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Fungi have unique ecosystem functions, such as organic matter decomposition, parasitism, and symbiosis with other organisms in terrestrial and aquatic ecosystems. Their taxonomic and functional diversities are essential factors for predicting ecosystem functions and their responses to environmental changes. With the widespread use of high‐throughput sequencing (HTS) in recent years, the detection of fungal DNA sequences in various regions and on different environmental substrates has advanced. HTS‐obtained DNA sequences can be compared with those in databases to identify the taxa of organisms from which they are derived. Therefore, a global DNA database containing taxonomic information has been developed. However, functional data on the distribution and function of individual taxa remain scarce. In this study, the ecological information of each fungal family was compiled from review papers and published books. Specifically, the following information was collected: reported distribution (11 categories including information on the presence of fungi in Japan) and function (38 categories related to ecological functional data, such as guilds and habitats) of 553 families included in the literature. These data will provide information on the ecology of specific fungi detected in the field and help estimate the functional group composition and diversity of fungi from their DNA assemblage data. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-02.1/jalter-en. [ABSTRACT FROM AUTHOR]

We present the largest freely available EcoPlate dataset for Japan, comprising data collected from a network of 33 natural forest sites (77 plots) in regions of East Asia ranging from cool temperate to subtropical. EcoPlate is a 96‐well microplate that contains three repeated sets of 31 response wells with different sole carbon substrates. The utilization of each carbon substrate by the microbial community is quantified by the color density of the well during incubation. EcoPlate can provide a multifunctional index of a soil microbial community. Soil properties (water content, carbon [C] and nitrogen [N] contents, the C/N ratio, and pH) that are essential for interpreting the EcoPlate results were also measured. The network is part of the Forest and Grassland Survey of the Monitoring Sites 1000 Project established by the Ministry of the Environment. Using a standardized protocol, soil was sampled between September and December 2020. A preliminary principal component analysis was performed on the temporal integration of color density using 31 substrates. For the temporal integration, we calculated the cumulative amount of color development by integrating the color density development curve. PC1 contributed 55.6% and is thought to represent the magnitude of the overall absorbance of all substrates. The model of environmental factors including elevation and the model of soil properties, including water content and pH, were selected as the best‐fit models for variation in PC1. EcoPlate data enable the meta‐analysis of comparative studies among forest types and testing community ecology and ecosystem function hypotheses at broad spatial scales. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP‐2022‐01.1/jalter‐en. [ABSTRACT FROM AUTHOR]

This data paper reports vegetation census data collected in a network of 28 grassland sites in Japan. This is the largest grassland data set freely available in Japan. The network is the project "Grassland Dynamics in Japan" launched by the Ministry of the Agriculture and Forestry and Fisheries, Japan. It consists of semi‐natural and artificial grasslands (pasture and meadow) and covers from Hokkaido to Kyushu area in Japan. Twenty to 12 permanent plots were established in each grassland. Censuses of plant species emerged in 1 m2 quadrat were conducted every year from 1972 to 1982 at longest. The data provide species abundance, plant coverage (%) and length (cm) of 484 quadrats. The censuses adopted common census protocol, which provide good opportunities for meta‐analyses and comparative studies among grasslands. The data have been used for ecological studies as well as for animal production reports published by the National Agriculture and Food Research Organization in Japan. The detailed Metadata for this abstract published in the Data Paper section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-22.1/jalter-en. [ABSTRACT FROM AUTHOR]

This paper reports the data collected in censuses of trees, litter fall and vegetation in a mountain riparian forest, upstream of the Watarase river, Gunma Prefecture in central Japan. A 1‐ha permanent plot (100 m × 100 m) subdivided into horizontal 10 m × 10 m grid cells was established in the forest in 2005. Tree census with woody species ≥15 cm girth at breast height was conducted every year from 2005. Twenty‐five litter traps were set in the permanent plot. The samples of litter fall were collected monthly, except in winter, between 2005 and 2008. And we sorted into leaves, branches, reproductive organs and other plant material, at species level as much as possible. The percentage cover of vascular plants was recorded at each vertical stratification (tree layer, subtree layer, shrub layer and herb layer) in 2008 and 2014 at the plot. These data are valuable for elucidating long‐term forest dynamics at mountain upstream areas experiencing frequent ground disturbances. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-15.1/jalter-en. [ABSTRACT FROM AUTHOR]

This paper describes the species occurrence record of zooxanthellate reef‐building corals at 1047 sites on the Japanese coast, recorded from 1929 to 2017. The dataset includes 484 confirmed scientific species names compiled from 152 literature sources, most of which were written in Japanese and published as gray literature in local journals or individual reports. Scientific names were consolidated under currently accepted nomenclature based on the World Register of Marine Species. Further revision of species names was made by referring to monographs on temperate coral species of Japan, along with expert knowledge. The dataset includes the coral species recorded each year at each study site, the geographical location of each site, and the scientific names of the corals. Three supporting datasets were created, containing a list of literature, the names of the sites and synonymization and confirmation of the coral names. This up‐to‐date collection of data is a contribution to the study of coral biogeography and conservation planning, as well as long‐term changes in coral species distributions in response to climate change. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-08.1/jalter-en. [ABSTRACT FROM AUTHOR]

