Group selection for adaptation to multiple-hen cages: selection program and direct responses

Shifting the Level of Selection in Science

Criteria for recognizing and rewarding scientists primarily focus on individual contributions. This creates a conflict between what is best for scientists' careers and what is best for science. In this article, we show how the theory of multilevel selection provides conceptual tools for modifying incentives to better align individual and collective interests. A core principle is the need to account for indirect effects by shifting the level at which selection operates from individuals to the groups in which individuals are embedded. This principle is used in several fields to improve collective outcomes, including animal husbandry, team sports, and professional organizations. Shifting the level of selection has the potential to ameliorate several problems in contemporary science, including accounting for scientists' diverse contributions to knowledge generation, reducing individual-level competition, and promoting specialization and team science. We discuss the difficulties associated with shifting the level of selection and outline directions for future development in this domain.

Indirect genetic effects are shaped by demographic history and ecology in Arabidopsis thaliana

The phenotype of an individual can be affected by the genes of its conspecifics through indirect genetic effects (IGEs). IGEs have been studied across different organisms including wild and domesticated animals and plants, but little is known about their genetic architecture. Here, in a large-scale intraspecific interaction experiment, we show that the contribution of IGEs to the biomass variation of Arabidopsis thaliana is comparable to values classically reported in animals. Moreover, we identify 11 loci explaining 85.1% of the variability in IGEs. We find that positive IGE alleles (that is, those with positive effects on neighbour biomass) occur both in relict accessions from southern Eurasia and in post-glacial colonizers from northern Scandinavia, and that they are likely to have two divergent origins: for nine loci, they evolved in the post-glacial colonizers independently from the relicts, while the two others were introgressed in the post-glacial colonizer from the relicts. Finally, we find that variation in IGEs probably reflects divergent adaptations to the contrasting environments of the edges and the centre of the native range of the species. These findings reveal a surprisingly tractable genetic basis of IGEs in A. thaliana that is shaped by the ecology and the demographic history of the species.

Increasing plant group productivity through latent genetic variation for cooperation

Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that-while beneficial to the group-decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields.

A complete absence of indirect genetic effects on brain gene expression in a highly social context

Genes not only control traits of their carrier organism (known as direct genetic effects or DGEs) but also shape their carrier's physical environment and the phenotypes of their carrier's social partners (known as indirect genetic effects or IGEs). Theoretical research has shown that the effects that genes exert on social partners can have profound consequences, potentially altering heritability and the direction of trait evolution. Complementary empirical research has shown that in various contexts (particularly in animal agriculture) IGEs can explain a large proportion of variation in specific traits. However, little is known about the general prevalence of IGEs. We conducted a reciprocal cross-fostering experiment with two genetic lineages of the clonal raider ant Ooceraea biroi to quantify the relative contribution of DGEs and IGEs to variation in brain gene expression (which underlies behavioural variation). We found that thousands of genes are differentially expressed by DGEs but not a single gene is differentially expressed by IGEs. This is surprising given the highly social context of ant colonies and given that individual behaviour varies according to the genotypic composition of the social environment in O. biroi. Overall, these findings indicate that we have a lot to learn about how the magnitude of IGEs varies across species and contexts.

Long-time behavior of a PDE replicator equation for multilevel selection in group-structured populations

In many biological systems, natural selection acts simultaneously on multiple levels of organization. This scenario typically presents an evolutionary conflict between the incentive of individuals to cheat and the collective incentive to establish cooperation within a group. Generalizing previous work on multilevel selection in evolutionary game theory, we consider a hyperbolic PDE model of a group-structured population, in which members within a single group compete with each other for individual-level replication; while the group also competes against other groups for group-level replication. We derive a threshold level of the relative strength of between-group competition such that defectors take over the population below the threshold while cooperation persists in the long-time population above the threshold. Under stronger assumptions on the initial distribution of group compositions, we further prove that the population converges to a steady state density supporting cooperation for between-group selection strength above the threshold. We further establish long-time bounds on the time-average of the collective payoff of the population, showing that the long-run population cannot outperform the payoff of a full-cooperator group even in the limit of infinitely-strong between-group competition. When the group replication rate is maximized by an intermediate level of within-group cooperation, individual-level selection casts a long shadow on the dynamics of multilevel selection: no level of between-group competition can erase the effects of the individual incentive to defect. We further extend our model to study the case of multiple types of groups, showing how the games that groups play can coevolve with the level of cooperation.

