Rare plant species identified in project areas where land is to be developed or altered may need to be extracted for ex-situ conservation under human control. During ex-situ conservation, it is important to minimize the impact of adverse factors including the potentially limited environmental adaptability of rare plants under cultivation and possible losses of genetic diversity due to inbreeding if the number of conserved individuals is low. Here we evaluate the conservation difficulty and genetic diversity of populations of the rare plant Violα raddeana at five sites based on harmful gene accumulation and gene duplication data gathered using RNA-seq. Moreover, we evaluate the genetic diversity and structure of these populations using SNP data acquired using MIG-seq. The results obtained indicate that the V. raddeana populations have declined but remain robust towards environmental changes and can undergo voluntary mating at all sites. Moreover, there is clear genetic differentiation between two populations in close geographic proximity. If the majority of the remaining individuals of V. raddeana in each genetically related population were transplanted and cultivated, it would be possible to maintain their genetic diversity through ex-situ conservation.

Brittle stars are marine invertebrates that often dominate the seafloor. Their global distribution range and abundance make them useful as marine environmental bio-indicators. Despite their importance, however, there is limited availability of data on brittle star specimens in Japan. In this study, we focused on Sagami Bay, one of the oldest Japanese sea areas for the study of brittle stars, and organized the data of the specimens obtained there. This collection included specimens collected between 2005 and 2021, with a total of 738 samples, which were identified as 112 species. In this data set we ignored the duplication at each sampling site. All data are deposited in the Global Biodiversity Information Facility (GBIF) through the Japan Node of GBIF and are thus accessible through the GBIF portal under the Creative Commons Attribution 4.0 International license. The complete data set for this abstract, published in the journal’s Data Paper section, is available in electronic format in MetaCat in JaLTER at http:/++++++(Scheduled to be obtained after acceptance).

Several attempts have been made to understand the population dynamics of fishery resources, such as tuna species using an integrated analysis model with multiple data sources. However, estimating absolute abundance levels in practical stock assessments remains a challenge. Close-kin mark–recapture (CKMR) methods provide information about the number of adults in a population using close-kinship pairs identified by genetic markers and statistical methods. In this study, we compared three methods for kinship identification using different algorithms in samples of wild Pacific bluefin tuna genotyped across 5,029 genome-wide single nucleotide polymorphisms in 4,108 samples. The fraRF method we developed employs pairwise identity-by-descent values as inputs for random-forest classification. The other two methods were CKMRsim and COLONY, which have been published and applied in several studies. These three methods were applied to the actual genotyping data with moderate missing genotypes, in addition to the pseudo-generated genotyping data for the simulation test. The simulation test mimicked genotyping data with physical linkage as well as genetic characteristics similar to those of actual samples. The three methods resulted in different numbers of inferred kinship pairs for both generated and actual data. Particularly for the half-sibling pairs, considerable number of false-positive and false-negative existed in the identification results. The differences in kinship identification results were interpreted based on a simulation test. This study may promote the understanding of behavior in each software when applying the software to SNP data with moderate missing genotypes as in the case of this study.

Malayan tapir is the only extant Asiatic species in the family Tapiridae, is endangered and threatened by risk of inbreeding from population structure. To elucidate the demographic and evolutionary history of the tapirs in Southeast Asia (SEA), this study analysed whole genome data from 10 individuals for historical effective population size (Ne) inference using sequentially Markovian coalescence (i.e., PSMC, MSMC, MSMC2), folded site frequency spectrum, (i.e., Stairway Plot 2), and their hybrid SMC++. The results revealed that tapir Ne ranged 6,000–12,000 in the last glacial period but went down to < 2,000 in recent time. Genomic analysis and population split time analysis (PSMC and SMC++) supported a population divergence (Fst > 0.25) between the Sumatran and mainland SEA tapirs since at least 6 kya. Subsidence of Sundaland and rainforest reduction were the major drivers for Ne decline. The timing of population split corresponded well with the inundation of Straits of Malacca to present-day levels by rapidly raising sea-levels during 10–6 kya. Results of this study, as well as contemporary geographical isolation, supports the subspecies status of the Sumatran population. This will have implication to the ex-situ conservation practices that may have produced hybrids of the isolated populations.

