cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27873999
title: Simulation dataset for Clustering-based loci subsampling helps for robust phylogenomics

description: Phylogenomic subsampling helps to mitigate data heterogeneity or reduce computational burden by selecting a subset of loci from genome-scale datasets for phylogenetic analysis. This approach typically involves filtering loci based on various properties of loci but lacks a consensus in practice. We proposed a novel multivariate, clustering-based approach that combines non-linear manifold learning UMAP dimension reduction with hierarchical clustering to identify and sort clusters based on their metrics possessing phylogenetic signal. Testing across 60 simulated and 16 empirical datasets, we evaluated its performance under varying data conditions including data source, subsampling size, species tree methods, and levels of incomplete lineage sorting (ILS). Combined summary statistics from both alignments and gene trees were preferred for clustering analyses, while statistics derived solely from gene trees (edge branch lengths and supports) were found to be less reliable, particularly at higher ILS levels. Subsampling strategies based on summary statistics or gene—species tree discordance consistently outperformed alternative approaches across all datasets. In empirical datasets, our method improved species tree accuracy even when filtering substantial portions of loci, with minimal adverse effects. Our clustering-based approach effectively identifies and retains loci with strong phylogenetic signals while excluding problematic sequences, demonstrating the potential for enhancing phylogenetic inference accuracy.
DOI: 10.6084/m9.figshare.27873999.v3
title: Simulation dataset for Clustering-based loci subsampling helps for robust phylogenomics

description: Phylogenomic subsampling helps to mitigate data heterogeneity or reduce computational burden by selecting a subset of loci from genome-scale datasets for phylogenetic analysis. This approach typically involves filtering loci based on various properties of loci but lacks a consensus in practice. We proposed a novel multivariate, clustering-based approach that combines non-linear manifold learning UMAP dimension reduction with hierarchical clustering to identify and sort clusters based on their metrics possessing phylogenetic signal. Testing across 60 simulated and 16 empirical datasets, we evaluated its performance under varying data conditions including data source, subsampling size, species tree methods, and levels of incomplete lineage sorting (ILS). Combined summary statistics from both alignments and gene trees were preferred for clustering analyses, while statistics derived solely from gene trees (edge branch lengths and supports) were found to be less reliable, particularly at higher ILS levels. Subsampling strategies based on summary statistics or gene—species tree discordance consistently outperformed alternative approaches across all datasets. In empirical datasets, our method improved species tree accuracy even when filtering substantial portions of loci, with minimal adverse effects. Our clustering-based approach effectively identifies and retains loci with strong phylogenetic signals while excluding problematic sequences, demonstrating the potential for enhancing phylogenetic inference accuracy.
DOI: 10.6084/m9.figshare.27873999.v2
title: Simulation dataset for Clustering-based loci subsampling helps for robust phylogenomics

description: Phylogenomic subsampling helps to mitigate data heterogeneity or reduce computational burden by selecting a subset of loci from genome-scale datasets for phylogenetic analysis. This approach typically involves filtering loci based on various properties of loci but lacks a consensus in practice. We proposed a novel multivariate, clustering-based approach that combines non-linear manifold learning UMAP dimension reduction with hierarchical clustering to identify and sort clusters based on their metrics possessing phylogenetic signal. Testing across 60 simulated and 16 empirical datasets, we evaluated its performance under varying data conditions including data source, subsampling size, species tree methods, and levels of incomplete lineage sorting (ILS). Combined summary statistics from both alignments and gene trees were preferred for clustering analyses, while statistics derived solely from gene trees (edge branch lengths and supports) were found to be less reliable, particularly at higher ILS levels. Subsampling strategies based on summary statistics or gene—species tree discordance consistently outperformed alternative approaches across all datasets. In empirical datasets, our method improved species tree accuracy even when filtering substantial portions of loci, with minimal adverse effects. Our clustering-based approach effectively identifies and retains loci with strong phylogenetic signal while excluding problematic sequences, demonstrating potential for enhancing phylogenetic inference accuracy.
DOI: 10.15468/dl.trxev7
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Guttigadus latifrons (Holt & Byrne, 1908)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 43 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023859-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3hp6e6
title: Occurrence Download

description: A dataset containing 157012 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The AAU Herbarium Database"
 ]
}

 The dataset includes 157012 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023857-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cg34nm
title: Occurrence Download

description: A dataset containing 3761 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mountain Invasion Research Network (MIREN) survey"
 ]
}

