Immune challenge affects reproductive behaviour in the guppy (Poecilia reticulata).

Immunocompetence and reproduction are among the most important determinants of fitness. However, energetic and metabolic constraints create conflict between these two life-history traits. While many studies have explored the relationship between immune activity and reproductive fitness in birds and mammals inoculated with bacterial endotoxin, very few have focused on fish. Fish have been neglected in this area due, in part, to the claim that they are largely resistant to the immune effects of endotoxins. However, the present study suggests that they are susceptible to significant effects with respect to reproductive behaviour. Here, we examined the reproductive behaviour of male guppies following exposure to bacterial lipopolysaccharides (LPS) in comparison to that of male guppies in a control treatment. Additionally, we investigated the responses of females to these males. We show that although immune challenge does not suppress general activity in male guppies, it significantly reduces mating effort. While females showed no difference in general activity as a function of male treatments, they did exhibit reduced group cohesion in the presence of LPS-exposed males. We discuss this in the context of sickness behaviours, social avoidance of immune-challenged individuals and the effects of mounting an immune response on reproductive behaviour.

Robust SNP-based prediction of rheumatoid arthritis through machine-learning-optimized polygenic risk score.

BACKGROUND: The popular statistics-based Genome-wide association studies (GWAS) have provided deep insights into the field of complex disorder genetics. However, its clinical applicability to predict disease/trait outcomes remains unclear as statistical models are not designed to make predictions. This study employs statistics-free machine-learning (ML)-optimized polygenic risk score (PRS) to complement existing GWAS and bring the prediction of disease/trait outcomes closer to clinical application. Rheumatoid Arthritis (RA) was selected as a model disease to demonstrate the robustness of ML in disease prediction as RA is a prevalent chronic inflammatory joint disease with high mortality rates, affecting adults at the economic prime. Early identification of at-risk individuals may facilitate measures to mitigate the effects of the disease. METHODS: This study employs a robust ML feature selection algorithm to identify single nucleotide polymorphisms (SNPs) that can predict RA from a set of training data comprising RA patients and population control samples. Thereafter, selected SNPs were evaluated for their predictive performances across 3 independent, unseen test datasets. The selected SNPs were subsequently used to generate PRS which was also evaluated for its predictive capacity as a sole feature. RESULTS: Through robust ML feature selection, 9 SNPs were found to be the minimum number of features for excellent predictive performance (AUC > 0.9) in 3 independent, unseen test datasets. PRS based on these 9 SNPs was significantly associated with (P < 1 × 10-16) and predictive (AUC > 0.9) of RA in the 3 unseen datasets. A RA ML-PRS calculator of these 9 SNPs was developed ( https://xistance.shinyapps.io/prs-ra/ ) to facilitate individualized clinical applicability. The majority of the predictive SNPs are protective, reside in non-coding regions, and are either predicted to be potentially functional SNPs (pfSNPs) or in high linkage disequilibrium (r2 > 0.8) with un-interrogated pfSNPs. CONCLUSIONS: These findings highlight the promise of this ML strategy to identify useful genetic features that can robustly predict disease and amenable to translation for clinical application.

Self-organization and information transfer in Antarctic krill swarms.

Antarctic krill swarms are one of the largest known animal aggregations, and yet, despite being the keystone species of the Southern Ocean, little is known about how swarms are formed and maintained. Understanding the local interactions between individuals that provide the basis for these swarms is fundamental to knowing how swarms arise in nature, and what potential factors might lead to their breakdown. Here, we analysed the trajectories of captive, wild-caught krill in 3D to determine individual-level interaction rules and quantify patterns of information flow. Our results demonstrate that krill align with near neighbours and that they regulate both their direction and speed relative to the positions of groupmates. These results suggest that social factors are vital to the formation and maintenance of swarms. Furthermore, krill operate a novel form of collective organization, with measures of information flow and individual movement adjustments expressed most strongly in the vertical dimension, a finding not seen in other swarming species. This research represents a vital step in understanding the fundamentally important swarming behaviour of krill.

