cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7280/d1xq2p
title: Dataset S2: Global Synechococcus pigment type distribution from metagenomes with co-located mixed layer depths and sea surface properties

description: Dataset containing Synechococcus metagenomes separated
 into pigment type abundance and proportion of light-harvesting
 generalists (capable of chromatic acclimation) at each sample location.
 Data are combined from GO-SHIP, GEOTRACES and TARA Oceans with
 co-located mixed layer depths and sea surface properties calculated from
 cruise CTD data. Additionally, the dataset contains co-located mixed layer
 depth climatology from ARGO; and sea surface height, and
 one-degree adjacent sea surface gradients via satellite atilmetry
 from AVISO.
description: Data was processed as fully described in the accompanying
 article—the manuscript that accompanies this dataset. Briefly,
 <em>Synechococcus</em> pigment types were derived from
 <em>mpeAB</em> gene coverage using methods previously
 described by Grebert et al (PNAS, 2018). Metagenomes used were taken from
 GO-SHIP, GEOTRACES, and TARA Oceans data and physical oceanographic
 parameters were obtained for the same month and location of the
 <em>Synechococcus</em> gene sample. Mixed layer depths were
 calculated using a threshold method of 0.2 <sup>o</sup>C from
 a surface reference of 10 m. The following datasets
 were used to derive <em>Synechococcus</em> gene coverage and
 calculate mixed layer depths: Bio-GO-SHIP metagenomes
 (https://doi:10.1038/s41597-021-00889-9) and GO-SHIP vertical profiles
 (https://cchdo.ucsd.edu), GEOTRACES metagenomes
 (https://doi.org/10.1038/sdata.2018.176) and GEOTRACES vertical profiles
 from IDP 2017 (https://doi.org/10.1016/j.chemgeo.2018.05.040); TARA Oceans
 metagenomes (https://doi.org/10.1126/science.1261359) and TARA Oceans
 vertical profiles (https://doi.org/10.1594/PANGAEA.836321). SSH was
 derived from AVISO L4 ADT (https://doi.org/10.5067/DYNTO-1D1M1) and sea
 surface gradients were calculated using the absolute difference in SSH of
 the nearest 1<sup>o</sup> grid to the
 <em>Synechococcus</em> gene location. Mixed layer depth
 climatology was calculated using ARGO data, available at
 https://doi.org/10.1002/2017GL073426
 and http://mixedlayer.ucsd.edu.
description: Data in the file accompanies the paper Lovindeer, R., Ustick, L.
 J., Primeau, F., Martiny, A. C., & Mackey, K. R. M. (2021).
 Modeling ocean color niche selection by Synechococcus blue-green
 acclimaters. Journal of Geophysical Research: Oceans:
 126 https://doi.org/10.1029/2021JC017434 Missing values
 are recorded as NaN. See accompanying README for details on the
 parameters. Note that either standard deviation (STD)
 or standard error (STDERR) are reported in the dataset and are indicated
 in the column header.
DOI: 10.5061/dryad.wdbrv15nx
title: Dataset for: Effects of oil and sediment properties and mixing states on the formation and settling of oil-particle aggregates

description: It is valuable to understand the interactive behavior of oil droplets with
 suspended particulate matter for sunken oil modeling and emergency
 response. In this Dataset, data acquired from a series of mesoscale wave
 tank experiments and sedimentation tests including oil dispersion
 efficiency, oil trapping efficiency, OPA density and size distribution of
 trapped oil were presented.
description: Files can be opened with the software Origin- OriginLab.
DOI: 10.5061/dryad.bzkh1898d
title: Illustrative inpatient blood glucose datasets for QcDM project