Shift in beneficial interactions during crop evolution

Plant domestication can be viewed as a form of co-evolved interspecific mutualism between humans and crops for the benefit of the two partners. Here, we ask how this plant-human mutualism has, in turn, impacted beneficial interactions within crop species, between crop species, and between crops and their associated microbial partners. We focus on beneficial interactions resulting from three main mechanisms that can be promoted by manipulating genetic diversity in agrosystems: niche partitioning, facilitation, and kin selection. We show that a combination of factors has impacted either directly or indirectly plant-plant interactions during domestication and breeding, with a trend toward reduced benefits arising from niche partitioning and facilitation. Such factors include marked decrease of molecular and functional diversity of crops and other organisms present in the agroecosystem, mass selection, and increased use of chemical inputs. For example, the latter has likely contributed to the relaxation of selection pressures on nutrient-mobilizing traits such as those associated to root exudation and plant nutrient exchanges via microbial partners. In contrast, we show that beneficial interactions arising from kin selection have likely been promoted since the advent of modern breeding. We highlight several issues that need further investigation such as whether crop phenotypic plasticity has evolved and could trigger beneficial interactions in crops, and whether human-mediated selection has impacted cooperation via kin recognition. Finally, we discuss how plant breeding and agricultural practices can help promoting beneficial interactions within and between species in the context of agroecology where the mobilization of diversity and complexity of crop interactions is viewed as a keystone of agroecosystem sustainability.

Capturing indirect genetic effects on phenotypic variability: Competition meets canalization

Phenotypic variability of a genotype is relevant both in natural and domestic populations. In the past two decades, variability has been studied as a heritable quantitative genetic trait in its own right, often referred to as inherited variability or environmental canalization. So far, studies on inherited variability have only considered genetic effects of the focal individual, that is, direct genetic effects on inherited variability. Observations from aquaculture populations and some plants, however, suggest that an additional source of genetic variation in inherited variability may be generated through competition. Social interactions, such as competition, are often a source of Indirect Genetic Effects (IGE). An IGE is a heritable effect of an individual on the trait value of another individual. IGEs may substantially affect heritable variation underlying the trait, and the direction and magnitude of response to selection. To understand the contribution of IGEs to evolution of environmental canalization in natural populations, and to exploit such inherited variability in animal and plant breeding, we need statistical models to capture this effect. To our knowledge, it is unknown to what extent the current statistical models commonly used for IGE and inherited variability capture the effect of competition on inherited variability. Here, we investigate the potential of current statistical models for inherited variability and trait values, to capture the direct and indirect genetic effects of competition on variability. Our results show that a direct model of inherited variability almost entirely captures the genetic sensitivity of individuals to competition, whereas an indirect model of inherited variability captures the cooperative genetic effects of individuals on their partners. Models for trait levels, however, capture only a small part of the genetic effects of competition. The estimation of direct and indirect genetic effects of competition, therefore, is possible with models for inherited variability but may require a two-step analysis.

The Impact of Probiotic Bacillus subtilis on Injurious Behavior in Laying Hens

Simple Summary

Injurious behavior prevention is a critical issue in the poultry industry due to increasing social stress, leading to negative effects on bird production and survivability, consequently enhancing gut microbiota dysbiosis and neuroinflammation via the microbiota–gut–brain axis. Probiotics have been used as potential therapeutic psychobiotics to treat or improve neuropsychiatric disorders or symptoms by boosting cognitive and behavioral processes and reducing stress reactions in humans and various experimental animals. The current data will first report that probiotic Bacillus subtilis reduces stress-induced injurious behavior in laying hens via regulating microbiota–gut–brain function with the potential to be an alternative to beak trimming during poultry egg production.

Abstract

Intestinal microbiota functions such as an endocrine organ to regulate host physiological homeostasis and behavioral exhibition in stress responses via regulating the gut–brain axis in humans and other mammals. In humans, stress-induced dysbiosis of the gut microbiota leads to intestinal permeability, subsequently affecting the clinical course of neuropsychiatric disorders, increasing the frequency of aggression and related violent behaviors. Probiotics, as direct-fed microorganism, have been used as dietary supplements or functional foods to target gut microbiota (microbiome) for the prevention or therapeutic treatment of mental diseases including social stress-induced psychiatric disorders such as depression, anxiety, impulsivity, and schizophrenia. Similar function of the probiotics may present in laying hens due to the intestinal microbiota having a similar function between avian and mammals. In laying hens, some management practices such as hens reared in conventional cages or at a high stocking density may cause stress, leading to injurious behaviors such as aggressive pecking, severe feather pecking, and cannibalism, which is a critical issue facing the poultry industry due to negative effects on hen health and welfare with devastating economic consequences. We discuss the current development of using probiotic Bacillus subtilis to prevent or reduce injurious behavior in laying hens.

Indirect Genetic Effects: A Cross-disciplinary Perspective on Empirical Studies

Indirect genetic effects (IGE) occur when an individual's phenotype is influenced by genetic variation in conspecifics. Opportunities for IGE are ubiquitous, and, when present, IGE have profound implications for behavioral, evolutionary, agricultural, and biomedical genetics. Despite their importance, the empirical study of IGE lags behind the development of theory. In large part, this lag can be attributed to the fact that measuring IGE, and deconvoluting them from the direct genetic effects of an individual's own genotype, is subject to many potential pitfalls. In this Perspective, we describe current challenges that empiricists across all disciplines will encounter in measuring and understanding IGE. Using ideas and examples spanning evolutionary, agricultural, and biomedical genetics, we also describe potential solutions to these challenges, focusing on opportunities provided by recent advances in genomic, monitoring, and phenotyping technologies. We hope that this cross-disciplinary assessment will advance the goal of understanding the pervasive effects of conspecific interactions in biology.