Functional coding haplotypes and machine-learning feature elimination identifies predictors of Methotrexate Response in Rheumatoid Arthritis patients.

BACKGROUND: Major challenges in large scale genetic association studies include not only the identification of causative single nucleotide polymorphisms (SNPs), but also accounting for SNP-SNP interactions. This study thus proposes a novel feature engineering approach integrating potentially functional coding haplotypes (pfcHap) with machine-learning (ML) feature selection to identify biologically meaningful, possibly causative genetic factors, that take into consideration potential SNP-SNP interactions within the pfcHap, to best predict for methotrexate (MTX) response in rheumatoid arthritis (RA) patients. METHODS: Exome sequencing from 349 RA patients were analysed, of which they were split into training and unseen test set. Inferred pfcHaps were combined with 30 non-genetic features to undergo ML recursive feature elimination with cross-validation using the training set. Predictive capacity and robustness of the selected features were assessed using six popular machine learning models through a train set cross-validation and evaluated in an unseen test set. FINDINGS: Significantly, 100 features (95 pfcHaps, 5 non-genetic factors) were identified to have good predictive performance (AUC: 0.776-0.828; Sensitivity: 0.656-0.813; Specificity: 0.684-0.868) across all six ML models in an unseen test dataset for the prediction of MTX response in RA patients. INTERPRETATION: Majority of the predictive pfcHap SNPs were predicted to be potentially functional and some of the genes in which the pfcHap resides in were identified to be associated with previously reported MTX/RA pathways. FUNDING: Singapore Ministry of Health's National Medical Research Council (NMRC) [NMRC/CBRG/0095/2015; CG12Aug17; CGAug16M012; NMRC/CG/017/2013]; National Cancer Center Research Fund and block funding Duke-NUS Medical School.; Singapore Ministry of Education Academic Research Fund Tier 2 grant MOE2019-T2-1-138.

Machine learning using genetic and clinical data identifies a signature that robustly predicts methotrexate response in rheumatoid arthritis.

OBJECTIVE: To develop a hypothesis-free model that best predicts response to MTX drug in RA patients utilizing biologically meaningful genetic feature selection of potentially functional single nucleotide polymorphisms (pfSNPs) through robust machine learning (ML) feature selection methods. METHODS: MTX-treated RA patients with known response were divided in a 4:1 ratio into training and test sets. From the patients' exomes, potential features for classifier prediction were identified from pfSNPs and non-genetic factors through ML using recursive feature elimination with cross-validation incorporating the random forest classifier. Feature selection was repeated on random subsets of the training cohort, and consensus features were assembled into the final feature set. This feature set was evaluated for predictive potential using six ML classifiers, first by cross-validation within the training set, and finally by analysing its performance with the unseen test set. RESULTS: The final feature set contains 56 pfSNPs and five non-genetic factors. The majority of these pfSNPs are located in pathways related to RA pathogenesis or MTX action and are predicted to modulate gene expression. When used for training in six ML classifiers, performance was good in both the training set (area under the curve: 0.855-0.916; sensitivity: 0.715-0.892; and specificity: 0.733-0.862) and the unseen test set (area under the curve: 0.751-0.826; sensitivity: 0.581-0.839; and specificity: 0.641-0.923). CONCLUSION: Sensitive and specific predictors of MTX response in RA patients were identified in this study through a novel strategy combining biologically meaningful and machine learning feature selection and training. These predictors may facilitate better treatment decision-making in RA management.

Social context affects camouflage in a cryptic fish species.

