cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/dxn-wzy-z1l
title: Sirenites

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/03e-a08-c1p
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/n9g-3gs-776
title: Arcestes

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/aan-8hc-l6z
title: Nuculana Link, 1807

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t47-456-3fs
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/df4-d8m-da4
title: Fusiturris Thiele, 1929

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/r3y-7f7-3s2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/5l9-rpb-bx4
title: Gastropoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e2p-qes-b56
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zg8-5x9-ny0
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9nd-dhc-c5a
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sh0-dpr-lcf
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a0x-2v4-g4e
title: Stomopneustes variolaris (Lamarck, 1816)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qsy-cjk-e6z
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/phd-bfx-xsk
title: †Spiropora elegans Lamouroux, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8ra-2vb-ccx
title: Cnidaria

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zbw-r8y-30t
title: Echinodermata

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/mcj-yyl-mml
title: †Androgynoceras capricornus (Schlotheim, 1820)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y99-wvd-3fm
title: Cephalopoda Cuvier, 1795

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.21233/s3zs-py78
title: Stordalen testate amoebae surface sample dataset

description: Raw data for the Stordalen testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22781714
title: Genome Analyses of 1,154 budding yeasts

description: Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation. 
<br>
This item includes the raw data for multiple analyses conducted on the genomic data. Each folder contains a readme.txt file that details the analysis and file formats. The analyses included in this folder are
<br>

 <strong>annotations_pep_interproscan.zip</strong>: InterPro - InterProScan was run on every genome annotation. The raw results are reported for all 1,154 yeasts. 
 <strong>y1000p_codetta_output.tar.gz</strong>: Codetta analysis - Codetta was run on every genome to determine the likely genetic code. 
 <strong>y1000p_orthofinder.tar.gz</strong>: Orthfinder Results - Orthofinder was run on all genome annotations to create orthogroups 
  <strong>y1000p_tRNA_scan.tar.gz</strong>: tRNAscan Results - tRNAscan was run on each genome assembly to determine the copy number, location and state of tRNAs within the genomes
 <strong>y1000plus_annotations_pep_kegg.tar.gz: </strong>KEGG Annotations - KEGG orthology was assigned to each genome annotation. 
 <strong>y1000p_repeatmsker_analysis.tar.gz: </strong>Repeatmasker analysis - Repeatmasker was run on all genome assemblies. A masked version of each genome is included in this folder
 <strong>Y1000p_BUCO_fulltable.tar.gz: </strong>BUSCO analysis - BUSCO was run on all genome assemblies. The "full table" results are reported for each genome
DOI: 10.21233/qbmv-wq98
title: Osoyoos Lake ostracode surface sample dataset

description: Raw data for the Osoyoos Lake ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22802147
title: Genomes and Annotations of 1,154 budding yeasts

description:   
<strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</strong>. 
<br>
This item contains the genomes and annotations for the 1,154 budding yeasts that were sequenced or re-annotated in this project. 
<br>

 <strong>y1000p_cds_files.tar.gz</strong> - Fasta files of the nucleotide sequences for the gene annotations in the format assembly_fullID.final.cds
 <strong>y1000p_gff3_files.tar.gz</strong> - GFF3 files of the gene annotations in the format assembly_fullID.final.gff3
 <strong>y1000p_gtf_files.tar.gz</strong> - GTF files of the gene annotations in the format assembly_fullID.final.gtf
 <strong>y1000p_pep_files.tar.gz</strong> - Fasta files of the amino acid sequences for the gene annotations in the format assembly_fullID.final.pep
 <strong>y1000p_genome_files.zip</strong> - Fasta files of the assembled genome sequences in the format assembly_fullID.fas.gz
DOI: 10.25452/figshare.plus.22802147.v1
title: Genomes and Annotations of 1,154 budding yeasts

description:   
<strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</strong>. 
<br>
This item contains the genomes and annotations for the 1,154 budding yeasts that were sequenced or re-annotated in this project. 
<br>

 <strong>y1000p_cds_files.tar.gz</strong> - Fasta files of the nucleotide sequences for the gene annotations in the format assembly_fullID.final.cds
 <strong>y1000p_gff3_files.tar.gz</strong> - GFF3 files of the gene annotations in the format assembly_fullID.final.gff3
 <strong>y1000p_gtf_files.tar.gz</strong> - GTF files of the gene annotations in the format assembly_fullID.final.gtf
 <strong>y1000p_pep_files.tar.gz</strong> - Fasta files of the amino acid sequences for the gene annotations in the format assembly_fullID.final.pep
 <strong>y1000p_genome_files.zip</strong> - Fasta files of the assembled genome sequences in the format assembly_fullID.fas.gz
DOI: 10.21233/mpsw-hc12
title: LDDsite296 ostracode surface sample dataset

description: Raw data for the LDDsite296 ostracode surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.sk2qf2
title: Occurrence Download

description: A dataset containing 137 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-82.54244 32.3894,-75.2174 32.3894,-75.2174 36.86798,-82.54244 36.86798,-82.54244 32.3894))",
 "OccurrenceStatus is Present",
 "TaxonKey is Parthenium integrifolium L."
 ]
}

