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

Cooperative Behaviors in Group-Living Spider Mites

Cooperative behaviors are evolutionary stable if the direct and/or indirect fitness benefits exceed the costs of helping. Here we discuss cooperation and behaviors akin to cooperation in subsocial group-living species of two genera of herbivorous spider mites (Tetranychidae), i.e., the largely polyphagous Tetranychus spp. and the nest-building Stigmaeopsis spp., which are specialized on grasses, such as bamboo. These spider mites are distributed in patches on various spatial scales, that is, within and among leaves of individual host plants and among individual hosts of single or multiple plant species. Group-living of spider mites is brought about by plant-colonizing foundresses ovipositing at local feeding sites and natal site fidelity, and by multiple individuals aggregating in the same site in response to direct and/or indirect cues, many of which are associated with webbing. In the case of the former, emerging patches are often composed of genetically closely related individuals, while in the case of the latter, local patches may consist of kin of various degrees and/or non-kin and even heterospecific spider mites. We describe and discuss ultimate and proximate aspects of cooperation by spider mites in host plant colonization and exploitation, dispersal, anti-predator behavior, and nesting-associated behaviors and conclude with theoretical and practical considerations of future research on cooperation in these highly rewarding model animals.

Contribution of social genetic effects in variance components estimation for body weight in Nigerian indigenous chickens raised in a tropical humid location

Social interactions among chickens can have a great unfavourable effect on economic returns in a poultry farm. The purpose of this study was to use four models to examine the influence of social genetic influences on the variation in body weight of Nigerian indigenous chickens. Sex was treated as the fixed effect within the models. Direct additive genetic, social genetic, and family effects and covariance between direct and social genetic effects were used as random effects. Data were analysed using single-trait animal models which include or exclude social genetic effects. Model comparison revealed that inclusion of full-sib family effect in model 3 did not cause any change in residual and additive genetic variances relative to estimates obtained with model 2. In general, social genetic variance was lower than the estimate for additive genetic variance, but substantially added to the overall heritable variance. For direct hereditary, full-sib family, and residual effects, accounting for heritable social effect in model 4 had a marginal effect on the size of the variances measured. All the estimated residual, additive genetic, social genetic effect, and family variances increased in comparison with model 3. The relationship between direct and social additive effects was positive and not significantly different from 0 (P > 0.05), suggesting autonomy between the direct and social breeding values. In conclusion, the use of models that account for direct effect and social genetic effect of the individual on its group members would entail an optimal individual selection scheme to increase the body weight of chickens.

The predictive ability of indirect genetic models is reduced when culled animals are omitted from the data

Background

Physical removal of individuals from groups causes reductions in group sizes and changes in group composition, which may affect the predictive ability of estimates of indirect genetic effects of animals on phenotypes of group mates. We hypothesized that including indirect genetic effects of culled animals and of animals without phenotypes in the analysis affects estimates of genetic parameters, improves predictive ability, and reduces bias of predicted breeding values. We tested this by applying different editing procedures, i.e. omission of individuals or groups from the data, and genetic models, i.e. a classical and an indirect genetic model (IGM) without or with weighting of indirect genetic effects based on the relative proportion of time spent in the pen or space allowance. Data consisted of average daily gain for 123,567 pigs in 11,111 groups, from which 3% of individuals in 25% of groups were prematurely removed from the group.

Results

The estimate of total heritability was higher (0.29 to 0.34) than that of direct heritability (0.23 to 0.25) regardless of the editing procedures and IGM used. Omission of individuals or groups from the data reduced the predictive ability of estimates of indirect genetic effects by 8 to 46%, and the predictive ability of estimates of the combined direct and indirect genetic effects by up to 4%. Omission of full groups introduced bias in predicted breeding values. Weighting of indirect genetic effects reduced the predictive ability of their estimates by at least 19% and of the estimates of the combined direct and indirect genetic effects by 1%.

Conclusions

We identified significant indirect genetic effects for growth in pigs. Culled animals should neither be removed from the data nor accounted for by weighting their indirect genetic effects in the model based on the relative proportion of time spent in the pen or space allowance, because it will reduce predictive ability and increase bias of predicted breeding values. Information on culled animals is important for prediction of indirect genetic effects and must be accounted for in IGM analyses by including fixed regressions based on relative time spent within the pen or relative space allowance.