 The dataset includes 3761 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023860-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s4aqav
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hoplostethus cadenati Quéro, 1974",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 100 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023861-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.waag28
title: Occurrence Download

description: A dataset containing 2132 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Bactrocera cucurbitae (Coquillett, 1899), Bactrocera dorsalis (Hendel, 1912))"
 ]
}

 The dataset includes 2132 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023862-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpjpm3
title: Occurrence Download

description: A dataset containing 5930913 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-70.26515 43.67481,-68.45543 43.67481,-68.45543 44.81498,-70.26515 44.81498,-70.26515 43.67481))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5930913 records from 561 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023855-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ykn57
title: Occurrence Download

description: A dataset containing 26633 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudoplatystoma magdaleniatum Buitrago-Suárez & Burr, 2007"
 ]
}

 The dataset includes 26633 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023863-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.apzf3k
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lampadena atlantica Maul, 1969",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 116 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023864-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qxpjzy
title: Occurrence Download

description: A dataset containing 3761 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mountain Invasion Research Network (MIREN) survey"
 ]
}

 The dataset includes 3761 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023865-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9nvhk9
title: Occurrence Download

description: A dataset containing 1186 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lampanyctus photonotus Parr, 1928",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1186 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023866-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mcs2f9
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lythrum virgatum L."
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023867-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ks6bkg
title: Occurrence Download

description: A dataset containing 686 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanostomias bartonbeani Parr, 1927",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 686 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023868-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kkgu5p
title: Occurrence Download

description: A dataset containing 7118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation, Living Specimen, Occurrence evidence)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sus scrofa Linnaeus, 1758"
 ]
}

 The dataset includes 7118 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023869-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rexhtg
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ficus gracilis (G.B.Sowerby I, 1825))",
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023870-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gngbsh
title: Occurrence Download

description: A dataset containing 1220 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polydactylus macrochir (Günther, 1867)"
 ]
}

 The dataset includes 1220 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023871-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.58ah6u
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is false",
 "TaxonKey is one of (Bactrocera cucurbitae (Coquillett, 1899), Bactrocera dorsalis (Hendel, 1912))"
 ]
}

 The dataset includes 112 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023872-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rtuzps
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nansenia tenera Kawaguchi & Butler, 1984",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 21 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023873-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13882909
title: Table 1 in A new species of bristletails of the genus Coryphophthalmus Verhoeff, 1910 (Microcoryphia: Machilidae) from Krasnodar Region, Russia

description: Table 1. Ratios of length to width of main leg segments of Coryphophthalmus aureaocellus sp. n. ТабΛица 1. Отношения ΑΛины к ширине сегментов ног Coryphophthalmus aureaocellus sp. n.
Sex, pair of legs ПоΛ, пара ногSegments Сегментыmale / самецfemale / самкаfore переΑняяmiddle среΑняяhind заΑняяfore переΑняяmiddle среΑняяhind заΑняяTarsa / Αапка4.815.046.0854.525.62Tibia / ГоΛень2.322.523.632.372.203.08Femur / БеΑро2.242.512.862.212.662.68
description: Published as part of Kaplin, V. G. & Koval, A. G., 2021, A new species of bristletails of the genus Coryphophthalmus Verhoeff, 1910 (Microcoryphia: Machilidae) from Krasnodar Region, Russia, pp. 157 in Caucasian Entomological Bulletin (Caucas. entomol. bull.) 17 (1) on page 157, DOI: 10.23885/181433262021171-155161, http://zenodo.org/record/13274173
DOI: 10.5281/zenodo.13882911
title: Table 2 in A new species of bristletails of the genus Coryphophthalmus Verhoeff, 1910 (Microcoryphia: Machilidae) from Krasnodar Region, Russia

