Reduced strength and increased variability of extinction selectivity during mass extinctions
Data files
Sep 14, 2023 version files 98.66 MB
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coeffs_bs_gr_Bambach_Pradel.txt
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coeffs_bs_gr_Big5_Pradel.txt
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coeffs_bs_gr_sansKPG_molluscs_Pradel.txt
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coeffs_bs_gr_sansLOME_brachiopods_Pradel.txt
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encounter_history_bs_gr_5class_Big5.Rdata
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genera_range_through.txt
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genus.sizes.ranges.cleaned.classes.csv
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pbdb.cleaned.classes.csv
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pbdbAnimals.Rdata
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README.md
Abstract
Two of the traits most often observed to correlate with extinction risk in marine animals are geographic range and body size. However, the relative effects of these two traits on extinction risk has not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographic range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographic range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographic range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographic range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.
README: Data from: Reduced Strength and Increased Variability of Extinction Selectivity Across Marine Clades During Mass Extinctions
GENERAL INFORMATION
- Author Information A. Principal Investigator Contact Information Name: Pedro M. Monarrez Institution: Stanford University Email: pmonarrez@stanford.edu <br> B. Associate or Co-investigator Contact Information Name: Jonathan L. Payne Institution: Stanford University Email: jlpayne@stanford.edu <br> C. Alternate Contact Information Name: Noel A. Heim Institution: Tufts University Email: noel.heim@tufts.edu
SHARING/ACCESS INFORMATION
- Licenses/restrictions placed on the data: CC0
- Links to publications that cite or use the data: TBD
- Links to other publicly accessible locations of the data: paleobiodb.org
- Links/relationships to ancillary data sets: NA
- Was data derived from another source? yes A. If yes, list source(s): Paleobiology Database
- Recommended citation for this dataset:
DATA & FILE OVERVIEW
File List:
genera_range_through.txt
pbdbAnimals.Rdata
pbdb.cleaned.classes.csv
genus.sizes.ranges.cleaned.classes.csv
encounter_history_bs_gr_5class_Big5.Rdata
coeffs_bs_gr_Big5_Pradel.txt
coeffs_bs_gr_Bambach_Pradel.txt
coeffs_bs_gr_sansLOME_brachiopods_Pradel.txt
coeffs_bs_gr_sansKPG_molluscs_Pradel.txt
Relationship between files, if important: should be read in order specified by R scripts. See R README in Zenodo.
METHODOLOGICAL INFORMATION
Every R script file starts with a number and each R script file should be run in numerical order (01-09). R scripts for ESM analysis are also numbered and should be run in order (S01-S16).
DATA-SPECIFIC INFORMATION FOR:
genera_range_through.txt
Text file with raw list of genera with first fossil occurrences (fad; first appearance datum) and last fossil occurrences (lad; last appearance datum) and body size data. Biovolume data is under calc_max_vol column. fad_age and lad_age correspond to the numeric geologic age of first and last occurrences and fad_int and lad_int correspond to the name of the interval in which a fad or lad occur. pbdb_taxon_no corresponds to the number assigned to a taxon by the Paleobiology Database. It is used to match our body size data set with occurrence data from the Paleobiology Database.
- Number of variables: 12
- Number of cases/rows: 33497
- Variable List: pbdb_taxon_no, taxon_name, phylum, class, order, family, max_length, fad_int, lad_int, fad_age, lad_age, calc_max_vol
- Missing data codes: NA
pbdbAnimals.Rdata
R data file containing raw download of fossil occurrences from the Paleobiology Database. Occurrences and genera are assigned numbers for multiple variables by the Paleobiology Database. early_interval, late_interval are equivalent to fad_int and lad_int respectively and max_ma and min_ma is equivalent to fad_age and lad_age respectively. Only taxon number, accepted name, phylum, class, max_ma, and min_ma are used from this file.
- Number of variables: 29
- Number of cases/rows: 585051
- Variable List: occurrence_no, record_type, reid_no, flags, collection_no, accepted_name, accepted_rank, accepted_no, early_interval, late_interval, max_ma, min_ma, reference_no, paleomodel, paleolng, paleolat, geoplate, phylum ,phylum_no, class, class_no, order, order_no, family, family_no, genus, genus_no, subgenus_no, genus_id
- Missing data codes: NA
pbdb.cleaned.classes.csv
Paleobiology Database occurrence file for genera with body size data with cleaned taxonomic names and complete stratigraphic range. logsize corresponds to the base 10 log of maximum body length and logvol is the base 10 log of maximum biovolume, which is the primary metric used for body size in this study. Only genus, class, logvol, and phylum are used from this file.
