair substitution rate is two orders of magnitude lower. The high rate of fitness-altering mutations observed in this species may be partially explained by a large mutational target relative to S. cerevisiae. Fitness-altering mutations also may occur primarily at simple sequence repeats, which are common throughout the genome, including in coding regions, and may represent a target that is particularly likely to give fitness effects upon mutation. The majority of mutations had deleterious effects on fitness, but there was evidence for a substantial fraction, up to 40%, being beneficial for some of the putative fitness traits. Competitive ability within the multicellular slug appears to be under weak directional selection, perhaps reflecting the fact that slugs are sometimes, but not often, comprised of multiple clones in nature. Evidence for pleiotropy among fitness components across MA lines was absent, suggesting that mutations tend to act on single fitness components.

Randomness and multilevel interactions in biology

The dynamic instability of living systems and the "superposition" of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems' dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing "order", induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.

Evolution of helping and harming in heterogeneous groups

Social groups are often composed of individuals who differ in many respects. Theoretical studies on the evolution of helping and harming behaviors have largely focused upon genetic differences between individuals. However, nongenetic variation between group members is widespread in natural populations, and may mediate differences in individuals' social behavior. Here, we develop a framework to study how variation in individual quality mediates the evolution of unconditional and conditional social traits. We investigate the scope for the evolution of social traits that are conditional on the quality of the actor and/or recipients. We find that asymmetries in individual quality can lead to the evolution of plastic traits with different individuals expressing helping and harming traits within the same group. In this context, population viscosity can mediate the evolution of social traits, and local competition can promote both helping and harming behaviors. Furthermore, asymmetries in individual quality can lead to the evolution of competition-like traits between clonal individuals. Overall, we highlight the importance of asymmetries in individual quality, including differences in reproductive value and the ability to engage in successful social interactions, in mediating the evolution of helping and harming behaviors.

Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection

High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation.

Horizontal gene transfer of epigenetic machinery and evolution of parasitism in the malaria parasite Plasmodium falciparum and other apicomplexans

Background

The acquisition of complex transcriptional regulatory abilities and epigenetic machinery facilitated the transition of the ancestor of apicomplexans from a free-living organism to an obligate parasite. The ability to control sophisticated gene expression patterns enabled these ancient organisms to evolve several differentiated forms, invade multiple hosts and evade host immunity. How these abilities were acquired remains an outstanding question in protistan biology.

Results

In this work, we study SET domain bearing genes that are implicated in mediating immune evasion, invasion and cytoadhesion pathways of modern apicomplexans, including malaria parasites. We provide the first conclusive evidence of a horizontal gene transfer of a Histone H4 Lysine 20 (H4K20) modifier, Set8, from an animal host to the ancestor of apicomplexans. Set8 is known to contribute to the coordinated expression of genes involved in immune evasion in modern apicomplexans. We also show the likely transfer of a H3K36 methyltransferase (Ashr3 from plants), possibly derived from algal endosymbionts. These transfers appear to date to the transition from free-living organisms to parasitism and coincide with the proposed horizontal acquisition of cytoadhesion domains, the O-glycosyltransferase that modifies these domains, and the primary family of transcription factors found in apicomplexan parasites. Notably, phylogenetic support for these conclusions is robust and the genes clearly are dissimilar to SET sequences found in the closely related parasite Perkinsus marinus, and in ciliates, the nearest free-living organisms with complete genome sequences available.

Conclusions

Animal and plant sources of epigenetic machinery provide new insights into the evolution of parasitism in apicomplexans. Along with the horizontal transfer of cytoadhesive domains, O-linked glycosylation and key transcription factors, the acquisition of SET domain methyltransferases marks a key transitional event in the evolution to parasitism in this important protozoan lineage.

