cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.hekmt3
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panicum humidorum Buch.-Ham. ex Hook.f."
 ]
}

 The dataset includes 38 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065395-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.czvy49
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ozoroa namaensis (Schinz & Dinter) R.Fern."
 ]
}

 The dataset includes 44 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065394-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yausfm
title: Occurrence Download

description: A dataset containing 24 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia rechingeri Chaudhri"
 ]
}

 The dataset includes 24 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065396-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9jqcgf
title: Occurrence Download

description: A dataset containing 62 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osbeckia leschenaultiana DC."
 ]
}

 The dataset includes 62 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065397-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8byku9
title: Occurrence Download

description: A dataset containing 628 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panicum humile Steud."
 ]
}

 The dataset includes 628 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065400-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ffdmw6
title: Occurrence Download

description: A dataset containing 1313 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Othonna quinquedentata Thunb."
 ]
}

 The dataset includes 1313 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065399-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9r32zq
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ozoroa namaquensis (Sprague) Von Teichman & A.E.van Wyk"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065401-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fk4s8m
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia saxatilis Chaudhri"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065402-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w7r75f
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osbeckia mehrana G.S.Giri & M.P.Nayar"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065403-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yq93ph
title: Occurrence Download

description: A dataset containing 472 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ophrys argolica H.Fleischm."
 ]
}

 The dataset includes 472 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065404-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.knn3sm
title: Occurrence Download

description: A dataset containing 343 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia sinaica Fresen."
 ]
}

 The dataset includes 343 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065406-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t744y4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osbeckia melastomacea Bakh.fil."
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065407-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d2a52n
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Othonna quinqueradiata DC."
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065405-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vnzgeq
title: Occurrence Download

description: A dataset containing 427 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panicum hygrocharis Steud."
 ]
}

 The dataset includes 427 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065409-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.37edpz
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ozoroa nigricans (Van der Veken) R.Fern. & A.Fern."
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065408-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24866076.v1
title: Effective elastic thickness of NA

description: This dataset contains the result of Effective elastic thickness of the lithosphere (Te) in North Atlantic Ocean. We use different central wavenumbers 2.668 and 5.336 before and after sediment correction. the f and err data represents for estimated loading ratio F and Te error, respectively.
DOI: 10.15468/dl.39n5au
title: Occurrence Download

description: A dataset containing 140 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ophrys atlantica Munby"
 ]
}

 The dataset includes 140 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065412-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ed4pza
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia sintenisii Chaudhri"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065411-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ynxprg
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osbeckia moonii Thwaites"
 ]
}

 The dataset includes 13 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065410-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yfvz2y
title: Occurrence Download

description: A dataset containing 154 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Othonna ramulosa DC."
 ]
}

 The dataset includes 154 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065413-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nqmf8p
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ozoroa nitida (Engl. & Brehmer) R.Fern. & A.Fern."
 ]
}

 The dataset includes 20 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065414-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24586032.v1
title: MCMCTREE

description: To assess the timing of historical processes that may have led to diversification in <i>Ocymyrmex</i>, a dated phylogeny for the genus was inferred using MCMCTREE v4.9j in the PAML package (Phylogenetic Analysis by Maximum Likelihood; (Yang, 2007)). Divergence ages were reconstructed using the 80% taxon completeness matrix, trimmed with 0.97 cut-off in SPRUCEUP v2020.2.19 (Borowiec, 2019), and the tree resulting from partitioned analysis of this data set as input topology (Appendix C). This tree was pruned to include only one representative of each <i>Ocymyrmex</i> species, and two outgroup taxa (<i>Nesomyrmex</i> <i>madecassus</i> and <i>Cardiocondyla thoracica</i>) were also removed prior to this analysis. Given the unknown fossil record of <i>Ocymyrmex</i>, secondary ages estimated by Blaimer et al. (2018) were used to calibrate two nodes in our tree. The split between <i>Ocymyrmex</i> and <i>Cardiocondyla</i> was calibrated with 46.5–71.9 Ma and the split between <i>Tetramorium </i>and the <i>Cataulacus</i> genus-group of which both <i>Ocymyrmex</i> and <i>Cardiocondyla</i> are part of (= root node) was calibrated with 60.1–84.9 Ma. Both calibration ranges were derived from 95% highest posterior density (HPD) intervals across four analyses from Blaimer et al. (2018) to account for uncertainty.We first estimated the Hessian gradient in MCMCTREE (set usedata = 3), then the estimates from the Hessian gradient were used to perform approximate likelihood estimation (usedata = 2). We performed four independent runs, with the following parameters: burnin was set to 500,000; sampling was performed every 100 iterations until 1,000,000 samples were gathered; the model was set to 7 (GTR); an independent rates model was applied (clock=2); and we used a single data partition. Convergence and effective sample size (ESS) were visualized in TRACER v1.7 (Rambaut et al., 2018).
DOI: 10.6084/m9.figshare.24586005.v1
title: Coalescent_analyses