- Number of variables: 34
- Number of cases/rows: 284309
- Variable List: genus, class, early_interval, occurrence_no, record_type, reid_no, flags, collection_no, accepted_rank, accepted_no, late_interval, reference_no, paleomodel, paleolng, paleolat, geoplate, phylum_no, class_no, order_no, family_no, genus_no, subgenus_no, genus_id, max_ma, min_ma, fad, lad, fad_age, lad_age, logsize, logvol, phylum, order, family
- Missing data codes: NA
genus.sizes.ranges.cleaned.classes.csv
List of genera from the Paleobiology Database occurrence file for with body size data with cleaned taxonomic names and stratigraphic ranges. logsize corresponds to the base 10 log of maximum body length and logvol is the base 10 log of maximum biovolume, which is the primary metric used for body size in this study. Only genus, class, logvol, phylum, fad, lad are used from this file.
- Number of variables: 9
- Number of cases/rows: 6702
- Variable List: genus, phylum, class, order, family, logsize, logvol, fad, lad
- Missing data codes: NA
encounter_history_bs_gr_5class_Big5.Rdata
R data file with the encounter history of each genus for each geologic stage within the study that have body size data and geographical range data. ch is a string of 0's and 1's and is the capture history of each genus. mass.ext and rec.mass are dummy variables indicating whether a geologic interval is background (0) or mass extinction/recovery (1).
- Number of variables: 262
- Number of cases/rows: 6,562
- Variable List: "ch" "class" "phylum" "logvol" "mass.ext1" "mass.ext2" "mass.ext3" "mass.ext4" "mass.ext5" "mass.ext6" "mass.ext7" "mass.ext8" "mass.ext9" "mass.ext10" "mass.ext11" "mass.ext12" "mass.ext13" "mass.ext14" "mass.ext15" "mass.ext16" "mass.ext17" "mass.ext18" "mass.ext19" "mass.ext20" "mass.ext21" "mass.ext22" "mass.ext23" "mass.ext24" "mass.ext25" "mass.ext26" "mass.ext27" "mass.ext28" "mass.ext29" "mass.ext30" "mass.ext31" "mass.ext32" "mass.ext33" "mass.ext34" "mass.ext35" "mass.ext36" "mass.ext37" "mass.ext38" "mass.ext39" "mass.ext40" "mass.ext41" "mass.ext42" "mass.ext43" "mass.ext44" "mass.ext45" "mass.ext46" "mass.ext47" "mass.ext48" "mass.ext49" "mass.ext50" "mass.ext51" "mass.ext52" "mass.ext53" "mass.ext54" "mass.ext55" "mass.ext56" "mass.ext57" "mass.ext58" "mass.ext59" "mass.ext60" "mass.ext61" "mass.ext62" "mass.ext63" "mass.ext64" "mass.ext65" "mass.ext66" "mass.ext67" "mass.ext68" "mass.ext69" "mass.ext70" "mass.ext71" "mass.ext72" "mass.ext73" "mass.ext74" "mass.ext75" "mass.ext76" "mass.ext77" "mass.ext78" "mass.ext79" "mass.ext80" "mass.ext81" "mass.ext82" "mass.ext83" "mass.ext84" "mass.ext85" "mass.ext86" "rec.mass1" "rec.mass2" "rec.mass3" "rec.mass4" "rec.mass5" "rec.mass6" "rec.mass7" "rec.mass8" "rec.mass9" "rec.mass10" "rec.mass11" "rec.mass12" "rec.mass13" "rec.mass14" "rec.mass15" "rec.mass16" "rec.mass17" "rec.mass18" "rec.mass19" "rec.mass20" "rec.mass21" "rec.mass22" "rec.mass23" "rec.mass24" "rec.mass25" "rec.mass26" "rec.mass27" "rec.mass28" "rec.mass29" "rec.mass30" "rec.mass31" "rec.mass32" "rec.mass33" "rec.mass34" "rec.mass35" "rec.mass36" "rec.mass37" "rec.mass38" "rec.mass39" "rec.mass40" "rec.mass41" "rec.mass42" "rec.mass43" "rec.mass44" "rec.mass45" "rec.mass46" "rec.mass47" "rec.mass48" "rec.mass49" "rec.mass50" "rec.mass51" "rec.mass52" "rec.mass53" "rec.mass54" "rec.mass55" "rec.mass56" "rec.mass57" "rec.mass58" "rec.mass59" "rec.mass60" "rec.mass61" "rec.mass62" "rec.mass63" "rec.mass64" "rec.mass65" "rec.mass66" "rec.mass67" "rec.mass68" "rec.mass69" "rec.mass70" "rec.mass71" "rec.mass72" "rec.mass73" "rec.mass74" "rec.mass75" "rec.mass76" "rec.mass77" "rec.mass78" "rec.mass79" "rec.mass80" "rec.mass81" "rec.mass82" "rec.mass83" "rec.mass84" "rec.mass85" "rec.mass86" "range1" "range2" "range3" "range4""range5" "range6" "range7" "range8" "range9""range10" "range11" "range12" "range13" "range14" "range15" "range16" "range17" "range18" "range19" "range20" "range21" "range22" "range23" "range24" "range25" "range26" "range27" "range28" "range29" "range30" "range31" "range32" "range33" "range34" "range35" "range36" "range37" "range38" "range39" "range40" "range41" "range42" "range43" "range44" "range45" "range46" "range47" "range48" "range49" "range50" "range51" "range52" "range53" "range54" "range55" "range56" "range57" "range58" "range59" "range60" "range61" "range62" "range63" "range64" "range65" "range66" "range67" "range68" "range69" "range70" "range71" "range72" "range73" "range74" "range75" "range76" "range77" "range78" "range79" "range80" "range81" "range82" "range83" "range84" "range85" "range86"
- Missing data codes: NA
coeffs_bs_gr_Big5_pradel.txt
File with raw coefficients of association for each taxonomic class from the CMR analysis. Phi corresponds to extinction and Gamma corresponds to origination. coef is used for coefficient estimate and se is used or standard error.
- Number of variables: 15
- Number of cases/rows: 28
- Variable List: class, BEB_Phi, BEB_SE, BEG_Phi, BEG_SE, MEB_Phi, MEB_SE, MEG_Phi, MEG_SE, BBG_Phi, BBG_SE, MBG_Phi, MBG_SE, p, p_SE
- Missing data codes: NA
coeffs_bs_gr_Bambach_Pradel.txt
File with raw coefficients of association for each taxonomic class from the CMR analysis. Phi corresponds to extinction and Gamma corresponds to origination. coef is used for coefficient estimate and se is used or standard error.
- Number of variables: 15
- Number of cases/rows: 20
- Variable List: class, BEB_Phi, BEB_SE, BEG_Phi, BEG_SE, MEB_Phi, MEB_SE, MEG_Phi, MEG_SE, BBG_Phi, BBG_SE, MBG_Phi, MBG_SE, p, p_SE
- Missing data codes: NA
- Acronyms: BEB: Background Extinction Body Size
BEG: Backgroud Extinction Geographic Range
MEB: Background Extinction Body Size
MEG: Mass Extinction Geographic Range
p: sampling estimate
Phi: extinction estimate
SE: Standard Error
ME: Mass Extinction covariate
Rec: mass extinction recovery covariate
coeffs_bs_gr_sansLOME_brachiopods_Pradel.txt
File with raw coefficients of association for each taxonomic class from the CMR analysis. Phi corresponds to extinction and Gamma corresponds to origination. coef is used for coefficient estimate and se is used or standard error.
- Number of variables: 15
- Number of cases/rows: 15
- Variable List: class, BEB_Phi, BEB_SE, BEG_Phi, BEG_SE, MEB_Phi, MEB_SE, MEG_Phi, MEG_SE, BBG_Phi, BBG_SE, MBG_Phi, MBG_SE, p, p_SE
- Missing data codes: NA
- Acronyms: BEB: Background Extinction Body Size
BEG: Backgroud Extinction Geographic Range
MEB: Background Extinction Body Size
MEG: Mass Extinction Geographic Range
p: sampling estimate
Phi: extinction estimate
SE: Standard Error
ME: Mass Extinction covariate
Rec: mass extinction recovery covariate
coeffs_bs_gr_sansKPG_molluscs_Pradel.txt
File with raw coefficients of association for each taxonomic class from the CMR analysis. Phi corresponds to extinction and Gamma corresponds to origination. coef is used for coefficient estimate and se is used or standard error.
- Number of variables: 15
- Number of cases/rows: 10
- Variable List: class, BEB_Phi, BEB_SE, BEG_Phi, BEG_SE, MEB_Phi, MEB_SE, MEG_Phi, MEG_SE, BBG_Phi, BBG_SE, MBG_Phi, MBG_SE, p, p_SE
- Missing data codes: NA
- Acronyms: BEB: Background Extinction Body Size
BEG: Backgroud Extinction Geographic Range
MEB: Background Extinction Body Size
MEG: Mass Extinction Geographic Range
p: sampling estimate
Phi: extinction estimate
SE: Standard Error
ME: Mass Extinction covariate
Rec: mass extinction recovery covariate