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

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aspidocarya uvifera Hook.fil. & Thomson"
 ]
}

 The dataset includes 81 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026047-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9x749g
title: Occurrence Download

description: A dataset containing 261264 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pandalus borealis Krøyer, 1838"
 ]
}

 The dataset includes 261264 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218714-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hoest4
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Narcissus ×aloysii-villarii Fern.Casas"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015637-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jc7c9
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zingiber monglaense S.J.Chen & Z.Y.Chen"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036554-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ffu8dd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schizura leptinoides Grote, 1864",
 {
 "not" : {
 "DatasetKey" : [
 "is Global database of alien macrofungi"
 ]
 }
 },
 {
 "or" : [
 "Country is Switzerland",
 "Country is Switzerland"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0396017-210914110416597/datasets/export for details.
DOI: 10.15468/dl.rn85n2
title: Occurrence Download

description: A dataset containing 539 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Bolborhynchus lineola (Cassin, 1853)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 539 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028104-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10996356
title: Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction

description: This repository contains the supplementary files for:

Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction.

Description of files

This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets.

Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database

Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers

dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database

tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips

change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses

BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models

BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies

Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models

Description of R code

The R code is subdivided into the following files:

Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses

PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints

BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models
DOI: 10.5281/zenodo.10996357
title: Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction

description: This repository contains the supplementary files for:

Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction.

Description of files

This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets.

Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database

Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers

dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database

tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips

change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses

BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models

BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies

Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models

Description of R code

The R code is subdivided into the following files:

Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses

PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints

BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models
DOI: 10.15468/dl.kmbbwh
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paronychia franciscana Eastw."
 ]
}

 The dataset includes 208 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036558-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.79kt8r
title: Occurrence Download

description: A dataset containing 1476 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-53.54296 -37.00196,-47.35547 -26.45508,-49.03857 -25.10376,-51.79834 -23.04712,-53.61987 -22.75818,-54.13843 -23.82166,-55.24365 -23.77222,-55.64795 -22.41431,-55.91162 -22.18579,-57.8562 -22.06165,-57.8584 -20.64111,-58.56592 -19.42603,-61.3103 -19.42493,-62.41553 -21.27173,-62.63416 -22.06549,-63.8064 -21.91223,-64.32166 -22.67194,-64.57654 -22.19733,-66.15967 -21.79907,-67.81201 -22.73071,-67.81201 -22.73071,-68.6206 -18.77563,-69.50773 -17.477,-69.92358 -18.20325,-70.34216 -18.31256,-98.82422 -25.33008,-88.69922 -57.11134,-57.48047 -57.11134,-53.54296 -37.00196))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Coccocypselum P.Browne"
 ]
}

 The dataset includes 1476 records from 72 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218728-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ey4oag
title: Occurrence Download

description: A dataset containing 4438 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Amazona finschi (P.L.Sclater, 1864)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4438 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028089-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxbf6p
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Andrographis paniculata (Burm.fil.) Nees",
 "Year 2003-2023"
 ]
}

 The dataset includes 28 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0128979-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fsakrc
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Penaeus merguiensis De Man, 1888"
 ]
}

 The dataset includes 18 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0422131-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rtvjcs
title: Occurrence Download

