cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.20783/dias.jle.24
title: Phytoplankton species abundance in Lake Inba (Japan) from 1986 to 2016

description: Lake Inba is one of the most eutrophic lakes in Japan. This data paper reports the abundance of phytoplankton species sampled biweekly from April 1986 to March 2016 at four stations in Lake Inba. Monitoring has been carried out by Chiba Prefectural Government, and phytoplankton count data have been collected since 1986. A total of 340 phytoplankton species were identified and enumerated by microscopy, as numbers of cells or colonies. The abundance of each species was expressed as cells per milliliter lake water. Total cell density ranged from 102 to 108 cells per ml. The dominant cell class density was Cyanobacteria throughout the year. Cyanobacteria, such as Phormidium spp., Microcystis aeruginosa, and Anabaena spp. (Dolicospermum spp.), were the most dense in all months. The dominant cyanobacteria species reached concentrations of 107 cells per ml. Diatoms, such as Aulacoseira granulata and A. ambigua, were also abundant, reaching 106 cells per ml. These data can be used to appreciate how anthropogenic disturbances, such as eutrophication and global warming, affect density and community composition of phytoplankton.
DOI: 10.3535/dng-ca8-d2a
title: Dryopteris expansa (C. Presl) Fraser-Jenk. & Jermy

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.23
title: Native Mediterranean plants as potential food sources for natural enemies of insect pests in olive groves

description: The diversity of native non-crop (“weed”) vegetation in agricultural landscapes can provide arthropod natural enemies with food sources and shelter, thus improving natural pest control and reducing dependence on chemical pesticides. Moreover, native plants to a region are uniquely positioned to provide cultural ecosystem services such as wild food and wild medicinal plants, as well as aesthetics values. The Mediterranean Basin is one of the world’s richest places in terms of plant diversity. Olive cultivation is the basic tree cultivation in the Mediterranean and dominates its rural landscape. The olive grove ecosystem, whose flora presents a notable resemblance to the flora of Mediterranean type ecosystems, is home to a myriad of species of insects, spiders and other arthropods. This includes over one hundred phytophagous species, plus an uncounted number of entomophagous that help to reduce phytophagous populations. Here we present data on flowering plant species from the ground cover of olive groves, store information on characteristics of plant species namely physiognomic type and flowering period, geographic information and some statistical values on olive groves study area and records in the flora of visitor arthropods and cultural ecosystem services. The data include information on 36 olive groves, 100 flora species (taxa), of which 86 native in Portugal, 5 endemic to Iberian Peninsula and 4 endemic to Portugal Continental, and present also a summary of the records of visitor arthropods in these flora (i.e. 2 classes, 6 orders and 12 families).
DOI: 10.20783/dias.jle.25
title: Acoustic monitoring data of avian species inside and outside the evacuation zone of the Fukushima Daiichi power plant accident

description: Large-scale land abandonment and reconstruction activity has altered the ecosystem structure in the evacuation area for the Fukushima Daiichi power plant accident in 2011. Despite social concerns about changes in the avian assemblages that occurred after the accident, publicly accessible data are quite limited. We engaged in acoustic monitoring of birds using digital voice recorders from 2014 in and around the Fukushima evacuation zone. All monitoring sites were located within schoolyards (including those that had been converted to community centers) to examine the bird assemblages in the urban and rural landscapes that were heavily altered by land abandonment due to the nuclear plant accident. A digital voice recorder was installed at each monitoring site during May–July, and we recorded 20 minutes a day using timer-recording mode. We divided the audio data into 1-minute segments and identified species occurred in sampled segments by experts. These data represent the presence-absence records from 52 sites monitored in 2014, 57 sites monitored in 2015, 54 sites monitored in 2016, 57 sites monitored in 2017, 56 sites monitored in 2018, 52 sites monitored in 2019 and 50 sites monitored in 2020. We identified the species for 7,222 segments in total and 68 species occurred in 2014, 8,017 segments in total and 64 species occurred in 2015, 5,289 segments in total and 58 species occurred in 2016, 4,092 segments in total and 60 species occurred in 2017, 4,200 segments in total and 65 species occurred in 2018, 4,000 segments in total and 59 species occurred in 2019 and 3,900 segments in total and 56 species　 occurred in 2020. We are continuing to monitor and intend to update the dataset with new observations hereafter. Our dataset will help people to recognize the status and dynamics of avian assemblage inside the evacuation zone, and will contribute to promote open science in avian ecological studies.
DOI: 10.3535/dng-hc1-a66
title: Lemna minor L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dng-z2k-1y6
title: Plantae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.33
title: A data set of long-term observation of aquatic vertebrates and associate environmental factors in a temperate stream, the Yura River, Kyoto, Japan

