Ecological Research

@ecologicalresearch.bsky.social

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Ecological Research publishes original papers on all aspects of #ecology, in both aquatic and terrestrial #ecosystems. ©The Ecological Society of Japan 🌐 https://esj-journals.onlinelibrary.wiley.com/journal/14401703 Original website: https://esj.ne.jp/er/

Graphical abstract: We developed a new version of the Multiplexed ISSR Genotyping by Sequencing (MIG-seq) method, called MIG-seq2. This improved protocol incorporates dual unique indices to distinguish more than 1344 samples and optimizes primer tail sequences to improve sequence quality. Additionally, we designed an optional degenerate primer set (dpMIG-seq2) to enhance amplification efficiency in low-diversity samples. The effectiveness of these improvements was confirmed by phylogenetic analyses of two closely related Plantago species, which yielded highly reproducible and well-supported trees.
Graphical abstract: We argue that personal and direct experiences of nature can influence biodiversity outcomes across multiple societal sectors, not only among the general public but also among actors such as policy makers, business leaders, educators, scientists, and journalists. By synthesizing existing evidence, we show that these experiences can shape biodiversity through sector-specific decisions and interconnected social, economic, and institutional pathways. Strengthening direct human-nature interactions across society may therefore represent a key approach for transformative biodiversity conservation.
Graphical abstract: This study provides a comprehensive dataset of actual and estimated ages, as well as inferred birth periods, for Indo-Pacific bottlenose dolphins (Tursiops aduncus) around Mikura Island, Japan. Using long-term individual identification surveys, speckle pattern analysis, and epigenetic data from fecal samples, age information was determined for 85.6% of the known population (268 of 313 individuals). The resulting dataset offers valuable insights into the population's demographics and reproductive seasonality, contributing to life history and conservation research.
Graphical abstract: The present study examined the succession and carbon source utilization of fungi associated with moss profiles and to identify the metabolic traits that were linked to the successional status. We showed that the successional status of microfungi in decomposing tissues of Hylocomium splendens was affected not by the taxonomic group but by the potential ability to utilize four carboxylic acids and two amino acids.
Graphical abstract: This study examined seasonal changes in the structure of intraguild predation systems involving cats, two rat species, and seabirds using stable isotope analysis. Our results showed that cats depended on seabirds (shared prey) as food when seabirds were present, but, when seabirds were absent, shifted their diet to Norway rats and subsequently showed increased reliance on black rats. In addition, Norway rats showed higher carbon and nitrogen stable isotope ratios than black rats, suggesting a stronger dependence on seabirds as a food source. These results suggest that, during periods when seabirds are absent, cats rely on two non-native rat species that serve as temporally compensatory prey.
Graphical abstract: Two sympatric crow species showed distinct resource use during the snow-free season, exploiting different environments and anthropogenic resources. In contrast, during winter, both species converged on similar habitats and food resources under snow cover. These results highlight flexible, season-dependent resource use in non-breeding crows.
Graphical abstract: The MorFunSeed dataset compiles standardized seed morphology and functional traits for 131 tree and shrub species native to Brazil's Cerrado and Atlantic Forest biomes. It includes 26 variables and 3406 records, providing a consistent and comparable structure across species. This dataset supports investigations into trait–environment relationships, germination strategies, and seedling establishment processes, while also contributes to improving species selection for large‑scale ecological restoration.
Graphical abstract: The aim of the present study was to evaluate the effect of fertilization regime (organic vs. inorganic) on the growth performance, nickel accumulation, and total nickel yield of the nickel hyperaccumulator Bornmuellera emarginata, cultivated under realistic field conditions in its native ultramafic environment in Northern Greece over a 3-year period.
Graphical abstract: We used camera traps in Ranthambhore National Park to study the ecology and behavior of chital and sambar with respect to seasonal variations. We found that body condition and foraging increased in winter, whereas summer conditions were associated with increased movement and reduced foraging. Our results demonstrate that camera traps can generate integrated demographic and behavioral indicators of ungulate performance, with direct relevance for monitoring prey populations in predator-dominated systems.