Efficient Allocation of Labor Maximizes Brood Development and Explains Why Intermediate-Sized Groups Perform Best During Colony-Founding in the Ant, Pogonomyrmex californicus

Cooperation in nature is usually between relatives, but unrelated individuals can also cooperate, requiring significant benefits to outweigh the costs of helping non-kin. Unrelated queens of the ant, Pogonomyrmex californicus, work together to found a new colony, a phenomenon known as pleometrosis. While previous studies have shown that pleometrosis improves queen survival and worker production, little is known of the behavioral interactions within nests that explain these advantages. We aimed to determine how the optimal group size for a small, simple social group is related to group productivity and the organization of work. Collecting queens from a known pleometrotic population, we established nests with either one, three, six, or nine foundresses and observed the resulting nascent colonies for 50 days. We found that queens in social founding groups survived longer and had higher productivity. While all social groups were equally successful in producing workers, intermediate-sized groups were most successful in terms of per capita production. Inactivity increased with group size. In addition, the proportion of essential colony growth tasks performed (such as foraging and brood care) was lowest in both solitary-founded groups and in groups of nine queens. As a result, intermediate sized groups outperformed both solitary queens and groups of nine in the efficiency with which they converted eggs into workers. These results emphasize the benefits of cooperation and the ways in which group size can influence fitness and the allocation of labor in social groups.

The quantitative genetics of the prevalence of infectious diseases: hidden genetic variation due to indirect genetic effects dominates heritable variation and response to selection

Infectious diseases have profound effects on life, both in nature and agriculture. However, a quantitative genetic theory of the host population for the endemic prevalence of infectious diseases is almost entirely lacking. While several studies have demonstrated the relevance of transmission of infections for heritable variation and response to selection, current quantitative genetics ignores transmission. Thus, we lack concepts of breeding value and heritable variation for endemic prevalence, and poorly understand response of endemic prevalence to selection. Here, we integrate quantitative genetics and epidemiology, and propose a quantitative genetic theory for the basic reproduction number R0 and for the endemic prevalence of an infection. We first identify the genetic factors that determine the prevalence. Subsequently, we investigate the population-level consequences of individual genetic variation, for both R0 and the endemic prevalence. Next, we present expressions for the breeding value and heritable variation, for endemic prevalence and individual binary disease status, and show that these depend strongly on the prevalence. Results show that heritable variation for endemic prevalence is substantially greater than currently believed, and increases strongly when prevalence decreases, while heritability of disease status approaches zero. As a consequence, response of the endemic prevalence to selection for lower disease status accelerates considerably when prevalence decreases, in contrast to classical predictions. Finally, we show that most heritable variation for the endemic prevalence is hidden in indirect genetic effects, suggesting a key role for kin-group selection in the evolutionary history of current populations and for genetic improvement in animals and plants.

Relationship between indirect genetic effects for growth, environmental enrichment, coping style and sex with the serum metabolome profile of pigs

Including Indirect Genetic Effects (IGE) in breeding programs to reduce aggression in group housed animals has been proposed. However, the effect of selection for IGE for growth on animal metabolism and physiology is unknown. The purpose of this study was twofold: (1) To investigate the effects of this new breeding method along with two housing (barren and straw), coping style (high and low resisters) and sex (female and castrated males) options on the metabolome profile of pigs. (2) To identify and map biological processes associated with a regrouping test at 9 weeks of age. We used Nuclear Magnetic Resonance to quantify 49 serum metabolites at week 8, 9 and 22. Also, we quantified 3 catecholamines (tyramine, epinephrine, phenylethylamine) and serotonin and three water soluble vitamins (B2, B5 and B7). Overall, no significant differences were observed between negative and positive IGE animals. The magnitude of change (delta) of many metabolites as a response to the regrouping test was significantly affected by IGE, especially that of the amino acids (P < 0.05), being greater in positive IGE pigs. The regrouping test was associated with alteration in glycine, serine and threonine metabolism. In conclusion positive and negative IGE animals respond differently to the regrouping test.

Comparison of Changes in the Plumage and Body Condition, Egg Production, and Mortality of Different Non-Beak-Trimmed Pure Line Laying Hens during the Egg-Laying Period

Simple Summary

The spread of both alternative and non-cage laying hen housing systems and the more forceful European refusal of beak trimming generate new problems in commercial egg production. The hybrid layers, which have been genetically selected under cage housing conditions for more decades, have lively temperament, are more susceptible for feather pecking and, in more cases, they are expressly aggressive, which led to permanent conflict situations in the large group keeping systems. Therefore, the omission of beak trimming could lead to an increased risk for feather pecking and consequently to a risk for increased mortality in the hen house by using the current commercial layers. Therefore, changes in the live weight, plumage and body condition, egg production, and mortality of different TETRA pure line non-beak-trimmed laying hens were compared during the egg-production period in our study, where the plumage condition was considered as an indicator trait for feather pecking. Our results confirm the findings of former studies that the genetic background of the hens is an important factor impacting feather pecking and suggest that breeding for an improved plumage condition might be a potential way to improve animal welfare in non-beak-trimmed layer flocks.