Mating system evolution and worker caste diversity in Pheidole ants

The efficiency of social groups is generally optimized by a division of labour, achieved through behavioural or morphological diversity of members. In social insects, colonies may increase the morphological diversity of workers by recruiting standing genetic variance for size and shape via multiply mated queens (polyandry) or multiple-breeding queens (polygyny). However, greater worker diversity in multi-lineage species may also have evolved due to mutual worker policing if there is worker reproduction. Such policing reduces the pressure on workers to maintain reproductive morphologies, allowing the evolution of greater developmental plasticity and the maintenance of more genetic variance for worker size and shape in populations. Pheidole ants vary greatly in the diversity of worker castes. Also, their workers lack ovaries and are thus invariably sterile regardless of the queen mating frequency and numbers of queens per colony. This allowed us to perform an across-species study examining the genetic effects of recruiting more patrilines on the developmental diversity of workers in the absence of confounding effects from worker policing. Using highly variable microsatellite markers, we found that the effective mating frequency of the soldier-polymorphic P. rhea (avg. meN = 2.65) was significantly higher than that of the dimorphic P. spadonia (avg. meN = 1.06), despite a significant paternity skew in P. rhea (avg. B = 0.10). Our findings support the idea that mating strategies of queens may co-evolve with selection to increase the diversity of workers. We also detected patriline bias in the production of different worker sizes, which provides direct evidence for a genetic component to worker polymorphism.

Dictyostelium development shows a novel pattern of evolutionary conservation

von Baer's law states that early stages of animal development are the most conserved. More recent evidence supports a modified "hourglass" pattern in which an early but somewhat later stage is most conserved. Both patterns have been explained by the relative complexity of either temporal or spatial interactions; the greatest conservation and lowest evolvability occur at the time of the most complex interactions, because these cause larger effects that are harder for selection to alter. This general kind of explanation might apply universally across independent multicellular systems, as supported by the recent finding of the hourglass pattern in plants. We use RNA-seq expression data from the development of the slime mold Dictyostelium to demonstrate that it does not follow either of the two canonical patterns but instead tends to show the strongest conservation and weakest evolvability late in development. We propose that this is consistent with a version of the spatial constraints model, modified for organisms that never achieve a high degree of developmental modularity.

A new social gene in Dictyostelium discoideum, chtB

Background

Competitive social interactions are ubiquitous in nature, but their genetic basis is difficult to determine. Much can be learned from single gene knockouts in a eukaryote microbe. The mutants can be competed with the parent to discern the social impact of that specific gene. Dictyostelium discoideum is a social amoeba that exhibits cooperative behavior in the construction of a multicellular fruiting body. It is a good model organism to study the genetic basis of cooperation since it has a sequenced genome and it is amenable to genetic manipulation. When two strains of D. discoideum are mixed, a cheater strain can exploit its social partner by differentiating more spore than its fair share relative to stalk cells. Cheater strains can be generated in the lab or found in the wild and genetic analyses have shown that cheating behavior can be achieved through many pathways.

Results

We have characterized the knockout mutant chtB, which was isolated from a screen for cheater mutants that were also able to form normal fruiting bodies on their own. When mixed in equal proportions with parental strain cells, chtB mutants contributed almost 60% of the total number of spores. To do so, chtB cells inhibit wild type cells from becoming spores, as indicated by counts and by the wild type cells’ reduced expression of the prespore gene, cotB. We found no obvious fitness costs (morphology, doubling time in liquid medium, spore production, and germination efficiency) associated with the cheating ability of the chtB knockout.

Conclusions

In this study we describe a new gene in D. discoideum, chtB, which when knocked out inhibits the parental strain from producing spores. Moreover, under lab conditions, we did not detect any fitness costs associated with this behavior.

First steps in experimental cancer evolution

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach - whereby evolution is observed in real time and which has typically employed microorganisms - can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research.

Collection and cultivation of dictyostelids from the wild

Dictyostelium discoideum is a commonly used model organism for the study of biological processes such as chemotaxis, cell communication, and development. While these studies primarily focus on a single clone, recent work has revealed a host of questions that can only be answered from studies of multiple genetically distinct clones. Understanding intraspecific clone conflict, kin recognition, differential adhesion, and other kinds of interactions likely to occur in the natural soil habitat can only come from studies of multiple clones. Studies of populations of wild isolates are also important for understanding the factors contributing to associations such as species co-occurrences and to observed inter- and intraspecific interactions such as those found between bacteria and D. discoideum. Natural isolates of Dictyostelium are easily found in soil and leaf litter in nearly all habitats. Here we describe a simple and successful method for isolating new wild clones from soil, then isolating single clonal strains, and storing them for future use.