Graphical abstract: This study indicates that exogenous glutathione (GSH) applied to the roots inhibits nickel (Ni) uptake and its translocation to the shoots in hydroponically grown Brassica napus. Micro-PIXE imaging further revealed that GSH reduces Ni accumulation near the stele, indicating inhibition of Ni radial transport toward the vascular tissues. Transcriptome analysis demonstrated that Ni-induced lignin biosynthesis genes are downregulated by GSH, suggesting that GSH modulates root cell wall structure to regulate Ni mobility at the molecular level.
Graphical abstract: Community scientists (citizen scientists) have monitored populations of early-spring-breeding frog species by counting egg masses at conservation sites across Japan. Using these long-term data, we examined shifts in breeding phenology in three frog species. All species showed trends toward earlier breeding, with population size influencing timing, while survey frequency had little effect. Our results indicate that warming advances amphibian breeding phenology in Japan and demonstrate the value of community science data. Photo by The Nature Conservation Society of Japan.
Graphical abstract: We developed a Random Forest model to assess vegetation conservation classes (VCCs) using 5779 national survey datasets in South Korea. The model not only achieved high classification accuracy (80.4%) but also demonstrated ecological validity by correctly identifying the successional trajectories and phytosociological species composition of Pinus and Quercus communities.
Graphical abstract: We investigated nest predation in the endangered Canarian houbara bustard using 229 artificial nests and camera traps. Ravens were identified as the main predators, and predation rates were influenced by raven density, vegetation cover, stone cover, and road density. These results provide practical recommendations for habitat management and strategies to reduce nest predation in houbara breeding areas.
Graphical abstract: The evergreen shrub Buxus microphylla, growing on ultramafic soils of Sugashima Island, Japan, develops crimson leaves each winter. Field and laboratory results indicate that nutrient limitation and light stress lead to chlorophyll degradation and carotenoid enrichment, rather than anthocyanin formation. This pigment imbalance highlights the roles of photoprotection and nutrient status in shaping the distinctive “crimson boxwood” phenotype.
Graphical abstract: Solar-induced chlorophyll fluorescence (SIF) and gross primary productivity decline at midday during a short heatwave in a tower site of a larch forest. High atmospheric vapor pressure deficit significantly reduced the photochemical reflectance index (PRI), light-use efficiency (LUE), and canopy fluorescence emission efficiency (ΔF). The study demonstrated that remote sensing of SIF and PRI effectively indicates heat- and drought-induced responses in photosynthetic activity in a forest ecosystem.
Graphical abstract: Two obligate ultramaficophytes, Balkana spergulifolia and Polygonum albanicum, were analyzed for elemental profiles and differences in response to ultramafic soils. Slight differences were observed between the soil samples, corresponding to some extent to the degree of serpentinization. The analyzed plants exhibited different strategies in response to excessive element concentrations in the soil.
Graphical Abstract: We found that the relative contributions of plant diversity and soil biodiversity to EMF changed significantly with increasing levels of shrub expansion. At lower levels of shrub expansion (shrub cover below 58%), plant diversity was a more prominent driver of EMF, whereas at higher levels of shrub expansion (shrub cover above 65%), the influence of soil biodiversity dominated. Shrub expansion has re-regulated the pattern of associations between above-ground and below-ground biodiversity and ecosystem functioning by altering vegetation structure and soil conditions. The present study provides new evidence that shrub expansion may shift ecosystem function maintenance mechanisms from plant diversity dominance to soil biodiversity dominance. This shift may be related to the simplification of plant community composition, changes in the quality of apoplastic material, and increased heterogeneity of the soil microenvironment during shrub expansion.
Graphical abstract: Latitudinal diversity gradients in species richness were observed in the coasts of Japan. Extensive tidal flats and biogeographical connectivity to the Eurasian Continent may cause the unexpected peak in species diversity at the Kyushu region. Mollusca was the dominant taxonomic group, followed by Malacostraca, Annelida, and other benthic groups.
