Biology subjects

Yagi, M.

Publications and source records attributed to Yagi, M..

16 recordsLinked to original sources

bioRxiv2026

Genetic polymorphisms in a mate choice locus are maintained by balancing selection in a wild medaka population

Sexual selection arises from individual differences in reproductive success, which can drive the maintenance of genetic polymorphisms in genes subject to balancing selection by the pleiotropic effects that trade-off between survival and reproduction. However, the extent to which sexual selection maintains genetic polymorphisms in wild populations remains unclear. Here, we explored on genomic signatures of balancing selection and selective sweep in the northern medaka, Oryzias sakaizumii in Japan by performing whole-genome resequencing of wild individuals. In addition, we re-evaluated the population genetic structure and admixture of Oryzias latipes and O. sakaizumii across the Japanese archipelago and detected genomic regions affected by introgression. Regions with signatures of selection from multiple statistics were located on eleven chromosomes. In particular, a region spanning 4.25 to 6.80 Mb on chromosome 18 showed high genetic diversity that could not be explained by sex differentiation or introgression from O. latipes in Eastern Japan. This pattern suggests that balancing selection maintains genetic polymorphisms in O. sakaizumii. Specifically, because a previously reported quantitative trait locus associated with female mating behavior overlaps with this region, we infer that sexual selection contributes to the maintenance of genetic polymorphism at this locus.

evolutionary biology↗

bioRxiv2026

Quantitative assessment of sea slugs (Heterobranchia) assemblages along the western coast of Kyushu, Japan: a baseline for long-term biodiversity monitoring

Quantitative information on the seasonal dynamics of heterobranch sea slug assemblages remains limited in warm-temperate coastal regions, despite their ecological importance as benthic consumers and indicators of environmental change. Here, we conducted a standardized, multi-seasonal SCUBA-based survey of sea slug assemblages at two rocky reef sites (Tatsunokuchi and Nomozaki-Akase) along the northwestern coast of Kyushu, Japan, from February 2024 to November 2025. Across the study period, a total of 81 species comprising 892 individuals were recorded. Species richness and total abundance exhibited pronounced seasonal variation at both sites, with higher values in winter-spring and marked declines during summer. Assemblage composition shifted seasonally from relatively even communities in winter-spring to dominance by a few taxa in summer, a pattern reflected by concurrent changes in diversity indices. Water temperature displayed clear seasonal cycles and was negatively correlated with both species richness and total abundance, indicating a close association between thermal conditions and seasonal changes in sea slug assemblages. While causal mechanisms were not explicitly tested, these consistent patterns highlight the importance of temporal environmental variability in structuring heterobranch communities in this region. This study provides one of the few quantitative, multi-seasonal baselines of heterobranch sea slug assemblages in warm-temperate coastal Japan, offering a reference framework for future ecological monitoring and assessments of environmental change.

ecology↗

bioRxiv2026

Size-invariant aerobic scope across ontogeny in a giant deep-sea scavenger

Aerobic scope is the aerobic metabolism left after maintenance costs are met, and it sets a simple limit on how much oxygen-dependent activity an animal can support. In many aquatic animals, this margin changes with body size because resting and active metabolic rates do not always scale in the same way. Large deep-sea scavengers are interesting in this respect because they live where food is sparse and unpredictable, but they must still move when carrion or food cues appear. We measured resting metabolic rate (RMR) and post-exercise peak oxygen consumption, here referred to as active metabolic rate (AMR), in the giant isopod Bathynomus doederleini across a body-mass range of 1.7-48.4 g using intermittent-flow respirometry at 10 {degrees}C. RMR and AMR both increased with body mass and had similar scaling exponents. As a result, factorial aerobic scope (FAS = AMR/RMR) did not change with body mass (median FAS = 2.83). A residual analysis also showed that mass-corrected RMR was not significantly related to mass-corrected AMR. Thus, individuals with relatively high maintenance metabolism did not necessarily have higher post-exercise aerobic capacity. These results show that exercise-induced aerobic scope was maintained across ontogeny in this deep-sea scavenger. They also show that body size and individual metabolic phenotype provide different information: body size explained the shared increase in RMR and AMR, whereas residual variation did not show a strong link between the two traits.

