Biology subjects

Sato, D. X.

Publications and source records attributed to Sato, D. X..

8 recordsLinked to original sources

bioRxiv2026

Phenotypic diversity acts as a higher-order functional trait of populations

Functional traits are usually assigned to individuals, yet some properties exist only as differences among population members. Whether such higher-order properties predict collective performance remains unclear. Here we used the aquatic plant Spirodela polyrhiza to test whether phenotypic and genetic differences among genotypes predict non-additive population growth. We grew twelve Japanese strains alone and in all pairwise mixtures and quantified their growth dynamics. Mixtures sometimes outperformed the mean of their component monocultures, and some exceeded the better-performing monoculture, although diversity effects were negative on average. Positive effects were most strongly associated with between-strain differences in frond colour and morphology, identifying specific dimensions of phenotypic diversity as population-level predictors of synergistic growth. Genome-wide higher-level association mapping identified loci where between-strain diversity was associated with growth effects, implicating stress responses, secondary metabolism and frond morphology. Loci associated with reduced performance implicated chemical perception and self/non-self recognition, whereas those associated with positive effects reflected functional differentiation in stress responses and physiological niches. Our findings suggest that some traits generate new functions at the population level through variation among individuals, making diversity itself a higher-order functional property.

ecology↗

bioRxiv2026

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

bioRxiv2026

Monoaminergic variation, cortical structure, and disaster trauma interact to shape emotional vulnerability

Emotional vulnerability arises from the interplay of genetic variation, cortical network capacity, and subjective processing of adverse experiences, yet these components are rarely examined together in population-scale datasets. Monoaminergic signaling offers an opportunity for understanding such interactions because variation in related genes shapes sensitivity to environmental inputs. Among them, the vesicular monoamine transporter 1 (VMAT1) Thr136Ile variant is notable for its functional effects and its long-term maintenance at intermediate frequencies, a pattern consistent with context-dependent selection. These properties make it an informative marker for investigating how genetic sensitivity interacts with neurobiological and experiential factors to shape affective functioning. Using data from up to 9,625 participants in the Tohoku Medical Megabank Project, a cohort established after the 2011 Great East Japan Earthquake, we investigated how monoaminergic variation, cortical morphology, and traumatic memory shape affective functioning. We found associations between the Thr136Ile variant and negative affectivity and depressive symptoms, consistent with prior reports of heightened emotional reactivity associated with the 136Thr allele. However, magnitude of these effects was substantially amplified in specific experiential and neurobiological contexts. Subjective trauma sensitivity, capturing the discrepancy between earthquake disruption and current traumatic memory, displayed a genotype-dependent association with depressive symptoms, and this relationship was strongest when parietal or insular cortical surface area was smaller. Together, these results identify a multilevel pathway through which monoaminergic variation contributes to emotional vulnerability by interacting with both cortical network capacity and trauma processing. The context-dependent influence of monoaminergic variation may further contribute to maintenance of affective diversity in human populations.

neuroscience↗

bioRxiv2025

Night light of a metropolitan coastline aligns with habitat segregation and divergent plasticity among closely related coastal isopods

Artificial light at night (ALAN) is a pervasive urban driver that can reshape coastal communities, yet its links to genetic structure and behavior remain unclear. Here, we examined two closely related isopods, Ligia laticarpa and L. furcata, across Tokyo Bay along a gradient from brightly lit inner-bay shorelines to darker, vegetated outer-bay coasts. Genomic and mitochondrial evidence consistently identified clear genetic segregation between outer- and inner-bay populations corresponding to the two species, with L. laticarpa predominating at inner-bay and L. furcata at outer-bay sites. While individual genetic profiles showed little indication of recent hybridization, population signals in several inner-bay sites pointed to historical inputs or local co-occurrence of distinct lineages, possibly mediated by ships. Bayesian modeling of 28 years of environmental data identified nighttime light intensity, salinity, and vegetation cover as major predictors of species occurrence, highlighting ALAN as a key environmental axis distinguishing their habitats. In laboratory assays, chronic ALAN exposure reduced growth and activity in L. furcata but had limited effects on L. laticarpa. These findings suggest that artificial lighting and maritime activity jointly shape patterns of genetic connectivity, habitat segregation, and physiological plasticity between closely related coastal species, providing insights into how anthropogenic disturbances influence ecological divergence.

ecology↗

bioRxiv2025

Genetic heterogeneity alleviates behavioral trade-off between exploration and vigilance in Drosophila

