cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.b5j6ay
title: Occurrence Download

description: A dataset containing 17205 records in GBIF matching the query:
SELECT
 '515' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 51.21395264452012
 AND decimalLatitude &lt;= 56.135291543055025
 AND decimalLongitude &gt;= 53.451504131127514
 AND decimalLongitude &lt;= 64.759591695172
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 17205 records were derived from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004382-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fxpnvx157
title: Data from: Phenotypic integration limits the variation in plant phenotypic plasticity among traits: a meta-analysis

description: This dataset contains the data associated with a meta-analysis on the
 relationship between phenotypic integration and phenotypic plasticity in
 plants, and the difference in phenotypic integration between a control and
 stress treatment. In most cases, the values and association among these
 two variables were calculated based on available datasets from each study
 included. 
description: # Dryad dataset Dataset DOI:
 [10.5061/dryad.fxpnvx157](10.5061/dryad.fxpnvx157) ## Description of the
 data and file structure A two part meta-analysis evaluating (1) the
 relationship between phenotypic plasticity and phenotypic integration and
 (2) the increase in phenotypic integration in response to stress ### Files
 and variables #### File: Data\_Stotz\_et\_al.\_Functional\_Ecology.xlsx
 **Description:** Dataset ##### Variables | **Column name** |
 **Description** | | :--------------------- |
 :---------------------------------------------------------------------------------------------------------------------------- | | StudyCase | Number asigned to separate study cases | | Citation  | Study citation | | species | Species scientific name | | genus | Genus name | | family | Family name | | Treatment type | Treatment applied to assess plasticity; it was standardized across studies | | Habit | Annual vs. perennial | | Ontogeny | Perennial species were classified as adult vs. seedlings | | CV\_Plasticidad | Phenotypic plasticity coefficient of variation among traits | | R\_stress\_env | Correlation coefficient between phenotypic plasticity and phenotypic integration at the trait level, in the stress treatment | | R\_con\_env | Correlation coefficient between phenotypic plasticity and phenotypic integration at the trait level, in the control treatment | | Control.Mean | Average phenotypic integration across traits in the control treatment | | Control.sd | Standard deviation in phenotypic integration across traits in the control treatment | | Control.n | Number of traits measured in the control treatment | | Stress.mean | Average phenotypic integration across traits in the stress treatment | | Stress.sd | Standard deviation in phenotypic integration across traits in the stress treatment | | Stress.n | Number of traits measured in the stress treatment | | Max\_integration\_prop | Maximum value of phenotypic integration across traits | Other: N/A: Indicates that data was not available or reported in the study NA: Indicates "not applicable", as annual plants were not classified based on ontogeny ### **Code/software** NA ## Access information Other publicly accessible locations of the data: * n/a Data was derived from the following sources: * n/a
DOI: 10.15468/dl.hfsech
title: Occurrence Download

description: A dataset containing 25329966 species occurrences available in GBIF matching the query:
{
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 25329966 records from 657 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004294-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2547d7x3s
title: Data from: Routine mitochondrial recombination drives rapid concerted evolution of duplicated control regions in a wild fish

