Phenotypic link between protein efficiency and pig welfare suggests no apparent trade-offs for mitigating nitrogen pollution.

Pig manure contributes significantly to environmental pollution through nitrogen compounds. Reducing protein in feed can help, but it may lead to damaging behaviors if pigs' nutritional needs are not met. Breeding pigs for higher protein efficiency (PE) is a long-term solution to reduce nitrogen pollution, but concerns about pig welfare remain. We studied 95 pigs involved in a project on the genetic basis of PE on a 20% protein restricted diet to investigate the phenotypic connection between PE and welfare. These pigs represented natural PE variations in the population. At around 100 days, before their PE was known, we observed their behaviors. Only three pigs engaged in tail biting and manipulation of vulnerable regions, but this was not associated with PE. There was no clear link between PE and manipulating pen mates' less vulnerable regions. Such behaviors are normal but can cause stress and injury if carried out excessively due to boredom or stress. Overall, pigs with higher PE showed no major behavioral abnormalities in this study. Considering the lack of genetic knowledge, the risk of increased harmful behaviors when selecting for higher PE appears low when inferred from this purely phenotypic association.

Genetic analysis of protein efficiency and its association with performance and meat quality traits under a protein-restricted diet.

BACKGROUND: An essential component in the development of sustainable pig production is the reduction of nitrogen excretion in fattening pigs. Pig feeds typically contain high levels of dietary crude protein, and due to incomplete conversion to muscle tissue, excess nitrogen is excreted, resulting in environmental problems such as nitrate pollution and greenhouse gas emissions. Therefore, improving protein efficiency (PE), i.e., the proportion of dietary protein that remains in the carcass, is desirable. The aim of this study was to estimate the heritability (h2) of PE and its genetic correlations with phosphorus efficiency, three performance, seven meat quality and two carcass quality traits when pigs were fed a 20% protein-restricted diet, using 1071 Swiss Large White pigs. To determine PE, the intake of feed with known nutrient content was accurately recorded for each pig and the nitrogen and phosphorus content of the carcass was determined using dual-energy X-ray absorptiometry. RESULTS: We found an average PE of 0.39 ± 0.04 and a heritability of 0.54 ± 0.10. PE showed a high genetic correlation with phosphorus efficiency (0.61 ± 0.16), moderate genetic correlations with feed conversion ratio (- 0.55 ± 0.14) and average daily feed intake (- 0.53 ± 0.14), and a low genetic correlation with average daily gain (- 0.19 ± 0.19). While PE has favourable genetic correlations with the performance traits and some meat quality traits, there is a potentially unfavourable correlation of PE with meat colour (redness [rg = - 0.27 ± 0.17]; yellowness [rg = - 0.31 ± 0.18]) and intra-muscular fat (IMF; rg = - 0.39 ± 0.15). Feed conversion ratio (FCR) also showed unfavourable genetic correlations with meat lightness, redness yellowness, IMF and cooking loss. CONCLUSIONS: PE is a heritable trait that can be considered in breeding programs to reduce the environmental impact of pig production. We found no strong negative correlation of PE with meat quality traits, and that there is potential to indirectly select for improved phosphorus efficiency. Selecting nutrient efficiencies might be a more suitable strategy to reduce nitrogen pollution from manure than focusing on FCR because the latter also shows genetic antagonism with some meat quality traits in our population.

Machine learning algorithms can predict tail biting outbreaks in pigs using feeding behaviour records.

Tail biting is a damaging behaviour that impacts the welfare and health of pigs. Early detection of precursor signs of tail biting provides the opportunity to take preventive measures, thus avoiding the occurrence of the tail biting event. This study aimed to build a machine-learning algorithm for real-time detection of upcoming tail biting outbreaks, using feeding behaviour data recorded by an electronic feeder. Prediction capacities of seven machine learning algorithms (Generalized Linear Model with Stepwise Feature Selection, random forest, Support Vector Machines with Radial Basis Function Kernel, Bayesian Generalized Linear Model, Neural network, K-nearest neighbour, and Partial Least Squares Discriminant Analysis) were evaluated from daily feeding data collected from 65 pens originating from two herds of grower-finisher pigs (25-100kg), in which 27 tail biting events occurred. Data were divided into training and testing data in two different ways, either by randomly splitting data into 75% (training set) and 25% (testing set), or by randomly selecting pens to constitute the testing set. In the first data splitting, the model is regularly updated with previous data from the pen, whereas in the second data splitting, the model tries to predict for a pen that it has never seen before. The K-nearest neighbour algorithm was able to predict 78% of the upcoming events with an accuracy of 96%, when predicting events in pens for which it had previous data. Our results indicate that machine learning models can be considered for implementation into automatic feeder systems for real-time prediction of tail biting events.

