Genetic control of interactions among individuals: contrasting outcomes of indirect genetic effects arising from neighbour disease infection and competition in a forest tree

Bring back the phenotype

When thinking about evolutionary change, many practicing biologists will focus on changes in allele frequencies over time. This gene-centric view of evolution has strongly impacted how evolution (and biological science in general) is thought, taught, and funded. In this viewpoint, we join recent criticisms of the gene-centric view and call for reinstalling a phenotypic view of evolution. The assumptions of the gene-centric view-enormous/nonstructured populations and totally random interactions between genes, individuals, and environments-are hard to imagine in the real world. A gene's effects on phenotype and fitness depend on its interactions with other genes (epistasis), other individuals, the microbiome, and the environment, and it changes between generations, populations, and environments. Incorrectly, genes have been given an agency and role in natural selection that they do not possess: they replicate, but they do not have phenotypic variation or differential proliferation through their traits (these are characteristics of the units of selection deemed 'interactors'). Here, we show how a phenotypic view of evolution is necessary to capture several widespread phenomena: epistasis, nongenetic inheritance, multilevel selection, and niche construction through plant-soil feedbacks, all of which have vast empirical evidence. Life is marvelous, complex, and certainly more than machinery and genetic information.

Indirect genetic effects increase the heritable variation available to selection and are largest for behaviors: a meta-analysis

The evolutionary potential of traits is governed by the amount of heritable variation available to selection. While this is typically quantified based on genetic variation in a focal individual for its own traits (direct genetic effects, DGEs), when social interactions occur, genetic variation in interacting partners can influence a focal individual's traits (indirect genetic effects, IGEs). Theory and studies on domesticated species have suggested IGEs can greatly impact evolutionary trajectories, but whether this is true more broadly remains unclear. Here, we perform a systematic review and meta-analysis to quantify the amount of trait variance explained by IGEs and the contribution of IGEs to predictions of adaptive potential. We identified 180 effect sizes from 47 studies across 21 species and found that, on average, IGEs of a single social partner account for a small but statistically significant amount of phenotypic variation (0.03). As IGEs affect the trait values of each interacting group member and due to a typically positive-although statistically nonsignificant-correlation with DGEs (r DGE-IGE = 0.26), IGEs ultimately increase trait heritability substantially from 0.27 (narrow-sense heritability) to 0.45 (total heritable variance). This 66% average increase in heritability suggests IGEs can increase the amount of genetic variation available to selection. Furthermore, whilst showing considerable variation across studies, IGEs were most prominent for behaviors and, to a lesser extent, for reproduction and survival, in contrast to morphological, metabolic, physiological, and development traits. Our meta-analysis, therefore, shows that IGEs tend to enhance the evolutionary potential of traits, especially for those tightly related to interactions with other individuals, such as behavior and reproduction.

Incorporating spatial and genetic competition into breeding pipelines with the R package gencomp

Genetic competition can obscure the true merit of selection candidates, potentially leading to altered genotype rankings and a divergence between expected and actual genetic gains. Despite a wealth of literature on genetic competition in plant and animal breeding, the separation of genetic values into direct genetic effects (DGE, related to a genotype's merit) and indirect genetic effects (IGE, related to the effects of a genotype's alleles on its neighbor's phenotype) in linear mixed models is often overlooked, likely due to the complexity involved. To address this, we introduce gencomp, a new R package designed to simplify the use of (spatial-) genetic competition models in crop and tree breeding routines. gencomp includes functions for constructing the genetic competition matrix, fitting (spatial-) genetic competition models via the variance-component approach, and extracting key results such as variance components, heritabilities, competition classes, and total genetic values. For tree breeding, gencomp also calculates the merit of different clonal mixtures using the estimated DGE and IGE of the selection candidates. In this paper, we first present the theoretical foundation of the methods implemented in the package. We then demonstrate the use of gencomp with two datasets: one simulated from a Eucalyptus spp. trial and a real potato dataset. We used both datasets to demonstrate the influence of genetic competition in variance component estimates, heritabilities and selection. Despite the dependency on ASReml-R, a paid resource, gencomp is a user-friendly tool that can popularize genetic competition models, contributing to more informed decision-making in plant breeding.

The genetic identity of neighboring plants in intraspecific mixtures modulates disease susceptibility of both wheat and rice

Mixing crop cultivars has long been considered as a way to control epidemics at the field level and is experiencing a revival of interest in agriculture. Yet, the ability of mixing to control pests is highly variable and often unpredictable in the field. Beyond classical diversity effects such as dispersal barrier generated by genotypic diversity, several understudied processes are involved. Among them is the recently discovered neighbor-modulated susceptibility (NMS), which depicts the phenomenon that susceptibility in a given plant is affected by the presence of another healthy neighboring plant. Despite the putative tremendous importance of NMS for crop science, its occurrence and quantitative contribution to modulating susceptibility in cultivated species remains unknown. Here, in both rice and wheat inoculated in greenhouse conditions with foliar fungal pathogens considered as major threats, using more than 200 pairs of intraspecific genotype mixtures, we experimentally demonstrate the occurrence of NMS in 11% of the mixtures grown in experimental conditions that precluded any epidemics. Thus, the susceptibility of these 2 major crops results from indirect effects originating from neighboring plants. Quite remarkably, the levels of susceptibility modulated by plant-plant interactions can reach those conferred by intrinsic basal immunity. These findings open new avenues to develop more sustainable agricultural practices by engineering less susceptible crop mixtures thanks to emergent but now predictable properties of mixtures.