Measuring cheating, fitness, and segregation in Dictyostelium discoideum

Dictyostelium has become a model organism for the study of social evolution because of the stage in its life cycle where thousands of independent amoebae together form a fruiting body. Some individuals die to form a stalk that holds aloft the remaining cells for dispersal to new environments as spores. Different genotypes can aggregate together, creating opportunities for exploitation by cheaters that contribute a smaller proportion of cells to the stalk. Clustering of genotypes into separate fruiting bodies reduces the opportunities for cheating. Some genotypes achieve this by segregating after aggregation. Here we describe techniques for assaying cheating and segregation in D. discoideum. We cover how to grow and maintain cells, fluorescently label genotypes, design experiments for accuracy and precision, calculate fitness and segregation, and interpret the results.

Simple system--substantial share: the use of Dictyostelium in cell biology and molecular medicine

Dictyostelium discoideum offers unique advantages for studying fundamental cellular processes, host-pathogen interactions as well as the molecular causes of human diseases. The organism can be easily grown in large amounts and is amenable to diverse biochemical, cell biological and genetic approaches. Throughout their life cycle Dictyostelium cells are motile, and thus are perfectly suited to study random and directed cell motility with the underlying changes in signal transduction and the actin cytoskeleton. Dictyostelium is also increasingly used for the investigation of human disease genes and the crosstalk between host and pathogen. As a professional phagocyte it can be infected with several human bacterial pathogens and used to study the infection process. The availability of a large number of knock-out mutants renders Dictyostelium particularly useful for the elucidation and investigation of host cell factors. A powerful armory of molecular genetic techniques that have been continuously expanded over the years and a well curated genome sequence, which is accessible via the online database dictyBase, considerably strengthened Dictyostelium's experimental attractiveness and its value as model organism.

Adaptation to a new environment allows cooperators to purge cheaters stochastically

Cooperation via production of common goods is found in diverse life forms ranging from viruses to social animals. However, natural selection predicts a "tragedy of the commons": Cheaters, benefiting from without producing costly common goods, are more fit than cooperators and should destroy cooperation. In an attempt to discover novel mechanisms of cheater control, we eliminated known ones using a yeast cooperator-cheater system engineered to supply or exploit essential nutrients. Surprisingly, although less fit than cheaters, cooperators quickly dominated a fraction of cocultures. Cooperators isolated from these cocultures were superior to the cheater isolates they had been cocultured with, even though these cheaters were superior to ancestral cooperators. Resequencing and phenotypic analyses revealed that evolved cooperators and cheaters all harbored mutations adaptive to the nutrient-limited cooperative environment, allowing growth at a much lower concentration of nutrient than their ancestors. Even after the initial round of adaptation, evolved cooperators still stochastically dominated cheaters derived from them. We propose the "adaptive race" model: If during adaptation to an environment, the fitness gain of cooperators exceeds that of cheaters by at least the fitness cost of cooperation, the tragedy of the commons can be averted. Although cooperators and cheaters sample from the same pool of adaptive mutations, this symmetry is soon broken: The best cooperators purge cheaters and continue to grow, whereas the best cheaters cause rapid self-extinction. We speculate that adaptation to changing environments may contribute to the persistence of cooperative systems before the appearance of more sophisticated mechanisms of cheater control.

Effects of plant host species and plant community richness on streptomycete community structure

We investigated soil streptomycete communities associated with four host plant species (two warm season C4 grasses: Andropogon gerardii, Schizachyrium scoparium and two legumes: Lespedeza capitata, Lupinus perennis), grown in plant communities varying in species richness. We used actinobacteria-selective PCR coupled with pyrosequencing to characterize streptomycete community composition and structure. The greatest pairwise distances between communities were observed in contrasts between monocultures of different plant species, indicating that plant species exert distinct selective effects on soil streptomycete populations. Increasing plant richness altered the composition and structure of streptomycete communities associated with each host plant species. Significant relationships between plant community characteristics, soil edaphic characteristics, and streptomycete community structure suggest that host plant effects on soil microbial communities may be mediated through changes to the soil environment. Co-occurring streptomycete taxa also shared consistent relationships with soil edaphic properties, providing further indication of the importance of habitat preference for taxon occurrence. Physical distance between sampling points had a significant influence on streptomycete community similarity. This work provides a detailed characterization of soil streptomycete populations across a field scale and in relation to plant host identity and plant community richness.

Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum

Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9), with a Poisson confidence interval of 4.1×10(-9) - 9.5×10(-9), per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10(-11), with a Poisson confidence interval ranging from 7.4×10(-13) to 1.6×10(-10), is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.