Trade-offs between conflicting behaviors fundamentally constrain animal performance, yet group living can alter how such trade-offs are expressed and alleviated. Here, we disentangled the effects of aggregation and heterogeneity, both arising from group living, on the exploration-vigilance trade-off in Drosophila. Using 78 genetically distinct strains from the Drosophila Genetic Reference Panel, we compared behavioral responses of single individuals, homogeneous groups (six individuals from the same strain), and heterogeneous groups (three individuals from each of two distinct strains) under predator-like looming stimuli. Pareto optimization analysis revealed that aggregation increased both exploratory and vigilance behavior, thereby exposing the underlying exploration-vigilance trade-off. In contrast, heterogeneity enhanced group performance beyond expected levels, alleviating the cost of balancing exploration and vigilance. To identify the phenotypic basis of this alleviation, we developed a phenome-wide higher-level association study (PheHAS) that screened 190 phenotypes across strain pairs. We found that heterogeneity in activity patterns and morphological traits promoted trade-off alleviation, whereas similarity in infection responses also contributed, suggesting that social facilitation may contribute. Our study provides the first explicit demonstration that aggregation and heterogeneity exert distinct effects on a group-level behavioral trade-off and introduces PheHAS as a generalizable framework for identifying the phenotypic bases underlying diversity effects in animal groups.

animal behavior and cognition↗

bioRxiv2024

Genetic heterogeneity induces nonadditive behavioural changes in Drosophila

The formation and dynamics of group behaviours are important topics in ecology and evolution. Although several theoretical studies assume homogeneity among individuals, real-world organisms often display remarkable behavioural diversity within groups. This study investigated the synergistic impact of genetic heterogeneity on group behaviour and reveals the behavioural underpinnings of diversity effects using 83 genetically distinct strains of Drosophila melanogaster. Various indices of foraging behaviour, including movement speed, search comprehensiveness, spatial preference and stopping time, were measured using homogeneous (single strain) and heterogeneous (mixing two distinct strains) groups of flies. The heterogeneous groups exhibited significant increases in spatial preference and stopping time compared with the homogeneous groups, suggesting that genetic heterogeneity induces nonadditive changes in group behaviour. Furthermore, the magnitude and direction of the behavioural change varied among different combinations. Multiple regression analysis showed that the phenotypic distance in some traits between mixed strains could explain the emergence of diversity effects on group behaviour. Specifically, interindividual heterogeneity in the locomotor activity level showed a positive correlation with diversity effects. These results emphasise the importance of intraspecific diversity in group dynamics and suggest that genetic heterogeneity can improve group performance through the acquisition of novel behavioural traits.

animal behavior and cognition↗

bioRxiv2024

Neurogenomic diversity enhances collective antipredator performance in Drosophila

Collective behavior is a unique social behavior that plays crucial roles in detecting and avoiding predators. Despite a long history of research on the ecological significance, its neural and genetic underpinnings remain elusive. Here we focus on the mesmerizing nature that visual cues from surrounding conspecifics alleviate the fear response to threatening stimuli in Drosophila melanogaster. A large-scale behavioral experiment and genome-wide association analysis utilizing 104 strains with known genomes uncovered the genetic foundation of the emergent behavioral properties of flies. We found genes involved in visual neuron development associated with visual response to conspecifics, and the functional assay confirmed the regulatory significance of lamina neurons. Furthermore, behavioral synchronization combined with interindividual heterogeneity in freezing drove nonadditive, synergistic changes in group performance for predatory avoidance. Our novel approach termed genome-wide higher-level association study (GHAS) identified loci whose within-group genetic diversity potentially contributes to such an emergent effect. Population genetic analysis revealed that selective pressure may favor increased responsiveness to conspecifics, indicating that by-productive genomic diversity within the group leads to a collective phenomenon. This work opens up a new avenue to understand the genomics underpinning the group-level phenotypes and offers an evolutionary perspective on the mechanism of collective behavior.

animal behavior and cognition↗

bioRxiv2021

Humanized substitutions of Vmat1 in mice induce changes in amygdala-dependent behaviors associated with the evolution of anxiety in humans

The human vesicular monoamine transporter 1 (VMAT1) harbors unique substitutions (Asn136Thr/Ile) that affect monoamine uptake into synaptic vesicles. These substitutions are absent in all known mammals, suggesting their contributions to distinct aspects of human behavior modulated by monoaminergic transmission, such as emotion and cognition. To directly test the impact of these human-specific mutations, we introduced the humanized residues into mouse Vmat1 via CRISPR/Cas9-mediated genome editing and examined changes at the behavioral, neurophysiological and molecular levels. Behavioral tests revealed reduced anxiety-related traits of Vmat1Ile mice, consistent with human studies, and electrophysiological recordings showed altered oscillatory activity in the amygdala under anxiogenic conditions. Transcriptome analyses further identified amygdala-specific changes in the expression of genes involved in neurodevelopment and emotional regulation, which may corroborate the observed phenotypes. This knock-in mouse model hence provides compelling evidence that the mutations affecting monoaminergic signaling and amygdala circuits have contributed to the evolution of human socio-emotional behaviors.

evolutionary biology↗