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs.

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies ("omics") study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

Investigating the potential for genetic improvement of nitrogen and phosphorus efficiency in a Swiss large white pig population using chemical analysis.

Pig production contributes to environmental pollution through excretion of phosphorus and nitrogenous compounds. European pig production requires annual imports of currently 36 million tons of soya bean, because domestic plant protein sources often do not meet the required protein quality. Most of the mineral phosphate sources are also imported. It is therefore desirable to improve nutrient deposition efficiency through selective breeding, that is to realise similar growth rates and carcass compositions as currently achieved but with a lower intake of dietary crude protein or phosphate. For a preliminary evaluation of the potential of selecting for increased nutrient deposition efficiency, we estimated genetic parameters for nitrogen and phosphorus efficiencies in a Swiss Large White pig population including 294 individuals. Nutrient efficiency phenotypes were obtained from wet-chemistry analyses of pigs of various live weights. Heritability of nitrogen efficiency was estimated at 41%. Heritability of phosphorus efficiency was very low (0.3%), but positive genetic correlations with nitrogen efficiency suggest that breeding for nitrogen efficiency would positively affect phosphorus efficiency. Further studies are needed to improve the quality of estimates and to obtain accurate high-throughput measures of nutrient efficiency to be implemented on farms.

Heritabilities, social environment effects and genetic correlations of social behaviours in a cooperatively breeding vertebrate.

Social animals interact frequently with conspecifics, and their behaviour is influenced by social context, environmental cues and the behaviours of interaction partners, allowing for adaptive, flexible adjustments to social encounters. This flexibility can be limited by part of the behavioural variation being genetically determined. Furthermore, behaviours can be genetically correlated, potentially constraining independent evolution. Understanding social behaviour thus requires carefully disentangling genetic, environmental, maternal and social sources of variations as well as the correlation structure between behaviours. Here, we assessed heritability, maternal, common environment and social effects of eight social behaviours in Neolamprologus pulcher, a cooperatively breeding cichlid. We bred wild-caught fish in a paternal half-sibling design and scored ability to defend a resource against conspecifics, to integrate into a group and the propensity to help defending the group territory ("helping behaviour"). We assessed genetic, social and phenotypic correlations within clusters of behaviours predicted to be functionally related, namely "competition," "aggression," "aggression-sociability," "integration" and "integration-help." Helping behaviour and two affiliative behaviours were heritable, whereas there was little evidence for a genetic basis in all other traits. Phenotypic social effects explained part of the variation in a sociable and a submissive behaviour, but there were no maternal or common environment effects. Genetic and phenotypic correlation within clusters was mostly positive. A group's social environment influenced covariances of social behaviours. Genetic correlations were similar in magnitude but usually exceeding the phenotypic ones, indicating that conclusions about the evolution of social behaviours in this species could be provisionally drawn from phenotypic data in cases where data for genetic analyses are unobtainable.

Divergent brain gene expression profiles between alternative behavioural helper types in a cooperative breeder.