description: Duplications and concerted evolution of control regions (CRs) in animal
 mitogenomes have been reported across diverse taxa, yet the tempo and
 mechanism of gene conversion remain poorly understood. Here, we assembled
 the complete mitochondrial genome of the western Indian ricefish Oryzias
 setnai and found that the CR is duplicated. Comparative analysis of CR1
 and CR2 sequences across individuals sampled throughout the species’ range
 revealed that they are identical in most individuals, and differ by only
 one or two mutations in the rest—indicating recent and ongoing concerted
 evolution. We estimated that gene conversion events occur at a rapid pace,
 on the order of once every &lt;1,000 years or less. Using both short-
 and long-read amplicon sequencing, we directly detected a substantial
 number of recombinant mitogenome molecules resulting from homologous
 recombination between CR paralogues. This provides the first clear
 evidence that homologous recombination is the mechanism driving
 mitochondrial gene conversion. Our findings challenge the prevailing view
 that recombination in animal mitochondria is exceedingly rare, and
 demonstrate that mitogenome recombination can occur routinely in natural
 populations.
description: # Data from: Routine mitochondrial recombination drives rapid concerted
 evolution of duplicated control regions in a wild fish README for data set
 from Nuryadi et al. 2025 Rapid concerted evolution of mitochondrial
 control regions by routine recombination. Proceedings of the Royal Society
 B. The data set accompanies one Dryad data file. Uploaded: May 2025
 Revised: Contact: Kazunori Yamahira
 ([yamahira@cs.u-ryukyu.ac.jp](mailto:yamahira@cs.u-ryukyu.ac.jp)) ---
 File_01_CR1_and_CR2_sequence.fas The fasta file containing mitochondrial
 control region 1 and control region 2 sequences (634 bp) of Oryzias
 setnai, which was used for the ML phylogeny in figure 4. ---
 File_02_File_02_Short_read_amplicon_sequence_and_count.txt The text file
 containing the data listed below. *Amplicon group*: Short-read amplicon
 group *Target region*: Target region (CR1 or CR2) amplified *Sequence*:
 Sequences obtained *Individual*: Individual ID of each sequence *Read
 type*: Read type of each sequence (CR1 or CR2) *Count*: Read number of
 each sequence --- File_03_Long_read_amplicon_sequence_and_count.txt The
 text file containing the data listed below. *Amplicon group*: Long-read
 amplicon group *Sequence ID*: ID of each sequence *Sequence*: Sequences
 obtained *Individual*: Individual ID of each sequence *Read type*: Read
 type of each sequence (CR1-CR2, CR1-CR1, CR2-CR2, or CR2-CR1) *Count*:
 Read number of each sequence
DOI: 10.5061/dryad.dncjsxmb6
title: Leatherback sea turtle (<em>Dermochelys coriacea</em>) presence locations used to generate distribution models in the Northwest Atlantic Ocean

description: Leatherback sea turtles (Dermochelys coriaces) are a highly migratory
 species of great conservation concern across the globe. Determining their
 distributions is important not only for establishing baselines to
 determine potential effects of altering ocean conditions but also for
 predicting potential interactions with anthropogenic activities. Here, we
 assembled a dataset of 82,963 ARGOS and FASTloc GPS locations from 75
 leatherbacks tagged with satellite transmitters off the east coast of the
 United States between 2017 and 2024. These locations have been filtered to
 exclude instances where the tag prematurely detached.
description: # Leatherback sea turtle (*Dermochelys coriacea*) presence locations used
 to generate distribution models in the Northwest Atlantic Ocean Dataset
 DOI: [10.5061/dryad.dncjsxmb6](10.5061/dryad.dncjsxmb6) ## Description of
 the data and file structure This dataset contains raw Argos and Fastloc
 GPS locations of leatherback sea turtles tagged with satellite
 transmitters off the east coast of the United States between 2017 and
 2024. We have rounded the latitude and longitude to the nearest 0.1
 decimal degree, as well as rounded the datetime stamp to the year, to
 reduce any potential adverse impacts to conservation efforts or introduce
 unintended risk to this population.  ### Files and variables The raw
 location data are provided as a .csv file named
 "raw_location_data.csv" which can be read and further processed
 in R to estimate true locations using continuous time correlated random
 walks (i.,e. R package aniMotum), and subsequently joining environmental
 data for assembling species distribution models. The file has X columns: 
 1. DeployID: Identification number of the satellite transmitter 2. Year -
 Year in which the location was recorded. 3. Type - How locations were
 derived: User (indicates tagging location), Argos, or Fastloc GPS. 4.
 Quality - Quality classes of locations. Argos location quality classes
 include Z, B, A, 0, 1, 2, 3, while Fastloc GPS locations include 4-9,
 which coordinates with the number of satellites used to estimate the GPS
 location.  5. Latitude - Rounded to the nearest 0.1 decimal degree.  6.
 Longitude - Rounded to the nearest 0.1 decimal degree. ## Access
 information Other publicly accessible locations of the data: * These data
 are in the process of being made available on NOAA's National Center
 for Environmental Information (NCEI). This process may take up to one
 year. The following link provides details on the dataset and will allow
 users to download these data once processed
 ([https://www.ncei.noaa.gov/archive/accession/0304726](https://www.ncei.noaa.gov/archive/accession/0304726)).
DOI: 10.15468/dl.wrhu78
title: Occurrence Download