description: The population dynamics of fishes are strongly affected by habitat characteristics, which are constantly changing due to seasonal and interannual variations in climatic, hydrological, and geographical processes. Seasonal and interannual variations in hydrological events directly affect the movement, growth, and mortality of stream fishes, and indirectly affect their population density and standing crop through changes in local-scale habitat structures. Characteristics of local-scale habitats directly affects on availability of foods, shelters, spawning sites, and interspecific interactions of stream fishes. Therefore, long-term data regarding the local-scale dynamics of habitat characteristics and its use by fish species over a few generations or longer would need for understanding the mechanism of the determinant process of fish population dynamics. When investigating the effects of habitat changes due to natural processes on the long-term dynamics of fish populations, removal of artificial influences such as changes in land use, dam constructions and channelization of riverrines is often problematic. Thereby, sampling sites where long-term observation of non-artificial changes in stream fish populations and habitats are very valuable. Here, I report the long-term seasonal and annual changes in stream fish populations and their habitat characteristics based on 75 snorkeling observations of fishes and environmental measurements in the upper reaches of the Yura River at Ashiu Research Forest, which has a 36.5-km2 catchment area with very little artificial disturbance, from May 2007 to June 2018. Snorkeling observations were conducted using the line-transect method during the day and at night, and microhabitat characteristics (water depth, current velocity, substratum characteristics, and presence/absence of cover) were determined for all individuals observed. A total of 56,042 individuals were observed, belonging to 17 fish and 7 other aquatic vertebrate species. These data may be used to examine the effects of habitat change on the processes that determine fish populations.
DOI: 10.3535/dng-znf-1y1
title: Potentilla crantzii (Crantz) Beck ex Fritsch

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnh-015-k8s
title: Alopecurus myosuroides Huds.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.27
title: Long-term data on forest regeneration after catastrophic windthrow in Tomakomai, Hokkaido, northern Japan

description: Typhoon No. 15 in 1954 (Marie) caused catastrophic windthrow in Hokkaido, northern Japan. The Tomakomai District of the National Forest was one of the forests severely damaged. A study site was established in a stand of the National Forest within the jurisdiction of the Iburi East District Forest Office. The stand was located on the eastern slope of Mt. Tarumae at an elevation of approximately 300–310 m a.s.l. at an angle of approximately 5°. Two belts sized 4 m × 40 m, crossing at right angles at the center, were established within the site in 1957, and censuses on regeneration were conducted in 1957, 1970, 1973, 1978, 1983, 1990, 1996, 2001, 2006, 2011, and 2016. All stems of coniferous tree species (height ≥ 10 cm) that regenerated in the belts were marked. For broadleaved tree species, all stems with height ≥ 1.3 m were marked in 1957–1990, but stems with height ≥ 10 cm were marked after 1996. Height was measured for all marked stems, and the diameter at breast height was measured for stems with height ≥ 1.3 m. During the censuses, 27 coniferous and broadleaved tree species were identified and three more species were identified to the genus level. There are 2,152 records for the occurrence data and 10,660 records for the measurement data, including missing values. The stem occurrence data were compiled following the Darwin Core format, and the measurement data were compiled following the Darwin Core Measurement or Fact Extension format. Finally all data were compiled for the Darwin Core Archive, an international standard format for biodiversity data. These data can help in understanding the succession of forests following large-scale disturbance and in managing this type of forest properly.
DOI: 10.3535/dnh-7mh-b18
title: Dryopteris expansa (C. Presl) Fraser-Jenk. & Jermy

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnh-brg-275
title: Brassica rapa L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnh-d04-1gg
title: Rumex longifolius DC.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnh-jq6-klp
title: Lathyrus aphaca L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.28
title: Image dataset of ophiuroid and other deep sea benthic organisms in 2015 extracted from the survey off Sanriku, Japan, by the research following the Great East Japan Earthquake 2011