physiology↗

bioRxiv2026

Three-dimensional redistribution of pelagic fish aggregations associated with floating offshore wind farms

Floating offshore wind farms (F-OWFs) are rapidly expanding into offshore pelagic environments, yet their ecological consequences remain poorly resolved because quantitative, non-invasive monitoring is challenging at sea. Here, we integrated environmental DNA (eDNA) metabarcoding and scientific echosounding to assess fish community composition and three-dimensional aggregation structure around a commercial-scale F-OWF off the Goto Islands, Japan. We compared four stations adjacent to turbines with four offshore control stations under comparable environmental conditions across five sampling periods (April and August 2024; May, June, and August 2025) and three depth layers (5, 50, and 80-160 m). eDNA metabarcoding detected 126 fish species, and community structure based on the 30 most frequently detected taxa did not differ significantly between the F-OWF and control areas (Bray-Curtis PERMANOVA, p = 0.60). Species richness varied strongly with sampling period and water layer, with a significant water layer x period interaction, whereas overall richness did not differ between areas (Mann-Whitney U test, p = 0.18). In contrast, acoustic surveys revealed a marked difference in vertical structuring of fish aggregations: in the control area, NASC per mile increased with depth, while this depth-dependence disappeared near turbines. Moreover, the weighted mean normalized depth (WMND) indicated a shallower vertical center of aggregation in the F-OWF area (0.34) than in the control area (0.24), consistent with turbine-associated redistribution in the water column. Although voyage-level integrated NASC per mile did not differ significantly between areas (t-test, p = 0.83), mean values were higher near turbines. Together, these results indicate that F-OWFs can be associated with changes in the three-dimensional organization of fish aggregations without producing pronounced shifts in dominant taxonomic composition. Our study demonstrates the value of combining eDNA metabarcoding and acoustics for evaluating ecological effects of offshore renewable-energy infrastructures and provides a framework for standardized, long-term monitoring as F-OWF deployment accelerates globally.

ecology↗

bioRxiv2025

Trophic transfer of nanoplastics reduces larval survival of marine fish more than waterborne exposure

Microplastics (MPs) and nanoplastics (NPs) are widespread contaminants in marine environments and pose significant risks to aquatic organisms. However, physiological effects and survival consequences of different MP and NP exposure pathways during early developmental stages of marine fish remain poorly understood. We investigated effects of direct and indirect consumption of MPs and NPs by larvae of red sea bream (Pagrus major) using a controlled laboratory system. Larvae were exposed to fluorescently labeled polystyrene particles (3 {micro}m and 0.2 {micro}m) either directly from the water or indirectly via contaminated zooplankton prey. MPs and NPs were detected in digestive tracts of all exposed individuals, regardless of the exposure route. However, survival was significantly reduced in larvae that consumed NPs via rotifer predation, suggesting that ingestion of contaminated prey organisms may represent a greater hazard than direct uptake from water. In both groups, antioxidant enzymes, superoxide dismutase (SOD) and catalase (CAT) were elevated, suggesting induction of oxidative stress. Relative gene expression revealed greater upregulation of several stress and immune-related genes in larvae exposed to MPs via rotifer predation than via direct consumption. Our findings provide clear evidence that both MPs and NPs can alter physiological and molecular responses in marine fish larvae, especially via rotifer predation. This study suggests the importance of considering trophic interactions in ecotoxicological assessments of plastic pollution to address plastic bioavailability and toxicity during early life stages. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/675286v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1de4a22org.highwire.dtl.DTLVardef@d53060org.highwire.dtl.DTLVardef@5b13fborg.highwire.dtl.DTLVardef@17cd662_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILarval survival was significantly reduced by nanoplastics via trophic transfer C_LIO_LIGrowth of larvae was not affected by micro-and nanoplastics C_LIO_LIMicro- and nanoplastics cause oxidative stress by both exposure routes C_LIO_LIUp-regulated gene expression revealed that larvae undergo various stresses C_LI

developmental biology↗

bioRxiv2025

A different world: temporal changes in nudibranch community structure over a half-century