Information on seed morphology and fruiting phenology related to fitness and reproductive strategy is important for plant ecology and evolution. Although seed morphology is highly variable across years, regions and mother trees even within the same species, seed mass and size are often reported as averages or ranges for each species in existing databases or picture books. Unfortunately, freely available seed trait data for individual seeds are limited. This paper reports data on morphology (seed length, width and height) and dry weight of individual seeds from 129 tree species in Japan. It includes data from 79 genera in 44 families collected from various forests located in cool temperate to subtropical regions in Japan, including species not reported in previous databases. We mainly used seeds from the collections of the Forest Tree Gene Bank Program, but new seeds were also collected. If possible, multiple seeds were collected from multiple mother trees of the same species. This paper also reports data of the sampling month and date, which indicates the fruiting season of trees at the sampling site. By comparing these data to past or future data, we hope that it will aid in understanding the effects of climate change on fruiting phenology. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-14.1/jalter-en. [ABSTRACT FROM AUTHOR]

To understand bee distributions in Japan, we started the citizen science program "Hanamaru‐Maruhana national census (Bumble bee national census in English)" from 2013, and collected bee photographs taken by citizens. Bee photographs were collected via e‐mail or "Mobile Phone System and Cloud Services" provided by Fujitsu FIP, Co. Species were identified from photographic images, and latitude‐longitude data were extracted from GPS data in Exif information of photographs or address in text of e‐mail. We have confirmed all 16 bumble bee species inhabiting in the Japanese archipelago excluding the Kurile Islands, and have got 5503 records of these bumble bees. In addition, we have got 380 records of three carpenter bee species that are often mistaken for bumble bees by citizens. This occurrence data cover the time range from September 2006 to October 2018, the latitudinal range from 26.45 to 45.29 and the longitudinal range from 127.80 to 145.82. The latitude–longitude data were rounded off to two decimal places in the published dataset for protecting privacy rights of citizens. In addition, the latitude–longitude data of five rare bumble bee species/subspecies were rounded off to one decimal place for protecting their habitats. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2021-04.1/jalter-en. [ABSTRACT FROM AUTHOR]

We present the largest freely available herbivory dataset for Japan representing data collected from a network of 19 natural forest sites across the country. Sampled network sites were part of the Monitoring Sites 1000 Project organized by the Ministry of the Environment. Sites were located across a range of climate zones, from subarctic to subtropical, and broadleaf trees (both evergreen and deciduous) were targeted at each site. Litterfall traps were used to assess leaf damage caused by leaf‐chewing insects in 2014 and 2015. Using a standardized protocol, we assessed herbivory on 117,918 leaves of 39 dominant tree species. Preliminary analyses suggest that insect herbivory increases with increasing latitude for deciduous broadleaf species. In particular, oak (Quercus crispula) and beech (Fagus crenata) were subject to increased insect herbivory with increasing latitude. In contrast, insect herbivory decreased with increasing latitude in evergreen broadleaf species. The latitudinal gradient of herbivory differed according to leaf type (i.e., evergreen or deciduous). This dataset offers excellent opportunities for meta‐analysis and comparative studies of herbivory among various forest types. The complete dataset for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2021-01.1/jalter-en. [ABSTRACT FROM AUTHOR]

Ground beetles of suborder Adephaga are often considered bioindicators of natural environments because their habitats and abundances strongly depend upon environmental factors. Although their importance and usefulness are already known, there are limited data regarding voucher specimens in Japan. Biodiversity data based on voucher specimens are of high quality and reliability. In this data paper, we compile the records of Caraboidea collected mainly by Dr. Kazuo Tanaka. We also detail the time and locality of collection based on the labels of specimens deposited in the Institute for Agro‐Environmental Sciences, National Agriculture and Food Research Organization, Japan. This collection facility contains 15,675 records of 673 species collected from 1947 to 1997. 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. [ABSTRACT FROM AUTHOR]

We collected information on the functional traits of the macrobenthos that inhabit mainly tidal flats along the Northwest Pacific coast of Tohoku, Japan, based on the species that were present during a survey after the Great East Japan Earthquake of 2011. The dataset contains information on 33 traits of 246 species and includes their taxonomic position, distribution, body length, habitat, reproduction type, and other characteristics such as diet type, migratory type, and invasiveness. Information about most basic traits such as body length, distribution, and habitat characteristics is complete, and more than 50% of trait information is complete for over 100 species, but information about reproduction is relatively limited. Although we did not limit our study to specific taxa and even included vegetation in the database, the majority of the taxa are Arthropoda, Mollusca, and Annelida. This file also has a table that compares the traits data to the existing traits database BIOTIC (Biological Traits Information Catalogue) to facilitate transformation and reuse of the data. Because the area of this survey was very adversely impacted by the Great East Japan Earthquake and Tsunami of March 11, 2011 and by post‐disaster anthropogenic activities, this database will be relevant to assessments of post‐disaster changes of the benthic community due to both the tsunami and human activities. The database is expected to fill the gap between the identification of species and assessments of community composition. The detailed Metadata for this abstract published in the Data Paper section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-23.1/jalter-en. [ABSTRACT FROM AUTHOR]