Five decades of monitoring data (1974-2022) at the acidified, acid-sensitive forested catchment of Langtjern in southern Norway document strong chemical recovery and browning of surface water, related to changes in sulfur (S) deposition. We used the process-oriented model MAGIC to simulate water chemistry from 1860 to 2100 using historical and projected deposition and climate. New in MAGIC is i) a solubility control of dissolved organic carbon (DOC) from S deposition, which allows inclusion of the changing role of organic acids in chemical recovery, and ii) climate-dependency of weathering rates. MAGIC successfully described measured chemical recovery and browning, and the change towards organic acid dominated acidification status. Hindcasts of pH suggested lower preindustrial pH than previously modelled with MAGIC, simulated without sulfate-dependency of DOC solubility. Climate scenarios indicated substantially wetter climate, leading to increased base cation losses and slight reacidification of the surface waters. A sensitivity analysis of weathering rates revealed that a doubling of weathering rates is needed to reach pre-industrial ANC in 2100, given that S deposition is expected to be reduced to a minimum. We conclude that impacts of climate change are most likely to lead to slight reacidification of surface waters, and that enhanced weathering rates could partly compensate this trend.

Excessive anthropogenic nitrogen fixation alters the nitrogen cycle and increases nitrogen deposition, leading to nitrogen saturation, which leads to forest decline and nitrate leakage into stream waters. Kureha Hill in Toyama Prefecture, Japan, is considered to be in nitrogen saturation, since many streams have contained high concentrations of nitrate for more than 20 years. This study verified the latest status of nitrogen saturation by comparing the latest data with 20-year observational data. Results showed that the current nitrate concentration in stream water is lower than that observed 20 years ago. However, the C/N ratio of the soil between 12 and 18, indicates that nitrogen saturation could take place. In addition, the net nitrogen mineralization and net nitrification rate showed no significant change from the past data. Based on the nitrogen leakage to the stream water, Kureha Hill’s nitrogen saturation was found to be less intense; however, its potential to produce nitrate has been unchanged for 20 years.

For 40 years MAGIC has been used to simulate the acidification of soils and waters due to acid deposition. The original model has now been updated and re-implemented in the C++ Mobius platform and is available as open source. New features include multipoint calibration, forest growth, and a soil carbon module. The Mobius platform facilitates automatic optimisation of calibrated parameters and multiple-calibrations using Monte-Carlo routines. The usefulness of MAGIC is demonstrated by application to the 50-year data series for deposition and runoff at Birkenes, a small, calibrated catchment in southern Norway. Acid deposition has declined dramatically at Birkenes since the peak in the 1970s. Sulphate is 90% lower. Stream water has recovered strongly. Decreased concentrations of sulphate have led to increased acid neutralising capacity, pH and reduced concentrations of toxic aluminium. These changes are well-simulated by MAGIC. The new features added as part of Mobius improve the simulations. The MAGIC-Mobius modelling tool is now available for applications to scenarios of land-use and climate change.

Although atmospheric nitrogen deposition due to throughfall has decreased in Tokyo metropolitan, the forested catchment which composed with Japanese cedar (Cryptomeria japonica), Japanese cypress (Chamaecyparis obtusa), and oak (Quercus serrata) was still nitrogen saturated. We aimed to elucidate effects of decrease in nitrogen deposition on aluminum (Al) dynamics in a forested Andisols. Throughfall and soil percolated water samples were taken under Japanese cedar stand and Japanese cypress stand in Hachioji, Tokyo (Field Museum Tamakyuryo). Major inorganic ions were determined by ion chromatography. Total Al concentrations were measured by atomic absorption spectrometry after concentrating under acidic condition. Aluminum concentrations were significantly correlated with nitrate (NO3-) concentration in both Japanese cedar stand and Japanese cypress stand. In case of Japanese cedar stand, Al concentrations tended to decrease with time. Acid load associated with N transformation ([H+]load), which was chosen as the sole factor for Al mobilization in Japanese cedar stand, has also decreased. Decrease in nitrogen deposition affected Al dynamics via decrease in [H+]load. It was suggested that the calcium (Ca) content in needles may promote recovery from soil acidification in Japanese cedar stand.