Graphical abstract: Ontogenetic shifts in flower-dwelling spiders alter their roles in pollination systems. Spiderlings preferentially prey on floral exploiters such as thrips, potentially reducing nectar and pollen loss, whereas adult spiders mainly capture effective pollinators. Considering predator ontogeny reveals stage-dependent and contrasting impacts of spiders on plant–pollinator interactions.
Graphical abstract: Large carnivores increasingly struggle to persist in human-dominated landscapes where conflict threatens both conservation and livelihoods. We examined human–leopard conflict in and around Jaisamand Wildlife Sanctuary, Rajasthan, India, documenting 572 incidents (2011–2024), predominantly livestock depredation near village peripheries, with risk shaped by elevation, land use, and proximity to human settlements. Our findings highlight that ineffective husbandry, inadequate compensation, and negative perceptions—particularly among less-educated residents—drive conflict, underscoring the need for secure livestock enclosures, timely payouts, education-based outreach, and landscape-level planning to promote human–leopard coexistence.
Graphical abstract: We compared the diet and assessed geographic and seasonal variations in the isotopic niches of red-footed boobies across three Indian Ocean atolls. Our results demonstrate plasticity in both diet and trophic niche, likely driven by local environmental conditions, breeding stages, and colony-specific factors. By establishing these ecological baselines, our study provides essential data to support the long-term monitoring of this widely occurring seabird within the rapidly changing tropical Indian Ocean.
Graphical abstract: Two helminth-rodent networks were analyzed for two distinct areas. Network modularity, nestedness, and degree of specialization were calculated for each network. Higher network modularity than nestedness and high network specialization were observed in both networks, suggesting functional and/or taxonomic specialization between helminth species and their hosts. Abundance was a more important predictor for explaining the topological role of host and parasite species than the functional attributes of the species, so that the most abundant host and parasite species played a central role in both networks.
Graphical abstract: Rinorea cf. bengalensis is a tropical nickel hyperaccumulator plant that can be dominant in forests locally. We investigated the partitioning of major and trace elements in a stand of R. cf. bengalensis in Borneo. Hyperaccumulators have a large impact on the cycling of Ni and other elements in their ecosystem.
Graphical abstract: Ultramafic (serpentine) soils create extreme edaphic conditions that drive plant adaptation and endemism. TĂŒrkiye hosts one of the richest ultramafic floras in the Northern Hemisphere, including many endemic and Ni-hyperaccumulating species. This review synthesizes current knowledge and highlights priorities for future research and conservation.
Graphical abstract: Selenium hyperaccumulators are plants able to accumulate over 1000 mg/kg in their shoots while growing in their natural environments. The distribution of selenium in the seeds of the three key hyperaccumulating species was elucidated using X-ray fluorescence microscopy computed tomography (XFM-CT).
Graphical abstract: Urbanization in India is increasing the demand for urban trees, but a lack of comprehensive data hinders effective management. To solve this, the Urban Trees of India (UTI) database was created, documenting 742 species across 380 urban areas. The database shows that most of these trees are native and evergreen, with the majority classified under “Least Concern” by the IUCN Red List.
Graphical abstract: Conducted continuous acoustic monitoring of cicadas at six sites in Tokyo–Kanagawa over 61 days in summer 2024, detecting six species. Seasonal calling patterns were broadly consistent, but some species extended their calls into nighttime hours at urban sites. Findings highlight interspecific variation in urban adaptation and demonstrate the effectiveness of audio recorders for long-term insect monitoring.
Graphical abstract: This study presents the first systematic inventory of street trees in MacapĂĄ, Northeastern Brazilian Amazon. Results reveal a dominance of exotic and fruit-bearing species, low tree density, and a replacement of large canopy trees by smaller ones, indicating potential losses in ecosystem services and the need for more biodiversity-focused afforestation planning.
