cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15587049
title: Supporting data for: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae

description: This is supporting sequence data for the paper: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae. It contains DNA and protein sequences as well as gene trees for 2135 loci for the investigation of the phylogenetic placement of the parasitic Rafflesiaceae and Apodannthaceae. Three datasets were included:

Data S1 Sequence alignments and gene trees for the 2135 loci analyzed in the study. The lists of loci included in the data subsets G446 and G829 are also provided. Both the raw alignments and masked alignments by HmmCleaner are provided for DNA and protein sequences. Each gene has 5 sets of gene trees inferred using different models in IQTREE:(1) *.GTR_codon.treefile: codon-based partition within gene (first, second, third codon in separate partitions) + forcing GTR (no +I or +R or +G); (2) *.MFP_codon.treefile: codon-based partition within gene + ModelFinder best fitting model; (3) *.msetGTR.treefile: no partition within gene + forcing GTR (with +I or +R or +G); (4) *.msetGTR_codon.treefile: codon-based partition within gene + forcing GTR (with +I or +R or +G); (5) *.na.mask.fas.treefile: no partition within gene + ModelFinder best fitting model.

Data S2 Species tree in newick format generated by the 22 analyses described in Cai et al. Table 1 and Appendix S9. For partition-based concatenation analyses, the best partition and substitution scheme in nexus format from IQ-TREE is also provided.The program and command line used to generate these species trees can be found on GitHub: https://github.com/lmcai/Rafflesiaceae_phylogenomics/tree/master/4_phylogeny_hypo_generation

Data S3 Log Likelihood per gene, log Likelihood per site, and rate per site estimated from the concatenated DNA sequence of the complete dataset. These likelihoods and rates are used for AU tests in Appendix S13 and the rate-sensitivity analysis in Figure 2.
DOI: 10.5281/zenodo.11643025
title: Supporting data for: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae

description: This is supporting sequence data for the paper: The danger zone: the joint trap of incomplete lineage sorting and long-branch attraction in resolving the Gondwanan origin of Rafflesiaceae and Apodanthaceae. It contains DNA and protein sequences as well as gene trees for 2135 loci for the investigation of the phylogenetic placement of the parasitic Rafflesiaceae and Apodannthaceae. Three datasets were included:

Data S1 Sequence alignments and gene trees for the 2135 loci analyzed in the study. The lists of loci included in the data subsets G446 and G829 are also provided. Both the raw alignments and masked alignments by HmmCleaner are provided for DNA and protein sequences. Each gene has 5 sets of gene trees inferred using different models in IQTREE:(1) *.GTR_codon.treefile: codon-based partition within gene (first, second, third codon in separate partitions) + forcing GTR (no +I or +R or +G); (2) *.MFP_codon.treefile: codon-based partition within gene + ModelFinder best fitting model; (3) *.msetGTR.treefile: no partition within gene + forcing GTR (with +I or +R or +G); (4) *.msetGTR_codon.treefile: codon-based partition within gene + forcing GTR (with +I or +R or +G); (5) *.na.mask.fas.treefile: no partition within gene + ModelFinder best fitting model.

Data S2 Species tree in newick format generated by the 22 analyses described in Cai et al. Table 1 and Appendix S9. For partition-based concatenation analyses, the best partition and substitution scheme in nexus format from IQ-TREE is also provided.The program and command line used to generate these species trees can be found on GitHub: https://github.com/lmcai/Rafflesiaceae_phylogenomics/tree/master/4_phylogeny_hypo_generation

Data S3 Log Likelihood per gene, log Likelihood per site, and rate per site estimated from the concatenated DNA sequence of the complete dataset. These likelihoods and rates are used for AU tests in Appendix S13 and the rate-sensitivity analysis in Figure 2.
DOI: 10.25549/uschist-c104-233043
title: Southern California alumni review, vol. 39, no. 3 (1957 Dec.)

description: Southern California alumni review, vol. 39, no. 3 (1957 December). Published monthly except June, July, August and September.
DOI: 10.25549/uschist-c104-233052
title: Southern California alumni review, vol. 39, no. 3 (1957 Dec.)

description: Southern California alumni review, vol. 39, no. 3 (1957 December). Published monthly except June, July, August and September.
DOI: 10.15468/dl.h8y5xp
title: Occurrence Download

description: A dataset containing 12975599 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 PRINTF('%04d-%02d', "year", "month") yearmonth,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, PRINTF('%04d-%02d', "year", "month"))) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, PRINTF('%04d-%02d', "year", "month"))) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.basisofrecord = 'HUMAN_OBSERVATION'
 AND (occurrence.coordinateuncertaintyinmeters &gt;= 0.0 AND occurrence.coordinateuncertaintyinmeters &lt;= 10000.0)
 AND occurrence.hascoordinate = TRUE
 AND occurrence.hasgeospatialissues = FALSE
 AND occurrence.license IN ('CC0_1_0', 'CC_BY_4_0')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL AND occurrence."month" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 PRINTF('%04d-%02d', "year", "month")

 The dataset's 12975599 records were derived from 18658 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033035-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1387403.10fu
title: SH1387403.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387404.10fu
title: SH1387404.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387406.10fu
title: SH1387406.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387408.10fu
title: SH1387408.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387409.10fu
title: SH1387409.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387412.10fu
title: SH1387412.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387413.10fu
title: SH1387413.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1387414.10fu
title: SH1387414.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15468/dl.vsfz5n
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Thailand",
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Mobula birostris (Walbaum, 1792)",
 "Year 2000-2024"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071949-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c29h57
title: Occurrence Download

description: A dataset containing 1372823060 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1372823060 records from 8697 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0099702-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7awcx3
title: Occurrence Download

description: A dataset containing 282184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Myanmar",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 282184 records from 501 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088436-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehkg7w
title: Occurrence Download

description: A dataset containing 2044 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Nonnula rubecula (von Spix, 1824)"
 ]
}

 The dataset includes 2044 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005577-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdzhzy
title: Occurrence Download

description: A dataset containing 2688 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiroptera",
 "Country is Mozambique"
 ]
}

 The dataset includes 2688 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025448-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mfm3rr
title: Occurrence Download

description: A dataset containing 2469 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Streptopelia dusumieri (Temminck, 1823))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2469 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004363-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vstru5
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phlox cluteana A.Nelson"
 ]
}

 The dataset includes 74 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075207-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ypd3tb
title: Occurrence Download

description: A dataset containing 111916 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phalacrocorax fuscicollis Stephens, 1826)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 111916 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005581-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cghknt
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Allium jubatum J.F.Macbr."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011686-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.69ya9h
title: Occurrence Download

description: A dataset containing 59166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Orchidaceae"
 ]
}

 The dataset includes 59166 records from 197 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021241-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufu33z
title: Occurrence Download

description: A dataset containing 30730 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Uria lomvia",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 30730 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088467-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xa4nmw
title: Occurrence Download

description: A dataset containing 780237 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Vireo flavifrons Vieillot, 1808)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 780237 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005584-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qu93du
title: Occurrence Download

description: A dataset containing 6910 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chiroptera",
 "Country is Nicaragua"
 ]
}

 The dataset includes 6910 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025461-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.