cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10684821
title: Data from:  Atlantic mackerel population structure does not support genetically distinct spawning components

description: The Atlantic mackerel, Scomber scombrus (Linnaeus, 1758) is a commercially valuable migratory pelagic fish inhabiting the northern Atlantic Ocean and the Mediterranean Sea. Given its highly migratory behaviour for feeding and spawning, several studies have been conducted to identify populations, assess differentiation among spawning components and define species connectivity, as well as to understand possible adaptation linked to recent range expansion northwards. However, the resulting findings did not resolve questions about the presence of genetically distinct spawning components for the species in the northern Atlantic. The increasing use of reference genomes in population genetics studies has proven fundamental to investigate genomic markers/regions potentially linked to differences at finer scale. Here, we sequenced and annotated a high-quality genome of S. scombrus, for a final assembly of 741 Mb in size, which we have used to map Restriction-site-associated sequencing (RAD-seq) reads for SNP discovery and genotyping. Our results based on thousands of SNP markers show that the Atlantic mackerel consist of three previously known genetically separated units (Northwest Atlantic, Northeast Atlantic, Mediterranean), and provide no evidence for genetically distinct spawning components within, nor for further differentiation that could be used to redefine management boundaries.
description: Metadata: Table with samples information for each dataset analysed. Data reporting all valuable information needed for data analysis such as samples ID, barcodes, sequencing pool,location and date of capture, groupings, age, size, sex and maturity stage. TableS1.xlsx

Supplementary S1: Document of Supplementary Tables and Figures. Data reporting additional Tables on (1) datasets compositions and filtering steps of each genotype table;(2) Pairwise FST estimates between NEA populations;(3) Pairwise FST estimates between NWA populations. Additionally, it includes supplementary Figures on (1) Workflow of the genome assembly process, (2) Workflow of the genome annotation process, (3) GenomeScope transformed linear plot, (4) Results of the ADMIXTURE analysis,(5) PCA plots of neutral and putative outlier SNPs for the different datasets and (6) using larvae and spawning adults only. Supplementary_Material.docx

R scripts used in the data analysisld_pruning.r : R script customized to filter SNPs in phisical linkages, customized to select bp range and preferential filtering approach (random SNPs vs SNPs with least amount of missing data).admixture.r : R script to plot admixture results 

Bash scripts for data analysis, from raw fastq file to the production of genotype tables. clean.sh: raw fastq to clean fastq for mappingmapping_ref.sh : mapping to reference genomegstacks_dedup.sh : gstack and de-duplicationadmixture_bash.sh : admxiture analysis bayescan.sh : bayescan analysis
DOI: 10.5281/zenodo.10684820
title: Data from:  Atlantic mackerel population structure does not support genetically distinct spawning components

description: The Atlantic mackerel, Scomber scombrus (Linnaeus, 1758) is a commercially valuable migratory pelagic fish inhabiting the northern Atlantic Ocean and the Mediterranean Sea. Given its highly migratory behaviour for feeding and spawning, several studies have been conducted to identify populations, assess differentiation among spawning components and define species connectivity, as well as to understand possible adaptation linked to recent range expansion northwards. However, the resulting findings did not resolve questions about the presence of genetically distinct spawning components for the species in the northern Atlantic. The increasing use of reference genomes in population genetics studies has proven fundamental to investigate genomic markers/regions potentially linked to differences at finer scale. Here, we sequenced and annotated a high-quality genome of S. scombrus, for a final assembly of 741 Mb in size, which we have used to map Restriction-site-associated sequencing (RAD-seq) reads for SNP discovery and genotyping. Our results based on thousands of SNP markers show that the Atlantic mackerel consist of three previously known genetically separated units (Northwest Atlantic, Northeast Atlantic, Mediterranean), and provide no evidence for genetically distinct spawning components within, nor for further differentiation that could be used to redefine management boundaries.
description: Metadata: Table with samples information for each dataset analysed. Data reporting all valuable information needed for data analysis such as samples ID, barcodes, sequencing pool,location and date of capture, groupings, age, size, sex and maturity stage. TableS1.xlsx

Updated version of "Extended_Data.docx" (originally "Supplementary_Material.docx") with amendments made following reviewers' comments. Document of Supplementary Tables and Figures:Data reporting additional Tables on (1) datasets compositions and filtering steps of each genotype table;(2) Pairwise FST estimates between NEA populations;(3) Pairwise FST estimates between NWA populations. Additionally, it includes supplementary Figures on (1) Workflow of the genome assembly process, (2) Workflow of the genome annotation process, (3) GenomeScope transformed linear plot, (4) Results of the ADMIXTURE analysis,(5) PCA plots of neutral and putative outlier SNPs for the different datasets and (6) using larvae and spawning adults only. 