As moths of the geometrid group usually live in forests and do not move long distances, they are considered to be valuable as environmental bio‐indicators. Biodiversity data based on voucher specimens should have high quality and reliability. Here, we publish the records of the family Geometridae and the superfamily Pyraloidea (Pyralidae and Crambidae) with time of collection and location information, that is, latitude and longitude on the basis of the collection of Dr. Hiroshi Inoue deposited at Institute for Agro‐Environmental Sciences, NARO (NIAES). The collection of Geometridae covers 653 records from 615 species, collected from 1926 to 1979. The collection of Pyraloidea covers 447 records from 418 species, collected from 1949 to 1985. For the purpose, all users can access the data from the Global Biodiversity Information Facility (GBIF) portal site with open data license CC BY 4.0; all data is published in the GBIF through the Japan node of GBIF (JBIF). The detailed Metadata for this abstract published in the Data Paper section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-21.1/jalter-en. [ABSTRACT FROM AUTHOR]

Long‐term record of leaf phenology of woody plants that have high longevity and that have been growing on the same site for a longer time could be one of the good indicators for assessing the effects of climate change on forest ecosystem functioning. Since climatic conditions could be different among locations, we need to record the phenology of forest plants growing under various climate types. Here, we report seasonal changes in leaf abundance of deciduous trees during a 13‐year period in the Sambe Forest of Shimane University located in northern Chugoku mountain range, western Japan (35°9′N, 132°37′–40′E, 300–628 m above sea level [asl]). Northern Chugoku mountain range is situated in the west end of Japan Sea side climate. Our study would provide the first record of tree phenology in this region. We examined eight species belonging to eight genera common in a secondary deciduous broad‐leaved forest in western Japan. Habitats of native trees ranged from canopy to understory in the forest and pioneers in an open site. Some of trees were exceptionally planted in an arboretum in the Sambe Forest. Leaf types included single leaf (i.e., Carpinus tschonoskii, Swida macrophylla, etc.) and pinnate leaves (i.e., Aesculus turbinata and Phellodendron amurense). We observed changes in the relative leaf abundance caused by budburst, leaf expansion and leaf shedding of the fixed shoots of targeted trees during 3‐day to 3‐week intervals from March to December each year from 2004 to 2016. Over the 13‐year period, we used a digital camera to take photographs of the shoots that were processed to estimate the leaf abundance. Our data was obtained from common tree species that have a wide habitat range and are distributed nationwide. Therefore, comparison of our data with those data in other climate types may significantly contribute to understand the effect of climate change across Japan on forest plants. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-20.1/jalter-en. [ABSTRACT FROM AUTHOR]

This is the first large dataset of underwater videos from which species occurrence and behavioral records of aquatic organisms were identified in Lake Biwa, the largest lake in Japan. We compiled 109 videos and 122 still‐images of fishes, diving birds and shrimps. The images were cropped from videos taken underwater with animal‐borne video cameras which were mounted on the backs of common carp (Cyprinus carpio). The attribute of each image and its occurrence of organisms were formatted according to the Darwin Core Archive which was developed by the Biodiversity Information Standards (TDWG), and the dataset is available via the Global Biodiversity Information Facility. Our dataset includes records of 10 species, 4 genera, 2 families and 1 infraorder which includes mostly fishes, several birds and a crustacean. The fish records include a threatened endemic fish, the "gengorou‐buna" crucian carp (Carassius cuvieri), and two alien fishes, largemouth bass (Micropterus salmoides) and bluegill sunfish (Lepomis macrochirus). We confirmed several types of intraspecific and interspecific relationships between video‐mounted carp and other organisms; for example, most video‐mounted carp frequently approached or chased conspecifics upon encountering, which sometimes led to two carp feeding side by side. At least three avian species also appeared in the dataset: Eurasian coot (Fulica atra), little grebe (Tachybaptus ruficollis), great crested grebe (Podiceps cristatus), but there was no apparent interaction between carp and these birds. Our underwater videos reveal and highlight the rich biodiversity of the lake today, providing clear evidence for behavior of aquatic organisms under natural conditions. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-18.1/jalter-en. [ABSTRACT FROM AUTHOR]

Apple snails Pomacea canaliculata and Pomacea maculata are herbivorous freshwater gastropods native to South America and are introduced species widespread in western and southern Japan. Although they affect rice culture and are invasive to native ecosystems, high‐resolution distribution data are not available for these species. I mapped the distribution of Pomacea species using the citizen science approach, by asking volunteers to report the geographical location along with the presence or absence of apple snail egg capsules or snail shells during 2017–2019. In total, 1,304 present and 508 absent records were collected, which revealed the distribution outlines of apple snails, especially in the Kansai area. Here, I provide a dataset of observation dates, location coordinates, volunteer names, and supplemental information. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-19.1/jalter-en. [ABSTRACT FROM AUTHOR]

Revealing how species assemblages are structured is one of the themes in community ecology and macroecology. The information of species traits as well as geographic occurrence would help analyze the pattern and process of species interactions and community assembly. Butterfly species are one of the best‐studied groups about their distribution and tons of their occurrence data exist. Also, life history traits, especially interaction with host plants are well‐described. However, the body size information is still poor although this is one of the most important characters affecting their distribution and life history traits. Here, we constructed a data set of the forewing length of butterflies by extracting the information from five Japanese and Taiwanese picture books. We measured 6,211 forewing lengths for a total of 524 species. Scientific, family and common names of the butterflies distributed in Japan were based on a Japanese picture book, and the other species distributed in Taiwan were based on Taiwanese picture books. Also, we added the information of butterfly names based on Binran database. Each record of butterflies is linked with the corresponding taxonomic names in the other two books to easily identify the species even when the names used in the three books and the Binran database are not the same. The dataset will be useful for basic and applied biological studies of butterflies because their forewing length is a proxy of their body size and dispersal ability, which could be important determinants of their physiology, distribution, ecosystem functioning and evolution. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-11.1/jalter-en. [ABSTRACT FROM AUTHOR]