Understanding long-term changes in marine biodiversity is essential for evaluating effects of climate change on coastal ecosystems. In this study, we compared nudibranch assemblages in northwestern Kyushu, Japan, during three time periods (1960-1980, 2001-2003, and 2023-2024), based on underwater surveys and historical records. In all, 47 nudibranch species were recorded during 27 diving surveys conducted in 2023 and 2024. Species diversity indices (Shannon-Wiener H and Simpson D) showed higher values during this survey than in 2001-2003. Comparative analysis of species composition revealed significant shifts, with 15 species exhibiting statistically significant differences in relative abundance from the past to the present. Notably, several species common in the past, such as Aplysia kurodai, were rarely observed in the recent survey, while many tropical-subtropical species appeared for the first time. The proportion of tropical-subtropical species increased markedly, whereas subarctic species were no longer detected. Similarity indices (Jaccards coefficient and Sorensen-Dice index) indicated that the current community differs markedly from those in earlier periods. These findings suggest a major community reorganization, potentially driven by rising sea water temperatures and other environmental changes. This study highlights the importance of long-term monitoring using multiple indicators to detect and interpret climate-driven biodiversity shifts in coastal marine ecosystems. HighlightsO_LILong-term changes in nudibranch assemblages were investigated using visual census surveys spanning 6 decades. C_LIO_LISpecies richness and tropical species have increased markedly in recent decades. C_LIO_LISubtropical species expanded their ranges, while some cold-water species declined. C_LIO_LIFindings suggest that community-level tropicalization is likely driven by ocean warming. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/668013v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@9d0182org.highwire.dtl.DTLVardef@1ce002borg.highwire.dtl.DTLVardef@16d3830org.highwire.dtl.DTLVardef@183ff06_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2025

Intraspecific differences in habitat depth in a deep-sea isopod, Bathynomus doederleini (Crustacea: Isopoda: Cirolanidae), off the west coast of Kyushu, Japan

The giant deep-sea isopod, Bathynomus doederleini, is a benthic scavenger distributed in the northwestern Pacific. Despite its ecological importance, little is known about its habitat use and intraspecific variation in body size in relation to depth. In this study, we examined the habitat depth, size structure, and distributional limits of B. doederleini off the western coast of Kyushu, Japan, using baited traps deployed at depths ranging from 151 to 821 m. A total of 1,152 individuals were collected, with the highest catch per unit effort (CPUE) observed between 300 and 500 m. CPUE declined sharply below 700 m, likely due to thermal constraints and interspecific competition. Body size distribution varied significantly with depth: minimum body size increased with depth, while maximum body size remained constant. Smaller individuals were more abundant in shallower, warmer waters, suggesting ontogenetic habitat segregation possibly driven by metabolic and competitive factors. No brooding individuals were captured, supporting previous findings that reproductive females avoid baited traps. These results suggest that B. doederleini forms a reproductively active population in the East China Sea, with ecological adaptations to thermal conditions and depth-related niche partitioning. This study highlights the importance of trap type and environmental gradients in understanding deep-sea species ecology.

ecology↗

bioRxiv2025

Primary and secondary microplastics do not affect hatching of Japanese flounder eggs