description: This is the first large image dataset and occurrence records of marine organisms in the Northwest Pacific off Tohoku, Japan. This area suffered by Great East Japan Earthquake 2011 and continental shelf and slope off of this area considered one of the most productive areas both for fishery and primary production in the world because of the complex mixture of the Kuroshio Current, Oyashio Current, and Tsugaru Warm Current. We compiled 3415 images of animals, stones, and sediments. Most of the images are of dominant species of Ophiuroidea (brittle stars), with 789 and 1421 images captured in two areas of different depth. These images are cropped from downward camera images collected during two dives in 2015 using remotely operated vehicles in a deeper area (670-800 m deep) off Kamaishi (cruise id KY15-08; dive no. HPD1812) and a shallower area (280 m deep) off Minami Sanriku town (cruise id NT15-E04; dive no. CRB17). The attribute of each image is listed in the subsequent comma delimited (csv) text file and the observed occurrence of each organisms was also converted into the text format used in Japan Ocean Biogeographic Information System Center (J-OBIS), which is comparable with Darwin Core 2.0. Basically, we recorded the higher taxonomic levels (e.g., order and class) that could be specified with certainty and added a list of potential species as an appendix. For better understanding the broad-scale impact of the earthquake along the continental shelf and slope, it is necessary to extract occurrence data of organisms from biological surveys. Gathering image or video data is appropriate for this purpose because most underwater surveys simultaneously record images and/or videos. This dataset will add the information of the status after 4 years of the disaster. These image data are also considered as training image data set for automatic extraction of organisms.
DOI: 10.3535/dnh-l8s-c5f
title: Lycopodium lagopus (Laest. ex C. Hartm.) Zinserl. ex Kuzen.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnh-lvr-jse
title: Ononis arvensis L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnh-ywh-4vx
title: Cardamine amara L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnj-58d-z8t
title: Oreojuncus trifidus (L.) Záv. Drábk. & Kirschner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.29
title: Fish–prey interactions in, and associated data from, a temperate stream of the Yura River, Kyoto, Japan

description: Although quantitative data on interspecific interactions within complex food webs are essential for evaluation of assumptions, hypotheses, and predictions of ecological theories; empirical studies yielding quantitative data on complex food webs are very limited. Ecological information on body size, habitat use, and seasonality of the component species of food webs aids in determining the mechanisms of food web structures. Ideally, ecological information on component species should be obtained contemporaneously when used to describe quantitative food webs, but such observations and sampling strategies are labor intensive and thus have been rarely described. We conducted year-round samplings of, and performed observations on, a temperate stream: the upper reaches of the Yura River, Kyoto, Japan. We derived quantitative data on the abundance, biomass, body mass, microhabitat use, and those seasonality of 7 fish species and 167 invertebrate taxa of the temperate stream food web. In addition, we estimated the per mass consumption rates of 7 predatory fish species, consuming 183 prey invertebrates, and the ratios between the per mass consumption rates of the 7 predatory fish species and the production rates of 78 prey invertebrates in each trophic link.
DOI: 10.3535/dng-s59-rvb
title: Sisymbrium orientale L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.32
title: Concentration of radioactive materials in small mammals collected from a restricted area in Fukushima, Japan since 2012

description: Fukushima Daiichi Nuclear Power Plant was struck by a huge earthquake and tsunami, which ultimately released a large amount of radioactive material owing to steam explosion in March 2011. This accident affected extensive area and resulted in soil contamination, which would prevail over a long period. The contaminants included various types of nuclear materials, among which cesium (134,137Cs) has a particularly long half-life. Organisms living in the contaminated area are presumably exposed to radiation caused by the presence of these radioactive contaminants in their environment, in addition to internal exposure owing to the intake of these contaminants through the food web. The purpose of our data collection is to monitor accumulation of radioactive materials in small mammals for a long period and to predict its effects. Reasons for focusing on small mammals include: i) mammals are the most sensitive to radiation, ii) small mammals have a smaller home range compared to large mammals; therefore, accumulation of radioactive materials in small mammals is considered to reflect the condition of the surrounding environment, and iii) among the small mammals, rodents are used as laboratory animals and provide a lot of information, from which we can expect to acquire much knowledge based on investigations. The dataset contains measurements of 134,137Cs and potassium (40K) concentrations in small terrestrial mammals collected in areas contaminated with radioactive contaminants from the Fukushima Daiichi Nuclear Power Plant accident. We established two fixed study sites and three temporary sites inside the zone from which humans were evacuated owing to high levels of radiation. Annual monitoring of Cs contamination in small mammals was started in 2012 at the fixed study sites. Until 2016, we collected 547 individuals of four species (Apodemus speciosus, A. argenteus, Microtus montebelli, and Urotrichus talpoides). Cs concentrations in each individual were measured using high-purity germanium detectors against a ground body after removing the internal organs and the head. Our data provide valuable information about temporal changes in 134Cs and 137Cs concentrations in small mammals following the Fukushima Daiichi Nuclear Power Plant accident. The study is continuing and the present dataset will be updated in the future.
DOI: 10.20783/dias.jle.30
title: Global dataset for carbon and nitrogen stable isotope ratios of lotic periphyton