The water chemistry of a stream reflects the biogeochemical processes occurring in upstream forests. Anthropogenic disturbances in forests, such as cutting trees, altering the nitrogen (N) cycle, and increase in N leaching from the soil to streams, potentially cause acidification or eutrophication downstream. In forests with dense understory vegetation, mechanical site preparation following tree cutting is commonly used to improve the early establishment of tree seedlings. In cool‐temperate forests in northern Hokkaido, Japan, dense understory vegetation (mainly comprising Sasa dwarf bamboo) inhibits forest regeneration after tree cutting. Soil scarification is a common site preparation technique for eliminating Sasa bamboo and improving forest regeneration. Long‐term data are useful for examining the temporal changes in stream water chemistry exposed to different specific forest management practices under changing environment (e.g., climate change and atmospheric N deposition). For 14 years (2003–2016), we observed the stream water chemistry in naturally forested watersheds and at one point after the confluence of all streams in Uryu Experimental Forest of Hokkaido University (North Hokkaido Experimental Forests Site of JaLTER) in northern Japan. We also monitored stream discharge, water level and stream water temperature in each watershed. Water samples were collected from the outlets of 10 watersheds. The forest management practice in each watershed includes clear‐cutting, soil scarification in sparse forest with dense understory Sasa, and clear‐cutting and soil scarification followed by soil replacement. Long‐term data in the six unmanaged watersheds are also valuable as a background information to analyze the effect of long‐term climate, environment and vegetation changes on stream water chemistry. The measured water quality data of 1,873 water samples include the ion concentrations (Cl−, NO3−, SO42−, Na+, NH4+, K+, Mg2+, and Ca2+), pH, and electrical conductivity (EC) in the stream water. The range of the concentrations of Cl−, NO3−, SO42−, Mg2+, and Ca2+ in the stream water across all the watersheds throughout the observed periods (minimum to maximum) were 3.35–23.67, 0.01–8.68, 0.83–4.01, 0.45–2.55 and 0.72–6.16 mg L−1, respectively. Similarly, the stream pH and EC ranged from 6.04 to 7.53 and 3.14 to 9.47 mS m−1, respectively. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/datapaper%202020‐04.1/jalter‐en. [Correction added on 7 September 2020, after first online publication: JaLTER URL has been updated.] [ABSTRACT FROM AUTHOR]

Plants generally use soil inorganic nitrogen, ammonium (NH4+–N), and nitrate (NO3−–N) as sources of nitrogen, an essential nutrient. The assimilation processes after uptake differ considerably from ammonium to nitrate. Nitrate must be reduced to ammonium in plant tissue before it is synthesized to amino acids, while ammonium is directly and immediately synthesized to amino acids after its uptake. Nitrate reductase is an enzyme that catalyzes the first and rate‐limiting step of nitrate assimilation, reducing nitrate to nitrite. It is a substrate‐inducible enzyme, and the capacity to induce nitrate reductase varies greatly among plant species. In vivo nitrate reductase activity (NRA) is generally measured as a nitrite production rate during incubation using fine cut pieces of plant tissue, and it is applicable as an indicator on plant nitrate use. Here we present in vivo NRA of leaves from a total of 108 species including arboreal trees, small trees, shrubs, herbs, a vine and a moss. For 75 of the species, NRA in fine roots was also determined. At least 20 species in sampled plants were imported and planted for scientific or industrial purposes, but most sampled species were native to Japan. Several inventory studies of plant NRA have been conducted, mainly in Europe, and they provided information on the species‐specific capacity of nitrate use by plants in Europe. However, to our best knowledge, there has been hitherto no published inventory of the NRA of plants in Japan where many endemic species are distributed. Our dataset contains plant NRA with species, family name, life form, leaf lifespan (evergreen or deciduous), growth stage, the season of sample collection, growth conditions (natural or cultivated) and other treatments/conditions when applicable. The data provided by this study may contribute to future works that require information regarding the plant species characteristics for nitrate use capacity or nitrate preference. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2019-06.1/jalter-en. [Correction added on 7 September 2020, after first online publication: JaLTER URL has been updated.] [ABSTRACT FROM AUTHOR]

In 2016, Ecological Research ( ER) celebrated its 30th anniversary. ER's goal is to be the leading ecological, evolutionary, and biodiversity journal in Asia. This article introduces the development of ER, improvements to its editorial system and their outcomes, and the strategies designed to achieve this goal. ER has already become a leading comprehensive and international publication as shown by statistical evidence and its strong editorial foundation. However, some members of the Ecological Society of Japan (ESJ) retain impressions of an old stereotype about ER. The discrepancy between the current status of the journal and its stereotype may explain why submissions from Japan remain static. A new article category for ER, Biodiversity in Asia, was created to encourage Asian studies. In addition, the Forum category is dedicated to promoting a broad understanding of the ESJ's various activities. To promote open science, the proportion of open access articles in the journal is increasing. The publication of Data papers has been accelerated to improve the public availability of excellent open data sets. ER symposia and seminars provide good opportunities for members to participate. ER financially supports the invitation of scientists internationally to facilitate research exchanges with other countries and consequently promotes the internationalization of the ESJ. The ESJ is open to the world's ecologists, and your participation in developing ER is welcome. [ABSTRACT FROM AUTHOR]

