DOI: 10.5061/dryad.931zcrjqw
title: Reduced strength and increased variability of extinction selectivity during mass extinctions

description: 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.
description: # Data from: Reduced Strength and Increased Variability of Extinction
 Selectivity Across Marine Clades During Mass Extinctions ## GENERAL
 INFORMATION 1. 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 1.
 Licenses/restrictions placed on the data: CC0 2. Links to publications
 that cite or use the data: TBD 3. Links to other publicly accessible
 locations of the data: paleobiodb.org 4. Links/relationships to ancillary
 data sets: NA 5. Was data derived from another source? yes A. If yes, list
 source(s): Paleobiology Database 6. 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. 1. Number of variables: 12
 2. Number of cases/rows: 33497 3. Variable List: pbdb\_taxon\_no,
 taxon\_name, phylum, class, order, family, max\_length, fad\_int,
 lad\_int, fad\_age, lad\_age, calc\_max\_vol 4. 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. 1. Number of variables: 29
 2. Number of cases/rows: 585051 3. 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 4. 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. 1. Number of variables: 34 2.
 Number of cases/rows: 284309 3. 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 4. 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. 1.
 Number of variables: 9 2. Number of cases/rows: 6702 3. Variable List:
 genus, phylum, class, order, family, logsize, logvol, fad, lad 4. 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). 1.
 Number of variables: 262 2. Number of cases/rows: 6,562 3. 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" 4. 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. 1. Number of variables: 15 2. Number of cases/rows: 28 3.
 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
 4. 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. 1. Number of variables: 15 2. Number of cases/rows: 20 3.
 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
 4. Missing data codes: NA 5. 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. 1. Number of variables: 15 2. Number of cases/rows: 15 3.
 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
 4. Missing data codes: NA 5. 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. 1. Number of variables: 15 2. Number of cases/rows: 10 3.
 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
 4. Missing data codes: NA 5. 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