The importance of distinguishing individual differences in 'social impact' versus 'social responsiveness' when quantifying indirect genetic effects on the evolution of social plasticity

Social evolution and the dynamics of social interactions have previously been studied under the frameworks of quantitative genetics and behavioural ecology. In quantitative genetics, indirect genetic effects of social partners on the socially plastic phenotypes of focal individuals typically lack crucial detail already included in treatments of social plasticity in behavioural ecology. Specifically, whilst focal individuals (e.g. receivers) may show variation in their 'responsiveness' to the social environment, individual social partners (e.g. signallers) may have a differential 'impact' on focal phenotypes. Here we propose an integrative framework, that highlights the distinction between responsiveness versus impact in indirect genetic effects for a range of behavioural traits. We describe impact and responsiveness using a reaction norm approach and provide statistical models for the assessment of these effects of focal and social partner identity in different types of social interactions. By providing such a framework, we hope to stimulate future quantitative research investigating the causes and consequences of social interactions on phenotypic evolution.

Linking leaf economic and hydraulic traits with early-age growth performance and survival of Eucalyptus pauciflora

Selection on plant functional traits may occur through their direct effects on fitness (or a fitness component), or may be mediated by attributes of plant performance which have a direct impact on fitness. Understanding this link is particularly challenging for long-lived organisms, such as forest trees, where lifetime fitness assessments are rarely achievable, and performance features and fitness components are usually quantified from early-life history stages. Accordingly, we studied a cohort of trees from multiple populations of Eucalyptus pauciflora grown in a common-garden field trial established at the hot and dry end of the species distribution on the island of Tasmania, Australia. We related the within-population variation in leaf economic (leaf thickness, leaf area and leaf density) and hydraulic (stomatal density, stomatal length and vein density) traits, measured from two-year-old plants, to two-year growth performance (height and stem diameter) and to a fitness component (seven-year survival). When performance-trait relationships were modelled for all traits simultaneously, statistical support for direct effects on growth performance was only observed for leaf thickness and leaf density. Performance-based estimators of directional selection indicated that individuals with reduced leaf thickness and increased leaf density were favoured. Survival-performance relationships were consistent with size-dependent mortality, with fitness-based selection gradients estimated for performance measures providing evidence for directional selection favouring individuals with faster growth. There was no statistical support for an effect associated with the fitness-based quadratic selection gradient estimated for growth performance. Conditional on a performance measure, fitness-based directional selection gradients estimated for the leaf traits did not provide statistical support for direct effects of the focal traits on tree survival. This suggested that, under the environmental conditions of the trial site and time period covered in the current study, early-stage selection on the studied leaf traits may be mediated by their effects on growth performance, which in turn has a positive direct influence on later-age survival. We discuss the potential mechanistic basis of the direct effects of the focal leaf traits on tree growth, and the relevance of a putative causal pathway of trait effects on fitness through mediation by growth performance in the studied hot and dry environment.

Linking quantitative genetics with community-level performance: Are there operational models for plant breeding?

Plant breeding is focused on the genotype and population levels while targeting effects at higher levels of biodiversity, from crop covers to agroecosystems. Making predictions across nested levels of biodiversity is therefore a major challenge for the development of intercropping practices. New prediction tools and concepts are required to design breeding strategies with desirable outcomes at the crop community level. We reviewed theoretical advances in the field of evolutionary ecology to identify potentially operational ways of predicting the effects of artificial selection on community-level performances. We identified three main types of approaches differing in the way they model interspecific indirect genetic effects (IIGEs) at the community level: (1) The community heritability approach estimates the variance for IIGE induced by a focal species at the community level; (2) the joint phenotype approach quantifies genetic constraints between direct genetic effects and IIGE for a set of interacting species; (3) the community-trait genetic gradient approach decomposes the IIGE for a focal species across a multivariate set of its functional traits. We discuss the potential operational capacities of these approaches and stress that each is a special case of a general multitrait and multispecies selection index. Choosing one therefore involves assumptions and goals regarding the breeding target and strategy. Obtaining reliable quantitative, community-level predictions at the genetic level is constrained by the size and complexity of the experimental designs usually required. Breeding strategies should instead be compared using theoretically informed qualitative predictions. The need to estimate genetic covariances between traits measured both within and among species (for IIGE) is another obstacle, as the two are not determined by the exact same biological processes. We suggest future research directions and strategies to overcome these limits. Our synthesis offers an integrative theoretical framework for breeders interested in the genetic improvement of crop communities but also for scientists interested in the genetic bases of plant community functioning.