description: Glucometrics is a set of measures designed to assess whether the blood
 glucose of patients with diabetes mellitus are
 effectively managed, and is useful in regular surveillance for
 adverse events such as hypoglycaemia and hyperglycaemia. To evaluate the
 quality of glycemic control using glucometrics, routinely collected blood
 glucose data needs to be consolidated, processed, and analysed in
 different units of analysis (i.e., patient-sample, patient-day, and
 patient-stay). Such procedure is challenging without dedicated manpower
 with specific professional skills.  We developed an open-source
 tool with a user-friendly graphical interface, named the Quality care for
 Diabetes Mellitus (QcDM) Project (available at:
 https://github.com/nyilin/QcDM_Project), to facilitate the monitoring of
 the quality of inpatient glycemic control. To illustrate the usage of the
 tool, we provide two datasets: test_format1.csv to generate glucometrics
 for monitoring glucose readings in an inpatient setting, and test1.csv to
 compare the glucometrics generated between different software programs.
description: The simulated dataset, test_format1.csv, contains blood glucose data with 5594 rows for 100 unique hospital stays in July 2020, randomly assigned into 4 ward locations. It has 4 columns: - ADMISSION.ID: integer-valued admission identifier for each unique hospital stay. - RESULT: blood glucose readings measured in mmol/L. To illustrate how the software program developed in the QcDM Project handles non-numerical values, three entries had non-numerical values. - RESULT.DATE: date-time stamp of glucose readings, in the format of "mm/dd/yyyy hh:mm".  - LOCATION: ward location of hospital stays where each unique hospital stay is assigned to one of the following labels: A, B, C, and D. This simulated dataset and the R script used to generate the dataset is available from the GitHub repository of the QcDM Project: https://github.com/nyilin/QcDM_Project/blob/main/data/Test1.   The anonymized dataset, test1.csv, is the test data from the Yale Glucometrics, with 2456 rows for 72 unique hospital stays in March and April. It has 3 columns without column headings: - Column 1: integer-valued admission identifier for each unique hospital stay. - Column 2: date stamp of glucose readings, in the format of "dd/mm/yyyy". The year of the anonymized date is further masked as 0000 and users are advised to replace it with a year of their choosing (e.g., 2005) before applying the QcDM tool. - Column 3: blood glucose readings measured in mg/dL. This dataset with the year of the anonymized date further masked as 0000 is also available from the GitHub repository of the QcDM Project: https://github.com/nyilin/QcDM_Project/blob/main/Supplementary_data/test1.csv.
DOI: 10.5061/dryad.4mw6m9096
title: Data from: Patterns of flammability after a sequence of mixed-severity wildfire in dry eucalypt forests of southern Australia

description: Fire severity is the impact of a fire on the landscape, particularly the
 physical impact on vegetation. Previous studies have established that the
 severity of a fire can be influenced by the severity of previous fires.
 Many of these studies were conducted in mixed-conifer forests, while
 little is known of this process in temperate eucalypt forests. Barker and
 Price (2018) found that high severity fire promotes high severity fire in
 eucalypt forests, but how is the severity of a fire in these systems
 affected by the severity of two sequential previous fires? This was
 investigated using remotely sensed and mapped fire severity data. We found
 that high severity fire is more likely after at least one previous high
 severity fire, regardless of its position in the sequence. A sequence of
 low or moderate severity fire followed by low severity fire resulted in
 the lowest proportion of high severity in the response fire. Our results
 suggest that low severity fire maintains the structure of forest fuels, so
 flammability remains relatively constant. A single high severity fire
 drives change, altering the structure and flammability of the vegetation
 and promoting more severe fire. However, the effects were small, so a
 cycle of high severity fire may be easily broken due to the influence of
 other variables, such as weather. Repeated high severity fire may also
 result in a decline in the ability of plants to recover from fire, leading
 to a compositional and structural change and potentially reducing the
 flammability of a forest.
DOI: 10.5061/dryad.cz8w9gj3h
title: Water uptake strategies by typical broadleaf and coniferous trees in the Loess Plateau mountain area of northern China