Since the first vascular plants appeared on land at least 430 million years ago, plant-soil feedback has started through the root-soil interface. Plant species have inherently specific and diverse root traits, but root functional and morphological plasticity is important to respond to soil changes or diversity in terms of nutrient forms and availabilities, especially in ecosystems with low plant species diversity. This paper synthesized how tree plasticity facilitates soil nutrient acquisition from the tropics to the Arctic. The fine roots of dipterocarp (Shore laevis) and rhizosphere microbes increase malate release in acidic soils for phosphorus solubilization, aluminum detoxification, and lignin degradation. The development of finer roots is a well-known strategy for the acquisition of limited nutrients, but the allocation of roots foraging “nutrient hotspots” in deeper soil is an alternative strategy. Scots pine increases the allocation of finer roots into the subsoil to solubilize P bonded to Al/Fe oxides in fine-textured podzol, but not in the coarse-textured podzol with deeper nutrient hotspots. The black spruce trees increase the biomass allocation to the belowground to acquire soil nitrogen, especially when black spruce roots absorb urea in the shallow soil on permafrost. Even in northern ecosystems with limited species diversity, a combination of functional plasticity and vertical plasticity of root system architecture facilitates soil phosphorus or nitrogen limitation.

Community assembly can change over time following variations in connectivity among habitats. Previous studies have demonstrated the influence of seasonal pulse floods on community structures by facilitating species dispersal, but the effects of short-term flash floods have been poorly investigated. We investigated fish community structures before and after a short-term flood in drainage ditches of paddy fields in the Kita River basin, Japan. The study sites were classified into three connectivity types, “Transient” (connected only during the flood, with a temporally-disappearing vertical gap between drainage ditches and downstream rivers), “Connected” (always connected, without the vertical gap), and “Disconnected” (always not connected, with the vertical gap). The abundance of Misgurnus anguillicaudatus, the only species that dispersed from paddy fields to drainage ditches, increased after the flood irrespective of the connectivity types, although the total abundance of the other species significantly increased after the flood only in the “Transient” sites. The dissimilarity of species composition between the (n-1)-th and n-th surveys at each site was consistently low in the “Connected” and “Disconnected” sites, whereas it rose just after the flood and gradually declined in the “Transient” sites. Species composition was significantly different among the connectivity types, indicating that some fish species need stable connectivity even during the non-flood period. The results showed that the short-term flood facilitated fish dispersal from paddy fields by the increased water discharge and that from downstream rivers by the temporary removal of vertical gap, emphasizing the importance of hydrological connectivity for biodiversity conservation in an agricultural landscape.

In the context of initiatives focused on captive breeding and reintroduction of endangered animal species, it is crucial to minimize any bias in reproductive success during the reintroduction phase in order to preserve genetic diversity. One population of Tachysurus ichikawai, a critically endangered bagrid catfish endemic to Japan, faces a threat from the construction of a dam. To address this, a captive breeding program followed by translocation is being implemented. Multiple breeding families are involved in this process; however, if there is a bias in reproductive success among them after release, it will result in a decline in genetic diversity. To identify potential biases in breeding lineages, we conducted kinship analysis between individuals born at the release site and breeding individuals. Because there were no samples available from the released individuals themselves, we examined distant kinship relationships, such as grandparent–grandchild and uncle–aunt–nephew–niece relationships, using a substantial number of single-nucleotide polymorphisms obtained from the whole genome re-sequence. Our findings indicate no bias between lineages in the first year after reintroduction, but a significant bias in the second year, emphasizing the need for continuous management and monitoring of reintroduced populations. This study demonstrates that monitoring kinship after reintroduction can correct lineage bias, which is critical for the prompt restoration of genetic diversity.