Social animal models for quantifying plasticity, assortment, and selection on interacting phenotypes

Both assortment and plasticity can facilitate social evolution, as each may generate heritable associations between the phenotypes and fitness of individuals and their social partners. However, it currently remains difficult to empirically disentangle these distinct mechanisms in the wild, particularly for complex and environmentally responsive phenotypes subject to measurement error. To address this challenge, we extend the widely used animal model to facilitate unbiased estimation of plasticity, assortment and selection on social traits, for both phenotypic and quantitative genetic (QG) analysis. Our social animal models (SAMs) estimate key evolutionary parameters for the latent reaction norms underlying repeatable patterns of phenotypic interaction across social environments. As a consequence of this approach, SAMs avoid inferential biases caused by various forms of measurement error in the raw phenotypic associations between social partners. We conducted a simulation study to demonstrate the application of SAMs and investigate their performance for both phenotypic and QG analyses. With sufficient repeated measurements, we found desirably high power, low bias and low uncertainty across model parameters using modest sample and effect sizes, leading to robust predictions of selection and adaptation. Our results suggest that SAMs will readily enhance social evolutionary research on a variety of phenotypes in the wild. We provide detailed coding tutorials and worked examples for implementing SAMs in the Stan statistical programming language.

Anticipated effects of abiotic environmental change on intraspecific social interactions

Social interactions are ubiquitous across the animal kingdom. A variety of ecological and evolutionary processes are dependent on social interactions, such as movement, disease spread, information transmission, and density-dependent reproduction and survival. Social interactions, like any behaviour, are context dependent, varying with environmental conditions. Currently, environments are changing rapidly across multiple dimensions, becoming warmer and more variable, while habitats are increasingly fragmented and contaminated with pollutants. Social interactions are expected to change in response to these stressors and to continue to change into the future. However, a comprehensive understanding of the form and magnitude of the effects of these environmental changes on social interactions is currently lacking. Focusing on four major forms of rapid environmental change currently occurring, we review how these changing environmental gradients are expected to have immediate effects on social interactions such as communication, agonistic behaviours, and group formation, which will thereby induce changes in social organisation including mating systems, dominance hierarchies, and collective behaviour. Our review covers intraspecific variation in social interactions across environments, including studies in both the wild and in laboratory settings, and across a range of taxa. The expected responses of social behaviour to environmental change are diverse, but we identify several general themes. First, very dry, variable, fragmented, or polluted environments are likely to destabilise existing social systems. This occurs as these conditions limit the energy available for complex social interactions and affect dissimilar phenotypes differently. Second, a given environmental change can lead to opposite responses in social behaviour, and the direction of the response often hinges on the natural history of the organism in question. Third, our review highlights the fact that changes in environmental factors are not occurring in isolation: multiple factors are changing simultaneously, which may have antagonistic or synergistic effects, and more work should be done to understand these combined effects. We close by identifying methodological and analytical techniques that might help to study the response of social interactions to changing environments, highlight consistent patterns among taxa, and predict subsequent evolutionary change. We expect that the changes in social interactions that we document here will have consequences for individuals, groups, and for the ecology and evolution of populations, and therefore warrant a central place in the study of animal populations, particularly in an era of rapid environmental change.

Indirect genetic and environmental effects on behaviors, morphology, and life-history traits in a wild Eastern chipmunk population

Additive genetic variance in a trait reflects its potential to respond to selection, which is key for adaptive evolution in the wild. Social interactions contribute to this genetic variation through indirect genetic effects-the effect of an individual's genotype on the expression of a trait in a conspecific. However, our understanding of the evolutionary importance of indirect genetic effects in the wild and of their strength relative to direct genetic effects is limited. In this study, we assessed how indirect genetic effects contribute to genetic variation of behavioral, morphological, and life-history traits in a wild Eastern chipmunk population. We also compared the contribution of direct and indirect genetic effects to traits evolvabilities and related these effects to selection strength across traits. We implemented a novel approach integrating the spatial structure of social interactions in quantitative genetic analyses, and supported the reliability of our results with power analyses. We found indirect genetic effects for trappability and relative fecundity, little direct genetic effects in all traits and a large role for direct and indirect permanent environmental effects. Our study highlights the potential evolutionary role of social permanent environmental effects in shaping phenotypes of conspecifics through adaptive phenotypic plasticity.