Graphical abstract: Long-term (1976–2015) field sign monitoring of brown bears in northern Hokkaido, Japan, yielded 2421 records (feeding signs, tracks, scats) along 9890 km of survey routes. The digitized spatiotemporal dataset provides insights into population dynamics, habitat use, and feeding behavior across a major wildlife management policy shift.
Graphical abstract: Our study demonstrated that the “safe site” function of coarse woody debris (CWD) is not inherent to the downed log itself, which is nutrient-poor and physically harsh. Instead, facilitation is driven by the associated bryophyte carpet and accumulated humus, which elevate nutrient availability to levels comparable to forest soil. The results highlight a clear mechanism that CWD provides the physical platform or microhabitat for bryophytes, and the bryophyte community provides the chemical and structural environment necessary for successful seedling establishment.
Graphical abstract: This study developed a novel system of functional groups for testate amoebae based on 18 functional traits and assessed its ecological significance. We used hierarchical clustering on a trait database encompassing 372 species from the Northern Holarctic realm. Our analysis identified seven distinct functional groups, offering a more ecologically informative framework than traditional morphological classification.
Graphical abstract: We investigated the factors influencing water deer occupancy and their activity patterns during the summer season. The results suggested that occupancy probability decreased with increasing NDVI (normalized difference vegetation index), indicating a preference for grasslands and shrublands. Additionally, water deer exhibited distinct crepuscular activity patterns.
Graphical abstract: We developed high-precision genome assemblies for two endangered avian species in Japan, the Okinawa rail and the Japanese golden eagle, using a hybrid approach combining short- and long-read whole genome sequencing technologies. This method improved assembly contiguity, reduced missing data, and enhanced completeness, improving the results of conservation genetic analyses. Our approach provides a cost-effective strategy for generating high-quality assemblies of non-model animals for population and conservation genetics.
Graphical abstract: Metal hyperaccumulation may enhance plant fitness through multiple, non-exclusive mechanisms, including elemental defense against herbivores and pathogens, altered pollinator interactions, and increased reproductive performance in metal-rich soils. Metals may also affect plant–plant interactions via elemental allelopathy and improve stress tolerance, such as drought resistance. In some systems, hyperaccumulation may confer incremental defensive benefits, arise as a by-product of efficient nutrient acquisition in nutrient-poor environments, or serve as a means of metal sequestration and disposal.
Graphical abstract: We applied the Elements of Metacommunity Structure (EMS) framework to macrophyte communities across coastal wetlands in southern Brazil, identifying distinct distribution patterns among functional groups. Our results show that environmental and climatic factors shape these patterns differently, with emergent species forming Clementsian communities and submerged species following Gleasonian patterns. This study enhances understanding of species distribution and community structuring in aquatic ecosystems.
Graphical abstract: We investigated how habitat amount (forest cover) and configuration (edge density, number of patches) interact to shape insectivorous bat diversity in 28 islands of a Malaysian hydroelectric reservoir. Forest cover directly increased sonotype richness, but its indirect effects through edge density were negative, especially in highly deforested landscapes. Our results show that habitat amount and configuration are interdependent, and minimizing habitat loss is crucial to mitigate the associated effects of fragmentation on tropical bats.
Graphical abstract: We investigated manganese (Mn) accumulation in 25 Ilex species using X-ray fluorescence analysis of 2655 herbarium specimens. Nine species were identified as Mn hyperaccumulators, with several consistently showing high Zn concentrations and a strong Mn–Zn correlation. These findings reveal Ilex as a distinct lineage of Mn hyperaccumulators in non-contaminated soils.
Graphical abstract: Stored carbon in the belowground organs was greatly depleted by the periodic reproductive event in the herbaceous species Veratrum album. The present study demonstrated the resource budget hypothesis based on carbon resources.
Graphical abstract: Satellite tracking of Black Wood Pigeons in the Izu Islands (2022–2025) revealed frequent interisland movements, with flights ranging from 4 to 170 km. Many individuals dispersed among islands after breeding and returned the following spring, indicating partial migratory or nomadic behavior at the archipelagic scale. Habitat selection shifted with movement, with a preference for afforestation areas and Sasa shrubs during breeding, suggesting flexible use of island habitats driven by individual movement decisions.