Microplastics (MPs) are pervasive pollutants that may threaten aquatic organisms, especially during early life stages. This study investigated effects of MPs on the hatching rate of Japanese flounder eggs. Fertilized eggs were exposed to polystyrene (PS) microbeads (primary microplastics) (3 and 10 {micro}m, at 20 and 200 particles/ml), and secondary MPs derived from coastal debris (rope, plastic bottles, fish net, string, and rubber pads) collected in Nagasaki, Japan. Hatching rates of flounder eggs were unaffected by either primary or secondary microplastics, suggesting limited impact of microplastics on this brief developmental stage.

developmental biology↗

bioRxiv2025

Floating offshore wind farms cause Japanese horse mackerel to congregate

Floating offshore wind farms (F-OWFs) are becoming key components of renewable energy production, yet their ecological impacts on marine ecosystems remain largely unexplored. Using environmental DNA (eDNA) analysis in the East China Sea, this study investigated the tendency for Japanese horse mackerel (Trachurus japonicus) to congregate beneath F-OWFs. Water samples were collected at stations near an F-OWF and control stations farther away at various depths and seasons. A total of 115 samples were analyzed, and eDNA of T. japonicus was detected in 83% of all samples. eDNA concentrations were significantly higher near an F-OWF (F-OWF stations) than at control stations. The highest recorded eDNA concentration reached 2,280 copies/L at an F-OWF station, whereas the maximum concentration at control stations was 783 copies/L. Seasonal variations were also observed, with lower concentrations in summer and higher concentrations from autumn to spring. Generalized linear model (GLM) analysis further revealed that wind turbines had a significant influence on eDNA concentration, whereas other environmental variables, such as water temperature and depth, were not significant. These findings suggest that F-OWFs may function as artificial reefs, providing habitat for commercially important fish and influencing fish distributions at both spatial and temporal scales. However, potential conflicts with fisheries due to spatial restrictions, displacement of fishery resources, and increased navigation costs necessitate further long-term ecological and socio-economic assessments. Integrating eDNA monitoring with traditional survey methods, such as acoustic surveys and ROV observations, is crucial for coexistence of adaptive offshore wind farm management and sustainable fisheries. Future research should also explore the long-term effects of F-OWFs on fish assemblages and biodiversity to support evidence-based decision-making for offshore energy development.

ecology↗

bioRxiv2025

Hematopoietic stem cells undergo bidirectional fate transitions in vivo.

Differentiation of haematopoietic stem and progenitor cells (HSPCs) is widely considered unidirectional in vivo. Here, we developed clonal phylogenetic tracing (CP-tracer) by sequential genetic barcoding, which enabled high-resolution analysis of 181,695 subclones derived from 847 individually labelled HSPCs. This approach uncovered bidirectional fate transitions between myeloid-biased (My-) and lineage-balanced haematopoietic stem cells (HSCs). Individual HSC clones, distinguished by temporally unique serial barcodes, exhibited durable lineage bidirectionality, with dynamics favouring progressive accumulation of My-HSCs over time. CRISPR-Cas9 screening identified the homeobox gene Hhex as a suppressor of myeloid differentiation that enables pivoting toward balanced output. Hhex function is age-dependent, with its expression declining in aged HSCs. Together, these findings demonstrate unexpected plasticity in HSC differentiation, modulated in part by Hhex-mediated repression, that shifts over time to drive the myeloid bias characteristic of ageing.

cell biology↗

bioRxiv2023

Environmental DNA Reveals the Geographic Distributions of Two Eel Species, Anguilla japonica and A. marmorata, in Western Kyushu, Japan