Breeding Beyond Monoculture: Putting the "Intercrop" Into Crops

Intercropping is both a well-established and yet novel agricultural practice, depending on one's perspective. Such perspectives are principally governed by geographic location and whether monocultural practices predominate. Given the negative environmental effects of monoculture agriculture (loss of biodiversity, reliance on non-renewable inputs, soil degradation, etc.), there has been a renewed interest in cropping systems that can reduce the impact of modern agriculture while maintaining (or even increasing) yields. Intercropping is one of the most promising practices in this regard, yet faces a multitude of challenges if it is to compete with and ultimately replace the prevailing monocultural norm. These challenges include the necessity for more complex agricultural designs in space and time, bespoke machinery, and adapted crop cultivars. Plant breeding for monocultures has focused on maximizing yield in single-species stands, leading to highly productive yet specialized genotypes. However, indications suggest that these genotypes are not the best adapted to intercropping systems. Re-designing breeding programs to accommodate inter-specific interactions and compatibilities, with potentially multiple different intercropping partners, is certainly challenging, but recent technological advances offer novel solutions. We identify a number of such technology-driven directions, either ideotype-driven (i.e., "trait-based" breeding) or quantitative genetics-driven (i.e., "product-based" breeding). For ideotype breeding, plant growth modeling can help predict plant traits that affect both inter- and intraspecific interactions and their influence on crop performance. Quantitative breeding approaches, on the other hand, estimate breeding values of component crops without necessarily understanding the underlying mechanisms. We argue that a combined approach, for example, integrating plant growth modeling with genomic-assisted selection and indirect genetic effects, may offer the best chance to bridge the gap between current monoculture breeding programs and the more integrated and diverse breeding programs of the future.

Feed competition reduces heritable variation for body weight in Litopenaeus vannamei

Background

Competition is a common social interaction among shrimp and depending on its intensity, it can affect heritable variation and response to selection. Little is known about the variance of indirect genetic effects (IGE) under competitive and non-competitive conditions in shrimp. In this study, we used extended mixed linear models to estimate genetic parameters for the direct genetic effect (DGE) and IGE on body weight in Litopenaeus vannamei raised under ad libitum (AF, non-competitive environment) and restricted (RF, competitive environment) feeding regimes.

Results

Estimates of heritabilities for body weight obtained with a traditional animal model (i.e. without accounting for IGE) were 0.11 ± 0.09 under AF and 0.25 ± 0.11 under RF. With extended animal models that accounted for IGE, the corresponding estimates for body weight were 0.07 ± 0.08 and 0.34 ± 0.11. Thus, heritabilities were higher under the RF regime than under the AF regime, regardless of whether IGE was accounted for or not. The log-likelihood ratio test revealed significant IGE under the RF regime. Although estimates of indirect genetic variance were low (0.0023 ± 0.0013 for AF and 0.0028 ± 0.0012 for RF), they contributed substantially to the total heritable variance: 66.8% for AF and 692.2% for RF. The total heritable variance was smaller under the RF regime (0.7 ± 1.3) than under the AF regime (5.8 ± 2.6) because of the high contribution of the negative covariance between DGE and IGE (− 7.03). Estimates of the correlation between DGE and IGE were 0.32 ± 0.47 under AF and − 0.93 ± 0.15 under RF, those of DGE and IGE for body weight between both regimes were 0.94 ± 0.07 and 0.67 ± 0.20, respectively, and those of IGE for body weight with DGE for survival were − 0.12 ± 0.22 under AF and − 0.58 ± 0.20 under RF.

Conclusions

These results indicate that strong competitive interactions occurred under the RF regime in L. vannamei. Significant reranking and variation in IGE of individuals were observed between the two feeding regimes. Strong competitive interactions reduced the total heritable variation for body weight when food was restricted. These results indicate that the extent of competition among L. vannamei depends on the feeding regime applied and that this competition affects the genetic basis of body weight.

Can breeders solve mortality due to feather pecking in laying hens?

Mortality due to feather pecking (FP) has large economic and welfare consequences in the commercial poultry industry, and reduces survival of birds. With FP, the survival time of a hen depends both on her own genetic ability to avoid becoming the victim of FP (direct genetic effect; DGE), and on the genetic tendency of her group mates to perform FP (indirect genetic effect; IGE). Thus, to improve survival time of laying hens, it is important to use a breeding strategy that captures both the DGE and the IGE of selection candidates. Here, we investigate the prospects for solving mortality due to FP in laying hens by genetic selection. First, we review genetic parameters for survival time. Second, we use deterministic simulation to predict response to selection for 2 multi-trait crossbred breeding programs, a traditional recurrent testing scheme (RT) and a genomic selection scheme (GS). Finally, we investigate the prospects for sustained improvement of survival time when mortality becomes low. Results show that survival time has considerable heritable variation; most estimates of the total additive genetic standard deviation are larger than 1 mo. As expected, predicted single generation response to selection in survival time with GS is substantial larger than with RT. Particularly when the correlation between survival time and other breeding goal traits is zero, the GS scheme yields substantial improvement in survival time. For example, when mortality is 35%, the genetic correlation between survival time and other traits is 0, allowing for a 10% reduction of response in other traits, and when selection takes place in both the sire line and dam line, survival time can be improved with ∼23 D in one generation, using GS. Results, however, also show a strong decrease in heritability when mortality decreases, indicating that continued improvement becomes increasingly difficult. In summary, our results show that breeders can considerably reduce mortality due to FP with limited reduction of improvement in other breeding goal traits.