description: Poor precipitation in the Loess Plateau area may significantly influence
 water uptake strategies of the plants growing there. The water sources of
 these trees have not been studied to date. We investigated the impacts of
 precipitation (before and after) on water uptake strategies of typical
 broadleaf and coniferous trees in the Loess Plateau mountain area of
 northern China by using hydrogen and oxygen stable isotope techniques. Our
 results indicated that water sources of these two tree types varied before
 and after rainfall. Robinia pseudoacacia, a broadleaf tree, absorbed water
 majorly from the 30–40 cm (57.8%) soil layer before precipitation and from
 the 20–30 cm (58.5%) soil layer after precipitation. However, Pinus
 tabuliformis, a coniferous tree, mainly absorbed water from 20–30 cm
 (24.9%) and 10–20 cm (21.6%) soil layers before precipitation and from
 0–10 cm (39.8%) and 10–20 cm (44%) soil layers after precipitation.
 Moreover, the herbaceous of broadleaf plant has higher complexity of the
 community through filed investigation. Thus, R. pseudoacacia and P.
 tabuliformis exhibited peculiar difference in terms of water uptake,
 indicating that they are suitable to grow together as forest vegetation in
 arid and semi-arid areas. Overall, our results provided vital information
 for sustainable afforestation management in the Loess Plateau mountain
 area of northern China.
description: This
 dataset corresponds to experimental estimates of stable isotope  of
 <i>P. tabuliformis</i><i>in</i>
 and <em>R. pseudoacacia</em> in Caijiachuan. It also contains
 local precipitation, temperature, sampling plots' understory and
 stable isotope before and after
 precipitation.
description: There are no missing
 values, and column names are self-explanatory.
DOI: 10.5061/dryad.t1g1jwt24
title: Social insect colonies are more likely to accept unrelated queens when they come with workers

description: Relatedness underlies the evolution of reproductive altruism, yet eusocial
 insect colonies occasionally accept unrelated reproductive queens. Why
 would workers living in colonies with related queens accept unrelated
 ones, when they do not gain indirect fitness through their reproduction?
 To understand this seemingly paradox, we investigated whether acceptance
 of unrelated queens by workers is an incidental phenomenon resulting from
 failure to recognize non-nestmate queens, or whether it is adaptively
 favored in contexts where cooperation is preferable to rejection. Our
 study system is the socially polymorphic Alpine silver ant, Formica
 selysi. Within populations some colonies have a single queen, and others
 have multiple, sometimes unrelated, breeding queens. Social organization
 is determined by a supergene with two haplotypes. In a first experiment we
 investigated whether the number of reproductive queens living in colonies
 affects the ability of workers at rejecting alien queens, as multiple
 matrilines within colonies could increase colony odor diversity and reduce
 workers’ recognition abilities. As workers rejected all alien queens,
 independently of the number of queens heading their colony, we then
 investigated whether their acceptance is flexible and favored in specific
 conditions. We found that workers frequently accepted alien queens when
 these queens came with a workforce. Our results show that workers flexibly
 adjust their acceptance of alien queens according to the situation. We
 discuss how this conditional acceptance of unrelated queens may be
 adaptive by providing benefits through increased colony size and/or
 genetic diversity, and by avoiding rejection costs linked to fighting.
DOI: 10.5061/dryad.37pvmcvk7
title: Spatial variation in antler investment of Apennine red deer

description: Heterogeneity in resource availability and quality can trigger spatial
 patterns in the expression of sexually selected traits such as body mass
 and weaponry. While relationships between habitat features and phenotypic
 quality are well established at a broad geographical scale, information is
 scanty on spatial patterns at a finer, intra-population scale. We used
 data collected on 1965 male red deer Cervus elaphus over 20 years from a
 non-migratory population living on two sides of a mountainous ridge with
 substantial differences in land cover and habitat quality but similar
 climate and population density. We investigate spatial patterns in (i)
 body mass, (ii) antler mass, (iii) antler investment. We also tested for
 site- and age-specific patterns in allometric relationship between body
 mass and antler mass. Statistically significant fine-scale spatial
 variations in body mass, antler mass and, to a lesser extent, antler
 allocation matched spatial differences in land cover. All three traits
 were greater in the northern slope, characterized by higher habitat
 heterogeneity and greater availability of open habitats, than in the
 southern slope. Moreover, the allometric relationship between body mass
 and antler mass differed among age classes, in a pattern that was
 consistent between the two mountain slopes. Our results support the
 occurrence of spatial patterns in the expression of individual attributes
 also at a fine, intra-population scale. Our findings emphasize the role of
 environmental heterogeneity in shaping spatial variations of key
 life-history traits, with potential consequences for reproductive success.
DOI: 10.5061/dryad.w9ghx3fpj
title: Inflow and meteorological data of the planned Longyangxia hydro–PV-wind power plant

