Indirect Genetic Effects Research Articles

Complex genotype interactions influence social fitness during the developmental phase of the social amoebaDictyostelium discoideum

When individuals interact, phenotypic variation can be partitioned into direct genetic effects (DGEs) of the individuals' own genotypes, indirect genetic effects (IGEs) of their social partners' genotypes and epistatic interactions between the genotypes of interacting individuals ('genotype-by-genotype (GxG) epistasis'). These components can all play important roles in evolutionary processes, but few empirical studies have examined their importance. The social amoeba Dictyostelium discoideum provides an ideal system to measure these effects during social interactions and development. When starved, free-living amoebae aggregate and differentiate into a multicellular fruiting body with a dead stalk that holds aloft viable spores. By measuring interactions among a set of natural strains, we quantify DGEs, IGEs and GxG epistasis affecting spore formation. We find that DGEs explain most of the phenotypic variance (57.6%) whereas IGEs explain a smaller (13.3%) but highly significant component. Interestingly, GxG epistasis explains nearly a quarter of the variance (23.0%), highlighting the complex nature of genotype interactions. These results demonstrate the large impact that social interactions can have on development and suggest that social effects should play an important role in developmental evolution in this system.

Indirect genetic effects in a sex‐limited trait: the case of breeding time in red‐billed gulls

Female reproductive performance can be strongly affected by male care, so that breeding time, a trait expressed only by females, can be seen as one trait determined by both male and female genotypes. Animal model analyses of a 46-year study of red-billed gulls (Larus novaehollandiae scopulinus) revealed that laying date was not heritable in females (h(2) = 0.001 +/- 0.030), but significantly so in males (h(2) = 0.134 +/- 0.029). Heritability of breeding time in males probably reflects genetic variability in some other trait such as courtship feeding ability. In line with predictions of evolutionary models incorporating indirect genetic effects, the strong and consistent directional selection for advanced breeding time has not resulted in detectable selection response in males. Our results demonstrate that a female trait is largely determined by genetic characteristics of its mate, and hence, any evolutionary change in red-billed gull breeding time depends critically on genetic variation in males.

Antagonistic Parent-Offspring Co-Adaptation

BackgroundIn species across taxa, offspring have means to influence parental investment (PI). PI thus evolves as an interacting phenotype and indirect genetic effects may strongly affect the co-evolutionary dynamics of offspring and parental behaviors. Evolutionary theory focused on explaining how exaggerated offspring solicitation can be understood as resolution of parent-offspring conflict, but the evolutionary origin and diversification of different forms of family interactions remains unclear.Methodology/Principal FindingsIn contrast to previous theory that largely uses a static approach to predict how “offspring individuals” and “parental individuals” should interact given conflict over PI, we present a dynamic theoretical framework of antagonistic selection on the PI individuals obtain/take as offspring and the PI they provide as parents to maximize individual lifetime reproductive success; we analyze a deterministic and a stochastic version of this dynamic framework. We show that a zone for equivalent co-adaptation outcomes exists in which stable levels of PI can evolve and be maintained despite fast strategy transitions and ongoing co-evolutionary dynamics. Under antagonistic co-adaptation, cost-free solicitation can evolve as an adaptation to emerging preferences in parents.Conclusions/SignificanceWe show that antagonistic selection across the offspring and parental life-stage of individuals favors co-adapted offspring and parental behavior within a zone of equivalent outcomes. This antagonistic parent-offspring co-adaptation does not require solicitation to be costly, allows for rapid divergence and evolutionary novelty and potentially explains the origin and diversification of the observed provisioning forms in family life.