description: The potential effects of independent lineage sorting on our dataset were explored by performing coalescent analyses with ASTRAL-III v. 5.7.7 (Zhang et al., 2018). ASTRAL-III is a java program for estimating a species tree given a set of unrooted gene trees, each inferred from a different part of a genome. This approach aims to explain the genealogical discordances between gene trees and species trees which might be caused by incomplete lineage sorting (Zhang et al., 2018). Gene trees were reconstructed from 2055 UCE loci retained in the 70% dataset, 1235 UCE loci retained by 80% dataset and 88 UCE loci retained by the 90% dataset. We estimated gene trees using the following command in IQ-TREE version 2.1.2 (Minh et al., 2020): iqtree2 -S ALN_DIR --prefix loci -T AUTO.
DOI: 10.6084/m9.figshare.24585954.v1
title: Concatenated analyses_unpartitioned

description: The demultiplexed FASTQ data were cleaned and trimmed of adapters using Illumiprocessor v.2.0 (Faircloth, 2013), based on the package Trimmomatic (Bolger et al., 2014). Data processing was done through a series of scripts available in the PHYLUCE package v.1.7.1 (Faircloth, 2015). Trimmed reads were assembled into contigs using a wrapper script (phyluce_assembly_assemblo_trinity.py) and the program TRINITY (version trinityrnaseq_r20140717) (Grabherr et al., 2011). We used the PHYLUCE pipeline to identify and extract contigs containing UCE loci. Species-specific contig assemblies were aligned to a FASTA file of all enrichment baits using phyluce_assembly_match_contigs_to_probes.py (min_coverage=50, min_identity=80). A list of UCE loci shared across all taxa was generated by using phyluce_assembly_get_match_counts.py. This list was then used to create FASTA files for each UCE locus using phyluce_get_fastas_from_match_counts.py. All sequence data in these FASTA files were aligned using MAFFT (Katoh and Standley, 2013) through phyluce_seqcap_align.py (min. length =100, no trim) and trimmed using a wrapper script (get_gblocks_trimmed_alignment_from_untrimmed.py) for Gblocks (Castresana, 2000) with the following settings: b1=0.5, b2=0.5, b3=12, b4=7. After trimming, multiple subsets based on filtering UCE loci for different levels of taxon occupancy (70%, 80% and 90% taxon completeness) were created using phyluce_get_only_loci_with_min_taxa.py, and we generated statistics across all subsets using get_align_summary_data.py. Individual alignments of UCE loci for each subset were then concatenated into one nexus alignment file with phyluce_align_format_nexus_files_for_raxml.py script for subsequent phylogenetic analyses. SPRUCEUP v2020.2.19 (Borowiec, 2019) was used to remove poorly aligned sequences or sequence fragments. The matrices were trimmed based on the following cut-off values: 95%, 97%, 98% and 99%. For this study, all the analyses here are based on 97% and 98% cut-off values, as a 95% cut-off was too stringent, and a 99% cut-off did not trim outlier sequences sufficiently.
DOI: 10.6084/m9.figshare.24585897.v1
title: Concatenated analyses_partitioned