Social biases determine spatiotemporal sparseness of ciliate mating heuristics

Ciliates become highly social, even displaying animal-like qualities, in the joint presence of aroused conspecifics and nonself mating pheromones. Pheromone detection putatively helps trigger instinctual and learned courtship and dominance displays from which social judgments are made about the availability, compatibility, and fitness representativeness or likelihood of prospective mates and rivals. In earlier studies, I demonstrated the heterotrich Spirostomum ambiguum improves mating competence by effecting preconjugal strategies and inferences in mock social trials via behavioral heuristics built from Hebbian-like associative learning. Heuristics embody serial patterns of socially relevant action that evolve into ordered, topologically invariant computational networks supporting intra- and intermate selection. S. ambiguum employs heuristics to acquire, store, plan, compare, modify, select, and execute sets of mating propaganda. One major adaptive constraint over formation and use of heuristics involves a ciliate’s initial subjective bias, responsiveness, or preparedness, as defined by Stevens’ Law of subjective stimulus intensity, for perceiving the meaningfulness of mechanical pressures accompanying cell-cell contacts and additional perimating events. This bias controls durations and valences of nonassociative learning, search rates for appropriate mating strategies, potential net reproductive payoffs, levels of social honesty and deception, successful error diagnosis and correction of mating signals, use of insight or analysis to solve mating dilemmas, bioenergetics expenditures, and governance of mating decisions by classical or quantum statistical mechanics. I now report this same social bias also differentially affects the spatiotemporal sparseness, as measured with metric entropy, of ciliate heuristics. Sparseness plays an important role in neural systems through optimizing the specificity, efficiency, and capacity of memory representations. The present findings indicate sparseness performs a similar function in single aneural cells by tuning the size and density of encoded computational architectures useful for decision making in social contexts.

The dynamics of cooperative bacterial virulence in the field

Laboratory experiments have shown that the fitness of microorganisms can depend on cooperation between cells. Although this insight has revolutionized our understanding of microbial life, results from artificial microcosms have not been validated in complex natural populations. We investigated the sociality of essential virulence factors (crystal toxins) in the pathogen Bacillus thuringiensis using diamondback moth larvae (Plutella xylostella) as hosts. We show that toxin production is cooperative, and in a manipulative field experiment, we observed persistent high relatedness and frequency- and density-dependent selection, which favor stable cooperation. Conditions favoring social virulence can therefore persist in the face of natural population processes, and social interactions (rapid cheat invasion) may account for the rarity of natural disease outbreaks caused by B. thuringiensis.

Structured growth and genetic drift raise relatedness in the social amoeba Dictyostelium discoideum

One condition for the evolution of altruism is genetic relatedness between altruist and beneficiary, often achieved through active kin recognition. Here, we investigate the power of a passive process resulting from genetic drift during population growth in the social amoeba Dictyostelium discoideum. We put labelled and unlabelled cells of the same clone in the centre of a plate, and allowed them to proliferate outward. Zones formed by genetic drift owing to the small population of actively growing cells at the colony edge. We also found that single cells could form zones of high relatedness. Relatedness increased at a significantly higher rate when food was in short supply. This study shows that relatedness can be significantly elevated before the social stage without a small founding population size or recognition mechanism.

Rapid antagonistic coevolution between strains of the social amoeba Dictyostelium discoideum

Social groups face a fundamental problem of overcoming selfish individuals capable of destroying cooperation. In the social amoeba Dictyostelium discoideum, there is evidence that some clones ('cheaters') contribute disproportionately to the viable spores in a fruiting body while avoiding the dead stalk cell fate. It remains unclear, however, whether this cheating is actually the product of selection. Here, I report the results of an experimental evolution study designed to test whether clones of D. discoideum will evolve resistance to cheating in the laboratory with genetic variation created only through spontaneous mutation. Two strains, one green fluorescent protein (GFP)-labelled and one wild-type, were allowed to grow and develop together before the wild-type strain was removed and replaced with a naïve strain evolving in parallel. Over the course of 10 social generations, the GFP-labelled strain reliably increased its representation in the spores relative to control populations that had never experienced the competitor. This competitive advantage extended to the non-social, vegetative growth portion of the life cycle, but not to pairwise competition with two other strains. These results indicate strong antagonism between strains, mediated by ample mutational variation for cheating and also suggest that arms races between strains in the wild may be common.