Selection, Epistasis, and Parent‐of‐Origin Effects on Deleterious Mutations across Environments inDrosophila melanogaster

Understanding the nature of selection against deleterious alleles is central to determining how populations are affected by the constant influx of new mutations. Important progress has been made in estimating basic attributes of the distribution of selection coefficients and gene interaction effects (epistasis). Although most aspects of selection are likely to be context dependent, little is known about the effect of stress on selection and epistasis at the level of individual genes, especially in multicellular organisms. Using Drosophila melanogaster, we measure how selection on 20 mutant alleles is affected by direct and indirect genetic factors across two environments. We find that environmental stress increases selection against individual mutations but reduces selection against combinations of mutations (i.e., epistasis becomes more positive). In addition, we find a high incidence of indirect genetic effects whereby the strength of selection against the alleles carried by offspring is dependent on the genotypes of their parents.

Adaptation and the genetics of social behaviour

In recent years much progress has been made towards understanding the selective forces involved in the evolution of social behaviour including conflicts over reproduction among group members. Here, I argue that an important additional step necessary for advancing our understanding of the resolution of potential conflicts within insect societies is to consider the genetics of the behaviours involved. First, I discuss how epigenetic modifications of behaviour may affect conflict resolution within groups. Second, I review known natural polymorphisms of social organization to demonstrate that a lack of consideration of the genetic mechanisms involved may lead to erroneous explanations of the adaptive significance of behaviour. Third, I suggest that, on the basis of recent genetic studies of sexual conflict in Drosophila, it is necessary to reconsider the possibility of within-group manipulation by means of chemical substances (i.e. pheromones). Fourth, I address the issue of direct versus indirect genetic effects, which is of particular importance for the study of behaviour in social groups. Fifth, I discuss the issue of how a genetic influence on dominance hierarchies and reproductive division of labour can have secondary effects, for example in the evolution of promiscuity. Finally, because the same sets of genes (e.g. those implicated in chemical signalling and the responses that are triggered) may be used even in species as divergent as ants, cooperative breeding birds and primates, an integration of genetic mechanisms into the field of social evolution may also provide unifying ideas.

From genes to ecosystems: an emerging synthesis of eco‐evolutionary dynamics

A synthesis is underway between ecology and evolution, partly brought about by the realization that evolutionary change can take place on ecological timescales (Hairston et al., 2005; Whitham et al., 2006; Carroll et al., 2007). This synthesis attempts to understand the dynamic interplay of ecological and evolutionary processes that results from natural or anthropogenic selective forces (Lankau & Strauss, 2007). Moreover, this synthesis represents an integration of several ‘genes to ecosystems’ approaches, including ‘ecological stochiometry’, ‘community genetics’ (Whitham et al., 2006) and ‘niche construction’. United under the framework of ‘eco-evolutionary dynamics’, these ideas seek to link genetic and phenotypic variation to population dynamics, biodiversity and ecosystem function, and place these disciplines in a dynamic evolutionary framework (i.e. understanding the ecological consequences of evolutionary processes and the evolutionary consequences of ecological interactions). This is not an easy endeavor because any such synthesis needs to be broadly multidisciplinary and integrative (Whitham et al., 2006). And yet the potential pay offs are large given that genetic variation across plant and animal systems can have extended consequences at the population, community and ecosystem levels. These consequences can come in the form of the vital rates of survival, reproduction and migration, as well as arthropod and aquatic macroinvertebrate diversity, soil microbial communities, trophic interactions, carbon storage, soil nitrogen availability, dissolved organic nitrogen and production of primary producers (Whitham et al., 2006; Bailey et al., 2009; Ezard et al., 2009; Harmon et al., 2009; Johnson et al., 2009; Palkovacs et al., 2009; Post & Palkovacs, 2009). The effects of genetic or phenotypic variation are not limited to single systems or to ecologically important species (i.e. keystone species, dominant species, foundation species, ecosystem engineers), although these are excellent places to start looking. Instead, genetic variation seems to have effects that are broadly distributed across plant and animal systems - and these effects can be similar in magnitude to those of nonevolutionary ecological variables, such as climate, species invasion and habitat quality (Hairston et al., 2005; Bailey et al., 2009; Ezard et al., 2009; Palkovacs et al., 2009; Post & Palkovacs, 2009).