Crypsis, or the ability to avoid detection and/or recognition, is an important and widespread anti-predator strategy across the animal kingdom. Many animals are able to camouflage themselves by adapting their body colour to the local environment. In particular, rapid changes in body colour are often critical to the survival of cryptic prey which rely on evading detection by predators. This is especially pertinent for animals subject to spatio-temporal variability in their environment, as they must adapt to acute changes in their visual surroundings. However, which features of the local environment are most relevant is not well understood. In particular, little is known about how social context interacts with other environmental stimuli to influence crypsis. Here, we use a common cryptic prey animal, the goby (Pseudogobius species 2) to examine how the presence and body colour of conspecifics influence the rate and extent to which gobies change colour. We find that solitary gobies change colour to match their background faster and to a greater extent than gobies in pairs. Further, we find that this relationship holds irrespective of the colour of nearby conspecifics. This study demonstrates the importance of social context in mediating colour change in cryptic animals.

Sentiments Regarding COVID-19 Vaccination among Graduate Students in Singapore.

As the COVID-19 pandemic rages unabated, and with more infectious variants, vaccination may offer a way to transit out of strict restrictions on physical human interactions to curb the virus spread and prevent overwhelming the healthcare system. However, vaccine hesitancy threatens to significantly impact our progress towards achieving this. It is thus important to understand the sentiments regarding vaccination for different segments of the population to facilitate the development of effective strategies to persuade these groups. Here, we surveyed the COVID-19 vaccination sentiments among a highly educated group of graduate students from the National University of Singapore (NUS). Graduate students who are citizens of 54 different countries, mainly from Asia, pursue studies in diverse fields, with 32% expressing vaccine hesitancy. Citizenship, religion, country of undergraduate/postgraduate studies, exposure risk and field of study are significantly associated with vaccine sentiments. Students who are Chinese citizens or studied in Chinese Universities prior to joining NUS are more hesitant, while students of Indian descent or studied in India are less hesitant about vaccination. Side effects, safety issues and vaccine choice are the major concerns of the hesitant group. Hence, this study would facilitate the development of strategies that focus on these determinants to enhance vaccine acceptance.

Social rank and not physiological capacity determines competitive success in zebrafish (Danio rerio).

Competition for resources shapes ecological and evolutionary relationships. Physiological capacities such as in locomotor performance can influence the fitness of individuals by increasing competitive success. Social hierarchy too can affect outcomes of competition by altering locomotor behaviour or because higher ranking individuals monopolize resources. Here, we tested the hypotheses that competitive success is determined by sprint performance or by social status. We show that sprint performance of individuals measured during escape responses (fast start) or in an accelerated sprint test did not correlate with realized sprint speed while competing for food within a social group of five fish; fast start and accelerated sprint speed were higher than realized speed. Social status within the group was the best predictor of competitive success, followed by realized speed. Social hierarchies in zebrafish are established within 7 days of their first encounter, and interestingly, there was a positive correlation between social status and realized speed 1 and 4 days after fish were placed in a group, but not after 7 days. These data indicate that physiological performance decreases in importance as social relationships are established. Also, maximal physiological capacities were not important for competitive success, but swimming speed changed with social context.

To clean or not to clean: Cleaning mutualism breakdown in a tidal environment.

The dynamics and prevalence of mutualistic interactions, which are responsible for the maintenance and structuring of all ecological communities, are vulnerable to changes in abiotic and biotic environmental conditions. Mutualistic outcomes can quickly shift from cooperation to conflict, but it unclear how resilient and stable mutualistic outcomes are to more variable conditions. Tidally controlled coral atoll lagoons that experience extreme diurnal environmental shifts thus provide a model from which to test plasticity in mutualistic behavior of dedicated (formerly obligate) cleaner fish, which acquire all their food resources through client interactions. Here, we investigated cleaning patterns of a model cleaner fish species, the bluestreak wrasse (Labroides dimidiatus), in an isolated tidal lagoon on the Great Barrier Reef. Under tidally restricted conditions, uniquely both adults and juveniles were part-time facultative cleaners, pecking on Isopora palifera coral. The mutualism was not completely abandoned, with adults also wandering across the reef in search of clients, rather than waiting at fixed site cleaning stations, a behavior not yet observed at any other reef. Contrary to well-established patterns for this cleaner, juveniles appeared to exploit the system, by biting ("cheating") their clients more frequently than adults. We show for the first time, that within this variable tidal environment, where mutualistic cleaning might not represent a stable food source, the prevalence and dynamics of this mutualism may be breaking down (through increased cheating and partial abandonment). Environmental variability could thus reduce the pervasiveness of mutualisms within our ecosystems, ultimately reducing the stability of the system.