Anguillid eels migrate thousands of kilometres from their spawning grounds, dispersing across a vast geographic area to fresh and brackish water habitats, where they settle and grow. Japanese eels (Anguilla japonica) and giant mottled eels (A. marmorata) are both found in Japan, although their distributions differ. However, details of these differences are unknown. We hypothesised that distribution patterns of Japanese and giant mottled eels must be different between and within rivers along the northwest coast of Kyushu, Japan. Environmental DNA (eDNA) analysis was conducted at 87 sites in 23 rivers. Japanese eel eDNA was detected in 19 rivers (82.6%) and that of giant mottled eels was detected in 8 (34.8%). eDNA for Japanese eels was detected at 6 of 9 sites in the North (66.7%), 13 of 23 sites in Omura (56.5%) and 37 of 55 sites in the South (67.3%). In contrast, giant mottled eel eDNA was detected at 1 of 9 sites in the North (11.1%), no sites in Omura and 15 of 55 sites in the South (27.3%). There was no correlation between eDNA concentrations of the two species at 10 sites in the five rivers where eDNA of both species was detected, implying that their habitat preference differ. This partially reveals dispersal and settlement mechanisms of these eel species.

ecology↗

bioRxiv2023

Metabolic responses to food and temperature in deep-sea isopods, Bathynomus doederleini

Metabolic rate, the energy required per unit of time for an organism to sustain life, is influenced by both intrinsic and extrinsic factors. Despite the similarities among living organisms across the various domains of life, it has been observed that those adapted to deep-sea environments exhibit notable distinctions from those in shallower waters, even when accounting for size and temperature. However, as deep-sea organisms are infrequently kept in captivity for prolonged periods, investigations into their potential metabolic responses to food and temperature have yet to be conducted. In this study, we demonstrate the impact of food (specific dynamic action: SDA) and temperature (Q10) on the metabolic rate of the deep-sea isopod Bathynomus doederleini. Positive correlations were found between SDA parameters (peak, time to peak, duration, and factorial scope) and meal size in deep-sea organisms. The postprandial metabolic rate, at a meal size of 45.4%, increased by approximately 6.5-fold, and the duration was 20 days. Within the temperature range of their natural habitat, the overall Q10 was 2.36, indicating that a 10 {degrees}C increase would lead to a 2.4-fold increase in resting metabolic rate. The mean metabolic rate of this species, corrected for the equivalent temperature, was significantly 63% lower than the metabolic scaling rule for aquatic invertebrates. This low metabolic rate suggests that deep-sea isopods can survive for a year on a mere few grams of whale blubber at a water temperature of 10.5 {degrees}C. This information is crucial for understanding the metabolic strategies and consequences of adaptation to a deep-sea environment.

ecology↗

bioRxiv2022

The Dynorphin/Kappa Opioid Receptor mediates adverse immunological and behavioral outcomes induced by repetitive blast trauma in male mice

BackgroundAdverse pathophysiological and behavioral outcomes related to mild traumatic brain injury (mTBI), posttraumatic stress disorder (PTSD), and chronic pain are common following blast exposure and contribute to decreased quality of life, but underlying mechanisms and prophylactic/treatment options remain limited. The dynorphin/kappa opioid receptor (KOR) system helps regulate behavioral and inflammatory responses to stress and injury; however, it has yet to be investigated as a potential mechanism in either humans or animals exposed to blast. We hypothesized that blast-induced KOR activation mediates adverse outcomes related to inflammation and affective behavioral response. MethodsC57Bl/6 adult male mice were singly or repeatedly exposed to either sham (anesthesia only) or blast delivered by a pneumatic shock tube. The selective KOR antagonist norBNI or vehicle (saline) was administered 72 hours prior to repetitive blast or sham exposure. Serum and brain were collected 10 minutes or 4 hours post-exposure for dynorphin A-like immunoreactivity and cytokine measurements, respectively. At one-month post-exposure, mice were tested in a series of behavioral assays related to adverse outcomes reported by humans with blast trauma. ResultsRepetitive but not single blast exposure resulted in increased brain dynorphin A-like immunoreactivity. norBNI pretreatment blocked or significantly reduced blast-induced increase in serum and brain cytokines, including IL-6, at 4 hours post exposure and aversive/anxiety-like behavioral dysfunction at one month post exposure. ConclusionsOur findings demonstrate a previously unreported role for the dynorphin/KOR system as a mediator of biochemical and behavioral dysfunction following repetitive blast exposure and highlight this system as a potential prophylactic/therapeutic treatment target.