Cryptomeria japonica (sugi) and Chamaecyparis obtusa (hinoki) are major Japanese timber species whose plantation area accounts for 44 and 25%, respectively, of the plantation forests in Japan. Physiology, anatomy and ecology of the species have been intensively studied for this half century, which now forms a huge stock of information. These data, however, were scattered in diverse sources, including papers, bulletins of research institutes, reports of other kinds and books, and were presented in nonstandardized, diverse styles in each source. This paper provides a database (SugiHinoki DB) that compiles 177 plant traits of sugi and hinoki from 364 primary sources published since 1950. The compiled traits include physiological, morphological, anatomical and biochemical features that are recognized as relevant to life history strategies, vegetation modeling and global change responses. Collected data have been obtained under different environmental conditions, for plants with different ages and for organs with a different age or different position, which provide information of within‐species variation for a given trait. Each data entry is accompanied by detailed ancillary information describing the site of measurement, stand of measurement and detailed measurement conditions, which help users account for data variations as a consequence of phenotypic plasticity and genetic variations and to filter data. To provide data in a consistent format, the data and the ancillary information were standardized, and units were converted. After data compilation, outliers were detected by calculating interquartile range for each trait per each species. As of August 2019, SugiHinokiDB contains 24,683 data entries (16,410 for sugi, 8,273 for hinoki). As sugi and hinoki are major plantation species in Japan, the data mostly came from study sites in Japan (from Hokkaido in the north to Yakushima island in Kyushu to the south) but were also obtained from arboretums or plantation forests in Taiwan, Korea and China. Data were largely obtained from plants in plantation forests but also from plants in natural forests and under experimental conditions. The improved availability of trait data offered by SugiHinokiDB provides new research opportunities, such as the intensive parameterization of vegetation models for a more accurate prediction of climate change impacts. [ABSTRACT FROM AUTHOR]

Species dynamics in an abandoned urban forest of Central Japan is described in this paper. The dominant species in the urban plantation were Cryptomeria japonica and Chamaecyparis obtusa. A variety of eight patches of the canopy was produced by previous forest management practices. Progressive and retrogressive species dynamics within these eight patches are investigated in this paper. The study elucidates the deterministic role of patchiness in the nature of species colonization and the maintenance of species diversity in an urban forest. Altogether 139 native and/or naturalized species, including 23 shrub and 35 tree species, were recorded in the study area of 3.2 ha. The performance of species varied according to their successional attributes indicating a selective canopy influence. Twenty percent of the tree species were shade-intolerant pioneers (e.g. Cornus spp., Rhus javanica var. roxburghii) re-established under selective tree-felling. Thirty percent were shade-tolerant climax species (e.g. Neolitsea sericea, Persea thunbergii) dominant in remnant closed patches. The remaining 50% belonged to various seral types with aggressive deciduous species (e.g. Aphananthe aspera, Celtis sinensis) in most of the patches. Some ruderal herbaceous species dominated heavily disturbed clear-felled patches. This study suggests that canopy modification influences the subsequent colonization pattern. Furthermore, heterogeneous patches contribute to greater species diversity and dynamics in isolated woodlands. [ABSTRACT FROM AUTHOR]

There are some recommendations for the use of species diversity indices in a paper recently published in this journal by M. Ohsawa on the species richness and composition of weevils in five forest types in the middle region of Japan. Because several factors, such as small sample size, calculation of Simpson’s diversity index by the use of the original equation of Simpson’s measure of concentration D, and a weak point in the Shannon–Wiener diversity index H′, may have led to biased estimates, I recalculated these indices using combined species diversity values of the five forest types. As the general tendencies of 1− D and H′ values calculated here were similar to those in Ohsawa’s paper, there is no need to propose any change to his view. However, these recalculated diversity indices indicated that they are values which are more suitable for use. It should be noted that the characteristics and weak point associated with the diversity indices need to be taken into account in future studies. [ABSTRACT FROM AUTHOR]

When we calculate mortality along a gradient such as size, dividing into size classes and calculating rates for every class often involves a trade-off: fine class intervals produce fluctuating rates along the gradient, whereas broad ones may miss some trends within an interval. The same trade-off occurs when we want to illustrate size distribution by a histogram. This paper introduces nonparametric methods, published in a statistical journal, into forest ecology, in which the fine-class strategy is used in an extreme way: (1) a smoothly changing pattern is approximated by a fine step function, (2) the goodness-of-fit to the data and the smoothness along the gradient are formulated as a weighting sum within a Bayesian framework, (3) the Akaike Bayesian Information Criterion (ABIC) selects the weighting system that most appropriately balances the two demands, and (4) the values of the step function are optimized by the maximum likelihood method. The nonparametric estimates enable us to represent various patterns visually and, unlike parametric modeling, calculations do not demand the determination of a functional form. Mortality and size distribution analyses were conducted on 12-year forest tree monitoring data from a 4 ha permanent plot in an old-growth warm–temperate evergreen broad-leaved forest in Japan. From trees of 11 evergreen species with a diameter at breast height (DBH) greater than 5 cm, we found three types of trend with increasing DBH: decreasing, ladle-shaped and constant mortality. These patterns reflect variations in life history particular to each species. [ABSTRACT FROM AUTHOR]