Testing for Direct and Indirect Effects of Mate Choice by Manipulating Female Choosiness

Despite a massive research effort, our understanding of the evolution of female mate choice remains incomplete [1, 2]. A central problem is that the predominating empirical research tradition has focused on male traits, yet the key question is whether female choice traits are maintained because of direct effects on female fitness or because of indirect genetic effects in offspring that may be associated with such traits. Here, we address this question by using a novel research strategy that employs experimental phenotypic manipulation of a female choice trait in an insect model system, the seed beetle Callosobruchus chinensis (Coleoptera: Bruchidae). We show that females with increased efficiency of choice enjoy strongly elevated fitness compared to females with reduced choice efficiency. In contrast, we found no effects of female choice efficiency on offspring fitness. Our results show that female choice is maintained by direct selection in females in this system, whereas indirect selection is relatively weak at most. We suggest that phenotypic engineering of female choice traits can greatly advance our ability to elucidate the relative importance of direct and indirect selection for the maintenance of female choice.

Multiple paternity and offspring quality in tree swallows

There is mounting evidence in a variety of taxa that females increase offspring quality by mating with multiple males, often resulting in multiple paternity. In birds, however, few studies have explicitly examined the benefits of mating with several different males; instead, the focus has been on whether or not extra-pair mating occurs, and its adaptive significance remains controversial. We examined the hypothesis that offspring quality, particularly immune response (phytohaemagglutinin assay) and growth, increases with the number of sires in broods of socially monogamous tree swallows (Tachycineta bicolor). We found one of the highest known levels of multiple paternity in birds (84% of nests with two or more extra-pair young had at least two extra-pair sires). Among nests with extra-pair young, the number and diversity of sires continued to increase linearly with the number of extra-pair young, so there was no evidence that some males monopolized paternity at high levels of extra-pair fertilization. Indeed, the number of sires was actually greater than expected in large broods, suggesting that some females might be seeking more mates. We found no effect of the number of sires on nestling immune response or growth. In mixed paternity broods, the immune response of extra-pair young did not differ from that of their within-pair half-siblings. However, among all broods, nestlings had a stronger immune response in nests with at least one extra-pair nestling than in nests with all within-pair nestlings. These results are not consistent with a good genes benefit of extra-pair mating, but they do suggest that there are environmental effects associated with extra-pair mating that increase nestling immune response. These environmental effects could produce indirect genetic effects on sexual selection if they are heritable. The extraordinarily high number of sires in this species highlights a relatively unexplored source of sexual selection in birds.

HOW TO MEASURE INDIRECT GENETIC EFFECTS: THE CONGRUENCE OF TRAIT-BASED AND VARIANCE-PARTITIONING APPROACHES

Indirect genetic effects (IGEs), which occur when phenotypic expression in one individual is influenced by genes in another conspecific individual, may have a drastic effect on evolutionary response to selection. General evolutionary models of IGEs have been developed using two distinct theoretical frameworks derived from maternal effects theory. The first framework is trait-based and focuses on how phenotypes are influenced by specific traits in a social partner, with the strength of interactions defined by the matrix Psi. The second framework partitions total genetic variance into components representing direct effects, indirect effects, and the covariance between them, without identifying specific social traits responsible for IGEs. The latter framework has been employed more commonly by empiricists because the methods for estimating variance components are relatively straightforward. Here, we show how these two theoretical frameworks are related to each other and derive equations that can be used to translate between them. This translation leads to a generalized method that can be used to estimate Psi via standard quantitative genetic breeding designs or pedigrees from natural populations. This method can be used in a very general set of circumstances and is widely applicable to all IGEs, including maternal effects and other interactions among relatives.