R scripts used in the data analysisld_pruning.r : R script customized to filter SNPs in phisical linkages, customized to select bp range and preferential filtering approach (random SNPs vs SNPs with least amount of missing data).admixture.r : R script to plot admixture results 

Bash scripts for data analysis, from raw fastq file to the production of genotype tables. clean.sh: raw fastq to clean fastq for mappingmapping_ref.sh : mapping to reference genomegstacks_dedup.sh : gstack and de-duplicationadmixture_bash.sh : admxiture analysis bayescan.sh : bayescan analysis
DOI: 10.5281/zenodo.14629129
title: Data from:  Atlantic mackerel population structure does not support genetically distinct spawning components

description: The Atlantic mackerel, Scomber scombrus (Linnaeus, 1758) is a commercially valuable migratory pelagic fish inhabiting the northern Atlantic Ocean and the Mediterranean Sea. Given its highly migratory behaviour for feeding and spawning, several studies have been conducted to identify populations, assess differentiation among spawning components and define species connectivity, as well as to understand possible adaptation linked to recent range expansion northwards. However, the resulting findings did not resolve questions about the presence of genetically distinct spawning components for the species in the northern Atlantic. The increasing use of reference genomes in population genetics studies has proven fundamental to investigate genomic markers/regions potentially linked to differences at finer scale. Here, we sequenced and annotated a high-quality genome of S. scombrus, for a final assembly of 741 Mb in size, which we have used to map Restriction-site-associated sequencing (RAD-seq) reads for SNP discovery and genotyping. Our results based on thousands of SNP markers show that the Atlantic mackerel consist of three previously known genetically separated units (Northwest Atlantic, Northeast Atlantic, Mediterranean), and provide no evidence for genetically distinct spawning components within, nor for further differentiation that could be used to redefine management boundaries.
description: Metadata: Table with samples information for each dataset analysed. Data reporting all valuable information needed for data analysis such as samples ID, barcodes, sequencing pool,location and date of capture, groupings, age, size, sex and maturity stage. TableS1.xlsx

Updated version of "Extended_Data.docx" (originally "Supplementary_Material.docx") with amendments made following reviewers' comments. Document of Supplementary Tables and Figures:Data reporting additional Tables on (1) datasets compositions and filtering steps of each genotype table;(2) Pairwise FST estimates between NEA populations;(3) Pairwise FST estimates between NWA populations. Additionally, it includes supplementary Figures on (1) Workflow of the genome assembly process, (2) Workflow of the genome annotation process, (3) GenomeScope transformed linear plot, (4) Results of the ADMIXTURE analysis,(5) PCA plots of neutral and putative outlier SNPs for the different datasets and (6) using larvae and spawning adults only. 

R scripts used in the data analysisld_pruning.r : R script customized to filter SNPs in phisical linkages, customized to select bp range and preferential filtering approach (random SNPs vs SNPs with least amount of missing data).admixture.r : R script to plot admixture results 

Bash scripts for data analysis, from raw fastq file to the production of genotype tables. clean.sh: raw fastq to clean fastq for mappingmapping_ref.sh : mapping to reference genomegstacks_dedup.sh : gstack and de-duplicationadmixture_bash.sh : admxiture analysis bayescan.sh : bayescan analysis
DOI: 10.5281/zenodo.14628098
title: Eukaryotic Voltage-gated Sodium Channel Protein Molecules Scaling Properties in the Context of Human Pain Disease

description: Finite-size scaling analysis of 50 eukaryotic voltage-gated sodium channel structures (resolution criterion < 4 Ang):

    1 NaVPas sructure 

    1 NaVEe1 structure 

    1 NaVEh structure

    47 NaV1_to_8 (NaV1.1, NaV1.2, NaV1.3, NaV1.4, NaV1.5, NaV1.6, NaV1.7, NaV1.8) structures

Machine learning experiments summarize the results obtained from classifying pain-disease-associated variants based on derived scaling characteristics. 

For details concerning how the data were produced, how to navigate through the data, and how to process the data toward producing scientific output, please see the corresponding GitHub repository.
DOI: 10.5281/zenodo.14628099
title: Eukaryotic Voltage-gated Sodium Channel Protein Molecules Scaling Properties in the Context of Human Pain Disease

description: Finite-size scaling analysis of 50 eukaryotic voltage-gated sodium channel structures (resolution criterion < 4 Ang):

    1 NaVPas sructure 

    1 NaVEe1 structure 

    1 NaVEh structure

    47 NaV1_to_8 (NaV1.1, NaV1.2, NaV1.3, NaV1.4, NaV1.5, NaV1.6, NaV1.7, NaV1.8) structures

Machine learning experiments summarize the results obtained from classifying pain-disease-associated variants based on derived scaling characteristics. 