Mid-sized groups perform best in a collective decision task in sticklebacks.

Numerous studies have reported functional improvements in collective behaviour with increasing group size, however, the possibility that such improvements may saturate or even decline as group size continues to grow have seldom been tested experimentally. Here, we tested the ability of solitary three-spined sticklebacks and those in groups, ranging from 2 to 29 fish, to leave an unfavourable patch of habitat. Our results replicate the findings of previous studies at low group sizes, with the fish initially showing a reduction in their latency to leave the unfavourable habitat as group size increased. As group size continued to increase, however, latency to leave the habitat increased, so that the functional relationship between group size and latency to depart was U-shaped. Our results suggest an optimum group size in this context of between 12 and 20 fish. Underlying this group-level trend was a similar U-shaped relationship between group size and the first fish to leave the habitat, suggesting that at larger group sizes, social conformity to the behaviour of the majority can stifle the ability of fish to innovate-in this case, to induce a collective movement from the unfavourable habitat.

Fine-scale behavioural adjustments of prey on a continuum of risk.

In the wild, prey species often live in the vicinity of predators, rendering the ability to assess risk on a moment-to-moment basis crucial to survival. Visual cues are important as they allow prey to assess predator species, size, proximity and behaviour. However, few studies have explicitly examined prey's ability to assess risk based on predator behaviour and orientation. Using mosquitofish, Gambusia holbrooki, and their predator, jade perch, Scortum barcoo, under controlled conditions, we provide some of the first fine-scale characterization of how prey adapt their behaviour according to their continuous assessment of risk based on both predator behaviour and angular distance to the predator's mouth. When these predators were inactive and posed less of an immediate threat, prey within the attack cone of the predator showed reductions in speed and acceleration characteristic of predator-inspection behaviour. However, when predators became active, prey swam faster with greater acceleration and were closer together within the attack cone of predators. Most importantly, this study provides evidence that prey do not adopt a uniform response to the presence of a predator. Instead, we demonstrate that prey are capable of rapidly and dynamically updating their assessment of risk and showing fine-scale adjustments to their behaviour.

Speed-mediated properties of schooling.

Collectively moving animals often display a high degree of synchronization and cohesive group-level formations, such as elongated schools of fish. These global patterns emerge as the result of localized rules of interactions. However, the exact relationship between speed, polarization, neighbour positioning and group structure has produced conflicting results and is largely limited to modelling approaches. This hinders our ability to understand how information spreads between individuals, which may determine the collective functioning of groups. We tested how speed interacts with polarization and positional composition to produce the elongation observed in moving groups of fish as well as how this impacts information flow between individuals. At the local level, we found that increases in speed led to increases in alignment and shifts from lateral to linear neighbour positioning. At the global level, these increases in linear neighbour positioning resulted in elongation of the group. Furthermore, mean pairwise transfer entropy increased with speed and alignment, implying an adaptive value to forming faster, more polarized and linear groups. Ultimately, this research provides vital insight into the mechanisms underlying the elongation of moving animal groups and highlights the functional significance of cohesive and coordinated movement.

Cohesion, order and information flow in the collective motion of mixed-species shoals.