description: The monthly measured streamflow data recorded at Tangnaihe hydrological
 station were chosen to represent the monthly inflow data of the hydropower
 plant. Meteorological data including daily solar duration,
 temperature, and wind speed data in Gonghe station were
 provided to calculate the monthly PV power output and wind power
 output.
description: Meteorological data including the daily solar duration,
 temperature, and wind speed data are from the China Meteorological
 Administration (http://data.cma.cn/); Streamflow data recorded at Tangnaihe hydrological station were provided by the China Yellow River Conservancy Commision.
DOI: 10.5061/dryad.6hdr7sr0n
title: Subcellular view of host–microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan–microbe symbiosis

description: Background: Sponges are increasingly recognised as key ecosystem engineers
 in many aquatic habitats. They play an important role in nutrient cycling
 due to their unrivalled capacity for processing both dissolved and
 particulate organic matter (DOM and POM) and the exceptional metabolic
 repertoire of their diverse and abundant microbial communities. Functional
 studies determining the role of host and microbiome in organic nutrient
 uptake and exchange, however, are limited. Therefore, we coupled
 pulse-chase isotopic tracer techniques with nanoscale secondary ion mass
 spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C-
 and 15N-labelled dissolved and particulate organic food at subcellular
 level in the high microbial abundance sponge Plakortis angulospiculatus
 and the low microbial abundance sponge Halisarca caerulea. Results: The
 two sponge species showed significant enrichment of DOM- and POM-derived
 13C and 15N into their tissue over time. Microbial symbionts were actively
 involved in the assimilation of DOM, but host filtering cells
 (choanocytes) appeared to be the primary site of DOM and POM uptake in
 both sponge species overall, via pinocytosis and phagocytosis,
 respectively. Translocation of carbon and nitrogen from choanocytes to
 microbial symbionts occurred over time, irrespective of microbial
 abundance, reflecting recycling of host waste products by the microbiome.
 Conclusions: Here, we provide empirical evidence indicating that the
 prokaryotic communities of a high and a low microbial abundance sponge
 obtain nutritional benefits from their host-associated lifestyle. The
 metabolic interaction between the highly efficient filter-feeding host and
 its microbial symbionts likely provides a competitive advantage to the
 sponge holobiont in the oligotrophic environments in which they thrive, by
 retaining and recycling limiting nutrients. Sponges present a unique model
 to link nutritional symbiotic interactions to holobiont function, and, via
 cascading effects, ecosystem functioning, in one of the earliest
 metazoan–microbe symbioses.
description: This dataset was collected in an experiment run between June and
 Juy 2018. It contains extracted values from NanoSIMS data, which gives the
 Atom% carbon and nitrogen from different cells of interest in sponge
 tissue over time. The last tab contains bulk stable isotope data (from
 EA-IRMS) from the sponges used in the experiment. Included are isotopic
 enrichment of sponge tissue in delta notation and carbon and nitrogen
 content (%) and dryweight of the sponge tissue. From these values,
 incoporation rates of dissolved and particulate organic matter are
 derived, which are provided in the main text and supplementary
 materials. 
description: There are no missing values.
DOI: 10.5061/dryad.rn8pk0p9c
title: Data for: Fishing triggers trophic cascade in terms of variation, not abundance, in an allometric trophic network model

description: Trophic cascade studies often rely on linear food chains instead of
 complex food webs and are typically measured as biomass averages, not as
 biomass variation. We study trophic cascades propagating across a complex
 food web including a measure of biomass variation in addition to biomass
 average. We examined whether different fishing strategies induce trophic
 cascades and whether the cascades differ from each other. We utilized an
 allometric trophic network (ATN) model to mechanistically study
 fishing-induced changes in food web dynamics. Different fishing strategies
 did not trigger traditional, reciprocal trophic cascades, as measured in
 biomass averages. Instead, fishing triggered a variation cascade that
 propagated across the food web, including fish, zooplankton and
 phytoplankton species. In fisheries that removed a large amount of
 top-predatory and cannibalistic fish, the biomass oscillations started to
 decrease after fishing was started. In fisheries that mainly targeted
 large planktivorous fish, the biomass oscillations did not dampen but
 slightly increased over time. Removing species with specific ecological
 functions might alter the food web dynamics and potentially affect the
 ecological resilience of aquatic ecosystems.
DOI: 10.5061/dryad.69p8cz91w
title: Land-use history alters the diversity, community composition and interaction networks of ectomycorrhizal fungi in beech forests