Globally, around half of all tropical forests are secondary communities which are recovering from previous disturbances. In these communities, dominant pioneers play a critical role in the successional dynamics due their ability to modify the environment, and thus to facilitate or hinder the performance of other species. In this study, we examined the population dynamics of the dominant pioneer species, Mimosa acantholoba var. eurycarpa, in a tropical dry forest during the process of secondary succession. We collected data from permanent plots over a period of 13 years and used integral projection models to analyze the vital rates and changes in population size. Most vital rates were negatively related to successional age, with resprouting, survival and recruitment of individuals responding more strongly, and individual growth rate more weakly. These vital-rate trends translated into significant variation of population size over succession, with a maximum size at year four and a rapid decline thereafter. Overall, our findings suggest that this species benefits from its ability to display a large number of resprouts in very early stages of succession, contributing to the rapid increase in population density. However, as succession unfolds, a lack of resprouting and a decline in survival reduce its population size, to the point of local extinction. These results highlight the importance of resprouting in the early dynamics of tropical dry forest communities recovering from disturbance.

The use of artificial intelligence (AI) and machine learning (ML) has significantly enhanced ecological research in Asia by improving data processing, analysis, and pattern extraction. Analyzing 1550 articles, I show an overview of the use of AI and ML for Asian ecological research. Following the last 20 year trend, I found that the topics in Asian ecological research have transitioned from technical perspectives to more applied issues, focusing on biodiversity conservation, climate change, land use change, and societal impacts. Non-Asian countries, on the other hand, have focused more on theoretical understanding and ecological processes. The difference between Asian and non-Asian regions may have emerged due to the ecological challenges faced by Asian countries, such as rapid economic growth, land development, and climate change impacts. In both regions, deep learning related technology has been emerging (e.g. big data collection including image and movement). Within Asia, China has been the Asia-leading country for AI/ML applications followed by Korea, Japan, India, and Iran. The number of computer science education programs for education in China has been increasing 3.5x times faster than that in the U.S., indicating that a nationwide strategy for computer science development is key for ecological science with AI. Overall, the adoption of AI and ML technologies in ecological studies in Asia has propelled the field forward and opened new avenues for innovative research and conservation practices.

Flowering phenology of alpine plant communities and seasonal dynamics of flower visitors have been scarcely studied in the tropical/subtropical alpine regions. We report flowering phenology, flower production, and flower-visiting insects in the alpine site of central Taiwan. Throughout the research period (2017–2018), we recorded flowering phenology of 130 plant species, flower production of 81 species, and 15,127 insects visiting alpine flowers. Most of the alpine plants were visited by dipteran insects and/or hymenopteran insects. The seasonal patterns of flowering were more apparent in bee-visited plants compared to fly-visited plants in which the flowering of bee-visited plants clearly increased as the season progressed. About 63% of flower visitors were dipteran insects (syrphid and non-syrphid flies), and 30% were hymenopteran insects (mostly bumble-bee workers). Although the seasonal trend in fly abundance was less clear between years, bumble-bee abundance consistently increased in the middle to late seasons, reflecting colony development. There was a positive correlation between bee abundance and the number of flowering species of bee-visited plants, but there was no correlation between fly abundance and the number of flowering species of fly-visited plants throughout the season. These results suggest that the flowering phenology of subtropical alpine communities is influenced by the seasonal availability of pollinators. Bumble bees, syrphid flies, and non-syrphid flies had wide ranges of foraging flowers, but their niche overlap was relatively small. Because cold-adapted bumble bees are threatened by climate change in Taiwan, plant–pollinator interactions may be disturbed by global warming.