INDIRECT GENETIC EFFECTS INFLUENCE ANTIPREDATOR BEHAVIOR IN GUPPIES: ESTIMATES OF THE COEFFICIENT OF INTERACTIONPSIAND THE INHERITANCE OF RECIPROCITY

How and why cooperation evolves, particularly among nonrelatives, remains a major paradox for evolutionary biologists and behavioral ecologists. Although much attention has focused on fitness consequences associated with cooperating, relatively little is known about the second component of evolutionary change, the inheritance of cooperation or reciprocity. The genetics of behaviors that can only be expressed in the context of interactions are particularly difficult to describe because the relevant genes reside in multiple social partners. Indirect genetic effects (IGEs) describe the influence of genes carried in social partners on the phenotype of a focal individual and thus provide a novel approach to quantifying the genetics underlying interactions such as reciprocal cooperation. We used inbred lines of guppies and a novel application of IGE theory to describe the dual genetic control of predator inspection and social behavior, both classic models of reciprocity. We identified effects of focal strain, social group strain, and interactions between focal and group strains on variation in focal behavior. We measured psi, the coefficient of the interaction, which describes the degree to which an individual's phenotype is influenced by the phenotype of its social partners. The genetic identity of social partners substantially influences inspection behavior, measures of threat assessment, and schooling and does so in positively reinforcing manner. We therefore demonstrate strong IGEs for antipredator behavior that represent the genetic variation necessary for the evolution of reciprocity.

GENES WITH SOCIAL EFFECTS ARE EXPECTED TO HARBOR MORE SEQUENCE VARIATION WITHIN AND BETWEEN SPECIES

The equilibrium sequence diversity of genes within a population and the rate of sequence divergence between populations or species depends on a variety of factors, including expression pattern, mutation rate, nature of selection, random drift, and mating system. Here, we extend population genetic theory developed for maternal-effect genes to predict the equilibrium polymorphism within species and sequence divergence among species for genes with social effects on fitness. We show how the fitness effects of genes, mating system, and genetic system affect predicted gene polymorphism. We find that, because genes with indirect social effects on fitness effectively experience weaker selection, they are expected to harbor higher levels of polymorphism relative to genes with direct fitness effects. The relative increase in polymorphism is proportional to the inverse of the genetic relatedness between individuals expressing the gene and their social partners that experience the fitness effects of the gene. We find a similar pattern of more rapid divergence between populations or species for genes with indirect social effects relative to genes with direct effects. We focus our discussion on the social insects, organisms with diverse indirect genetic effects, mating and genetic systems, and we suggest specific examples for testing our predictions with emerging sociogenomic tools.

On the adjustment for covariates in genetic association analysis: a novel, simple principle to infer direct causal effects

In genetic association studies, different complex phenotypes are often associated with the same marker. Such associations can be indicative of pleiotropy (i.e. common genetic causes), of indirect genetic effects via one of these phenotypes, or can be solely attributable to non-genetic/environmental links between the traits. To identify the phenotypes with the inducing genetic association, statistical methodology is needed that is able to distinguish between the different causes of the genetic associations. Here, we propose a simple, general adjustment principle that can be incorporated into many standard genetic association tests which are then able to infer whether an SNP has a direct biological influence on a given trait other than through the SNP's influence on another correlated phenotype. Using simulation studies, we show that, in the presence of a non-marker related link between phenotypes, standard association tests without the proposed adjustment can be biased. In contrast to that, the proposed methodology remains unbiased. Its achieved power levels are identical to those of standard adjustment methods, making the adjustment principle universally applicable in genetic association studies. The principle is illustrated by an application to three genome-wide association analyses.

Selection, Epistasis, and Parent-of-Origin Effects on Deleterious Mutations across Environments in Drosophila melanogaster

Understanding the nature of selection against deleterious alleles is central to determining how populations are affected by the constant influx of new mutations. Important progress has been made in estimating basic attributes of the distribution of selection coefficients and gene interaction effects (epistasis). Although most aspects of selection are likely to be context dependent, little is known about the effect of stress on selection and epistasis at the level of individual genes, especially in multicellular organisms. Using Drosophila melanogaster, we measure how selection on 20 mutant alleles is affected by direct and indirect genetic factors across two environments. We find that environmental stress increases selection against individual mutations but reduces selection against combinations of mutations (i.e., epistasis becomes more positive). In addition, we find a high incidence of indirect genetic effects whereby the strength of selection against the alleles carried by offspring is dependent on the genotypes of their parents.