Abstract

The experiment was carried out with altogether 1740 non-beak-trimmed laying hens, which originated from Bábolna TETRA Ltd., representing two different types (Rhode Island Red (RIR) and Rhode Island White (RIW)) and four different lines (Lines 1–2: RIR, Lines 3–4: RIW). The plumage and body condition of randomly selected 120 hens (30 hens/line) was examined at 20, 46, and 62 weeks of age. The egg production and the mortality of the sampled hens were recorded daily. Based on the results, it was established that the lines differ clearly in most of the examined traits. It was also pointed out that injurious pecking of the hens resulted not only in damages in the plumage but also in the body condition. The results obviously demonstrated that the highest egg production and the lowest mortality rate were reached by those hens, which had the best plumage and body condition. Because the occurrence of injurious pecking seems to depend on the genetic background, selection of the hens (lines, families, individuals) for calm temperament will be very important in the future in order to maintain the high production level in non-beak-trimmed layer flocks.

Advances in genetic selection and breeder practice improve commercial layer hen welfare

Modern commercial layer breeds represent the culmination of ~7000 years of natural genetic selection. This selection was driven in former times by a combination of genetic-shift and -drift events, that led to chickens being favoured as domesticated species for meat and egg production. More recently, in the early 20th century, the concept of hybrid vigour was discovered and accelerated the natural breeding progress that delivered new genetic lines and more favourable production traits. In the mid-20th century, the broiler-type and egg layer-type lines diverged and, in the 21st century, genetic analysis has further accelerated the progress made towards extended primary breeding characteristics such as egg quality, production and feed-intake traits, together with secondary breeding characteristics such as behavioural traits that have improved robustness in different housing systems, climates and feed types, which together have significantly improved welfare traits. Most recently, there has been the adoption of higher-powered computational analytics together with quantitative trait loci and single-nucleotide polymorphism assessment, which have further improved the uniformity of production traits within breeds. Most importantly, this has provided the primary breeding companies with improved and broader basis of selection of the modern commercial layer breeds, which also improved the alignment of layer strains with market requirements, and diverse variations in housing, nutritional and environmental conditions. This is also testament to the speed with which the commercial layer geneticists can respond to changing welfare policy on factors such as stocking density and beak treatment. The present paper reviews the modern approaches to genetic selection, including considerations of and benefits to the welfare state of commercial layers.

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.

Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding

Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.

Farming plant cooperation in crops

Selection of the fittest can promote individual competitiveness but often results in the erosion of group performance. Recently, several authors revisited this idea in crop production and proposed new practices based on selection for cooperative phenotypes, i.e. phenotypes that increase crop yield through decreased competitiveness. These recommendations, however, remain difficult to evaluate without a formal description of crop evolutionary dynamics under different selection strategies. Here, we develop a theoretical framework to investigate the evolution of cooperation-related traits in crops, using plant height as a case study. Our model is tailored to realistic agricultural practices and shows that combining high plant density, high relatedness and selection among groups favours the evolution of shorter plants that maximize grain yield. Our model allows us to revisit past and current breeding practices in light of kin selection theory, and yields practical recommendations to increase cooperation among crops and promote sustainable agriculture.

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.

Artificially selecting microbial communities: If we can breed dogs, why not microbiomes?

Natural microbial communities perform many functions that are crucial for human well-being. Yet we have very little control over them, and we do not know how to optimize their functioning. One idea is to breed microbial communities as we breed dogs: by comparing a set of microbiomes and allowing the best-performing ones to generate new communities, and so on. Although this idea seems simple, designing such a selection experiment brings with it many decisions with surprising outcomes. Xie and colleagues developed a computational model that reveals this complexity and shows how different experimental design decisions can impact the success of such an experiment.

Simulations reveal challenges to artificial community selection and possible strategies for success

Multispecies microbial communities often display "community functions" arising from interactions of member species. Interactions are often difficult to decipher, making it challenging to design communities with desired functions. Alternatively, similar to artificial selection for individuals in agriculture and industry, one could repeatedly choose communities with the highest community functions to reproduce by randomly partitioning each into multiple "Newborn" communities for the next cycle. However, previous efforts in selecting complex communities have generated mixed outcomes that are difficult to interpret. To understand how to effectively enact community selection, we simulated community selection to improve a community function that requires 2 species and imposes a fitness cost on one or both species. Our simulations predict that improvement could be easily stalled unless various aspects of selection are carefully considered. These aspects include promoting species coexistence, suppressing noncontributors, choosing additional communities besides the highest functioning ones to reproduce, and reducing stochastic fluctuations in the biomass of each member species in Newborn communities. These considerations can be addressed experimentally. When executed effectively, community selection is predicted to improve costly community function, and may even force species to evolve slow growth to achieve species coexistence. Our conclusions hold under various alternative model assumptions and are therefore applicable to a variety of communities.