Despite the frequency with which mixed-species groups are observed in nature, studies of collective behaviour typically focus on single-species groups. Here, we quantify and compare the patterns of interactions between three fish species, threespine sticklebacks (Gasterosteus aculeatus), ninespine sticklebacks (Pungitius pungitius) and roach (Rutilus rutilus) in both single- and mixed-species shoals in the laboratory. Pilot data confirmed that the three species form both single- and mixed-species shoals in the wild. In our laboratory study, we found that single-species groups were more polarized than mixed-species groups, while single-species groups of threespine sticklebacks and roach were more cohesive than mixed shoals of these species. Furthermore, while there was no difference between the inter-individual distances between threespine and ninespine sticklebacks within mixed-species groups, there was some evidence of segregation by species in mixed groups of threespine sticklebacks and roach. There were differences between treatments in mean pairwise transfer entropy, and in particular we identify species-differences in information use within the mixed-species groups, and, similarly, differences in responses to conspecifics and heterospecifics in mixed-species groups. We speculate that differences in the patterns of interactions between species in mixed-species groups may determine patterns of fission and fusion in such groups.

Familiarity affects collective motion in shoals of guppies (Poecilia reticulata).

The coordinated and synchronized movement of animals in groups often referred to as collective motion emerges through the interactions between individual animals within the group. Factors which affect these interactions have the potential to shape collective movement. One such factor is familiarity, or the tendency to bias behaviour towards individuals as a result of social recognition. We examined the effect of familiarity on the expression of collective motion in small shoals of female guppies (Poecilia reticulata). Groups comprising familiar individuals were more strongly polarized than groups of unfamiliar individuals, particularly when in novel surroundings. The ability to form more strongly polarized shoals potentially promotes information transfer and enhances the anti-predator benefits of grouping.

Local interactions and global properties of wild, free-ranging stickleback shoals.

Collective motion describes the global properties of moving groups of animals and the self-organized, coordinated patterns of individual behaviour that produce them. We examined the group-level patterns and local interactions between individuals in wild, free-ranging shoals of three-spine sticklebacks, Gasterosteus aculeatus. Our data reveal that the highest frequencies of near-neighbour encounters occur at between one and two body lengths from a focal fish, with the peak frequency alongside a focal individual. Fish also show the highest alignment with these laterally placed individuals, and generally with animals in front of themselves. Furthermore, fish are more closely matched in size, speed and orientation to their near neighbours than to more distant neighbours, indicating local organization within groups. Among the group-level properties reported here, we find that polarization is strongly influenced by group speed, but also the variation in speed among individuals and the nearest neighbour distances of group members. While we find no relationship between group order and group size, we do find that larger groups tend to have lower nearest neighbour distances, which in turn may be important in maintaining group order.

The effects of external cues on individual and collective behavior of shoaling fish.

Collective animal behavior is an emergent phenomenon arising from the local interactions of the members of animal groups. Considerable progress has been made in characterizing these interactions, particularly inferring rules that shape and guide the responses of animals to their near neighbors. To date, experimental work has focused on collective behavior within a single, stable context. We examine the individual and collective behavior of a schooling fish species, the x-ray tetra (Pristella maxillaris), identifying their response to changes in context produced by food cues or conspecific alarm cues. Fish exposed to alarm cues show pronounced, broad-ranging changes of behavior, including reducing speed and predictability in their movements. Alarmed fish also alter their responses to other group members, including enacting a smaller zone of repulsion and increasing their frequency of observation of, and responsiveness to, near neighbors. Fish subject to food cues increased speed as a function of neighbor positions and reduced encounter frequency with near neighbors. Overall, changes in individual behavior and the interactions among individuals in response to external cues coincide with changes in group-level patterns, providing insight into the adaptability of behavior to changes in context and interrelationship between local interactions and global patterns in collective behavior.

Body size affects the strength of social interactions and spatial organization of a schooling fish (Pseudomugil signifer).