description: A dataset containing 124652 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chalcorana Dubois, 1992, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiasmocleis Méhely, 1904, Chiromantis Peters, 1854, Chiromantis Giglio-Tos, 1915, Chiromantis Rondani, 1856, Chiromantes Gistel, 1848, Chyromantis Rondani, 1856, Chiromantes, Chersomantis Gistel, 1856, Chiromanthes Gistel, 1848, Chloromantis Kaltenbach, 1998, Cliomantis Giglio-Tos, 1913, Chonomantis Glaw & Vences, 1994, Chiromantis Peters, 1854, Chiromantis Giglio-Tos, 1915, Chiromantis Rondani, 1856, Chiromantes Gistel, 1848, Chyromantis Rondani, 1856, Chiromantes, Chersomantis Gistel, 1856, Chiromanthes Gistel, 1848, Chloromantis Kaltenbach, 1998, Cliomantis Giglio-Tos, 1913, Chonomantis Glaw & Vences, 1994, Chiromantis Peters, 1854, Chiromantis Giglio-Tos, 1915, Chiromantis Rondani, 1856, Chiromantes Gistel, 1848, Chyromantis Rondani, 1856, Chiromantes, Chersomantis Gistel, 1856, Chiromanthes Gistel, 1848, Chloromantis Kaltenbach, 1998, Cliomantis Giglio-Tos, 1913, Chonomantis Glaw & Vences, 1994, Chiromantis Peters, 1854, Chiromantis Giglio-Tos, 1915, Chiromantis Rondani, 1856, Chiromantes Gistel, 1848, Chyromantis Rondani, 1856, Chiromantes, Chersomantis Gistel, 1856, Chiromanthes Gistel, 1848, Chloromantis Kaltenbach, 1998, Cliomantis Giglio-Tos, 1913, Chonomantis Glaw & Vences, 1994, Chiromantis Peters, 1854, Chiromantis Giglio-Tos, 1915, Chiromantis Rondani, 1856, Chiromantes Gistel, 1848, Chyromantis Rondani, 1856, Chiromantes, Chersomantis Gistel, 1856, Chiromanthes Gistel, 1848, Chloromantis Kaltenbach, 1998, Cliomantis Giglio-Tos, 1913, Chonomantis Glaw & Vences, 1994, Chiromantis Peters, 1854, Chiromantis Giglio-Tos, 1915, Chiromantis Rondani, 1856, Chiromantes Gistel, 1848, Chyromantis Rondani, 1856, Chiromantes, Chersomantis Gistel, 1856, Chiromanthes Gistel, 1848, Chloromantis Kaltenbach, 1998, Cliomantis Giglio-Tos, 1913, Chonomantis Glaw & Vences, 1994, Chrysopaa Ohler & Dubois, 2006, Chrysopa Leach, 1815, Chrysopia Noronha ex Thouars, Conraua Nieden, 1908, Conrana Bauer, 1985, Conraua Nieden, 1908, Conrana Bauer, 1985, Cornufer Tschudi, 1838, Cornifer Agassiz, 1846, Corythomantis Boulenger, 1896, Craugastor Cope, 1862, Craugastor Cope, 1862, Craugastor Cope, 1862, Crinia Tschudi, 1838, Cainia, Crania Retzius, 1781, Crinita Dirsh, 1949, Crisia Lamouroux, 1812, Cronia H.Adams & A.Adams, 1853, Clinia Thomson, 1857, Crania Hirst & Maulik, 1926, Crinita Houtt., Crinita Moench, Cainia Arx & E.Müll., Chinia Leng, 1985)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 124652 records from 451 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011258-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x3w6yh
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centaurea cheirolopha (Fenzl) Wagenitz"
 ]
}

 The dataset includes 127 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0128989-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qe7vmj
title: Occurrence Download

description: A dataset containing 2338 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phylloicus Mueller, 1880"
 ]
}

 The dataset includes 2338 records from 74 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0422827-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.crk6ue
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 {
 "or" : [
 "Country is Canada",
 "Country is United States of America"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is 28eb1a3f-1c15-4a95-931a-4af90ecb574d",
 "TaxonKey is Anthocoridae",
 "Year 2008-2021"
 ]
}

 The dataset includes 105 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0072980-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r953c9
title: Occurrence Download

description: A dataset containing 1053 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Centaurea cineraria L."
 ]
}

 The dataset includes 1053 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0129002-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aa5zv9
title: Occurrence Download

description: A dataset containing 427 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calceolaria filicaulis Clos"
 ]
}

 The dataset includes 427 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218761-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6rgn6o
title: Occurrence Download

description: A dataset containing 1783 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 1783 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001940-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k6gv6y
title: Occurrence Download

description: A dataset containing 37497 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trifolium subterraneum L."
 ]
}

 The dataset includes 37497 records from 599 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021183-230810091245214/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.byxrsk
title: Occurrence Download

description: A dataset containing 1274504 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Hylocichla mustelina (Gmelin, 1789)"
 ]
}

 The dataset includes 1274504 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0218746-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gm7vxg
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caragana chinghaiensis Y.X.Liou"
 ]
}

 The dataset includes 29 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0080731-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.drewe4
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Prunus huantensis Pilg."
 ]
}

 The dataset includes 91 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004931-210819072339941/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ofj930
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psychotria pleiocephala Müll.Arg."
 ]
}

 The dataset includes 173 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021417-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qhry8s
title: Occurrence Download

description: A dataset containing 1488 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-88.6782 -40.15429,-29.81756 -40.15429,-29.81756 11.15877,-88.6782 11.15877,-88.6782 -40.15429))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Taquara micrantha (Kunth) I.L.C.Oliveira & R.P.Oliveira"
 ]
}

 The dataset includes 1488 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0141553-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uvhcjn
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hedysarum drobovii Korotkova"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0017544-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5hjmxg
title: Occurrence Download

description: A dataset containing 3332 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Trichechus manatus Linnaeus, 1758"
 ]
}

 The dataset includes 3332 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175194-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hpyqne
title: Occurrence Download

description: A dataset containing 227 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Protea longifolia Andrews"
 ]
}

 The dataset includes 227 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021419-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bgumf6
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hieracium helenae T.Tyler"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022098-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x62nsa
title: Occurrence Download

description: A dataset containing 5037 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gopherus agassizii (Cooper, 1861)"
 ]
}

 The dataset includes 5037 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175198-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ufehoe
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alstroemeria pseudospathulata Ehr.Bayer"
 ]
}

 The dataset includes 23 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021419-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eknf37
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dietes flavida Oberm."
 ]
}

 The dataset includes 44 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026927-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.