In community ecology, trait‐based approaches have been strongly recommended in recent years to understand the responses of community functions against environmental changes. Trait‐based approaches have been used to solve the mechanistic rules in the relationship between soil animal communities and environmental change. However, databases of functional traits of soil animals are still lacking. Collembola is one of the most abundant and diverse group in land ecosystems, with more than 400 identified species in Japan. This data set provides taxonomic information, geographic, habitat distributions and 13 morphological trait items of 407 species of Japanese Collembola: described in Japanese literature. The workshop of Japanese Collembola, supported by the Japanese Society of Soil Zoology, summarized the taxonomy for the Japanese Collembola species. The data set presented here is mainly based on their work. The spatial coverage of this data set is in the land area of Japan. Suborder, superfamily, family, subfamily, genus and species names, as well as common Japanese names, are listed in this paper. The species distributions of Japanese Collembola in each global ecozone and in each area within Japan were described. Habitat preference for soil, cave, seashore and tree trunk habitats was recorded. The 13 morphological traits of Collembola species, which are body length; body weight of adult individual; body form; antenna length; furca length; body pigmentation; pairs of ocelli (eyes); post‐antennal organ; pseudocelli; body scale; anal spine; mandible and molar plate are listed in this dataset. These 13 morphological traits in this dataset are covered the most of trait items which have been internationally used in Collembola study. Trait‐based studies of Collembola have mainly been for European species, most of which are not found in Japan or East Asia. These data sets may provide an important first step to incorporating community data from the Asian region to the trait‐based global ecology. Data files are stored in the Ecological Research Data Archives at http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/archives/2019/ERDP-2019-03. [ABSTRACT FROM AUTHOR]

This data paper reports census data of ground-dwelling beetle and other fauna of the forest floor environment; collections were made from a network of 22 forest sites in Japan. To our knowledge, this represents the largest dataset for long-term monitoring of a ground-dwelling beetle community and other taxa in a ground environment in forests, which covers a broad climatic range in the temperate zone and is freely available. The network forms part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subalpine, cool- and warm-temperate and subtropical climatic zones and the four major forest types of Japan. Thirty-three permanent plots usually 1 ha in size were established in old-growth, secondary natural and a few plantation forests. Censuses of the ground-dwelling beetle community were conducted using pitfall trapping and forest floor environment monitoring every year from 2004 to the present. During the initial 9 years of the census (2004-2012), 59,762 beetle individuals (including 3182 larvae) of more than 314 species were recorded. This dataset includes taxonomy and biomass of each beetle individual and each taxonomic group of other invertebrates coincidently captured in pitfall trapping. The dataset also includes data related to ground coverage by forest floor vegetation, dry mass of the accumulated organic litter layer, and carbon and nitrogen contents and cellulose decomposition rate in organic layer and surface mineral soil. The data could be used to investigate geographical patterns and intra- and inter-annual dynamics of individual body mass, populations and community structures of ground-dwelling beetles, and their relationships with the forest floor environment. Furthermore, the data could be analyzed with other open datasets related to tree community dynamics and litter fall continuously measured in the same study plots. This dataset also provides information related to the distribution and average body mass of each beetle species. [ABSTRACT FROM AUTHOR]

This paper reports seasonal data regarding leaf litter for 14 deciduous broad-leaved species and one evergreen coniferous species as well as leaf area index (LAI) data for the 14 deciduous broad-leaved species in a cool-temperate deciduous broad-leaved forest in Japan. The seasonal leaf biomass of various tree species is important for accurately evaluating ecosystem functions such as photosynthesis and evapotranspiration under climate change. However, there is a lack of freely available, long-term data. We collected litterfall every 1 to 4 weeks from September or October to November or December each year from 2005 to 2014 in Takayama, Japan (36°08′46″N, 137°25′23″E, 1420 m a.s.l.). After sorting the litter into leaves (according to species categories), stems + branches, and 'other', we dried and weighed the litter groups. We also collected seasonal leaf data (number of leaves and leaf length and width) for each broad-leaved species, which we recorded every 1 to 4 weeks from April or May to October or November using multiple target shoots. To estimate the LAI in autumn for each deciduous broad-leaved species, we used a semi-empirical model of the vertical integration of leaf dry mass per unit leaf area. To estimate the LAI in spring and summer, we used the relationship between the LAI in autumn and the seasonal leaf data. Our data provide input, calibration, and validation parameters for determining LAI based on satellite remote-sensing observations or radiative transfer models and for use in ecosystem models. [ABSTRACT FROM AUTHOR]

