cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.20783/dias.jle.40
title: Plant trait database for Cryptomeria japonica and Chamaecyparis obtusa (SugiHinoki DB)—their physiology, morphology, anatomy and biochemistry

description: 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 form 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 non-standardized, 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 had been obtained under different environmental conditions, for plants with different age, and for organs with 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 to 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 rage (IQR) for each trait per each species. In Aug 2019, SugiHinokiDB contains 24683 data entries (16410 for sugi, 8273 for hinoki). As sugi and hinoki are major plantation species in Japan, the data were mostly come from study sites in Japan (from Hokkaido in the north to Yakushima island in Kyushu, to the south), but were also from arboretums or plantation forests in Taiwan, Korea and China. Data were largely obtained for plants in plantation forests but also plants in natural forests and under experimental conditions. The improved availability of trait data offered by SugiHinokiDB provide new research opportunities such as intensive parameterization of vegetation models for more accurate prediction of climate change impacts.
DOI: 10.3535/dmx-php-7eq
title: Hammarbya paludosa (L.) Kuntze

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-10m-rla
title: Rorippa palustris (L.) Besser

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.47
title: Field data for satellite validation and forest structure modeling in a pure and sparse forest of Picea glehnii in northern Hokkaido

description: To validate and to improve ecological products obtained from satellites, such as a leaf area index (LAI), above-ground biomass (AGB), and a fraction of photosynthetically active radiation (fAPAR), in-situ accurate data are indispensable. They must be not a single point-data but an areal data representing the satellite footprint. Their accuracy needs to be much higher than the required accuracy for the satellite products. The quantitative assessment of their error is necessary for evaluating the satellite products' error from the discrepancy between the satellite products and the in-situ data. However, such data had not been available. In particular, there had been few data of LAI in a sparse evergreen needle-leaved forest, because of difficulty of accuracy control of in-situ observation in such a forest. To overcome the difficulty and to obtain the representative LAI, we made an allometric equation to estimate the leaf mass of Picea glehnii in northern Hokkaido. We report the allometric equations of leaf mass and above-ground biomass of P. glehnii, its leaf mass per area (LMA), its leaf life span, its leaf distribution, its crown shapes, its wood specific gravity, and tree locations. We also report LAI, AGB, and fAPAR within the 500 m × 500 m area, which is the footprint scale of the Global Change Observation Mission-Climate (GCOM-C) satellite, in a pure and sparse forest of P. glehnii in northern Hokkaido. These precise data are useful for validation of other satellite data, especially with higher spatial resolution, and forest structure modeling.
DOI: 10.3535/dmy-80j-qal
title: Lolium arundinaceum (Schreb.) Darbysh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-84q-d4b
title: Alopecurus geniculatus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-884-rl7
title: Polypodium vulgare L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.45
title: Stream water quality in relation to watershed-scale practical forest management in a cool-temperate natural forest in northern Japan

description: The water chemistry of a stream reflects the biogeochemical processes occurring in upstream forests. Anthropogenic disturbances in forests, such as cutting of 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 ten 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 to 23.67, 0.01 to 8.68, 0.83 to 4.01, 0.45 to 2.55, and 0.72 to 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.
DOI: 10.3535/dmx-tr4-095
title: Draba verna L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.44
title: Long-term monthly climate data at the forest stations of Kyoto University

description: Long-term climate monitoring by universities provides fundamental data for various disciplines in the natural sciences. Kyoto University once managed ten university forest stations and is currently managing five. At these stations, climate data have been monitored almost since the establishment of each station until today, with the exception of the stations in foreign countries. We compiled and report the monthly climate data at these forest stations from the start of monitoring until December 2018. These data are important for investigating environmental changes in East Asia, including China (Taiwan), South Korea (Chosen), and Russia (Sakhalin, Karafuto) over the last 100 years. Long-term monitoring often involves minor and major changes in the monitoring procedures, devices, and even monitoring sites due to unavoidable circumstances, such as technological advances, changes in standard methods, and climatic and anthropogenic disasters. Therefore, associated metadata on the monitoring methods are also important. We also compiled metadata on changes in monitoring methods. In addition, to examine the effects of changes in the methods on the observed climate data, we compared the values recorded before and after the change for each climate variable at each monitoring site. Methodological changes affected only a few variables, with the exception of humidity. Careful interpretation may be required when a researcher uses humidity data in any analysis.
DOI: 10.20783/dias.jle.49
title: Data on coral species occurrences in Japan since 1929

description: 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.
DOI: 10.3535/dmy-kw3-mn0
title: Hepatica nobilis Schreb.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.55
title: Seed size and weight of 129 tree species in Japan

description: Information on seed morphology and fruiting phenology related to fitness and reproductive strategy are 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. Through comparing these data to past or future data, we hope that it will aid in understanding the effects of climate change on fruiting phenology.
DOI: 10.3535/dmy-lkl-jhm
title: Trifolium montanum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-nxa-2s4
title: Vahlodea atropurpurea (Wahlenb.) Fr.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-ssd-2hn
title: Dryopteris carthusiana (Vill.) H. P. Fuchs