Juveniles of the cooperatively breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care ("cleaners") or consistently abstain from helping ("noncleaners"). These phenotypes are not based on heritable genetic differences. Instead, they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and noncleaners in two experimental conditions, a helping opportunity and a control condition. We aimed to identify (a) expression differences between cleaners and noncleaners in the control, (b) changes in gene expression induced by the opportunity and (c) differences in plasticity of gene expression between cleaners and noncleaners. Control cleaners and noncleaners differed in the expression of a single gene, irx2, which regulates neural differentiation. During the opportunity, cleaners and noncleaners had three upregulated genes in common, which were implicated in neuroplasticity, hormonal signalling and cell proliferation. Thus, the stimulus in the opportunity was sufficiently salient. Cleaners also showed higher expression of seven additional genes that were unique to the opportunity. One of these cleaner-specific genes is implicated in neuropeptide metabolism, indicating that this process is associated with cleaning performance. This suggests that the two types employed different pathways to integrate social information, preparing them for accelerated reaction to future opportunities. Interestingly, three developmental genes were downregulated between the control and the opportunity in cleaners only. Our results indicate that the two behavioural types responded differently to the helping opportunity and that only cleaners responded by downregulating developmental genes.

Brain activation patterns following a cooperation opportunity in a highly social cichlid fish.

In highly social species, individuals frequently face opportunities to cooperate. The molecular and neural mechanisms that integrate internal and external information prior to cooperative responses are not well understood. Using expression levels of egr-1, a genomic marker of neural activity, we quantified the neural response to an alloparental-care opportunity in a cooperatively breeding fish, a component of cooperative behaviour, across brain regions and time. In this species, alloparental care and submission are considered alternative strategies to appease dominants. We therefore investigated whether brood care and defence as well as submissive displays were associated with egr-1 expression. Finally, we predicted potential targets of the egr-1 transcription factor in the cichlid genome. This target prediction suggested that egr-1 regulates the expression of transcription factors involved in nervous system development, which could be implicated in social memory formation associated with cooperation. Egr-1 expression levels differed between test and control individuals and across time. Compared to a control, individuals experiencing the cooperation opportunity expressed less egr-1 in two brain regions, the cerebellum and the telencephalon. This down-regulation was independent of their behavioural reaction, i.e. whether they cooperated or not. However, within the subset of test individuals, egr-1 expression increased as a function of the amount of submissive behaviours, but not of cooperative behaviours, in the hypothalamus and potentially the telencephalon. These regions host structures that play a role in social decision-making; suggesting that egr-1 might be a suitable proxy for neural activation due to the social interaction component of the cooperation opportunity, rather than the actual alloparental care component.

Consistent cooperation in a cichlid fish is caused by maternal and developmental effects rather than heritable genetic variation.

Studies on the evolution of cooperative behaviour are typically confined to understanding its adaptive value. It is equally essential, however, to understand its potential to evolve, requiring knowledge about the phenotypic consistency and genetic basis of cooperative behaviour. While previous observational studies reported considerably high heritabilities of helping behaviour in cooperatively breeding vertebrates, experimental studies disentangling the relevant genetic and non-genetic components of cooperative behaviour are lacking. In a half-sibling breeding experiment, we investigated the repeatability and heritability of three major helping behaviours performed by subordinates of the cooperatively breeding fish Neolamprologus pulcher To experimentally manipulate the amount of help needed in a territory, we raised the fish in two environments differing in egg predation risk. All three helping behaviours were significantly repeatable, but had very low heritabilities. The high within-individual consistencies were predominantly due to maternal and permanent environment effects. The perceived egg predation risk had no effect on helping, but social interactions significantly influenced helping propensities. Our results reveal that developmentally plastic adjustments of provided help to social context shape cooperative phenotypes, whereas heritable genetic variation plays a minor role.

Genetics and developmental biology of cooperation.

Despite essential progress towards understanding the evolution of cooperative behaviour, we still lack detailed knowledge about its underlying molecular mechanisms, genetic basis, evolutionary dynamics and ontogeny. An international workshop "Genetics and Development of Cooperation," organized by the University of Bern (Switzerland), aimed at discussing the current progress in this research field and suggesting avenues for future research. This review uses the major themes of the meeting as a springboard to synthesize the concepts of genetic and nongenetic inheritance of cooperation, and to review a quantitative genetic framework that allows for the inclusion of indirect genetic effects. Furthermore, we argue that including nongenetic inheritance, such as transgenerational epigenetic effects, parental effects, ecological and cultural inheritance, provides a more nuanced view of the evolution of cooperation. We summarize those genes and molecular pathways in a range of species that seem promising candidates for mechanisms underlying cooperative behaviours. Concerning the neurobiological substrate of cooperation, we suggest three cognitive skills necessary for the ability to cooperate: (i) event memory, (ii) synchrony with others and (iii) responsiveness to others. Taking a closer look at the developmental trajectories that lead to the expression of cooperative behaviours, we discuss the dichotomy between early morphological specialization in social insects and more flexible behavioural specialization in cooperatively breeding vertebrates. Finally, we provide recommendations for which biological systems and species may be particularly suitable, which specific traits and parameters should be measured, what type of approaches should be followed, and which methods should be employed in studies of cooperation to better understand how cooperation evolves and manifests in nature.