Expression of aggressiveness modulates mesencephalic c-fos activation during a social interaction test in Japanese quail (Coturnix japonica)

It is well known that during a social conflict, interactions are dependent on the animal's propensity to behave aggressively as well as the behavior of the opponent. However, discriminating between these two confounding factors was difficult. Recently, a Social Interaction (SI) test using photocastrated males as non-aggressive stimuli was proposed as a useful tool to evaluate aggressiveness. The avian Intercollicular- Griseum centralis complex (comparable to mammalian periaqueductal gray) has been reported as a crucial node in the descending pathways that organize behavioral and autonomic aspects of defensive responses and aggressiveness. Herein, using the SI test, we evaluated whether mesencephalic areas are activated (expressed c-fos) when photostimulated adult males are confronted with non-responsive (non-aggressive) opponents. Furthermore, we also examined whether mesencephalic activation is related to male performance during the SI test (i.e., aggressive vs. non-aggressive males) in birds reared in enriched or in standard environments. Five mesencephalic areas at two anatomic levels (intermediate and rostral) and locomotion during SI testing were studied. Aggressive males showed increased c-fos expression in all areas studied, and moved at faster speeds in comparison to their non-aggressive and control counterparts. Non-aggressive males and the test controls showed similar c-fos labeling. In general, rearing condition did not appear to influence c-fos expression nor behavior during the SI test. Findings suggest that mesencephalic activation is involved when males are actively expressing aggressive behaviors. This overall phenomenon is shown regardless of both the environmental stimuli provided during the birds´ rearing and the potentially stressful stimuli during the SI trial.

Review of Sensor Technologies in Animal Breeding: Phenotyping Behaviors of Laying Hens to Select Against Feather Pecking

Simple Summary

The European Cooperation in Science and Technology (COST) Action GroupHouseNet aims to provide synergy among scientists to prevent damaging behavior in group-housed pigs and laying hens. One goal of this network is to determine how genetic and genomic tools can be used to breed animals that are less likely to perform damaging behavior on their pen-mates. In this review, the focus is on feather-pecking behavior in laying hens. Reducing feather pecking in large groups of hens is a challenge, because it is difficult to identify and monitor individual birds. However, current developments in sensor technologies and animal breeding have the potential to identify individual animals, monitor individual behavior, and link this information back to the underlying genotype. We describe a combination of sensor technologies and “-omics” approaches that could be used to select against feather-pecking behavior in laying hens.

Abstract

Damaging behaviors, like feather pecking (FP), have large economic and welfare consequences in the commercial laying hen industry. Selective breeding can be used to obtain animals that are less likely to perform damaging behavior on their pen-mates. However, with the growing tendency to keep birds in large groups, identifying specific birds that are performing or receiving FP is difficult. With current developments in sensor technologies, it may now be possible to identify laying hens in large groups that show less FP behavior and select them for breeding. We propose using a combination of sensor technology and genomic methods to identify feather peckers and victims in groups. In this review, we will describe the use of “-omics” approaches to understand FP and give an overview of sensor technologies that can be used for animal monitoring, such as ultra-wideband, radio frequency identification, and computer vision. We will then discuss the identification of indicator traits from both sensor technologies and genomics approaches that can be used to select animals for breeding against damaging behavior.

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.

Genetic selection for growth performance and thermal tolerance under high ambient temperature after two generations using heat shock protein 90 expression as an index

Genetic selection for productive performance in high ambient temperatures was performed on two chicken strains, Rhode Island Red and Sinai, for two generations, and the heritable responses to tolerance were estimated using heat shock protein 90 (HSP90) gene expression. The results are summarised as follows: (1) heat stress negatively affected some economic traits, mainly bodyweight. This effect was more pronounced in the parent stock than in the first generation (F1) and second generation (F2). (2) This effect was modulated by the chicken strain, and the decreased bodyweight was more pronounced in RI strain than in the Sinai strain, indicating that the Sinai strain is more tolerant to high ambient temperature. (3) The offspring (F1 and F2) of both strains were more tolerant to high ambient temperature; this trend was also true for the parents of these two strains. (4) HSP90 mRNA expression was the same in both strains under normal conditions in all three generations. (5) Under high ambient temperature conditions, the Sinai strain (all generations) showed significantly increased HSP90 mRNA expression compared with the Rhode Island Red strain. These findings suggest that heat tolerance is passed from parents to offspring. We recommended that selection for heat-stress tolerance be applied to producing commercial strains reared in hot climate conditions.