neuroscience↗

bioRxiv2022

Microplastic pollution in aquatic environments may facilitate misfeeding by fish

Numerous recent studies have documented ingestion of microplastics (MPs) by many aquatic animals, yet an explanation for misfeeding by fish remains unexplained. Here we tested the hypothesis that biofilm (biofouling) on MP surfaces due to exposure in the aquatic environment facilitates misfeeding in fish. Spherical polystyrene (PS) was cultured for 0 to 22 weeks in a freshwater environment to grow biofilm on the MP. Goldfish were employed in a simple feeding experiment with and without provision of genuine food at ecologically relevant MP concentrations. The absorbance (ABS), which is a proxy for biofilm formation increased exponentially within three weeks of initiation and reached a plateau after approximately five weeks. Although fish did not swallow the MPs, "capture" occurred when food pellets were in the vicinity and significantly increased in probability with exposure time. Duration of capture also increased significantly with increasing exposure. These results suggest that the drift of MPs in aquatic environments may facilitate fish misidentification of MPs as edible prey.

ecology↗

bioRxiv2021

Microplastic pollution of commercial fishes from coastal and offshore waters, Japan

Microplastics (MPs) pollution is a worldwide issue in the marine environment. There is growing concern of consuming MPs through fish, yet the current contamination status of fish collected from the deep sea surrounding Japan remains limited. We present baseline data on MPs in commercially important fishes from the coastal and offshore waters near Kyushu, Japan (East China Sea). We examined the MPs in the digestive tracts of two pelagic (n = 150 in total) and five demersal species (n = 235 in total). The fish were caught by pole and line, and bottom trawl at different geographical positions. The MPs in pelagic fish (39.1 %) were higher than demersal fish (10.3 %) and of larger sizes. The MPs correlated with habitat depth and type. There was species variation in the shape and polymer composition of MPs. These results increase our understanding of the heterogeneous uptake of MPs by fishes.

ecology↗

bioRxiv2021

Spatiotemporal variations of surface water microplastics near Kyushu, Japan: A quali-quantitative analysis

Microplastics in the ocean are threatening marine ecosystems. Although plastic contaminants are ubiquitous from rivers to polar oceans, their distribution is thought to be heterogeneous, implying that both spatial and temporal variability exist. Here, we elucidate the significant spatial and temporal (seasonal) variations in the quanti-qualitative characteristics of microplastics off the west coast of Kyushu, Japan in the East China Sea. Six surveys across nine stations (n = 54) were conducted over a 14-month period, and a total of 6131 plastic items were identified. The average microplastic abundance (items {middle dot}m-3) and size (mm) {+/-} S.D. were 0.49 {+/-} 0.92 (n = 54), and 1.71 {+/-} 0.93 (n = 6131), respectively. Differences between the highest and lowest abundances were 50-fold among monthly means (1.97 {+/-} 1.49, n = 9; 0.04 {+/-} 0.03, n = 9), and 550-fold across all net tows (5.50; 0.01). With respect to colour, polymer type, and shape, white and transparent (68.5%), polyethylene (80%) fragments (76.0%) were the dominant composition. There were statistically significant differences for each of the analytical microplastic parameters among survey months (p < 0.02). Our results provide baseline data, and lead to a more comprehensive understanding of the spatiotemporal characteristics of microplastic pollution. HighlightsO_LISignificant spatiotemporal variability in microplastic litter was detected based on the quali-quantitative analyses. C_LIO_LIAverage ({+/-} S.D.) microplastic abundance was 0.49 {+/-} 0.92 (items {middle dot}m-3) and size was 1.71 {+/-} 0.93 (mm). C_LIO_LIDifferences between highest and lowest abundances were 50-fold among monthly means, and 550-fold across all net tows. C_LIO_LIWhite and transparent polyethylene fragments were the dominant composition. C_LI

ecology↗