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

description: A dataset containing 36360 records in GBIF matching the query:
SELECT
 '513' 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;= 40.08862809834564
 AND decimalLongitude &lt;= 50.36857131846712
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 36360 records were derived from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004335-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j3tx95xsj
title: Statistical code from: Passive acoustic monitoring with AI-based detection and identification reveal sooty grouse hooting patterns in western Oregon

description: We estimated sooty grouse hooting patterns, both daily and seasonal, using
 generalized additive mixed models (GAMMs) using hooting data. The
 influence of weather, topographic, and study region were examined using
 these models, as were time since sunrise (daily) and day of year
 (seasonal). For both daily and seasonal frameworks, we compare models that
 incorporate both smooth and fixed terms using the mgcv package in Program
 R using the percent of deviance explained.
description: # Statistical code from: Passive acoustic monitoring with AI-based
 detection and identification reveal sooty grouse hooting patterns in
 western Oregon Dataset DOI:
 [10.5061/dryad.j3tx95xsj](10.5061/dryad.j3tx95xsj) ## Description of the
 data and file structure ### Files and variables #### File:
 Daily_GAMM_models.R **Description:** Daily GAMM models run in R with mgcv
 package. #### File: df_daily.csv **Description:** Daily data used as input
 for GAMM models **Column definitions:** * Year_Station_ARU: Unique ID for
 each ARU by location and year * Route_ID: Route ID of the sooty grouse
 hooting survey route the ARU was deployed on * Ecoregion: Physiographic
 province. These provinces represent different forest zones and
 environmental factors across western Oregon. * Date: Date * Time: Time
 (Start time of the 10 minute block) * hootsPer10Minutes: Number of sooty
 grouse hoots detected by PNW-Cnet for that 10 minute block of time * Year:
 Year * Elevation: Elevation, in meters * dayOfYear: Julian day of year *
 timeSinceSunrise_min: Time since sunrise, in minutes * dailyPrecip_mm:
 Daily precipitation, in millimeters * minTemp_c: Minimum daily
 temperature, in Celsius #### File: Seasonal_GAMM_models.R
 **Description:** Seasonal GAMM models run in R with mgcv package ####
 File: df_seasonal.csv **Description:** Seasonal data used as input for
 GAMM models **Column definitions:** * Year_Station_ARU: Unique ID for each
 ARU by location and year * Route_ID: Route ID of the sooty grouse hooting
 survey route the ARU was deployed on * Ecoregion: Physiographic province.
 These provinces represent different forest zones and environmental factors
 across western Oregon. * Date: Date * dailyHoots: Number of sooty grouse
 hoots detected by PNW-Cnet for that day * Year: Year * Latitude: Latitude,
 in decimal degrees * Elevation: Elevation, in meters * dayOfYear: Julian
 day of year * dailyPrecip_mm: Daily precipitation, in millimeters *
 minTemp_c: Minimum daily temperature, in Celsius * recordingTime_hours:
 Number of hours the ARU recorded that day ## Code/software We ran the
 generalized additive models in program R (R Core Team 2023) using package
 mgcv (Wood 2006). We used gam() for the seasonal models and bam() for the
 daily models, since the daily model was a very large dataset and bam()
 uses less memory.
DOI: 10.15468/dl.hu6ts5
title: Occurrence Download

description: A dataset containing 324 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-114.55537 14.97164,-84.44463 14.97164,-84.44463 27.02836,-114.55537 27.02836,-114.55537 14.97164))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mimosa luisana"
 ]
}

 The dataset includes 324 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004354-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3r2280gtq
title: Data from: Links between leaf morphology and ecological strategy across secondary succession in a temperate deciduous forest (North Carolina, USA): Implications for the fossil record