The evergreen oak Quercus glauca often dominates secondary broadleaved forests in Western Japan. It is regarded as a mid-successional species, whose diameter and height growth fall between those of early- and late-successional species. Despite the ecological importance of this evergreen oak in the secondary succession of the evergreen broadleaved forest zone in Japan, tree-felling data that allow estimations of tree mass and leaf area from non-destructive measurements are lacking. This paper provides stem growth data, read from tree rings on disks sampled from 13 Q. glauca stems, and their allometric data. The samples were collected in 1994 from the Ginkakuji-san National Forest, Kyoto City, Japan. Allometric data comprised data on stem age, diameter at breast height, diameter at 10% height, tree height, height of the lowest living branch, height of the lowest living leaf in the crown, volume of the main stem, squared stem diameter just below the lowest living branch, total leaf area of the stem, dry weight of the total leaves, dry weight of all branches, dry weight of the main stem, total aboveground dry weight, mean relative photosynthetic photon flux density (PPFD) above the crown, mean relative PPFD below the crown, crown projection area, and specific leaf area. These data can be helpful for estimating the biomass and leaf area index of a Q. glauca stand by enabling the derivation of allometric relationships between non-destructive measurements (such as stem diameter at breast height, and tree height) and tree mass or leaf area. Diameters (including bark thickness) at ground height and above (at 0.5- or 1-m intervals) for each stem are also provided. Stem growth data were based on tree-ring reads from disks taken from heights of 0.0 and 0.3 m, and at 0.5-m (stem height <7 m) or 1.0-m (stem height ≥7 m) intervals above that. Stem volume growth derived from these tree-ring data can be converted into stem mass growth if combined with an analysis of the allometric data, which may serve as a useful resource for the estimation of carbon fixation by evergreen oaks in relation to global climate change. [ABSTRACT FROM AUTHOR]

This paper reports seasonal data regarding leaf number, leaf length and width, leaf area, leaf angle, and SPAD (leaf chlorophyll content index) for 11 genera (12 species) in a cool-temperate deciduous broadleaved forest in Japan. Knowing the leaf phenology of tree species is important for accurately evaluating the temporal variability of ecosystem functions (e.g., photosynthesis and evapotranspiration) under rapid climate change. However, there is a lack of freely available long-term observation data regarding leaf phenological characteristics for many tree species. We collected leaf phenological data from tagged shoots every 1-4 weeks from April or May to October or November each year from 2005 to 2014 in Takayama, Japan (36°08′46″N, 137°25′23″E, 1420 m a.s.l.). We targeted typical dominant, codominant, and understory tree species at the site. To evaluate differences among individuals and between sunlit and shaded leaves, we measured one to four shoots of some species and individuals. Our data provide input, calibration, and validation parameters for a terrestrial ecosystem and for radiative-transfer models and remote-sensing observations. [ABSTRACT FROM AUTHOR]

This data paper reports the abundance of phytoplankton species in monthly or biweekly samples collected from May 1978 through March 2010 at two stations on Lake Kasumigaura, a shallow lake that is the second-largest lake in Japan. The data set of quantitatively over several decades is unique among the available published data papers concerning lakes or plankton and continues to be freely available. The monitoring has been performed as a component of the Lake Kasumigaura Long-term Environmental Monitoring program, conducted by the National Institute for Environmental Studies since 1977. The data set details 173 phytoplankton species (or taxa), which can be identified by using an optical microscope and records their abundance. The abundance of each species is expressed in units of volume (μm) per milliliter of lake water. This approach allows quantitative comparisons among taxa because the cell size of phytoplankton varies by several orders of magnitude among taxa. The phytoplankton data include 39 species (taxa) of Cyanophyta, 67 Chlorophyceae (Chlorophyta), 3 Prasinophyceae (Chlorophyta), 1 Raphidophyceae (Heterokontophyta), 6 Euglenophyceae (Euglenozoa), 4 Dinophyceae (Dinophyta), 38 Bacillariophyceae (Heterokontophyta), 6 Chrysophyceae (Heterokontophyta), 7 Xanthophyceae (Heterokontophyta), 1 Cryptophyceae (Cryptophyta) and 1 Prymnesiophyceae (Haptophyta). The data have been used for ecological and environmental studies and for studies on lake management. [ABSTRACT FROM AUTHOR]

This data paper describes the densities of the bacterioplankton, picocyanobacteria, eukaryotic picoplankton, heterotrophic nanoflagellates and ciliates in the water of Lake Kasumigaura-a shallow, eutrophic lake that is the second largest in Japan. All of these planktonic organisms are components of a microbial loop and are countable using an epifluorescence microscope. These data represent the results of monthly collections from April 1996 through March 2010 at two sites on the lake, and this data set is unique among the available published data papers concerning lakes or plankton and continues to be freely available. The monitoring was performed as a component of the Lake Kasumigaura Long-term Environmental Monitoring program conducted by National Institute for Environmental Studies since 1977 and includes water quality, plankton, and benthos. The data have been used for ecological studies and for studies on the management of water quality. [ABSTRACT FROM AUTHOR]

This paper describes the flora of habitat-forming seaweeds (fucoids and temperate kelps) at 7673 sites of the Japanese coast encompassing its warm to cold temperate zone, recorded from 1887 to 2014. The data set includes 86 species (21,168 presence and 20,845 absence records), compiled from 355 literature sources, most of which were written in Japanese and published as grey literature in local journals or individual reports. Scientific names were consolidated under currently-accepted nomenclature based on Algaebase (). The data set compiled the seaweed flora at each study site each year, the geographical location and the scientific names. Additionally, three supporting data sets were created respectively including name of each site, synonyms of the seaweeds, and the corresponding literature list. This rich collection of data can be used to study the biogeography and long-term changes of particular species and the diversity of habitat-forming seaweeds of the Japanese coast. [ABSTRACT FROM AUTHOR]