Indirect genetic effects and the evolution of aggression in a vertebrate system

Aggressive behaviours are necessarily expressed in a social context, such that individuals may be influenced by the phenotypes, and potentially the genotypes, of their social partners. Consequently, it has been hypothesized that indirect genetic effects (IGEs) arising from the social environment will provide a major source of heritable variation on which selection can act. However, there has been little empirical scrutiny of this to date. Here we test this hypothesis in an experimental population of deer mice (Peromyscus maniculatus). Using quantitative genetic models of five aggression traits, we find repeatable and heritable differences in agonistic behaviours of focal individuals when presented with an opponent mouse. For three of the traits, there is also support for the presence of IGEs, and estimated correlations between direct and indirect genetic (rAO,F) effects were high. As a consequence, any selection for aggression in the focal individuals should cause evolution of the social environment as a correlated response. In two traits, strong positive rAO,F will cause the rapid evolution of aggression, while in a third case changes in the phenotypic mean will be constrained by negative covariance between direct and IGEs. Our results illustrate how classical analyses may miss important components of heritable variation, and show that a full understanding of evolutionary dynamics requires explicit consideration of the genetic component of the social environment.

Social Context Influences Chemical Communication in D. melanogaster Males

Chemical communication mediates social interactions in insects. For the fruit fly, D. melanogaster, the chemical display is a key fitness trait because it leads to mating. An exchange of cues that resembles a dialogue between males and females is enacted by pheromones, chemical signals that pass between individual flies to alter physiology and behavior. Chemical signals also affect the timing of locomotor activity and sleep. We investigated genetic and environmental determinants of chemical communication. To evaluate the role of the social environment, we extracted a chemical blend from individual males selected from groups composed of one genotype and compared these extracts to those from groups of mixed genotypes. To evaluate the role of the physical environment, these comparisons were performed under a light-dark cycle or in constant darkness. Here, we show that chemical signaling is affected by the social environment, light-dark cycle, and genotype as well as the complex interplay of these variables. Gene-by-environment interactions produce highly significant effects on chemical signaling. We also examined individual responses within the groups. Strikingly, the response of one wild-type fly to another is modulated by the genotypic composition of his neighbors. Chemical signaling in D. melanogaster may be a "fickle" trait that depends on the individual's social background.

The joint effects of kin, multilevel selection and indirect genetic effects on response to genetic selection

Kin and levels-of-selection models are common approaches for modelling social evolution. Indirect genetic effect (IGE) models represent a different approach, specifying social effects on trait values rather than fitness. We investigate the joint effect of relatedness, multilevel selection and IGEs on response to selection. We present a measure for the degree of multilevel selection, which is the natural partner of relatedness in expressions for response. Response depends on both relatedness and the degree of multilevel selection, rather than only one or the other factor. Moreover, response is symmetric in relatedness and the degree of multilevel selection, indicating that both factors have exactly the same effect. Without IGEs, the key parameter is the product of relatedness and the degree of multilevel selection. With IGEs, however, multilevel selection without relatedness can explain evolution of social traits. Thus, next to relatedness and multilevel selection, IGEs are a key element in the genetical theory of social evolution.