For details concerning how the data were produced, how to navigate through the data, and how to process the data toward producing scientific output, please see the corresponding GitHub repository.
DOI: 10.15468/dl.govzmz
title: Occurrence Download

description: A dataset containing 131000 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anura",
 "Geometry POLYGON((-141.20 0.31,-141.20 33.32,-86.09 33.32,-86.09 0.31,-141.20 0.31))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 131000 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023085-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m7rvy5
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ormosia microphylla Merr.",
 "Year 1980-2023"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019563-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qrn8qx
title: Occurrence Download

description: A dataset containing 2929 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidothrix isidorei (P.L.Sclater, 1852)"
 ]
}

 The dataset includes 2929 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074555-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxxdpw
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liabum sublobatum B.L.Rob."
 ]
}

 The dataset includes 18 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023086-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fd2eyj
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Breynia discocalyx (Welzen) Welzen & Pruesapan"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0074553-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g64we6
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Elachistocleis surinamensis (Daudin, 1802))"
 ]
}

 The dataset includes 158 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020723-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9auedi
title: Occurrence Download

description: A dataset containing 19004353 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Canada",
 "Country is United States of America"
 ]
 },
 "BasisOfRecord is Specimen",
 "EventDate is greater than or equal to 1900-01-01"
 ]
}

 The dataset includes 19004353 records from 909 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023088-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11091097
title: 9. FRACTESUS_FRAMATOME_ANP-4_KJc_MCT_-100_BL3E1

description: Fractesus project. Fracture test mini-CT. Raw data ANP-4. Framatome.
DOI: 10.5281/zenodo.11091098
title: 9. FRACTESUS_FRAMATOME_ANP-4_KJc_MCT_-100_BL3E1

description: Fractesus project. Fracture test mini-CT. Raw data ANP-4. Framatome.
DOI: 10.15468/dl.338kda
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tremulina cracens B.G.Briggs & L.A.S.Johnson"
 ]
}

 The dataset includes 73 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018696-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2d29q
title: Occurrence Download

description: A dataset listing the 44 species recorded in GBIF matching the query:
{
 "and" : [
 "GadmGid is COL.27.36_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphibia"
 ]
}

 The dataset's 44 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0298088-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c4z82s
title: Occurrence Download

description: A dataset containing 2324848 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Garrulus glandarius (Linnaeus, 1758)"
 ]
}

 The dataset includes 2324848 records from 2997 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0384720-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e1xh3x
title: Occurrence Download

description: A dataset containing 1096 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus coulteri D.Don"
 ]
}

 The dataset includes 1096 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046063-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vhd2ht
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "TaxonKey is Rhododendron adenopodum Franch.",
 "TaxonKey is Rhododendron aberconwayi Cowan"
 ]
 }
 ]
}

 The dataset includes 41 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214836-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8y3epe
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ficus ampulliformis Corner"
 ]
}

 The dataset includes 11 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006140-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nc5xuq
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calathea neurophylla H.Kenn."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149513-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8sa8gr
title: Occurrence Download

description: A dataset containing 1096 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus coulteri D.Don"
 ]
}

 The dataset includes 1096 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046065-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fkhqnr
title: Occurrence Download

description: A dataset containing 132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Machine Observation",
 "PublishingOrg is e2e717bf-551a-4917-bdc9-4fa0f342c530",
 "TaxonKey is Falco deiroleucus Temminck, 1825"
 ]
}

 The dataset includes 132 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032776-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dfj4me
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cleistocactus laniceps (K.Schum.) Rol.-Goss."
 ]
}

 The dataset includes 31 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0149512-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vfzm3u
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fordiophyton jinpingense J.H.Dai & Z.Y.Yu"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006161-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pag8qj
title: Occurrence Download

description: A dataset containing 1250 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ficus benghalensis L."
 ]
}

 The dataset includes 1250 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234654-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oqy6wu
title: Occurrence Download

description: A dataset containing 4242135 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "StateProvince is nsw",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 4242135 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046067-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8m2jf2
title: Occurrence Download

description: A dataset containing 10760 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Carex trinervis Degl."
 ]
}

 The dataset includes 10760 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0214855-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a8aysc
title: Occurrence Download

description: A dataset containing 1781 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Anabazenops dorsalis (P.L.Sclater & Salvin, 1880)"
 ]
}

 The dataset includes 1781 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006216-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ixbkv
title: Occurrence Download

description: A dataset containing 1507 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-35.03789 20.20433,67.61836 20.20433,67.61836 61.24925,-35.03789 61.24925,-35.03789 20.20433))",
 "DatasetKey is The French Collection of Medicago truncatula",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1507 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046070-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.npxpk7
title: Occurrence Download

description: A dataset containing 766031 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lauraceae"
 ]
}

 The dataset includes 766031 records from 1352 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0237720-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.