description: A dataset containing 962 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Axius stirynchus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 962 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004394-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wdbrv161k
title: Complete genome sequence of Picosynechococcus sp. strain NKBG15041c, a fast-growing marine cyanobacterium

description: Here, we report the complete genome sequence of Picosynechococcus sp.
 strain NKBG15041c, which was isolated from coastal seawater in Okinawa
 prefecture, Japan. Additionally, we determined the complete sequences of
 three associated plasmids. The genomic DNA was sequenced using both
 Illumina and PacBio platforms. Genome assembly, integrating PacBio long
 reads and Illumina short reads, was performed using B-assembler. The
 longest circular contig represents the complete genome of P. NKBG1504c,
 comprising 2,845,435 bp with a G+C content of 49.8%. The three circular
 contigs showed high homology with plasmids from Synechococcus sp.
 NIES-970.
description: # Complete genome sequence of Picosynechococcus sp. strain NKBG15041c, a
 fast-growing marine cyanobacterium This Readme file lists the raw sequence
 files of Illumina short reads and PacBio Long reads for the genome of
 *Picosynechococcus* sp. strain NKBG1504c. Dataset DOI:
 [10.5061/dryad.wdbrv161k](10.5061/dryad.wdbrv161k) ## Description of the
 data and file structure *P*. NKBG15041c was cultivated in BG11 medium
 supplemented with 3% NaCl under continuous illumination (50 µmol
 photons m⁻² s⁻¹) at 30 °C with shaking at 100 rpm. Cells were grown until
 the OD₆₆₀ reached 0.4, and then harvested by centrifugation at 8,000×g for
 10 minutes at 4℃. Genomic DNA was extracted from bacterial pellets using
 ISOIL for Bead Beating (NIPPON GENE) according to the manufacturer’s
 instructions. Following RNase treatment for 30 minutes at 4 °C, the DNA
 was purified by phenol-chloroform extraction and ethanol precipitation.
 For Illumina sequencing, 500 ng of genomic DNA was fragmented to a target
 size of 350 bp (range: 250–650 bp) using a Covaris M220
 Focused-ultrasonicator and purified using PCR Clean DX Beads (Aline
 Biosciences). Library preparation was performed using the NEB Next Ultra
 II DNA Library Prep Kit for Illumina (NEB). The resulting sequencing
 libraries were quantified using the Qubit DNA Assay (Thermo Fisher
 Scientific), and their fragment size distribution was assessed using the
 TapeStation D1000 ScreenTape (Agilent). The library was sequenced with
 150-bp pair-end reads on the Novaseq 6000 Sequencing System. For PacBio
 sequencing, 3 μg of genomic DNA was sheared to an appropriate fragment
 length by g-TUBE (Covaris) and used for library construction with the
 SMRTbell® Prep Kit 3.0 (PacBio). The library concentration was quantified
 using a Qubit 3.0 Fluorometer (Invitrogen), and its size distribution was
 assessed using an Agilent 2100 Bioanalyzer System. Subsequent steps were
 carried out according to the manufacturer's instructions. The library
 was sequenced using HiFi chemistry on the PacBio Sequel IIe platform. ####
 Files ##### **Illumina short read** 15041c-genome_R1_001.fastq.gz
 15041c-genome_R2_001.fastq.gz ##### **PacBio long read**
 15041c_genome_LGK9224.hifi_reads.fastq
DOI: 10.5281/zenodo.18408044
title: Data for the research "Chemical Geodynamics of Granitoid Magmatism During a Pacific-Philippine Sea Plate Transition in Southwest Japan"
DOI: 10.5281/zenodo.18408043
title: Data for the research "Chemical Geodynamics of Granitoid Magmatism During a Pacific-Philippine Sea Plate Transition in Southwest Japan"
DOI: 10.5061/dryad.f7m0cfz7t
title: Isolation and computer-based structural determination of madangolide b