description: The demultiplexed FASTQ data were cleaned and trimmed of adapters using Illumiprocessor v.2.0 (Faircloth, 2013), based on the package Trimmomatic (Bolger et al., 2014). Data processing was done through a series of scripts available in the PHYLUCE package v.1.7.1 (Faircloth, 2015). Trimmed reads were assembled into contigs using a wrapper script (phyluce_assembly_assemblo_trinity.py) and the program TRINITY (version trinityrnaseq_r20140717) (Grabherr et al., 2011). We used the PHYLUCE pipeline to identify and extract contigs containing UCE loci. Species-specific contig assemblies were aligned to a FASTA file of all enrichment baits using phyluce_assembly_match_contigs_to_probes.py (min_coverage=50, min_identity=80). A list of UCE loci shared across all taxa was generated by using phyluce_assembly_get_match_counts.py. This list was then used to create FASTA files for each UCE locus using phyluce_get_fastas_from_match_counts.py. All sequence data in these FASTA files were aligned using MAFFT (Katoh and Standley, 2013) through phyluce_seqcap_align.py (min. length =100, no trim) and trimmed using a wrapper script (get_gblocks_trimmed_alignment_from_untrimmed.py) for Gblocks (Castresana, 2000) with the following settings: b1=0.5, b2=0.5, b3=12, b4=7. After trimming, multiple subsets based on filtering UCE loci for different levels of taxon occupancy (70%, 80% and 90% taxon completeness) were created using phyluce_get_only_loci_with_min_taxa.py, and we generated statistics across all subsets using get_align_summary_data.py. Individual alignments of UCE loci for each subset were then concatenated into one nexus alignment file with phyluce_align_format_nexus_files_for_raxml.py script for subsequent phylogenetic analyses. SPRUCEUP v2020.2.19 (Borowiec, 2019) was used to remove poorly aligned sequences or sequence fragments. The matrices were trimmed based on the following cut-off values: 95%, 97%, 98% and 99%. For this study, all the analyses here are based on 97% and 98% cut-off values, as a 95% cut-off was too stringent, and a 99% cut-off did not trim outlier sequences sufficiently.
DOI: 10.6084/m9.figshare.24585888.v1
title: Phyluce_commands

description: Phyluce commands
DOI: 10.15468/dl.f8pxqg
title: Occurrence Download

description: A dataset containing 230690 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alburnoides bipunctatus (Bloch, 1782)"
 ]
}

 The dataset includes 230690 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065383-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qjxtbt
title: Occurrence Download

description: A dataset containing 190 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panicum ibitense A.Camus"
 ]
}

 The dataset includes 190 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065415-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6a22tn
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia somaliensis Baker"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065416-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c82z8j
title: Occurrence Download

description: A dataset containing 7633 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ophrys bertolonii Moretti"
 ]
}

 The dataset includes 7633 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065418-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.423rdv
title: Occurrence Download

description: A dataset containing 117 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Othonna retrofracta Jacq."
 ]
}

 The dataset includes 117 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065420-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.njfb42
title: Occurrence Download

description: A dataset containing 233089 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Poecile hudsonicus (J.R.Forster, 1772)"
 ]
}

 The dataset includes 233089 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065384-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9b8rtk
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panicum impeditum Launert"
 ]
}

 The dataset includes 74 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065422-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z78w5j
title: Occurrence Download

description: A dataset containing 597 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ozoroa obovata (Oliv.) R.Fern. & A.Fern."
 ]
}

 The dataset includes 597 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065421-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rh5eab
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Osbeckia muralis Naudin"
 ]
}

 The dataset includes 81 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065419-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q25ybx
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia splendens Steven"
 ]
}

 The dataset includes 6 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065423-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24866076
title: Effective elastic thickness of NA

description: This dataset contains the result of Effective elastic thickness of the lithosphere (Te) in North Atlantic Ocean. We use different central wavenumbers 2.668 and 5.336 before and after sediment correction. the f and err data represents for estimated loading ratio F and Te error, respectively.
DOI: 10.15468/dl.xh8a2d
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Othonna retrorsa DC."
 ]
}

 The dataset includes 123 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065424-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.