description: Table 2. Length ratios of urosternites and urocoxites of Coryphophthalmus aureaocellus sp. n. ТабΛица 2. Отношения ΑΛины стернитов и кокситов брюшка Coryphophthalmus aureaocellus sp. n.
Urites / Сегменты брюшкаUrosternite: urocoxite Стернит: кокситы брюшкаUrostyli (not including apical spines): urocoxites / ГрифеΛьки (не вкΛючая апикаΛьные игΛы): кокситы брюшкаApical spines: styli АпикаΛьные игΛы: грифеΛькиmale/ самецfemale / самкаmale / самецfemale / самкаmale / самецfemale / самкаII0.560.60.640.510.430.47III0.580.620.620.510.40.5IV0.580.630.620.50.440.46V0.580.630.620.510.450.48VI0.560.620.610.540.340.5VII0.460.50.770.560.430.48VIII0.40.710.730.450.45IX––0.830.660.260.32
description: Published as part of Kaplin, V. G. & Koval, A. G., 2021, A new species of bristletails of the genus Coryphophthalmus Verhoeff, 1910 (Microcoryphia: Machilidae) from Krasnodar Region, Russia, pp. 158 in Caucasian Entomological Bulletin (Caucas. entomol. bull.) 17 (1) on page 158, DOI: 10.23885/181433262021171-155161, http://zenodo.org/record/13274173
DOI: 10.5281/zenodo.13882913
title: Table 3 in A new species of bristletails of the genus Coryphophthalmus Verhoeff, 1910 (Microcoryphia: Machilidae) from Krasnodar Region, Russia

description: Table 3. Posterior angle of urosternites and distribution of sublateral spines on urotergites and on urosternites of Coryphophtaalmus aureaocellus sp. n. ТабΛица 3. ЗаΑний угоΛ стернитов и распреΑеΛение субΛатераΛьных игΛ на тергитах и кокситах брюшка Coryphophtaalmus aureaocellus sp. n.
Urites / Сегменты брюшкаPosterior angle of urosternite, degrees ЗаΑний угоΛ стернита, граΑусыNumber of sublateral spines on urites КоΛичество субΛатераΛьных игΛ на сегментах брюшка urocoxites urotergites кокситы брюшка тергиты брюшкаmale / самецfemale / самкаmale / самецfemale / самкаmale / самец female / самкаI––000 0II7682000 0III7682000 0IV7880000 0V7678001 + 1 1 + 1VI72780–1 + 0–103–4 + 3–4 1 + 1VII84834 + 42–3 + 2–35 + 5 2 + 2VIII96–5–6 + 5–65 + 56 + 6 5 + 5IX––2/8 + 9/3*2/5 + 8/15 + 5 4 + 4X––––4 + 4 4 + 4
Note. * – outer/inner spines.
Примечание. * – наружные/внутренние шипики.
description: Published as part of Kaplin, V. G. & Koval, A. G., 2021, A new species of bristletails of the genus Coryphophthalmus Verhoeff, 1910 (Microcoryphia: Machilidae) from Krasnodar Region, Russia, pp. 158 in Caucasian Entomological Bulletin (Caucas. entomol. bull.) 17 (1) on page 158, DOI: 10.23885/181433262021171-155161, http://zenodo.org/record/13274173
DOI: 10.15468/dl.up5y6k
title: Occurrence Download

description: A dataset containing 6866 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Myocastor coypus (Molina, 1782)"
 ]
}

 The dataset includes 6866 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023874-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.umhu7a
title: Occurrence Download

description: A dataset containing 722 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Mergus squamatus Gould, 1864",
 "Year 2014-2024"
 ]
}

 The dataset includes 722 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023875-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u7kwj8
title: Occurrence Download

description: A dataset containing 1553 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is University of Texas, Biodiversity Center, Entomology Collection (UTIC)",
 "Geometry POLYGON((-98.14106 30.32952,-98.13678 30.32952,-98.13678 30.3329,-98.14106 30.3329,-98.14106 30.32952))"
 ]
}

 The dataset includes 1553 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023876-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7gkbwm
title: Occurrence Download

description: A dataset containing 757 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nessorhamphus ingolfianus (Schmidt, 1912)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 757 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023877-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whj4km
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cycas segmentifida D.Yue Wang & C.Y.Deng"
 ]
}

 The dataset includes 92 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023878-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eqqz6v
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lythrum virgatum L."
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023879-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gg7vzm
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oxynotus paradoxus Frade, 1929",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 41 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023881-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ypr6wu
title: Occurrence Download

description: A dataset containing 7118 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen, Occurrence evidence)",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sus scrofa Linnaeus, 1758"
 ]
}

 The dataset includes 7118 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023880-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y8rrbz
title: Occurrence Download

description: A dataset containing 581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Nipponia nippon (Temminck, 1835)",
 "Year 2014-2024"
 ]
}

 The dataset includes 581 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023882-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s36qwa
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Paraliparis membranaceus Günther, 1887",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023883-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.