description: Forests have expanded across Europe over the last centuries as a
 consequence of farmland (agricultural and pasture) abandonment.
 Agricultural practices usually increase soil fertility and reduce the
 diversity and abundance of ectomycorrhizal (ECM) fungi, essential
 mutualists of many woody species in temperate and Mediterranean forests.
 The recovery of this biotic interaction after the cessation of human
 activities is, thus, crucial for the re-establishment of functional forest
 ecosystems. Here we addressed the legacies of past land use and the
 recovery of the mutualism between ECM fungi and Fagus sylvatica trees in
 recent beech forests (&lt; 50 years) in Northeast Spain. Soil and root
 samples were collected in 6 long-established and 8 recent beech forests to
 analyse soil abiotic properties and the ECM fungi associated
 with beech roots (Illumina DNA metabarcoding of ECM tips). Up to
 609 amplicon sequence variants (ASV) of ECM fungi were identified, with
 220 ASV found in both forest types. Recent forests had a significantly
 lower soil organic matter and phosphorus content, which had a significant
 effect on the community structure of ECM fungi in beech roots. Moreover,
 beech trees in recent forests interacted with less fungal taxa but had a
 higher relative abundance of Ascomycota. Tarzetta spp. (Ascomycota,
 Pezizales) and Lactarius blennius (Basidiomycota, Russulales) emerges as
 the particular taxa associated with recent and long-established forests,
 respectively. More specialized mutualistic networks with a lower species
 normalized degree were found in recent forests, which might result in a
 lower quality and resilience of the ectomycorrhizal mutualism. Synthesis:
 Land-use history modulated the mycorrhizal symbioses in regenerating beech
 forests through changes in soil organic matter and nitrogen, which were
 the main drivers of the differences in fungal community composition and
 functional types associated with beech trees in recent forests.
description: <i>Fagus sylvatica</i> trees in recent beech forests
 (&lt; 50 years) and in long-established forests in Northeast Spain
 were selected and sampled. Soil and root samples were collected in 6
 long-established and 8 recent beech forests to analyse soil abiotic
 properties and the ECM fungi associated to beech roots (Illumina DNA
 metabarcoding of ECM tips).
description: In addition to the data provided in this Dryad and in the
 supporting information section of this article, the raw reads (DNA) have
 been deposited in the sequence read archive and are available under the
 BioProject ID PRJNA622562.
DOI: 10.5061/dryad.5x69p8d2q
title: Drivers of change in the realised climatic niche of terrestrial mammals

description: The breadth of a species’ climatic niche is an important ecological trait
 that allows adaptation to climate change, but human activities often
 reduce realised niche breadth by impacting species distributions. Some
 life-history traits, such as dispersal ability and reproductive speed,
 allow species to cope with both human impact and climate change. But how
 do these traits interact with human pressure to determine niche change?
 Here we investigate the patterns and drivers of change in the realised
 climatic niche of 258 terrestrial mammal species. Our goal is to
 disentangle the impacts of human land use, climate change, and life
 history. We quantified the past and present climatic niches of each
 species by considering past climatic conditions (Mid Holocene) within
 their pre-human impact distributions, and current climatic conditions
 within the current distributions. Depending on the difference between past
 and current niche, we defined four categories of change: “shrink”,
 “shift”, “stable”, and “expand”. We found over half of the species in our
 sample have undergone niche shrink, while only one in six retained a
 stable niche. Climate change and distribution change were the strongest
 correlates of species niche change, followed by biogeography,
 anthropogenic land use, and life-history traits. Factors that increased
 the probability of niche shrink included: overall climatic instability,
 reduction in distribution range, historical land use, large body mass, and
 long weaning age. Species with these characteristics might require
 interventions that facilitate natural dispersal or assisted colonisation
 to survive rapidly changing climates.
description: Climatic, Biological, and human-pressure
 variables measured for each species, under each climate scenario. All
 methods and primary data sources are described in the associated
 article.
description: Please refer to the readme file associated with the dataset.