The recovery of mammalian species in the US Midwest through natural recolonization constitutes a conservation success story, yet management remains challenging due to many unknowns related to population dynamics and abundance. Abundance is a critical parameter for management decisions, and estimating the density and abundance of elusive species, such as terrestrial carnivores, remains challenging despite recent technological advances. In this study, we evaluated density and abundance of a recovering carnivore species, the bobcat (Lynx rufus) in two areas of Ohio using non-invasive DNA from scat. The target areas in eastern and southern Ohio have been shown to have uneven dynamics and recolonization success and we expected that this would be reflected in differences in density and abundance. We collected 298 bobcat scats between July 2018 and April 2019 on 150 km of repeated transects. Of these, 102 scats were successfully genotyped, and 55 individuals were identified (33 in eastern Ohio and 22 in southern Ohio). Using Spatially Explicit Capture-Recapture models, we estimated 17.9 ± 4.3 and 11.3 ± 2.9 bobcats/100 km2 in eastern and southern Ohio study areas, respectively. Our results support prior telemetry data which indicated that bobcats in eastern Ohio had smaller home-ranges than bobcats in southern Ohio, and thus could support a higher density of individuals. The higher densities were similar to other eastern US populations and are much higher than other Midwestern recovering populations. Our results provide a snapshot of the population status and can be used to determine sustainable management strategies for Ohio’s bobcat population

A subtropical mangrove along the Miyara River in Ishigaki Island, Japan was studied for evaluating the carrying capacity for biomass of the monospecific stands. Rhizophora stylosa and Bruguiera gymnorrhiza were dominant in the downstream area whereas B. gymnorrhiza in the upstream. The stem diameter D, stem height H, fine roots mass were measured and, aboveground biomass AGB, belowground coarse root biomass BGBcoarse were estimated. The AGB, BGBcoarse and fine root mass were estimated as 128.46 Mg ha-1, 31.01 Mg ha-1 and 12.75 Mg ha-1 in the R. stylosa; 269.82 Mg ha-1, 93.68 Mg ha-1 and 11.13 Mg ha-1 in the downstream B. gymnorrhiza; and, 227.94 Mg ha-1, 81.05 Mg ha-1 and 6.35 Mg ha-1 in the upstream B. gymnorrhiza plots, respectively. The AGB did not differ among the plots, meanwhile BGBcoarse was significantly lower and fine root mass was significantly higher in the R. stylosa plots than in the downstream B. gymnorrhiza plots. Significantly lower mean individual phytomass wt specific to tree density  of R. stylosa plots than B. gymnorrhiza plots in the  – wt relationship was found, which denoted the lower carrying capacity for AGB of R. stylosa than that of B. gymnorrhiza. The results rejected our hypothesis that the stressful edaphic conditions, such as high soil salinity and low pH at the downstream, limit biomass and potential canopy height Hmax of mangrove along a river gradient but partly supported another hypothesis that biomass and Hmax differs between different mangrove species at the same edaphic environment.

Plants, as immobile organisms, depend on their roots to access soil resources efficiently and cost-effectively. To achieve this goal as well as develop more productive crops and adapt to variable challenging conditions plants rely on root phenotypic plasticity. This includes changes in root morphology, growth angles, diameter, elongation, branching density, and rotation rate. In simpler terms, a plant root system is a dynamic structure that can change its branching structure in response to changes in biotic and abiotic conditions such as water availability, soil mineral nutrient content, soil compaction, salinity, and the formation of symbiotic relationships with other organisms or anchored in the substrate. However, the complexity of these responses and their impact on plant fitness are not well understood. In this study, we have reviewed different aspects of the morphological plasticity of the root system. The results show that root flexibility can greatly help plant adaptation. Thus, gaining a comprehensive understanding of root plasticity can lead to improved and sustainable plant production.