description: Carbon and nitrogen stable isotope ratios (δ13C and δ15 N) have been widely employed in food web analysis. In lotic environments, periphyton is a major primary producer that makes a large contribution to food web production as well as carbon and nitrogen cycling. While the δ13C and δ15N values have many advantages as a natural tracer, the controls over their high spatial and temporal variability in stream periphyton are not well known. Here, we present the global dataset of δ13C and δ15N values of lotic periphyton from 54 published and two unpublished sources, including 978 observations from 148 streams/rivers in 38 regions around the world, from arctic to tropical sites. The 54 published sources were articles recorded during the period of 1994–2016 in 25 academic journals. The two unpublished sources were from the authors’ own data. The dataset showed that δ13C and δ15N values of periphyton ranged from −47.3 to −9.3‰ and from −5.6 to +22.6‰, respectively. The dataset also includes physicochemical factors (altitude, coordinates, catchment area, width, depth, geology, vegetation, canopy coverage, biome, season, presence of anadromous salmon, temperature, pH, current velocity, and discharge), nutrient data (nitrate and ammonium concentrations), and algal attributes (chlorophyll a concentration, algal species compositions, and carbonates removal) in streams/rivers studied, all of which may help interpret the δ13C and δ15N values of periphyton. The metadata file outlines structure of all the data and with references for data sources, providing a resource for future food web studies in stream and river ecosystems.
DOI: 10.3535/dnj-dxx-ptg
title: Salix glauca L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnj-g80-se6
title: Barbarea stricta Andrz.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnj-hhg-qfx
title: Stellaria nemorum L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnj-jf8-2qg
title: Carex oederi var. bergrothii (Palmgr.) Hedrén & Lassen

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.31
title: 8 million phenological and sky images from 29 ecosystems from the Arctic to the tropics: the Phenological Eyes Network

description: We report long-term continuous phenological and sky images taken by time-lapse cameras through the Phenological Eyes Network (http://www.pheno-eye.org) in various ecosystems from the Arctic to the tropics. Phenological images are useful in recording the year-to-year variability in the timing of flowering, leaf-flush, leaf-coloring, and leaf-fall and detecting the characteristics of phenological patterns and timing sensitivity among species and ecosystems. They can also help interpret variations in carbon, water, and heat cycling in terrestrial ecosystems, and be used to obtain ground-truth data for the validation of satellite-observed products. Sky images are useful in continuously recording atmospheric conditions and obtaining ground-truth data for the validation of cloud contamination and atmospheric noise present in satellite remote-sensing data. We have taken sky, forest canopy, forest floor, and shoot images of a range of tree species and landscapes, using time-lapse cameras installed on forest floors, towers, and rooftops. In total, 84 time-lapse cameras at 29 sites have taken 8 million images since 1999. Our images provide (1) long-term, continuous detailed records of plant phenology that are more quantitative than in situ visual phenological observations of index trees; (2) basic information to explain the responsiveness, vulnerability, and resilience of ecosystem canopies and their functions and services to changes in climate; and (3) ground-truthing for the validation of satellite remote-sensing observations.
DOI: 10.3535/dnj-kkj-3zt
title: Carex dioica L.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.20783/dias.jle.35
title: Longitudinal and microhabitat distributions of fishes, amphibians, and reptiles and the environmental characteristics in the upper Yura River, Kyoto, Japan

description: Quantitative data on the distribution of aquatic vertebrate species along environmental gradients at multiple spatial scales are useful for assessing habitat quality, understanding habitat selection, and predicting the population structures of focal species. In addition, comparable datasets for multiple species enable the examination of the interspecific differences in habitat niches and their differentiation or aggregation patterns in a stream assemblage, as well as the theory of species coexistence. The distributions of aquatic vertebrates and environmental characteristics on longitudinal and microhabitat scales were investigated at 21 sites in a temperate stream, the Yura River, Kyoto, Japan, during the day and at night from August to September 2009. The sites were located from the headwaters to about 40 km downstream along the main channel of the river. Snorkeling observations were conducted using the line-transect method following a standardized procedure at each sampling site with a detailed description of the spatial structure of aquatic vertebrate habitats. The microhabitat environments (water depth, current velocity, substratum characteristics, and presence/absence of vegetation cover) could be determined for all observed individuals. A total of 11,724 individuals belonging to 28 fish, two amphibian, and one reptile species were observed. The data can be used to examine the spatial patterns of focal aquatic vertebrate species and assemblages, and interspecific differences in habitat use among sympatric aquatic vertebrate species at multiple spatial scales.
DOI: 10.3535/dnk-7yx-2sx
title: Alopecurus aequalis Sobol.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dnk-ang-ydd
title: Equisetum pratense Ehrh.

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.