Unexpected results when assessing underlying aggressiveness in Japanese quail using photocastrated stimulus birds

Aggressive behaviors can affect both animal welfare and productivity. Because the expression of aggressive behaviors is dependent on the quality of the opponent, they reflect relative rather than absolute levels of underlying aggressiveness. This study was aimed to characterize the aggressive responsiveness of photostimulated (14:10 h light:dark photoperiod) adult Japanese quail when interacting with a photocastrated (6:18 h light:dark photoperiod) counterpart in a novel test environment and to assesses interindividual variations. This was based on the assumption that photocastrated birds will not actively provoke an aggressive confrontation. Birds were reared in male-female pairs. Frequencies of behaviors (i.e., pecks, threats, chases, grabs, mounts) were determined during 10 min social interactions in a novel environment. A first experiment evaluated 78 encounters between a photostimulated male or female with either a photocastrated male or female (photocastration of sexually mature birds started at 11 wk of age). High interindividual variability was observed and in general, highly aggressive birds (performing 20 or more aggressive interactions) received little or no aggression from their test counterpart. However, unexpectedly, we also found that 37% and 32% of photocastrated males and females, respectively, performed aggressions toward their photostimulated counterparts, and initiated the aggressive interactions in a similar proportion than photostimulated males. Aggressive photocastrated males did not perform reproductive-type behaviors (i.e., grabs, mounts). Aggressiveness in the photocastrated birds was attributed to their social experience prior to photocastration. Therefore, a second experiment evaluated 106 encounters between a photostimulated male or female and a naive photocastrated male (photocastration started at 4 wk of age, prior to sexual development). Photocastrated males performed no aggressions toward their photostimulated counterparts. Consistently with previous studies, our findings show that naive photocastrated males can be used as a non-aggressive stimulus during a social interaction aimed to assess expression of aggressiveness in photostimulated birds. However, caution should be taken when applying the photocastration protocol considering that prior fighting and sexual experience or other physiological changes related with maturation can interfere during subsequent aggressive testing.

Modelling the co-evolution of indirect genetic effects and inherited variability

When individuals interact, their phenotypes may be affected not only by their own genes but also by genes in their social partners. This phenomenon is known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, however, competition not only affects trait levels of individuals, but also inflates variability of trait values among individuals. In the field of quantitative genetics, the variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Such studies, however, consider only the genetic effect of the focal individual on trait variability and do not make a connection to competition. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, the current quantitative genetic models of IGE and inherited variability do not allow for such a relationship. The lack of quantitative genetic models that connect IGEs to inherited variability limits our understanding of the potential of variability to respond to selection, both in nature and agriculture. Models of trait levels, for example, show that IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to variability of trait values. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of the genetic and environmental effects of the focal individual and of the difference in trait value between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait, which is a measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. In contrast to the existing quantitative genetic models, our model allows for co-evolution of IGEs and variability, as the regression coefficient can respond to selection. Our simulations show that the model results in increased variability of body weight with increasing competition. When competition decreases, i.e., cooperation evolves, variability becomes significantly smaller. Hence, our model facilitates quantitative genetic studies on the relationship between IGEs and inherited variability. Moreover, our findings suggest that we may have been overlooking an entire level of genetic variation in variability, the one due to IGEs.

Evolutionary agroecology: individual fitness and population yield in wheat (Triticum aestivum)

Although the importance of group selection in nature is highly controversial, several researchers have argued that plant breeding for agriculture should be based on group selection, because the goal in agriculture is to optimize population production, not individual fitness. A core hypothesis behind this claim is that crop genotypes with the highest individual fitness in a mixture of genotypes will not produce the highest population yield, because fitness is often increased by "selfish" behaviors, which reduce population performance. We tested this hypothesis by growing 35 cultivars of spring wheat (Triticum aestivum L.) in mixtures and monocultures, and analyzing the relationship between population yield in monoculture and individual yield in mixture. The relationship was unimodal, as predicted. The highest-yielding populations were from cultivars that had intermediate fitness, and these produced, on average, 35% higher yields than cultivars with the highest fitness. It is unlikely that plant breeding or genetic engineering can improve traits that natural selection has been optimizing for millions of years, but there is unutilized potential in traits that increase crop yield by decreasing individual fitness.

Estimation of total genetic effects for survival time in crossbred laying hens showing cannibalism, using pedigree or genomic information

Mortality of laying hens due to cannibalism is a major problem in the egg-laying industry. Survival depends on two genetic effects: the direct genetic effect of the individual itself (DGE) and the indirect genetic effects of its group mates (IGE). For hens housed in sire-family groups, DGE and IGE cannot be estimated using pedigree information, but the combined effect of DGE and IGE is estimated in the total breeding value (TBV). Genomic information provides information on actual genetic relationships between individuals and might be a tool to improve TBV accuracy. We investigated whether genomic information of the sire increased TBV accuracy compared with pedigree information, and we estimated genetic parameters for survival time. A sire model with pedigree information (BLUP) and a sire model with genomic information (ssGBLUP) were used. We used survival time records of 7290 crossbred offspring with intact beaks from four crosses. Cross-validation was used to compare the models. Using ssGBLUP did not improve TBV accuracy compared with BLUP which is probably due to the limited number of sires available per cross (~50). Genetic parameter estimates were similar for BLUP and ssGBLUP. For both BLUP and ssGBLUP, total heritable variance (T² ), expressed as a proportion of phenotypic variance, ranged from 0.03 ± 0.04 to 0.25 ± 0.09. Further research is needed on breeding value estimation for socially affected traits measured on individuals kept in single-family groups.