Heritable spouse effects increase evolutionary potential of human reproductive timing

Sexual reproduction is inherently interactive, especially in animal species such as humans that exhibit extended pair bonding. Yet we have little knowledge of the role of male characteristics and their evolutionary impact on reproductive behavioural phenotypes, to the extent that biologists typically consider component traits (e.g. reproductive timing) as female-specific. Based on extensive genealogical data detailing the life histories of 6435 human mothers born across four centuries of modern history, we use an animal modelling approach to estimate the indirect genetic effect of men on the reproductive phenotype of their partners. These analyses show that a woman's reproductive timing (age at first birth) is influenced by her partner's genotype. This indirect genetic effect is positively correlated with the direct genetic effect expressed in women, such that total heritable variance in this trait is doubled when heritable partner effects are considered. Our study thus suggests that much of the heritable variation in women's reproductive timing is mediated via partner effects, and that the evolutionary potential of this trait is far greater than previously appreciated.

Opposite responses to selection and where to find them

We generally expect traits to evolve in the same direction as selection. However, many organisms possess traits that appear to be costly for individuals, while plant and animal breeding experiments reveal that selection may lead to no response or even negative responses to selection. We formalize both of these instances as cases of "opposite responses to selection." Using quantitative genetic models for the response to selection, we outline when opposite responses to selection should be expected. These typically occur when social selection opposes direct selection, when individuals interact with others less related to them than a random member of the population, and if the genetic covariance between direct and indirect effects is negative. We discuss the likelihood of each of these occurring in nature and therefore summarize how frequent opposite responses to selection are likely to be. This links several evolutionary phenomena within a single framework.

Comparison of host susceptibilities to native and exotic pathogens provides evidence for pathogen-imposed selection in forest trees

The extent to which spatial structuring of host resistance in wild plant populations reflects direct pathogen-imposed selection is a subject of debate. To examine this issue, genetic susceptibilities to an exotic and a coevolved native fungal pathogen were compared using two Australian host tree species. Damage to common host germplasm of Corymbia citriodora ssp. variegata (CCV) and Eucalyptus globulus, caused by recently introduced (Austropuccinia psidii) and native (Quambalaria pitereka and Teratosphaeria sp.) pathogens was evaluated in common-garden experiments. There was significant additive genetic variation within host species for susceptibility to both the exotic and native pathogens. However, susceptibility to A. psidii was not genetically correlated with susceptibility to either native pathogen, providing support for pathogen-specific rather than general mechanisms of resistance. Population differentiation (Q_ST ) for susceptibility to the native pathogens was greater than neutral expectations (molecular F_ST ), arguing for divergent selection. Coupled with lower native, but not exotic, pathogen susceptibility in host populations from areas climatically more prone to fungal proliferation, these findings suggest that pathogen-imposed selection has contributed directly to a geographic mosaic of host resistance to native pathogens.

Increased developmental density decreases the magnitude of indirect genetic effects expressed during agonistic interactions in an insect

The expression of aggression depends not only on the direct genetic effects (DGEs) of an individual's genes on its own behavior, but also on indirect genetic effects (IGEs) caused by heritable phenotypes expressed by social partners. IGEs can affect the amount of heritable variance on which selection can act. Despite the important roles of IGEs in the evolutionary process, it remains largely unknown whether the strength of IGEs varies across life stages or competitive regimes. Based on manipulations of nymphal densities and > 3000 pair-wise aggression tests across multiple life stages, we experimentally demonstrate that IGEs on aggression are stronger in field crickets (Gryllus bimaculatus) that develop at lower densities than in those that develop at higher densities, and that these effects persist with age. The existence of density-dependent IGEs implies that social interactions strongly determine the plastic expression of aggression when competition for resources is relaxed. A more competitive (higher density) rearing environment may fail to provide crickets with sufficient resources to develop social cognition required for strong IGEs. The contribution of IGEs to evolutionary responses was greater at lower densities. Our study thereby demonstrates the importance of considering IGEs in density-dependent ecological and evolutionary processes.

Indirect Genetic Effects for Growth in Pigs Affect Behaviour and Weight Around Weaning

Selection for indirect genetic effects (IGE), i.e. the genetic effect of an individual on a trait of another individual, is a promising avenue to increase trait values in plant and animal breeding. Studies in livestock suggest that selection for IGE for growth (IGEg) might increase animals' capacity to tolerate stress. We assessed the effect of a stressful phase (weaning) on the behaviour and performance of pigs (n = 480) divergently selected for high or low IGEg. High IGEg pigs were significantly slower to explore the feed and gained less weight than low IGEg pigs in the days after weaning. In line with previous findings, high IGEg animals may have prioritized the formation of social ranks.