description: The fossil record offers important opportunities to reconstruct plant
 community responses to past disturbance events. Yet, reconstructions are
 hindered by limited empirical evidence of successional variation in
 functional traits measurable on fossil leaves, including leaf morphology
 and δ13C. In addition, the role the leaf economic spectrum (LES) plays
 across succession within temperate deciduous forests is unresolved.
 Lastly, it is unclear to what degree disturbance confounds the leaf
 morphology-climate relationships utilized in paleoclimate proxies. We
 utilize a chronosequence spanning forest stands varied by time since
 logging (4, 21, 44, 94 years old), and one old-growth stand, in North
 Carolina. Leaf traits of woody non-monocot angiosperms (WNMA) leaves,
 including all trees and prominent understory plants, were measured to
 document patterns relating to the LES (e.g., leaf mass per area [LMA]),
 patterns of leaf morphology and δ13C, and the confounding influence on
 climatic estimates using the digital leaf physiognomy proxy.
description: # Data from: Links between leaf morphology and ecological strategy across
 secondary succession in a temperate deciduous forest (North Carolina,
 USA): Implications for the fossil record Dataset DOI:
 [10.5061/dryad.3r2280gtq](10.5061/dryad.3r2280gtq) ## Description of the
 data and file structure This dataset contains three data files. The first
 contains metadata and other data collected at the time of leaf collection,
 including the site the leaf was sampled in and the taxa it was sampled
 from. The second contains raw measurements of leaf morphology and the
 third contains diameter at breast height measurements of all trees with
 DBH equal to or greater than 10 cm in each study plot used for
 abundance-weighting trait values at a site-level.  In each spreadsheet, a
 "Headers" tab exists and provides detail for the meaning of all
 column headers.  ### Files and variables #### File: Leaf\_metadata.xlsx
 **Description:** Metadata and other data collected at the time of leaf
 collection, including the site the leaf was sampled in and the taxa it was
 sampled from ##### Variables * See "Headers" column #### File:
 Plot\_DBH-SBA.xlsx **Description:** Diameter at breast height measurements
 of all trees with DBH equal to or greater than 10 cm in each study plot
 used for abundance-weighting trait values at a site-level.  #####
 Variables * See "Headers" column #### File: Leaf\_traits.xlsx
 **Description:**  Raw measurements of leaf morphology. Note, n/a values
 designate values which are not possible to measure (e.g., tooth variables
 on untoothed leaves), we were unable to measure because of damage to the
 leaf, or in the case of chemical data (C and N), were not measured because
 of constraints on time and cost.  ##### Variables * See
 "Headers" column ## Code/software All files are Microsoft Excel
 files.
DOI: 10.15468/dl.ypknje
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polymorphus contortus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 24 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004353-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wkhq3r
title: Occurrence Download

description: A dataset containing 14981 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Icaricia icarioides"
 ]
}

 The dataset includes 14981 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004355-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xgxd254t2
title: Gene turnover and contingency facilitated the repeated evolution of C<sub>4</sub> photosynthesis in grasses

description: In grasses, almost all species belong to two evenly sized clades (BOP and
 PACMAD), yet the &gt;20 independent origins of C4 photosynthesis in
 this family only occur in the PACMAD lineage. Here, we identify potential
 genetic precursors for C4 photosynthesis that were present at the base of
 the PACMAD clade, representing the last common ancestor of all C4 grasses.
 We generated the first reference genomes for Aristidoideae species
 (Aristida adscensionis and Stipagrostis hirtigluma), the sister lineage of
 all other PACMAD grasses. In combination with 34 other Poales genomes, we
 identify gene gains at the base of the PACMAD clade, and genes lost in the
 sister BOP lineage. Candidate C4 precursors include β-carbonic anhydrase,
 as well as genes involved in amino acid and nitrate transport, carbon
 metabolism, oxidative stress management and transcription regulation. Gene
 turnover created the necessary genetic contingency, facilitating the
 independent recruitment and refinement of C4 genes in multiple independent
 origins. Our results support the idea that the repeated evolution of C4
 photosynthesis in PACMAD grasses was not driven by a single genetic event
 but was instead underwritten by chance genetic changes that originated
 long before there was selection for the trait itself.
description: # Gene turnover and contingency facilitated the repeated evolution of
 C<sub>4</sub>photosynthesis in grasses Dataset DOI:
 [10.5061/dryad.xgxd254t2](10.5061/dryad.xgxd254t2) ## Description of the
 data and file structure We generated HiFi reads of two Aristidoideae
 species, *Aristida adscensionis* and *Stipagrostis hirtigluma* (grasses
 from the PACMAD clade), assembled a draft genome, and performed gene
 annotation for each of them.  ### Files and variables #### File:
 Stipagrostis_4n_nuclear-softMasked.gff3 **Description:** Gene annotation
 for *Stipagrostis hirtigluma* using Helixer. #### File:
 Stipagrostis_4n_nuclear-softMasked.fna **Description:** Fasta file
 containing all the contig sequences assembled for *Stipagrostis
 hirtigluma*. #### File: Aristida_nuclear-softMasked.gff3
 **Description:** Gene annotation for *Aristida adscensionis* using
 Helixer. #### File: Aristida_nuclear-softMasked.fna **Description:** Fasta
 file containing all the contig sequences assembled for *Aristida
 adscensionis*. #### **File: Re-annotations-Helixer.zip** **Description:**
 GFF3 files for the 7 re-annotated grass genomes detailed in Table S1. ####
 **File: Core-set-OF.zip** **Description:** Trees and multiple sequence
 alignments generated by OrthoFinder for the core set of candidate genes.
 #### **File: ML_trees.zip** **Description:** Maximum likelihood trees
 constructed with PhyML. ## Code/software The used software is detailed in
 the associated preprint article. ## Access information Other publicly
 accessible location of the data: NCBI
 bioproject [PRJNA1254624](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1254624)
DOI: 10.6073/pasta/89360462123ccb4b0391868078a7e0fd
title: Stream and lake water chemistry data for Green Lakes Valley, 1998 - ongoing.