Revisiting social recognition systems in invertebrates

Since the 1970s, the ability of some invertebrate species to recognize individual conspecifics has attracted increased scientific interest. However, there is still confusion in the literature, possibly due to the lack of unambiguous criteria for classifying social recognition in its different forms. Here, we synthesize the results of studies on invertebrates and provide a framework with the purpose of identifying research needs and directions for future investigations. Following in part Sherman et al.'s (Behavioural ecology: an evolutionary approach. Blackwell Science, Oxford, pp 69-96, 1997) definition of 'recognition systems' and Tibbetts and Dale's (Trends Ecol Evol 22:529-537, 2007) classification of 'individual recognition,' we first discuss different case studies that exemplify the categories of 'familiar recognition' and 'class-level recognition.' Then, through the analysis of the invertebrate literature, we illustrate eight key properties that characterize 'true individual recognition' systems. We are confident that the proposed framework will provide opportunities for exciting discoveries of the cognitive abilities in invertebrates.

Understanding microbial cooperation

The field of microbial cooperation has grown enormously over the last decade, leading to improved experimental techniques and a growing awareness of collective behavior in microbes. Unfortunately, many of our theoretical tools and concepts for understanding cooperation fail to take into account the peculiarities of the microbial world, namely strong selection strengths, unique population structure, and non-linear dynamics. Worse yet, common verbal arguments are often far removed from the math involved, leading to confusion and mistakes. Here, we review the general mathematical forms of Price's equation, Hamilton's rule, and multilevel selection as they are applied to microbes and provide some intuition on these otherwise abstract formulas. However, these sometimes overly general equations can lack specificity and predictive power, ultimately forcing us to advocate for more direct modeling techniques.

Detecting the molecular signature of social conflict: theory and a test with bacterial quorum sensing genes

Extending social evolution theory to the molecular level opens the door to an unparalleled abundance of data and statistical tools for testing alternative hypotheses about the long-term evolutionary dynamics of cooperation and conflict. To this end, we take a collection of known sociality genes (bacterial quorum sensing [QS] genes), model their evolution in terms of patterns that are detectable using gene sequence data, and then test model predictions using available genetic data sets. Specifically, we test two alternative hypotheses of social conflict: (1) the "adaptive" hypothesis that cheaters are maintained in natural populations by frequency-dependent balancing selection as an evolutionarily stable strategy and (2) the "evolutionary null" hypothesis that cheaters are opposed by purifying kin selection yet exist transiently because of their recurrent introduction into populations by mutation (i.e., kin selection-mutation balance). We find that QS genes have elevated within- and among-species sequence variation, nonsignificant signatures of natural selection, and putatively small effect sizes of mutant alleles, all patterns predicted by our evolutionary null model but not by the stable cheater hypothesis. These empirical findings support our theoretical prediction that QS genes experience relaxed selection due to nonclonality of social groups, conditional expression, and the individual-level advantage enjoyed by cheaters. Furthermore, cheaters are evolutionarily transient, persisting in populations because of their recurrent introduction by mutation and not because they enjoy a frequency-dependent fitness advantage.

High relatedness in a social amoeba: the role of kin-discriminatory segregation

A major challenge for social theory is to explain the importance of kin discrimination for the evolution of altruism. One way to assess the importance of kin discrimination is to test its effects on increasing relatedness within groups. The social amoeba Dictyostelium discoideum aggregates to form a fruiting body composed of dead stalk and live spores. Previous studies of a natural population showed that where D. discoideum occurs in the soil, multiple clones are often found in the same small soil samples. However, actual fruiting bodies usually contain only one clone. We here performed experiments to gauge the effect of kin-discriminatory segregation on increasing relatedness. We mixed co-occurring clones from this population using a relatedness level found in small soil samples. We found a lower proportion of uniclonal fruiting bodies and a lower level of relatedness compared with natural fruiting bodies. We found that the amount of relatedness increase attributable to kin-discriminatory segregation was small. These findings suggest a relatively minor influence of kin-discriminatory segregation on relatedness in D. discoideum. We discuss our results comparing with the results of previous studies, including those of wild clones and laboratory mutants. We ask why wild clones of D. discoideum exhibit a low degree of kin-discriminatory segregation, and what alternative factors might account for high relatedness in D. discoideum.