Network measures for dyadic interactions: stability and reliability.

Social network analysis (SNA) is a general heading for a collection of statistical tools that aim to describe social interactions and social structure by representing individuals and their interactions as graph objects. It was originally developed for the social sciences, but more recently it was also adopted by behavioral ecologists. However, although SNA offers a full range of exciting possibilities for the study of animal societies, some authors have raised concerns about the correct application and interpretation of network measures. In this article, we investigate how reliable and how stable network measures are (i.e. how much variation they show under re-sampling and how much they are influenced by erroneous observations). For this purpose, we took a data set of 44 nonhuman primate grooming networks and studied the effects of re-sampling at lower re-sampling rates than the originally observed ones and the inclusion of two types of errors, "mis-identification" and "mis-classification," on six different network metrics, i.e. density, degree variance, vertex strength variance, edge weight disparity, clustering coefficient, and closeness centrality. Although some measures were tolerant toward reduced sample sizes, others were sensitive and even slightly reduced samples could yield drastically different results. How strongly a metric is affected seems to depend on both the sample size and the structure of the specific network. The same general effects were found for the inclusion of sampling errors. We, therefore, emphasize the importance of calculating valid confidence intervals for network measures and, finally, we suggest a rough research plan for network studies.

A social network analysis of primate groups.

Primate social systems are difficult to characterize, and existing classification schemes have been criticized for being overly simplifying, formulated only on a verbal level or partly inconsistent. Social network analysis comprises a collection of analytical tools rooted in the framework of graph theory that were developed to study human social interaction patterns. More recently these techniques have been successfully applied to examine animal societies. Primate social systems differ from those of humans in both size and density, requiring an approach that puts more emphasis on the quality of relationships. Here, we discuss a set of network measures that are useful to describe primate social organization and we present the results of a network analysis of 70 groups from 30 different species. For this purpose we concentrated on structural measures on the group level, describing the distribution of interaction patterns, centrality, and group structuring. We found considerable variability in those measures, reflecting the high degree of diversity of primate social organizations. By characterizing primate groups in terms of their network metrics we can draw a much finer picture of their internal structure that might be useful for species comparisons as well as the interpretation of social behavior.

Social structure of primate interaction networks facilitates the emergence of cooperation.

Animal cooperation has puzzled biologists for a long time as its existence seems to contravene the basic notion of evolutionary biology that natural selection favours 'selfish' genes that promote only their own well-being. Evolutionary game theory has shown that cooperators can prosper in populations of selfish individuals if they occur in clusters, interacting more frequently with each other than with the selfish. Here we show that social networks of primates possess the necessary social structure to promote the emergence of cooperation. By simulating evolutionary dynamics of cooperative behaviour on interaction networks of 70 primate groups, we found that for most groups network reciprocity augmented the fixation probability for cooperation. The variation in the strength of this effect can be partly explained by the groups' community modularity-a network measure for the groups' heterogeneity. Thus, given selective update and partner choice mechanisms, network reciprocity has the potential to explain socially learned forms of cooperation in primate societies.

Tolerated mouth-to-mouth food transfers in common marmosets.

In this paper we describe tolerated mouth-to-mouth food transfers in captive adult common marmosets, where an animal approached a conspecific that has recently received a piece of food, opened the other's mouth forcefully, and picked food pieces out of it. Tolerated mouth-to-mouth food transfers occurred between animals of both sexes. They were observed when the possessor was subordinate as well as when it was dominant, and in four dyads they were observed in both directions. We argue that this behaviour might have a social function and that the cooperative breeding system of marmosets might have facilitated its evolution.