Direct and indirect genetic effects on reproductive investment in a grasshopper

A fundamental part of the quantitative genetic theory deals with the partitioning of the phenotypic variance into additive genetic and environmental components. During interaction with conspecifics, the interaction partner becomes a part of the environment from the perspective of the focal individual. If the interaction effects have a genetic basis, they are called indirect genetic effects (IGEs) and can evolve along with direct genetic effects. Sexual reproduction is a classic context where potential conflict between males and females can arise from trade-offs between current and future investments. We studied five female fecundity traits, egg length and number, egg pod length and number and latency to first egg pod, and estimated the direct and IGEs using a half-sib breeding design in the grasshopper Chorthippus biguttulus. We found that the male IGEs were an order of magnitude lower than the direct genetic effects and were not significantly different from zero. However, there was some indication that IGEs were larger shortly after mating, consistent with the idea that IGEs fade with time after interaction. Female direct heritabilities were moderate to low. Simulation shows that the variance component estimates can appear larger with less data, calling for care when interpreting variance components estimated with low power. Our results illustrate that the contribution of male IGEs is overall low on the phenotypic variance of female fecundity traits. Thus, even in the relevant context of sexual conflict, the influence of male IGEs on the evolutionary trajectory of female reproductive traits is likely to be small.

Indirect genetic effect model using feeding behaviour traits to define the degree of interaction between mates: an implementation in pigs growth rate

An alternative implementation of the animal model including indirect genetic effect (IGE) is presented considering pair-mate-specific interaction degrees to improve the performance of the model. Data consisted of average daily gain (ADG) records from 663 pigs kept in groups of 10 to 14 mates during the fattening period. Three types of models were used to fit ADG data: (i) animal model (AM); (ii) AM with classical IGE (AM-IGE); and (iii) AM fitting IGE with a specific degree of interaction between each pair of mates (AM-IGE_i). Several feeding behavior phenotypes were used to define the pair-mate-specific degree of interaction in AM-IGE_i: feeding rate (g/min), feeding frequency (min/day), the time between consecutive visits to the feeder (min/day), occupation time (min/day) and an index considering all these variables. All models included systematic effects batch, initial age (covariate), final age (covariate), number of pigs per pen (covariate), plus the random effect of the pen. Estimated posterior mean (posterior SD) of heritability was 0.47 (0.15) using AM. Including social genetic effects in the model, total heritable variance expressed as a proportion of total phenotypic variance (T²) was 0.54 (0.29) using AM-IGE, whereas it ranged from 0.51 to 0.55 (0.12 to 0.14) with AM-IGE_i, depending on the behavior trait used to define social interactions. These results confirm the contribution of IGEs to the total heritable variation of ADG. Moreover, important differences between models were observed in EBV rankings. The percentage of coincidence of top 10% animals between AM and AM-IGE_i ranged from 0.44 to 0.89 and from 0.41to 0.68 between AM-IGE and AM-IGE_i. Based on the goodness of fit and predictive ability, social models are preferred for the genetic evaluation of ADG. Among models including IGEs, when the pair-specific degree of interaction was defined using feeding behavior phenotypes we obtained an increase in the accuracy of genetic parameters estimates, the better goodness of fit and higher predictive ability. We conclude that feeding behavior variables can be used to measure the interaction between pen mates and to improve the performance of models including IGEs.

Social genetic effects for growth in pigs differ between boars and gilts

Background

Average daily gain (ADG) in pigs is affected by the so-called social (or indirect) genetic effects (SGE). However, SGE may differ between sexes because boars grow faster than gilts and their social behaviours differ. We hypothesized that direct genetic effects (DGE) and SGE for ADG in pigs differ between boars and gilts and that accounting for these differences will improve the predictive ability of a social genetic effects model (SGM). Our data consisted of ADG from 30 to 94 kg for 32,212 uncastrated males (boars) and 48,252 gilts that were raised in sex-specific pens. Data were analyzed using a univariate model with sex as a fixed effect and a bivariate model with ADG in boars and gilts as separate traits using both a classical animal model (CM) and a SGM.

Results

With the univariate model, the heritability for ADG was 0.22 ± 0.01 for the CM, while the estimate of the total heritable variance (T²) was 0.23 ± 0.01 with the SGM. With the bivariate model, the genetic variance for SGE was higher for boars (13.8 ± 5.8) than for gilts (9.3 ± 3.9). For the bivariate model, T² was 0.32 ± 0.02 for boars and 0.27 ± 0.01 for gilts. Estimates of the genetic correlations between DGE (0.88 ± 0.02) and SGE (0.30 ± 0.30) for boars versus gilts indicated that ADG in boars and gilts are different traits. Moreover, the estimate of the genetic correlation between DGE and SGE indicated presence of genetic effects of competition among gilts but not among boars. Compared to a CM, the univariate SGM improved predictive ability significantly only for gilts and the bivariate SGM improved predictive ability significantly for both boars and gilts.

Conclusions

We found significant genetic variances of SGE for ADG. The covariance between DGE and SGE was much more negative for gilts than for boars when applying the bivariate model. Because the estimate of the genetic correlation for ADG between gilts and boars differed significantly from 1 and the predictive ability for boars and gilts was improved significantly with the bivariate model, we recommend the use of a bivariate model to estimate both SGE and DGE for ADG in pigs.

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 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.