Intraspecific genetic diversity modulates plant-soil feedback and nutrient cycling

Plant genetic diversity can affect ecosystem functioning by enhancing productivity, litter decomposition and resistance to natural enemies. However, the mechanisms underlying these effects remain poorly understood. We hypothesized that genetic diversity may influence ecosystem processes by eliciting functional plasticity among individuals encountering kin or genetically diverse neighbourhoods. We used soil conditioned by groups of closely related (siblings) and diverse genotypes of Deschampsia cespitosa - a species known to exhibit kin recognition via root exudation - to investigate the consequences of kin interactions for root litter decomposition and negative feedback between plants and soil biota. Genetically diverse groups produced root litter that had higher nitrogen (N) content, decomposed faster and resulted in greater N uptake by the next generation of seedlings compared with litter produced by sibling groups. However, a similar degree of negative soil feedback on plant productivity was observed in soil conditioned by siblings and genetically diverse groups. This suggests that characteristics of roots produced by sibling groups slow down N cycling but moderate the expected negative impact of soil pathogens in low-diversity stands. These findings highlight interactions between neighbouring genotypes as an overlooked mechanism by which genetic diversity can affect biotic soil feedback and nutrient cycling.

Indirect genetic effects: a key component of the genetic architecture of behaviour

Behavioural ecology research increasingly focuses on why genetic behavioural variation can persist despite selection. Evolutionary theory predicts that directional selection leads to evolutionary change while depleting standing genetic variation. Nevertheless, evolutionary stasis may occur for traits involved in social interactions. This requires tight negative genetic correlations between direct genetic effects (DGEs) of an individual’s genes on its own phenotype and the indirect genetic effects (IGEs) it has on conspecifics, as this could diminish the amount of genetic variation available to selection to act upon. We tested this prediction using a pedigreed laboratory population of Mediterranean field crickets (Gryllus bimaculatus), in which both exploratory tendency and aggression are heritable. We found that genotypes predisposed to be aggressive (due to DGEs) strongly decreased aggressiveness in opponents (due to IGEs). As a consequence, the variance in total breeding values was reduced to almost zero, implying that IGEs indeed greatly contribute to the occurrence of evolutionary stasis. IGEs were further associated with genetic variation in a non-social behaviour: explorative genotypes elicited most aggression in opponents. These key findings imply that IGEs indeed represent an important overlooked mechanism that can impact evolutionary dynamics of traits under selection.

Genetic-based interactions among tree neighbors: identification of the most influential neighbors, and estimation of correlations among direct and indirect genetic effects for leaf disease and growth in Eucalyptus globulus

An individual's genes may influence the phenotype of neighboring conspecifics. Such indirect genetic effects (IGEs) are important as they can affect the apparent total heritable variance in a population, and thus the response to selection. We studied these effects in a large, pedigreed population of Eucalyptus globulus using variance component analyses of Mycosphearella leaf disease, diameter growth at age 2 years, and post-infection diameter growth at ages 4 and 8 years. In a novel approach, we initially modeled IGEs using a factor analytic (FA) structure to identify the most influential neighbor positions, with the FA loadings being position-specific regressions on the IGEs. This involved sequentially comparing FA models for the variance-covariance matrices of the direct and indirect effects of each neighbor. We then modeled IGEs as a distance-based, combined effect of the most influential neighbors. This often increased the magnitude and significance of indirect genetic variance estimates relative to using all neighbors. The extension of a univariate IGEs model to bivariate analyses also provided insights into the genetic architecture of this population, revealing that: (1) IGEs arising from increased probability of neighbor infection were not associated with reduced growth of neighbors, despite adverse fitness effects being evident at the direct genetic level; and (2) the strong, genetic-based competitive interactions for growth, established early in stand development, were highly positively correlated over time. Our results highlight the complexities of genetic-based interactions at the multi-trait level due to (co)variances associated with IGEs, and the marked discrepancy occurring between direct and total heritable variances.

Air-borne genotype by genotype indirect genetic effects are substantial in the filamentous fungus Aspergillus nidulans

Genotype by genotype indirect genetic effects (G × G IGEs) occur when the phenotype of an individual is influenced by an interaction between its own genotype and those of neighbour individuals. Little is known regarding the relative importance of G × G IGEs compared with other forms of direct and indirect genetic effects. We quantified the relative importance of IGEs in the filamentous fungus Aspergillus nidulans, a species in which IGEs are likely to be important as air-borne social interactions are known to affect growth. We used a collection of distantly related wild isolates, lab strains and a set of closely related mutation accumulation lines to estimate the contribution of direct and indirect genetic effects on mycelium growth rate, a key fitness component. We found that indirect genetic effects were dominated by G × G IGEs that occurred primarily between a focal genotype and its immediate neighbour within a vertical stack, and these accounted for 11% of phenotypic variation. These results indicate that G × G IGEs may be substantial, at least in some systems, and that the evolutionary importance of these interactions may be underappreciated, especially in microbes. We advocate for a wider use of the IGE framework in both applied (for example, choice of varietal mixtures in plant breeding) and evolutionary genetics (kin selection/kin competition studies).