This data paper reports litter fall data collected in a network of 21 forest sites in Japan. This is the largest litter fall data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Twenty-three permanent plots in which usually 25 litter traps were installed were established in old-growth or secondary natural forests. Litter falls were collected monthly from 2004, and sorted into leaves, branches, reproductive structures and miscellaneous. The data provide seasonal patterns and inter-annual dynamics of litter falls, and their geographical patterns, and offer good opportunities for meta-analyses and comparative studies among forests. [ABSTRACT FROM AUTHOR]

This data paper reports tree census data collected in a network of 34 forest sites in Japan. This is the largest forest data set freely available in Japan to date. The network is a part of the Monitoring Sites 1000 Project launched by the Ministry of the Environment, Japan. It covers subarctic to subtropical climate zones and the four major forest types in Japan. Forty-two permanent plots, usually 1 ha in size, were established in old-growth or secondary natural forests. Censuses of woody species ≥15 cm girth at breast height were conducted every year or once during 2004 to 2009. The data provide species abundance, survivorship and stem girth growth of 52,534 individuals of 334 tree and liana species. The censuses adopted common census protocol, which provide good opportunities for meta-analyses and comparative studies among forests. The data have been used for ecological studies as well as for the biodiversity reports published by the Ministry of the Environment. [ABSTRACT FROM AUTHOR]

Land use data serve as an essential part of large-scale ecological research, such as landscape ecology and macroecological studies. For agricultural fields in Japan, existing time series statistical records can be used to convert map data according to a map of municipality units. In this data paper, we determined the areas of agricultural land use in Japan from 1970 to 2005, excluding small islands, at spatial resolutions of 5- and 10-km mesh grid units, which are often referred to as the Five-fold Mesh and Japanese Second-order Mesh, respectively. The elements considered included total farmland, paddy fields, dry farmland, and orchards. In 2005, we included abandoned agricultural areas because the related data were available in the agricultural statistical records. The source data came from the Census for Agriculture, Forestry and Fisheries conducted by the Ministry of Agriculture, Forestry and Fisheries, Japan. The Datum was the Japanese Geodetic Datum 2000 (JGD2000). All of the datasets have open data licenses under the rules of the Creative Commons CC-BY 4.0 International (). [ABSTRACT FROM AUTHOR]

This data paper describes the native vascular aquatic plant floras of 268 Japanese lakes recorded from 1899-2011. The data were compiled from 201 literature sources, most of which were written in Japanese and published in local journals or individual reports rather than in major scientific journals. The literature was searched using web-based services (i.e., Google Scholar, ; CiNii, ; JDreamII, ; and ISI, ) and by private communication with experts or local governments. Scientific names were consolidated under currently-accepted nomenclature. Four datasets, FloraDB, LakeDB, SpeciesDB, and LiteratureDB, were created to include records of the flora of each lake in each year, the names and locations of the lakes, the scientific names and synonyms of the aquatic vascular plants, and a literature list, respectively. These data can be used to study long-term changes in the species composition and/or richness of aquatic plants in Japanese lakes. [ABSTRACT FROM AUTHOR]

This data paper reports spectral reflectance and transmittance data of leaves from 21 terrestrial vascular plant species (seven herbaceous, and 14 broadleaf and long-needle coniferous tree species) and of shoots from one short-needle coniferous tree species. The reflectance spectra of branches of one tree species, of the trunks of 12 tree species and ground surface of one deciduous broad-leaf forest are also reported. Optical measurements and leaf samplings were made at five sites on Honshu Island, Japan, which are typical vegetation types in East Asia, i.e., grassland, paddy field, and deciduous broad-leaf or coniferous forests. The collection and measurements were conducted for main species in each site. To include other common vegetation types in East Asia, such as evergreen broad-leaf or coniferous forests, the sample collection and the measurements were conducted at gardens and an experimental forest. Leaves of ten deciduous species were measured at different phenological stages from leaf expansion to senescence since those species shows significant seasonal changes in spectral reflectance and transmittance of leaves. Leaves at different position in a canopy (e.g., sunlit versus shaded leaves) were also measured for eight of 21 species. The spectral reflectance and transmittance from both adaxial and abaxial sides of the all leaves or needles, expect Picea abies needles. The measurements of the leaves were conducted with a spectroradiometer attached via an optical fiber to an integrating sphere. Two types of integrating spheres were used: a model LI-1800-12 (Li-Cor) and an RTS-3ZC integrating sphere (Analytical Spectral Devices). A leaf clip accessory was also used instead of an integrating sphere for measuring the leaves of two species. All data were measured within the 350-2,500-nm spectral range with 1-nm steps between measurements but the data obtained by LI-1800 is unavailable in 1,650-1,740, 1,890-1,950, and 2,050-2,500 nm because of a large amount of noise. These data are used as input parameters in a radiative transfer model designed to estimate the leaf area index from radiation reflected from a canopy surface. [ABSTRACT FROM AUTHOR]

Focuses on authors of research papers published in 2002 "Ecological Research" journal, who received the Ecological Research Award from the Ecological Society of Japan. 'Effects of rainfall events in soil CO2 flux in a cool temperate deciduous broad-leaved forest," by Mi-sun Lee, Kaneyuki Nakane, Takayuki Nakatsubo, Wen-hong Mo and Hiroshi Koizumi; "Factors affecting seedling recruitment and survivorship of Japanese subalpine stone pine, Pinus pumila, after seed dispersal by nutcrackers," by Takuya Kajimoto.