While a rich variety of self-propelled particle models propose to explain the collective motion of fish and other animals, rigorous statistical comparison between models and data remains a challenge. Plausible models should be flexible enough to capture changes in the collective behaviour of animal groups at their different developmental stages and group sizes. Here, we analyse the statistical properties of schooling fish (Pseudomugil signifer) through a combination of experiments and simulations. We make novel use of a Boltzmann inversion method, usually applied in molecular dynamics, to identify the effective potential of the mean force of fish interactions. Specifically, we show that larger fish have a larger repulsion zone, but stronger attraction, resulting in greater alignment in their collective motion. We model the collective dynamics of schools using a self-propelled particle model, modified to include varying particle speed and a local repulsion rule. We demonstrate that the statistical properties of the fish schools are reproduced by our model, thereby capturing a number of features of the behaviour and development of schooling fish.

Morphological differences between habitats are associated with physiological and behavioural trade-offs in stickleback (Gasterosteus aculeatus).

Local specialization can be advantageous for individuals and may increase the resilience of the species to environmental change. However, there may be trade-offs between morphological responses and physiological performance and behaviour. Our aim was to test whether habitat-specific morphology of stickleback (Gasterosteus aculeatus) interacts with physiological performance and behaviour at different salinities. We rejected the hypothesis that deeper body shape of fish from habitats with high predation pressure led to decreases in locomotor performance. However, there was a trade-off between deeper body shape and muscle quality. Muscle of deeper-bodied fish produced less force than that of shallow-bodied saltmarsh fish. Nonetheless, saltmarsh fish had lower swimming performance, presumably because of lower muscle mass overall coupled with smaller caudal peduncles and larger heads. Saltmarsh fish performed better in saline water (20 ppt) relative to freshwater and relative to fish from freshwater habitats. However, exposure to salinity affected shoaling behaviour of fish from all habitats and shoals moved faster and closer together compared with freshwater. We show that habitat modification can alter phenotypes of native species, but local morphological specialization is associated with trade-offs that may reduce its benefits.

Initiation and spread of escape waves within animal groups.

The exceptional reactivity of animal collectives to predatory attacks is thought to be owing to rapid, but local, transfer of information between group members. These groups turn together in unison and produce escape waves. However, it is not clear how escape waves are created from local interactions, nor is it understood how these patterns are shaped by natural selection. By startling schools of fish with a simulated attack in an experimental arena, we demonstrate that changes in the direction and speed by a small percentage of individuals that detect the danger initiate an escape wave. This escape wave consists of a densely packed band of individuals that causes other school members to change direction. In the majority of cases, this wave passes through the entire group. We use a simulation model to demonstrate that this mechanism can, through local interactions alone, produce arbitrarily large escape waves. In the model, when we set the group density to that seen in real fish schools, we find that the risk to the members at the edge of the group is roughly equal to the risk of those within the group. Our experiments and modelling results provide a plausible explanation for how escape waves propagate in nature without centralized control.

Personality affects the foraging response of a mammalian herbivore to the dual costs of food and fear.

Predators attack and plants defend, so herbivores face the dilemma of how to eat enough without being eaten. But do differences in the personality of herbivores affect the foraging choices of individuals? We explored the ecological impact of personality in a generalist herbivore, the brushtail possum (Trichosurus vulpecula). After quantifying personality traits in wild individuals brought temporarily into captivity, we tested how these traits altered foraging by individuals when free-ranging in their natural habitat. To measure their responses to the dual costs of predation risk and plant toxin, we varied the toxin concentration of food in safe foraging patches against paired, non-toxic risky patches, and used a novel synthesis of a manipulative Giving-Up-Density (GUD) experiment and video behavioural analysis. At the population level, the cost of safe patches pivoted around that of risky patches depending on food toxin concentration. At the individual level, boldness affected foraging at risky high-quality food patches (as behavioural differences between bold and shy), and at safe patches only when food toxin concentration was low (as differences in foraging outcome). Our results ecologically validate the personality trait of boldness, in brushtail possums. They also reveal, for the first time, a nuanced link between personality and the way in which individuals balance the costs of food and fear. Importantly, they suggest that high plant defence effectively attenuates differences in foraging behaviour arising from variation in personality, but poorly defended plants in safe areas should be differentially subject to herbivory depending on the personality of the herbivore.