Indirect genetic effects and the lek paradox: inter-genotypic competition may strengthen genotype × environment interactions and conserve genetic variance

Understanding the evolutionary mechanisms that maintain genetic variation in natural populations is one of the fundamental goals of evolutionary biology. There is growing evidence that genotype-by-environment interaction (G x E) can maintain additive genetic variance (V (A)), but we lack information on the relative performance of genotypes under the competitive situations encountered in the field. Competing genotypes may influence each other, and this interaction is also subject to selection through indirect genetic effects (IGE). Here, we explore how genotypes perform when interacting and evaluate IGE in order to understand its influence on V (A) for sexually-selected traits in the lesser waxmoth, Achroia grisella. We found that inter-genotype differences and crossover interactions under joint rearing are equal to or greater than values when reared separately. A focal genotype exhibited different performances when jointly reared with various genotypes-suggesting that IGE may be responsible for the increased levels of crossover and differences in performance observed. We suggest that some genotypes are superior competitors for food acquisition in the larval stage, and that these differences influence the development and evolution of other genotypes through IGE. We reaffirm the role of G x E in maintaining V (A) and note the general importance of IGE in studies of evolutionary mechanisms.

“HIDDEN” REPRODUCTIVE CONFLICT BETWEEN MATES IN A WILD BIRD POPULATION

Environmental conditions experienced by a female prior to reproducing may be influenced by her mate. Part of such an indirect effect of a male on his partner's reproduction may be genetic (indirect genetic effect). However, a female's direct and a male's indirect genetic effects need not align. We analyzed 10,652 records of seasonal timing of laying, an important reproductive trait in many organisms, of 1864 male and 1916 female common gulls Larus canus collected during 37 years. We show that there is both a direct (female) and an indirect (male) genetic effect (explaining 14.5% and 4.8% of the REML estimated variance in laying date, respectively), but these are significantly negatively correlated (-0.53+/-0.22 SE), indicating that genes for early laying in females are associated with genes for a delaying male effect on his partner's laying date (and vice versa). There is strong selection for laying early in this population, and these sexually antagonistic genetic effects may contribute in maintaining the variation in laying date. Our findings provide an empirical demonstration of a hitherto largely unstudied level of conflict between mates, with important ramifications for our understanding of evolutionary dynamics and mate choice in nature.

Current analyses do not resolve whether extra-pair paternity is male or female driven

Recent studies question the importance of indirect genetic effects in explaining female benefits of extra-pair matings in socially monogamous species. Compiling data on 14 wild bird species, Arnqvist and Kirkpatrick (Am Nat 165:S26–S37, 2005) estimated the average direct cost in terms or reduced parental care to be an order of magnitude larger than the potential effect of genetic benefits. This study has sparked a debate regarding potential confounding factors but no consensus appears to have been reached. Here we focus on the implicit assumption that all individuals face the same selective pressures and argue that this assumption is probably too strong in most cases. Using a theoretical model we show that when the amount of resources that a male provides depends on territory quality, his physical condition or prospects for alternative breeding opportunities, a female may respond to such differences by altering her mating behaviour. Such confounding factors may lead to direct fitness effects that result in negative correlations between paternal care and paternity even if females that produce extra-pair young experience a net benefit. Negative correlations can also result when males forcefully seek copulations and females resist them. We discuss the studies included in the analysis in this light, and conclude that current analyses on the net selective pressures remain uninformative. In addition to considering average effects across individuals and species we suggest giving attention to individual differences and the influence of ecological factors such as territory quality and predation pressures on female mating behaviour.

Age Structure and Senescence in Long-Term Cohorts of Eisenia andrei (Oligochaeta: Lumbricidae)

HEN and colleagues (1) discussed fitness and aging relationships, considering senescence evolution in laboratory lines of nematodes. They concluded that fitness costs for Caenorhabditis elegans are consistent with antagonistic pleiotropy. Fitness and demography might be dominated by indirect genetic effects in other organisms too. We provide an additional explanation for senescence evolution by allometric mass-specific costs, as shown by long-term dynamics of reproduction, growth, and mortality of Eisenia andrei age cohorts. Empirical results collected during a 9-year experiment are provided and discussed. In this context we introduced mass-derived Gompertzian Metabolic Rates (GMR), which are benchmarks in com