description: This is a summary of major ion concentrations for lake water at
 selected depths as well as for the inlets and outlets of Green Lakes
 1, 4, and Lake Albion. On some occasions the same samples were also
 taken from other lakes in the Green Lakes Valley, such as Green
 Lakes 2, 3 and 5.
DOI: 10.5517/ccdc.csd.cc2mccx9
title: CCDC 2424011: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mccyb
title: CCDC 2424012: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mcczc
title: CCDC 2424013: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mcd0f
title: CCDC 2424014: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mcd1g
title: CCDC 2424015: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2mcd2h
title: CCDC 2424016: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p8nbz
title: CCDC 2480971: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p8nc0
title: CCDC 2480972: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p8nd1
title: CCDC 2480973: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p8nf2
title: CCDC 2480974: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p8ng3
title: CCDC 2480975: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.mgqnk999w
title: Data from: A target capture-based phylogeny of emerald moths (Lepidoptera: Geometridae: Geometrinae) provides new insights into tribal-level classification

description: The emerald moths (Lepidoptera: Geometridae: Geometrinae) are a
 cosmopolitan subfamily with over 275 genera and 2,600 species. Most of
 these moths are characterized by a green ground color, with different
 lineages exhibiting different shades of green. The monophyly of
 Geometrinae has been confirmed by multiple phylogenetic analyses. However,
 the relative placement of many of the geometrine tribes is poorly
 supported. In this study, we use anchored hybrid enrichment to obtain
 phylogenomic data from over 400 loci for 63 genera of emerald moths, with
 complete taxon sampling at the tribe level (representing all 23 proposed
 tribal hypotheses), and generate a maximum likelihood tree to assess the
 status of these tribes. We treat Dichordophorini Ferguson as a junior
 synonym (syn.n.) of Nemoriini Gumppenberg, and propose two new subtribes
 of Hemitheini Bruand: Oospilina subtr.n. and Xanthoxenina subtr.n.
description: # A target capture-based phylogeny of emerald moths (Lepidoptera:
 Geometridae: Geometrinae) provides new insights into tribal-level
 classification Dataset DOI:
 [10.5061/dryad.mgqnk999w](10.5061/dryad.mgqnk999w) ## Description of the
 data and file structure In this study, we used anchored hybrid enrichment
 to obtain phylogenomic data from over 400 loci for 63 genera of emerald
 moths (Lepidoptera: Geometridae: Geometrinae), with complete taxon
 sampling at the tribe level (representing all 23 proposed tribal
 hypotheses), and generated a maximum likelihood tree to assess the status
 of these tribes. ### Files and variables **File:
 all_genetrees_for_ASTRAL.txt** Description: Text file listing all 405 gene
 trees (in newick format) used as input for the ASTRAL analysis **File:
 Degen_partitionscheme.nex** Description: Partition scheme used to generate
 the ML tree in Fig. S2 **File: Degen_supermatrix.fas** Description: Fasta
 file containing the aligned, concatenated Degen dataset used to generate
 the ML tree displayed in Fig. S2 **File: FigS1_nt123.tre**
 Description: Unrooted tree file corresponding to the ML tree in Fig. S1
 **File: FigS2_Degen.tre** Description: Unrooted tree file corresponding to
 the ML tree in Fig. S2 **File: FigS3_ASTRAL.tre** Description: Unrooted
 tree file corresponding to the ASTRAL tree in Fig. S3 **File:
 individual_loci.zip** Description: Individual fasta files corresponding to
 each of the 405 loci used to generate datasets for tree-building **File:
 nt123_partitionscheme.nex** Description: Partition scheme used to generate
 the ML tree in Fig. 2 and Fig. S1 **File: nt123_supermatrix.fas**
 Description: Fasta file containing the aligned, concatenated nt123 dataset
 used to generate the ML tree displayed in Fig. 2 and Fig. S
DOI: 10.5517/ccdc.csd.cc2p8nh4
title: CCDC 2480976: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2p8nj5
title: CCDC 2480977: Experimental Crystal Structure Determination

description: Related Article: Huaiyuan Zhu, Shicheng Dong, Xufang Liu, Xiyuan Li, Tobias Weng, Jun Zhu, Shigeyoshi Inoue|2025|Angew.Chem.,Int.Ed.|65|e18102|doi:10.1002/anie.202518102
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.