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-tn9-fs4
title: Elymus caninus (L.) L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.46
title: Systematic forest inventory plots and their contribution to plant distribution and climate change impact studies in Thailand

description: Thailand is recognized as having high species richness both flora and fauna. The systematic plant taxonomy and collection was initiated in 1957–58. However, the distribution of specimen collections is uneven and mainly located near road networks. The Royal Forest Department (RFD) has since 2001 initiated the systematic uniformly fixed grids of 20 km × 20 km for measuring trees and their environments with the financial and technical support from the International Tropical Timber Organization. After the reorganization of the RFD in 2002, the Department of National Parks, Wildlife and Plant Conservation of Thailand, which then was separated from the RFD, has carried on this project and added the uniformly fixed grids ranging from 2.5 km × 2.5 km to 10 km × 10 km over the entire protected areas in Thailand. Throughout three project phases (2001-present), there are over 3,150 plots collected from 59 provinces, while the remaining 18 provinces do not have monitoring plots because of either the security issue or no forest covers. There were, based on altogether 24,605 occurrence records of trees with a diameter greater than 4.5 cm at breath high level from 363 species from 81 families and 222 genera. Trees belong to Dipterocarpaceae, Lamiaceae, Burseraceae, Phyllanthaceae, Malvaceae and Fabaceae families are dominant. Besides for simple estimation of tree density and volume, the data were used for bio-geographical and climate change impact studies.
DOI: 10.3535/dmy-z4v-ryv
title: Elymus caninus (L.) L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmz-097-v68
title: Salix myrsinites L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.48
title: Quantitative records of habitat-forming seaweeds found in Japanese temperate and subtropical zones (fucoids and kelps)

description: This data paper introduces a data set of quantitative records, including biomass (wet and dry weight), cover, shoot density, and shoot length, of habitat-forming seaweeds (temperate kelps and fucoids) collected at 400 sites (2,115 sampling points) of a warm-to-cold temperate zone of the Japanese coast from 1957 to 2013. The data set includes 8,885 occurrence records of 58 species, extracted from 64 literature sources, most of which were written in local language. The data set compiled the quantitative records of seaweeds at each study site, each year and each month; the geographical location; the vertical distribution; and the scientific names. Furthermore, one supporting data set was added that included the name of the corresponding literature list. The data set was formatted as Darwin Core and its extension, “Sample-based Data.” Scientific names were updated to ones that are currently accepted based on Algaebase (http://www.algaebase.org). A comprehensive distribution (presence and absence) data set of Japanese habitat-forming seaweeds has been published (Kumagai et al. 2016 Ecological Research 31: 759), which covers geographic distribution and the associated long-term changes in seaweeds found in Japanese temperate and subtropical zones. Here, this data set focuses more on changes in seaweed quantity according to season and depth. This rich data set can be used to analyze the seasonal, long-term changes and spatial differences in the biomass and community structure of habitat-forming seaweeds along the Japanese coast. These datasets are published under a Creative Commons attribution license CC-BY NC 4.0 (https://creativecommons.org/licenses/by-nc/4.0/).
DOI: 10.3535/dmz-3ev-yyx
title: Salix caprea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmz-7e5-vc0
title: Allium cepa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmz-axq-64v
title: Salix caprea L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.50
title: Long-term observation of fish community in streams inside and outside road construction of Teshio River system, northern Hokkaido, Japan

description: Nakagawa experimental forest of Hokkaido University is located in the middle Teshio River and some tributaries flow through the forest. The construction of Otoineppu bypass route started in 2007. This bypass route will passes through the forest. In order to evaluate the impacts of the road construction on stream ecosystem, a long-term monitoring of fish community and stream environmental characteristics have been conducted including before, during and after the road construction. The survey has been implemented on five streams in Teshio River (three streams inside the bypass construction zone and two streams outside the zone). Here, we report the data of species, body size and body weight of fish sampled using an electrofishing unit and the data of stream environmental characteristics such as water temperature, water surface area, pH, and EC. The three-pass removal method for fish sampling and measurement of stream environmental characteristics were conducted three times a year (mainly June, August and October) from 1999 to 2018. A total of 57,203 individuals were observed, belonging to 11 species in 7 families. After bypass road construction started (2007), the number of fishes gradually increased at both of bypass road construction and control sites. Occasionally, the number of fishes at the bypass construction site tended to be lower than at the control site, but there was not always noticeable difference between them. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in Ecological Research Data Paper Archives at http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/archives/2020/ERDP-2020-09.
DOI: 10.3535/dmz-b18-mp5
title: Gagea minima (L.) Ker Gawl.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmz-crg-kwl
title: Chenopodium L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.56
title: Structure and dynamics of a mountain riparian forest at an upstream valley in central Japan

description: 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 &gt; 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, sub-tree 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.
DOI: 10.3535/dmz-qhp-yq5
title: Amaranthus retroflexus L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-q2z-15p
title: Rumex acetosella L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dmy-qdm-m7q
title: Ceratophyllum demersum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.59
title: Underwater video and still-image dataset of fishes and other aquatic animals in Lake Biwa, Japan, observed via carp-mounted video loggers

description: 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 (GBIF). 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 intra- and inter-specific 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 showcase 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 Ecological Research Data Paper Archives at http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/archives/2020/ERDP-2020-18