Graphical abstract: The three-field plot shows how leading researchers, functional traits, and biomes are interconnected in Brazilian bryophyte ecology. It highlights strong links between reproductive traits and the Atlantic Forest, reflecting research focus and collaboration patterns.
Graphical abstract: Subterranean ecosystems in the Bodoquena karst region were studied to understand how microhabitat features influence invertebrate diversity across different spatial scales. The study found that species richness is positively related to trophic diversity and negatively to distance from cave entrances, with temperature and shelter availability also affecting community composition. The presence of 20 troglomorphic species underscores the region's conservation value, emphasizing the need for ongoing monitoring amid increasing human pressures.
Graphical abstract: This study presents a novel biodiversity dataset comprising 737 endemic tree taxa in India. The endemic tree species distribution varies significantly among the states of India. Temperature seasonality emerged as the major driver of the endemic tree diversity. To date, only 30% of the species have been evaluated for threat status. The findings can contribute in guiding global and national conservation priorities.
Graphical abstract: Fly-derived iDNA can detect more vertebrate species than leech-derived iDNA.
Graphical Abstract: The Asian black bear populations in Japan experienced three distinct periods of population decline in the past. The first decline began approximately between 800,000 and 300,000 years ago, the second occurred around 150,000 to 70,000 years ago, and the third took place roughly from 50,000 to 18,000 years ago.
Graphical Abstract: This study examined the impact of farmland abandonment on biodiversity in Japanese Satoyama using spiders as indicators. In 2023, 629 individuals from 94 taxa were collected in Machida City, suggesting that farmland abandonment may enhance landscape diversity.
Graphical abstract: Excessive deer browsing leads to the spread of the unpalatable shrub Pieris japonica, which forms monodominant stands (a) and suppresses other vegetation. In contrast to areas without Pieris dominance (b, d), we found that the modified organic horizon under these shrubs specifically inhibits seedling root growth, thereby limiting plant establishment (c).
Graphical Abstract: Estimation of palatability and browsing pressure are key techniques for ecosystem management. We compared four methods to estimate palatability based on browsing scar survey and proposed the reference palatability values for the Japanese flora as plant ecological trait. Browsing pressure, defined as the threshold palatability value between browsed and unbrowsed plants, is depicted as a map. Such maps can help identify locations where damage-control measures should be implemented.
Graphical abstract: In this paper, we synthesize studies that integrally examine geological and ecological processes across different scales and components of riverscapes, including geohydrological processes. Finally, we identify both scientific and practical challenges that must be addressed to bridge the gap between basic-science implications and their implementation in riverscape restorations.
Graphical abstract: Our results reveal that arthropods, particularly chewing arthropods, were the dominant predators, and their activity was strongly influenced by both habitat type and canopy cover. Predation probability increased with canopy cover in forest plots but decreased in silvo-pastures, highlighting an important interaction between vegetation structure and habitat degradation. Furthermore, predation rates were consistently higher at lower elevations, possibly due to microclimatic conditions or changes in predator community composition.
Graphical abstract: We compared the community structure of Aculeata bees and wasps in natural deciduous broadleaved forests and two coniferous plantations (Cryptomeria japonica, “Sugi” and Chamaecyparis obtusa, “Hinoki”) in southern Kyushu, Japan. Compared with natural forests, the dependence of Aculeata communities on the detritus-based food chain increased in both plantations. In addition, Aculeata communities in plantations exhibited lower seasonal segregation of food resources and wider foraging ranges.
Graphical abstract: We present an expanded 28S rRNA reference dataset for environmental DNA (eDNA) detection of deep-sea octocorals in the Western Pacific. The dataset includes 269 specimens spanning 52 genera across 24 families, with sequences obtained via Sanger sequencing and genome skimming. This curated resource will support more accurate biodiversity assessments and conservation of cold-water coral ecosystems.