Direct and indirect genetic effects in life-history traits of flour beetles (Tribolium castaneum)

Indirect genetic effects (IGEs) are the basis of social interactions among conspecifics, and can affect genetic variation of nonsocial and social traits. We used flour beetles (Tribolium castaneum) of two phenotypically distinguishable populations to estimate genetic (co)variances and the effect of IGEs on three life-history traits: development time (DT), growth rate (GR), and pupal body mass (BM). We found that GR was strongly affected by social environment with IGEs accounting for 18% of the heritable variation. We also discovered a sex-specific social effect: male ratio in a group significantly affected both GR and BM; that is, beetles grew larger and faster in male-biased social environments. Such sex-specific IGEs have not previously been demonstrated in a nonsocial insect. Our results show that beetles that achieve a higher BM do so via a slower GR in response to social environment. Existing models of evolution in age-structured or stage-structured populations do not account for IGEs of social cohorts. It is likely that such IGEs have played a key role in the evolution of developmental plasticity shown by Tenebrionid larvae in response to density. Our results document an important source of genetic variation for GR, often overlooked in life-history theory.

The prospects of selection for social genetic effects to improve welfare and productivity in livestock

Social interactions between individuals living in a group can have both positive and negative effects on welfare, productivity, and health of these individuals. Negative effects of social interactions in livestock are easier to observe than positive effects. For example, laying hens may develop feather pecking, which can cause mortality due to cannibalism, and pigs may develop tail biting or excessive aggression. Several studies have shown that social interactions affect the genetic variation in a trait. Genetic improvement of socially-affected traits, however, has proven to be difficult until relatively recently. The use of classical selection methods, like individual selection, may result in selection responses opposite to expected, because these methods neglect the effect of an individual on its group mates (social genetic effects). It has become clear that improvement of socially-affected traits requires selection methods that take into account not only the direct effect of an individual on its own phenotype but also the social genetic effects, also known as indirect genetic effects, of an individual on the phenotypes of its group mates. Here, we review the theoretical and empirical work on social genetic effects, with a focus on livestock. First, we present the theory of social genetic effects. Subsequently, we evaluate the evidence for social genetic effects in livestock and other species, by reviewing estimates of genetic parameters for direct and social genetic effects. Then we describe the results of different selection experiments. Finally, we discuss issues concerning the implementation of social genetic effects in livestock breeding programs. This review demonstrates that selection for socially-affected traits, using methods that target both the direct and social genetic effects, is a promising, but sometimes difficult to use in practice, tool to simultaneously improve production and welfare in livestock.

Indirect genetic effects from competition in the clonal herb Sedum album (Crassulaceae)

Recent years have seen increasing interest in indirect genetic effects, i.e. influences on the phenotype that depend on the genotype of other conspecific individuals; however, the empirical evidence for such effects is still limited, especially in wild plant species. The present study of the clonal herb Sedum album assessed direct and indirect genetic effects on performance-related traits in a 4-year experiment with clonally replicated genotypes, grown in pairs and differing in anthocyanin pigmentation to allow separation of individuals during data collection. In agreement with the existence of indirect genetic effects, the experimentally-paired plants not only expressed their own genotype but were also affected by the genotype of their pair mate. The effect of neighbour genotype explained up to one-fourth of the variation in performance and most likely resulted from competition, imposed by the close physical contact between paired individuals and the limiting conditions used in the garden environment. Indirect genetic effects from competition have the potential to enhance the efficacy of group-level selection relative to individual selection, given the nutrient-poor and spatially-confined substrate available to plants of S. album in the natural habitat.

Indirect genetic effects contribute substantially to heritable variation in aggression-related traits in group-housed mink (Neovison vison)

BACKGROUND

Since the recommendations on group housing of mink (Neovison vison) were adopted by the Council of Europe in 1999, it has become common in mink production in Europe. Group housing is advantageous from a production perspective, but can lead to aggression between animals and thus raises a welfare issue. Bite marks on the animals are an indicator of this aggressive behaviour and thus selection against frequency of bite marks should reduce aggression and improve animal welfare. Bite marks on one individual reflect the aggression of its group members, which means that the number of bite marks carried by one individual depends on the behaviour of other individuals and that it may have a genetic basis. Thus, for a successful breeding strategy it could be crucial to consider both direct (DGE) and indirect (IGE) genetic effects on this trait. However, to date no study has investigated the genetic basis of bite marks in mink.