description: Madangolide (1) is a 17-membered cyclic enamide isolated from the marine
 cyanobacterium Lyngbya bouillonii. Since its discovery in 1999, the
 relative and absolute configurations of 1 have remained unknown. Here, we
 report the isolation, structural determination, and biological activity of
 a new analog of madangolide (1), madangolide B (2), from a marine Moorena
 sp. cyanobacterium. The planar structure of 2 was established using
 conventional two-dimensional NMR spectroscopy. The absolute configuration
 was clarified by comparing the experimental and theoretical data,
 including the chemical shifts, homonuclear and heteronuclear coupling
 constants, and ECD spectra. Based on the similarity of the NMR data, we
 proposed an absolute configuration of madangolide (1) and verified it
 through degradation and derivatization reactions. This study demonstrates
 the effectiveness of modern computational chemistry in revealing the
 stereochemistry of complex natural products with conformational
 flexibility.
description: All NMR spectral data
 were recorded on a JEOL JNM-ECX-400 or a JNM-ECS-400
 spectrometer.
description: # Spectroscopic data for madangolide and madangolide B ## Description of
 the data and file structure NMR data is grouped in appropriately named
 folders. In each folder, raw NMR data (jdf format), structure file (mol
 format), and a short description for the NMR device and processing
 software are provided. The raw NMR data can be processed by various
 programs, such as DELTA, provided by JEOL. ### Files and variables File:
 madangolide1.zip Description: (1) 1H NMR data for madangolide (jdf
 format); (2) structure file of madangolide (mol format); (3) Short
 description for NMR data (txt format). File: mdaongolideB2.zip 
 Description: (1) 1H NMR, 13C NMR, COSY, HMBC, HMQC, NOESY data for
 madangolide B (jdf format); (2) structure file of madangolide B (mol
 format); (3) Short description for NMR data (txt format). Abbreviation
 COSY: correlation spectroscopy, HMBC: heteronuclear multiple-bond
 correlation, HMQC: heteronuclear multiple-quantum correlation, NOESY:
 nuclear Overhauser effect spectroscopy, NMR: nuclear magnetic resonance.
 ## Code/software NMR data can be processed by various software, such as
 DELTA. DELTA can be freely provided from the JEOL website
 ([https://nmrsupport.jeol.com/](https://nmrsupport.jeol.com/)).
DOI: 10.5061/dryad.kprr4xhhg
title: Data from: Counteracting cascades challenge the heterogeneity – stability relationship