Genomic prediction of survival time in a population of brown laying hens showing cannibalistic behavior

BACKGROUND

Mortality due to cannibalism causes both economic and welfare problems in laying hens. To limit mortality due to cannibalism, laying hens are often beak-trimmed, which is undesirable for animal welfare reasons. Genetic selection is an alternative strategy to increase survival and is more efficient by taking heritable variation that originates from social interactions into account, which are modelled as the so-called indirect genetic effects (IGE). Despite the considerable heritable variation in survival time due to IGE, genetic improvement of survival time in laying hens is still challenging because the detected heritable variation of the trait with IGE is still limited, ranging from 0.06 to 0.26, and individuals that are still alive at the end of the recording period are censored. Furthermore, survival time records are available late in life and only on females. To cope with these challenges, we tested the hypothesis that genomic prediction increases the accuracy of estimated breeding values (EBV) compared to parental average EBV, and increases response to selection for survival time compared to a traditional breeding scheme. We tested this hypothesis in two lines of brown layers with intact beaks, which show cannibalism, and also the hypothesis that the rate of inbreeding per year is lower for genomic selection than for the traditional breeding scheme.

RESULTS AND DISCUSSION

The standard deviation of genomic prediction EBV for survival time was around 22 days for both lines, indicating good prospects for selection against mortality in laying hens with intact beaks. Genomic prediction increased the accuracy of the EBV by 35 and 32 % compared to the parent average EBV for the two lines. At the current reference population size, predicted response to selection was 91 % higher when using genomic selection than with the traditional breeding scheme, as a result of a shorter generation interval in males and greater accuracy of selection in females. The predicted rate of inbreeding per generation with truncation selection was substantially lower for genomic selection than for the traditional breeding scheme for both lines.

CONCLUSIONS

Genomic selection for socially affected traits is a promising tool for the improvement of survival time in laying hens with intact beaks.

Breeding for improved welfare in pigs: a conceptual framework and its use in practice

Welfare of animals can be defined as the kind of feelings the environmental conditions bring about in the animals. These feelings depend on the needs of the animals and their degree of satisfaction. Needs of animals, and so their welfare, are partly genetically determined. Therefore, welfare can be changed by breeding. The aim of this study was to investigate how welfare of pigs under modern intensive farm conditions can be improved by genetic selection, with emphasis on the precise definition of the breeding goal and determination of the animal characteristics on which selection can be based in practice.

The existing thermoregulation model was used to develop a conceptual framework that describes welfare of growing pigs and production sows with respect to each of their needs as a curvilinear function of the respective environmental conditions. The framework assumes that welfare in terms of feelings is reflected by the physiological and behavioural mechanisms the pig has to activate in order to cope with the various environmental conditions it encounters. Based on those physiological and behavioural responses to changing conditions, five welfare zones can be distinguished for each need. Breeding goals for welfare were defined in terms of the transition points between these welfare zones, such that future pigs would better cope with unfavourable or unfamiliar farming conditions, therewith quickening the domestication process, to some extent. However, as long as genetic parameters for these transition points are not available, more common welfare-related characteristics like temperament, stress resistance and robustness can be included in the breeding goal, as an alternative.

For selection among potential breeding candidates, transition points between welfare zones can be determined in sib tests, thereby also collecting the data for estimating genetic parameters. As a cheaper alternative, breeding candidates could be tested under hard conditions and selected on their coping success. In addition, various behavioural tests and operant conditioning tests (to test a pig's motivation to change its actual environment) can be carried out. Under common conditions on the farm, problems associated with coping (like incidences of diseases, injuries, and stereotypies) and/or other relevant traits (e.g. saliva cortisol levels, longevity and even production traits) should be recorded routinely and used as selection index information. Selection for improved welfare should lead to more tolerant pigs that are better able to cope with possible unfavourable farm conditions by a more efficient use of the adaptation mechanisms they already possess. It should, however, not result in lowering husbandry standards. More research is needed to assess genetic correlations among various welfare aspects and with production traits to prevent undesired side effects in future populations of pigs.