RESULT AND DISCUSSION

A model that included DGE and IGE fitted the data significantly better than a model with DGE only, and IGE contributed a substantial proportion of the heritable variation available for response to selection. In the model with IGE, the total heritable variation expressed as the proportion of phenotypic variance (T2) was six times greater than classical heritability (h2). For instance, for total bite marks, T2 was equal to 0.61, while h2 was equal to 0.10. The genetic correlation between direct and indirect effects ranged from 0.55 for neck bite marks to 0.99 for tail bite marks. This positive correlation suggests that mink have a tendency to fight in a reciprocal way (giving and receiving bites) and thus, a genotype that confers a tendency to bite other individuals can also cause its bearer to receive more bites.

CONCLUSION

Both direct and indirect genetic effects contribute to variation in number of bite marks in group-housed mink. Thus, a genetic selection design that includes both direct genetic and indirect genetic effects could reduce the frequency of bite marks and probably aggression behaviour in group-housed mink.

Indirect genetic effects and kin recognition: estimating IGEs when interactions differ between kin and strangers

Social interactions among individuals are widespread, both in natural and domestic populations. As a result, trait values of individuals may be affected by genes in other individuals, a phenomenon known as indirect genetic effects (IGEs). IGEs can be estimated using linear mixed models. The traditional IGE model assumes that an individual interacts equally with all its partners, whether kin or strangers. There is abundant evidence, however, that individuals behave differently towards kin as compared with strangers, which agrees with predictions from kin-selection theory. With a mix of kin and strangers, therefore, IGEs estimated from a traditional model may be incorrect, and selection based on those estimates will be suboptimal. Here we investigate whether genetic parameters for IGEs are statistically identifiable in group-structured populations when IGEs differ between kin and strangers, and develop models to estimate such parameters. First, we extend the definition of total breeding value and total heritable variance to cases where IGEs depend on relatedness. Next, we show that the full set of genetic parameters is not identifiable when IGEs differ between kin and strangers. Subsequently, we present a reduced model that yields estimates of the total heritable effects on kin, on non-kin and on all social partners of an individual, as well as the total heritable variance for response to selection. Finally we discuss the consequences of analysing data in which IGEs depend on relatedness using a traditional IGE model, and investigate group structures that may allow estimation of the full set of genetic parameters when IGEs depend on kin.

The quantitative genetics of indirect genetic effects: a selective review of modelling issues

Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits subject to IGEs have been developed within two frameworks; a trait-based framework in which IGEs are specified as a direct consequence of individual trait values, and a variance-component framework in which phenotypic variance is decomposed into a direct and an indirect additive genetic component. This work is a selective review of the quantitative genetics of traits affected by IGEs, with a focus on modelling, estimation and interpretation issues. It includes a discussion on variance-component vs trait-based models of IGEs, a review of issues related to the estimation of IGEs from field data, including the estimation of the interaction coefficient Ψ (psi), and a discussion on the relevance of IGEs for response to selection in cases where the strength of interaction varies among pairs of individuals. An investigation of the trait-based model shows that the interaction coefficient Ψ may deviate considerably from the corresponding regression coefficient when feedback occurs. The increasing research effort devoted to IGEs suggests that they are a widespread phenomenon, probably particularly in natural populations and plants. Further work in this field should considerably broaden our understanding of the quantitative genetics of inheritance and response to selection in relation to the social organisation of populations.

Indirect genetic effects and housing conditions in relation to aggressive behaviour in pigs

Indirect Genetic Effects (IGEs), also known as associative effects, are the heritable effects that an individual has on the phenotype of its social partners. Selection for IGEs has been proposed as a method to reduce harmful behaviours, in particular aggression, in livestock and aquaculture. The mechanisms behind IGEs, however, have rarely been studied. The objective was therefore to assess aggression in pigs which were divergently selected for IGEs on growth (IGEg). In a one generation selection experiment, we studied 480 offspring of pigs (Sus scrofa) that were selected for relatively high or low IGEg and housed in homogeneous IGEg groups in either barren or enriched environments. Skin lesion scores, a proxy measure of aggression, and aggressive behaviours were recorded. The two distinct IGEg groups did not differ in number of skin lesions, or in amount of reciprocal fighting, both under stable social conditions and in confrontation with unfamiliar pigs in a 24 h regrouping test. Pigs selected for a positive effect on the growth of their group members, however, performed less non-reciprocal biting and showed considerably less aggression at reunion with familiar group members after they had been separated during a 24 h regrouping test. The enriched environment was associated with more skin lesions but less non-reciprocal biting under stable social conditions. Changes in aggression between pigs selected for IGEg were not influenced by G×E interactions with regard to the level of environmental enrichment. It is likely that selection on IGEg targets a behavioural strategy, rather than a single behavioural trait such as aggressiveness.