 The dataset includes 137 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022184-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/0017-2n24
title: Fleet Moss testate amoebae surface sample dataset

description: Raw data for the Fleet Moss testate amoebae surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22806416
title: Dataset supporting Figure 2: Phylogenomics

description: <br><b>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</b>.<br>This item includes raw and underlying data associated with Figure # 2 in the manuscript. Input files and results from the construction of the phylogenetic tree of the Saccharomycotina subphylum.<br>Each item contains a README.txt file that gives specific details on the analysis, file structure, and folder structure.<br><b>y1000p_1403_OG_files.tar.gz </b>- The 1403 ortho groups used to construct the phylogeny of the subphylum<b>1154yeasts_1403OGs_ml_timetree.tree</b> - Tree file containing the time tree calibrated phylogeny<b>1154yeasts_1403OGs_ml_timetree_times.txt</b> - File containing the estimated times associated with the time tree<b>1175taxa_1403OGs_iqtree_ML_rooted.nex</b> - Nexus tree file containing the rooted tree file used in Figure 2 and the supplemental tree file<b>1175taxa_1403OGs_astral_length_rooted_lpp_added.tre - </b>Tree file containing the yeast phylogeny estimated using ASTRAL<b>1000_strip*.txt </b>- iTOL (itol.com) files to identify the isolation environment of the strains. <b>itol_color_strip.txt </b> - Add colors to the tree in iTOL<b>ALL_NAMES_FILE.xlsx </b>- The names on the tree have been adjusted to reflect the most recent naming conventions (as of November 2023). This file contains the matching names across the dataset, including earlier versions of the phylogenetic trees which were used for some analyses<br><br>
DOI: 10.21233/3kyw-bp04
title: Gerlach Pond diatom surface sample dataset

description: Raw data for the Gerlach Pond diatom surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22806455
title: Dataset supporting Figure 3: Generalist/Specialist Analyses

description:   
<strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</strong>. 
<br>
This item includes raw and underlying data associated with Figure 3 in the manuscript. 
<br>
These items were used to assess the evolution and frequency of the generalist and specialist niche breadth in the budding yeasts.
<br>
Each item includes a README.txt file that includes specific information about the analysis, file structure, and folder structure. 
<br>

 <strong>bayes_carb_v_class_coevolution.tar.gz </strong> - Bayestraits outputs to compare gain and loss of carbon metabolism traits in generalist and specialist backgrounds. Includes data shown in Fig 3D
 <strong>bayes_carbon_nitrogen_coevolution.tar.gz</strong> - Bayestraits outputs for the analysis that modeled co-evolution between carbon and nitrogen breadth. Data discussed in the manuscript
  <strong>carbon_breadth_reconstruction.tar.gz</strong> - Bayestraits ancestral reconstruction of carbon breadth
 <strong> CarbonNitrogen_Classifications.zip </strong>- Data file containing information about carbon and nitrogen classifications
DOI: 10.21233/3whj-bt69
title: Lily Pond water chemistry dataset

description: Raw data for the Lily Pond water chemistry dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22840730
title: Phenotyping Data for Saccharomycotina Yeasts

description:   
<strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation</strong>. 
<br>
Phenotypic data for 853 yeast strains in 24 conditions. These data include the raw optical density (OD) reads from the plate reader and the average growth rates quantified from those raw reads. These data were used throughout the manuscript.
<br>
The data is further described in the<strong> README_PhenotypingData.txt</strong>
DOI: 10.21233/mxfv-1595
title: Geneva Lake diatom dataset

description: Raw data for the Geneva Lake diatom dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/6kgm-zr91
title: Maly Suszek pollen dataset

description: Raw data for the Maly Suszek pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22903130
title: Dataset supporting Figure 5: Environmental Data

description: <strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.</strong>
<br>
This item includes raw and underlying data associated with Figure 5 in the manuscript. 
<br>
These items were used to assess differences in isolation environments between generalist and specialist yeasts. 
<br>
Each item (when appropriate) includes a README.txt file that includes specific information about the analysis, file structure, and folder structure. 
<br>

 <strong>budding_yeasts_isolations.owl </strong>- Ontology of isolation environments generated for the budding yeasts. This file is in OWL (web ontology language)  format. Details on this file format can be found here: https://www.w3.org/TR/owl2-primer/ 
 <strong>budding_yeasts_isolations.owx </strong>- Ontology of isolation environments generated for the budding yeasts. This file is in OWX format. Details on this file format can be found here: https://www.w3.org/TR/owl-xml-serialization/
  <strong>PCA_distance_matrix.csv</strong> - CSV file containing the species-to-species distances generated from the phylogenetic PCA of growth rate data. These distances are used in Fig C and a subset of the PCA is shown in Fig 5D.
DOI: 10.21233/dgtd-b361
title: Denny Pond diatom dataset

description: Raw data for the Denny Pond diatom dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.25452/figshare.plus.22904597
title: Dataset supporting Figure 6: Power of y1000+

description: <strong>Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,090 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.</strong>
<br>
This item includes raw and underlying data associated with Figure 5 in the manuscript. 
<br>
These items were used to assess differences in pathogenicity between generalist and specialist yeasts. 
<br>
Each item (when appropriate) includes a README.txt file that includes specific information about the analysis, file structure, and folder structure. 
<br>

 <strong> y1000p_growth_at_37.xlsx </strong>- Excel file that categorizes each of the species as being able to grow at 37C or not. Column names are: assembly_fullID_updated, at_37_C, and Temp_Source. 

         -<em> assembly_fullID_updated</em> - the assemblyID of each species analyzed
         - <em>at_37_C </em>- growth at 37 including Y (yes), N (no), W (weak), V (variable), S (slow)
         - <em>Temp_Source </em>- the resource that was used to identify growth or no growth including the Yeast Book     (Kurtzman CP, Fell JW, Boekhout T, editors. The yeasts: a taxonomic study. Elsevier; 2011 May 9.) and the CBS database (https://wi.knaw.nl/fungal_table)
<br>

  <strong>y1000p_HSP_seqs.zip </strong>- HSP annotation information used in Figure 6

<br>
DOI: 10.21233/44bw-eg51
title: NEWSU 24 pollen surface sample dataset

description: Raw data for the NEWSU 24 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.