description: Spatial environmental heterogeneity is widely assumed to enhance
 ecological stability by promoting refugia, biodiversity, and asynchrony.
 Yet, we lack field experiments testing this fundamental relationship and
 its underlying mechanisms in naturally assembled multitrophic systems. To
 address this gap, we monitored experimental substrates replicating
 topographic heterogeneity on a rocky shore over three years. Contrary to
 theory, heterogeneity showed no net effect on community stability due to
 four counteracting pathways. Heterogeneity increased stability by i)
 providing refugia that enhanced population stability and ii) boosting
 species richness, which promoted asynchrony. At the same time, it
 decreased stability by iii) reducing a dominant non-native species and iv)
 suppressing consumers, both of which otherwise stabilised community
 composition. These opposing processes cancelled out the
 heterogeneity-stability relationship, highlighting the complex and
 multi-causal nature of this relationship. We caution against the
 assumption that increasing heterogeneity universally enhances stability,
 particularly in systems with strong consumer interactions and dominant
 species.
description: # Data from: Counteracting Cascades Challenge the Heterogeneity–Stability
 Relationship This repository provides the data used in the study: **Sola,
 J., Fairchild, T.P., Perkins, M.J., Bull, J.C., & Griffin, J.N.
 (2025).** *Counteracting cascades challenge the heterogeneity–stability
 relationship.* *Ecology Letters*. Dataset DOI:
 [10.5061/dryad.kprr4xhhg](10.5061/dryad.kprr4xhhg) The study is based on a
 three-year field experiment on a temperate rocky shore, testing the widely
 held ecological assumption that spatial heterogeneity promotes community
 temporal stability. Contrary to theoretical expectations, we found that
 heterogeneity had no net stabilising effect, due to opposing cascades
 involving species richness, population variability, and suppression of
 dominant species. This repository enables full reproducibility of all
 analyses, figures, and models presented in the paper. ### Repository
 Contents The following files are included: * **Raw_community_tax.csv**:
 Species-level percent cover data by tile and sampling date. *
 **Community_data.csv**: Processed dataset containing diversity metrics. *
 **ShoreHeight.csv**: Shore height measurements per experimental plot. *
 **Stability_metrics.csv**: Final dataset derived from the above,
 containing all calculated temporal stability metrics. * **Metadata.xlsx**:
 Description of all variables included in the datasets above, including
 units and data types. ### Citation If using these data, you are encouraged
 to cite both the publication and the Dryad dataset DOI. ## Other sources
 for these data: The datasets used in the analyses are also available at
 the companion GitHub repository:
 [https://github.com/JSolaC/Solaetal2025-Stability](https://github.com/JSolaC/Solaetal2025-Stability)
DOI: 10.15468/dl.vwv2z3
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudione confusa",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004396-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8cz8w9h49
title: Productivity-driven decoupling of microbial carbon use efficiency and respiration across global soils

description: Despite extensive research on soil microbial carbon use efficiency (CUE),
 its linkage to actual soil organic C dynamics remains ambiguous. A key
 uncertainty is that CUE estimates derived from short-term labeling
 incubations assume a linear negative relationship with pulse respiration
 rates, thereby overlooking widespread nonlinear interactions and long-term
 microbial acclimation in natural ecosystems. Here, we synthesized 1,094
 paired observations of CUE and average annual heterotrophic respiration
 rate (Rh) across global natural ecosystems, and found a nonlinear
 relationship between them governed by ecosystem productivity. In
 low-productive arid and cold regions, CUE declined with increasing Rh. In
 contrast, in high-productivity tropical and temperate regions, CUE
 stabilized at a low level (0.27±0.11) as Rh exceeded a threshold of
 340±10.8 g C m-2 y-1. This shift reflects a fundamental microbial
 trade-off between C assimilation and the maintenance of stoichiometric
 homeostasis.
description: # Productivity-driven decoupling of microbial carbon use efficiency and
 respiration across global soils Dataset DOI:
 [10.5061/dryad.8cz8w9h49](https://doi.org/10.5061/dryad.8cz8w9h49) ##
 Description of the data and file structure The dataset (Raw_Data.csv)
 include 1094 pried observations of CUEst and Rh, as well as other
 environmental variables (Soil_MAT, MAP, LAI, and Soil_pH). | Variables |
 Full name | Unit | | :-------------- |
 :------------------------------------------------------ | :---------- | |
 Paper\_ID | Unique number of publication | - | | Climatic\_Group | global
 Köppen-Geiger classification of climate | - | | Soil\_MAT | Soil mean
 annual temperature | ℃ | | MAP | Mean annual precipitation | mm | | LAI |
 Leaf area index | m2 m-2 | | Soil\_pH | Soil pH | - | | CUEst |
 Stoichiometry-estimated microbial carbon use efficiency | - | | Rh |
 Average annual soil heterotrophic respiration rates | g C m-2 y-1 |
DOI: 10.6084/m9.figshare.31175359
title: Data for Obesity Publication

description: Data on the food environment for South Los Angeles and the San Fernando Valley.
DOI: 10.6084/m9.figshare.31175359.v1
title: Data for Obesity Publication

description: Data on the food environment for South Los Angeles and the San Fernando Valley.
DOI: 10.15468/dl.ynxsdr
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aega bicarinata",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 51 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004397-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.