Growth dynamics and the evolution of cooperation in microbial populations

Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of colonies, promote cooperation. Biased by population dynamics these fluctuations result in two qualitatively distinct regimes of robust cooperation under repetitive fragmentation into groups. First, if the level of cooperation exceeds a threshold, cooperators will take over the whole population. Second, cooperators can also emerge from a single mutant leading to a robust coexistence between cooperators and free-riders. We find frequency and size of population bottlenecks, and growth dynamics to be the major ecological factors determining the regimes and thereby the evolutionary pathway towards cooperation.

High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium

Most complex multicellular organisms develop clonally from a single cell. This should limit conflicts between cell lineages that could threaten the extensive cooperation of cells within multicellular bodies. Cellular composition can be manipulated in the social amoeba Dictyostelium discoideum, which allows us to test and confirm the two key predictions of this theory. Experimental evolution at low relatedness favored cheating mutants that could destroy multicellular development. However, under high relatedness, the forces of mutation and within-individual selection are too small for these destructive cheaters to spread, as shown by a mutation accumulation experiment. Thus, we conclude that the single-cell bottleneck is a powerful stabilizer of cellular cooperation in multicellular organisms.

Kin discrimination and cooperation in microbes

Recognition of relatives is important in microbes because they perform many behaviors that have costs to the actor while benefiting neighbors. Microbes cooperate for nourishment, movement, virulence, iron acquisition, protection, quorum sensing, and production of multicellular biofilms or fruiting bodies. Helping others is evolutionarily favored if it benefits others who share genes for helping, as specified by kin selection theory. If microbes generally find themselves in clonal patches, then no special means of discrimination is necessary. Much real discrimination is actually of kinds, not kin, as in poison-antidote systems, such as bacteriocins, in which cells benefit their own kind by poisoning others, and in adhesion systems, in which cells of the same kind bind together. These behaviors can elevate kinship generally and make cooperation easier to evolve and maintain.

Evolution and stability of altruist strategies in microbial games

When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory (EGT). We study the predictions of EGT for the bacterial "suicide bomber" game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

Evolution and diversity of dictyostelid social amoebae

Dictyostelid social amoebae are a large and ancient group of soil microbes with an unusual multicellular stage in their life cycle. Taxonomically, they belong to the eukaryotic supergroup Amoebozoa, the sister group to Opisthokonta (animals + fungi). Roughly half of the ~150 known dictyostelid species were discovered during the last five years and probably many more remain to be found. The traditional classification system of Dictyostelia was completely overturned by cladistic analyses and molecular phylogenies of the past six years. As a result, it now appears that, instead of three major divisions there are eight, none of which correspond to traditional higher-level taxa. In addition to the widely studied Dictyostelium discoideum, there are now efforts to develop model organisms and complete genome sequences for each major group. Thus Dictyostelia is becoming an excellent model for both practical, medically related research and for studying basic principles in cell-cell communication and developmental evolution. In this review we summarize the latest information about their life cycle, taxonomy, evolutionary history, genome projects and practical importance.

Evolutionary and population dynamics: a coupled approach

We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by population dynamics in general. Especially for fast reproducing microbes which are subject to selection, both types of dynamics are often closely intertwined. We illustrate this by considering different growth scenarios. Depending on whether microbes die or stop to reproduce (dormancy), qualitatively different behaviors emerge. For cooperating bacteria, a permanent increase of costly cooperation can occur. Even if not permanent, cooperation can still increase transiently due to demographic fluctuations. We validate our analysis via stochastic simulations and analytic calculations. In particular, we derive a condition for an increase in the level of cooperation.

Nuclear and genome dynamics in multinucleate ascomycete fungi

Genetic variation between individuals is essential to evolution and adaptation. However, intra-organismic genetic variation also shapes the life histories of many organisms, including filamentous fungi. A single fungal syncytium can harbor thousands or millions of mobile and potentially genotypically different nuclei, each having the capacity to regenerate a new organism. Because the dispersal of asexual or sexual spores propagates individual nuclei in many of these species, selection acting at the level of nuclei creates the potential for competitive and cooperative genome dynamics. Recent work in Neurospora crassa and Sclerotinia sclerotiorum has illuminated how nuclear populations are coordinated for fungal growth and other behaviors and has revealed both molecular and physical mechanisms for preventing and policing inter-genomic conflict. Recent results from population-level genomic studies in a variety of filamentous fungi suggest that nuclear exchange between mycelia and recombination between heterospecific nuclei may be of more importance to fungal evolution, diversity and the emergence of newly virulent strains than has previously been recognized.