The presence of extreme feather peckers in groups of laying hens

Feather pecking is a serious economic and welfare problem in laying hens. Feather damage occurs mainly through severe feather pecking (SFP). Selection experiments have proved that this behavior is heritable and lines have been divergently selected for high (HFP) and low feather pecking (LFP). The number of bouts of SFP per hen follows a Poisson distribution with a maximum nearby 0. A few studies indicate that the distribution within flocks is not homogenous but contains sub-groups of birds showing extremely high levels of feather pecking (EFP). It was the aim of the current study to re-analyze data on SFP of lines selected for HFP/LFP and their F2 cross so as to uncover hidden sub-populations of EFP birds. Data of seven selection generations of HFP and LFP selection lines as well as their F2 cross have been used. We fitted a two-component mixture of Poisson distributions in order to separate the sub-group of EFP from the remaining birds. HFP and LFP lines differed mainly in mean bouts per bird. The proportion of EFP was only marginal in the LFP as compared with the HFP and the F2 population. Selection for LFP did not result in total elimination of EFP. The presence of even small proportions of EFP may play an important role in initiating outbreaks of feather pecking in large flocks. Further studies on feather pecking should pay special attention to the occurrence of EFP sub-groups.

Local competition increases people's willingness to harm others

Why should organisms incur a cost in order to inflict a (usually greater) cost on others? Such costly harming behavior may be favored when competition for resources occurs locally, because it increases individuals' fitness relative to close competitors. However, there is no explicit experimental evidence supporting the prediction that people are more willing to harm others under local versus global competition. We illustrate this prediction with a game theoretic model, and then test it in a series of economic games. In these experiments, players could spend money to make others lose more. We manipulated the scale of competition by awarding cash prizes to the players with the highest payoffs per set of social partners (local competition) or in all the participants in a session (global competition). We found that, as predicted, people were more harmful to others when competition was local (Study 1). This result still held when people "earned" (rather than were simply given) their money (Study 2). In addition, when competition was local, people were more willing to harm ingroup members than outgroup members (Study 3), because ingroup members were the relevant competitive targets. Together, our results suggest that local competition in human groups not only promotes willingness to harm others in general, but also causes ingroup hostility.

On the effectiveness of multilevel selection

Experimental studies of group selection show that higher levels of selection act on indirect genetic effects, making the response to group and community selection qualitatively different from that of individual selection. This suggests that multilevel selection plays a key role in the evolution of supersocial societies. Experiments showing the effectiveness of community selection indicate that we should consider the possibility that selection among communities may be important in the evolution of supersocial species.

Kin and multilevel selection in social evolution: a never-ending controversy?

Kin selection and multilevel selection are two major frameworks in evolutionary biology that aim at explaining the evolution of social behaviors. However, the relationship between these two theories has been plagued by controversy for almost half a century and debates about their relevance and usefulness in explaining social evolution seem to rekindle at regular intervals. Here, we first provide a concise introduction into the kin selection and multilevel selection theories and shed light onto the roots of the controversy surrounding them. We then review two major aspects of the current debate: the presumed formal equivalency of the two theories and the question whether group selection can lead to group adaptation. We conclude by arguing that the two theories can offer complementary approaches to the study of social evolution: kin selection approaches usually focus on the identification of optimal phenotypes and thus on the endresult of a selection process, whereas multilevel selection approaches focus on the ongoing selection process itself. The two theories thus provide different perspectives that might be fruitfully combined to promote our understanding of the evolution in group-structured populations.

Resilience in farm animals: biology, management, breeding and implications for animal welfare

A capacity for the animal to recover quickly from the impact of physical and social stressors and disease challenges is likely to improve evolutionary fitness of wild species and welfare and performance of farm animals. Salience and valence of stimuli sensed through neurosensors, chemosensors and immunosensors are perceived and integrated centrally to generate emotions and engage physiological, behavioural, immune, cognitive and morphological responses that defend against noxious challenges. These responses can be refined through experience to provide anticipatory and learned reactions at lower cost than innate less-specific reactions. Influences of behaviour type, coping style, and affective state and the relationships between immune responsiveness, disease resistance and resilience are reviewed. We define resilience as the capacity of animals to cope with short-term perturbations in their environment and return rapidly to their pre-challenge status. It is manifested in response to episodic, sporadic or situation-specific attributes of the environment and can be optimised via facultative learning by the individual. It is a comparative measure of differences between individuals in the outcomes that follow exposure to potentially adverse situations. In contrast, robustness is the capacity to maintain productivity in a wide range of environments without compromising reproduction, health and wellbeing. Robustness is manifested in response to persistent or cyclical attributes of the environment and is effected via activity of innate regulatory pathways. We suggest that for farm animals, husbandry practices that incorporate physical and social stressors and interactions with humans such as weaning, change of housing, and introduction to the milking parlour can be used to characterise resilience phenotypes. In these settings, resilience is likely to be more readily identified through the rate of return of variables to pre-challenge or normal status rather than through measuring the activity of diverse stress response and adaptation mechanisms. Our strategy for phenotyping resilience of sheep and cattle during weaning is described. Opportunities are examined to increase resilience through genetic selection and through improved management practices that provide emotional and cognitive enrichment and stress inoculation.