Data and code from: Interactions between intrinsic and extrinsic factors in island bat survival and extirpation in a global extinction hotspot
Data files
Jul 24, 2026 version files 8.64 MB
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folder4dryad.zip
8.63 MB
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README.md
15.66 KB
Abstract
Caribbean islands are hotspots of mammalian biodiversity and extinction, where only a few intermediate-sized non-volant species survived. Despite numerous extirpations and extinctions, how body size (intrinsic trait) or island features (extrinsic environmental variables) contribute to the survival and extirpation of 479 Caribbean bat populations is poorly known. We used phylogenetic hierarchical models to impute missing body mass data for several fossil species and then to model extirpation probability as a function of intrinsic traits and extrinsic variables. Data inputs and scripts for replicating analyses in Interactions between intrinsic and extrinsic factors shape island bat survival and extirpation in a global extinction hotspot. Data may be reused; citation is recommended.
Dataset DOI: 10.5061/dryad.wwpzgmt0b
Article DOI: https://doi.org/10.1093/evolinnean/kzag014
Description of the data and file structure
README
July 24, 2026
Download all supplementary data from manuscript available at Evolutionary Journal of the Linnean Society online (https://doi.org/10.1093/evolinnean/kzag014).
All abbreviations and units of measure are described and listed as a note in each supplementary table.
All files from the supplement should be placed into a folder before proceeding.
Save tables 2-8 as a csv and rename appropriately (e.g. Table_S2 - compilation.csv, Table_S3 - compilation.csv, etc.) to correspond to the script.
Place all tables into the source folder
Do not tamper with NAs in the csv/tsv files, leave them as is.
Unzip folder4dryad.zip.
Interactions between intrinsic and extrinsic factors in bat survival and extirpation in the Caribbean
0a. Run pruningCode_MamPhy-to-CaribbeanTaxa.R in the caribbeanBats_Nov2025 folder, must include:
input:
##sample from https://doi.org/10.1371/journal.pbio.3000494
/caribbeanBats_Nov2025/MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_v2_sample100_nexus.trees
##taxonomy from https://doi.org/10.1371/journal.pbio.3000494
/caribbeanBats_Nov2025/taxonomy_mamPhy_5911species_toPublish.csv
##Caribbean bat list
/caribbeanBats_Nov2025/Updated_Species_List_Bats.tsv
##full rows of MRCAs; Do not tamper with NAs, leave as is.
/caribbeanBats_Nov2025/nameToAdd_mrca1_mrca2_caribbeanBATS.txt
##list of species to extract from trees; Do not tamper with NAs, leave as is.
/caribbeanBats_Nov2025/MamPhy_CaribbeanTaxaToPruneOut_BATS.tsv
key output: CaribbeanBATS_76_taxa_MamPhy_added17taxa_random100trees_resolvedUltra_FINAL.nex
0b. This is code for an alternate tree that has monophyletic Mormoopidae. Run pruningCode_mamphy-to-CaribbeanTaxa.R in the caribbeanBats_May2026 folder, must include:
input:
download from 4705sp_mean.nwk https://figshare.com/articles/dataset/Data_for_A_Species-Level_Timeline_of_Mammal_Evolution_Integrating_Phylogenomic_Data_/14885691?file=31403983
place in
/caribbeanBats_May2026/
##Caribbean bat list
/caribbeanBats_May2026/Updated_Species_List_Bats.tsv
##full rows of MRCAs, do not modify, leave
/caribbeanBats_May2026/nameToAdd_mrca1_mrca2_caribbeanBATS.txt
##list of species to extract from trees
/caribbeanBats_May2026/mamphy_CaribbeanTaxaToPruneOut_Bats.tsv
key output (this is only one tree): CaribbeanBATS_76_taxa_MamPhy_added17taxa_resolvedUltra_FINAL.nex
1. Run bat_island_data_process.R in the data folder must include:
input:
##data from https://doi.org/10.7208/chicago/9780226649214.003.0009
/sources/appendix9_2.csv
## data from the article https://doi.org/10.1098/rspb.2020.2905
## download data from https://doi.org/10.6084/m9.figshare.14124211
## rename as Final_WTWTW_dataset_July2020 and save as a csv file
## add dataset to sources folder
/sources/Final_WTWTW_dataset_July2020.csv
##new island data compiled for our analysis
/sources/Table_S6 - compilation.csv
##data from https://doi.org/10.1002/ece3.399 that was not published then
/sources/Table_S7 - compilation.csv
output:
bat_island_data.RData
2. Run bat_island_data_corr.R in same folder as bat_island_data.RData
input:
bat_island_data.RData
output:
bat_island_data.RData (modified from step 1)
3. Run bat_traits_data_process.R in the data folder must include:
input:
##compiled body mass data
/sources/Table_S2 - compilation.csv
##compiled greatest length of skull data
/sources/Table_S3 - compilation.csv
##compiled roost type data
/sources/Table_S4 - compilation.csv
##compile diet type data
/sources/Table_S5 - compilation.csv
output:
bat_traits.RData
4a. Run impute_vars_phyr_v2.R in same folder as bat_traits.RData and CaribbeanBATS_76_taxa_MamPhy_added17taxa_random100trees_resolvedUltra_FINAL.nex must include:
input:
bat_traits.RData
CaribbeanBATS_76_taxa_MamPhy_added17taxa_random100trees_resolvedUltra_FINAL.nex
output:
impute_traits_phyr_v2.RData
4b. This is code for an alternate tree that has monophyletic Mormoopidae. Run impute_vars_phyr_alt.R in same folder as bat_traits.RData and CaribbeanBATS_76_taxa_MamPhy_added17taxa_resolvedUltra_FINAL.nex must include:
input:
bat_traits.RData
CaribbeanBATS_76_taxa_MamPhy_added17taxa_resolvedUltra_FINAL.nex
output:
impute_traits_phyr_alt.Rdata.RData
5a. Run bat_model_v10.R in same folder as bat_island_data.RData and impute_traits_phyr_v2.RData
must include:
input:
bat_island_data.RData
impute_traits_phyr_v2.RData
output:
##this is the equivalent of WTWTW dataset from https://doi.org/10.1098/rspb.2020.2905
Caribbean_island_bat_Nov2025.csv
bat_model_v10.RData
5b. This is code for an alternate tree that has monophyletic Mormoopidae. Run bat_model_alt.R in same folder as bat_island_data.RData and impute_traits_phyr_alt.RData
must include:
input:
bat_island_data.RData
impute_traits_phyr_alt.RData
output:
##this is a summary of regressions with alternate tree that has monophyletic Mormoopidae. Subsequent runs do not apply as there is only one mean tree, not 100 as in the Upham tree sample.
bat_binomial_models_alt.txt
bats_model_alt.Rdata
6. Requires multi-core system. Run phylo_phyr_binomial_bat_v10.R in same folder as bat_model_v10.RData must include:
input:
bats_v10.Rdata
output:
bats_impu_mods_v10.RData
7. Run summarize_phyr_binomial_fbat_v10.R in same folder as bats_impu_mods_v10.RData must include:
input:
bats_impu_mods_v10.RData
key output:
bats_fbat_vis.RData
8. Run summarize_phyr_binomial_fsig_v10.R in same folder as bats_impu_mods_v10.RData must include:
input:
bats_impu_mods_v10.RData
key output:
bats_fsig_vis.RData
9. Run plot_phyr_binomial_fbat_v10.R in same folder as bats_fbat_vis.RData must include:
input:
bats_fbat_vis.RData
key output:
bats_fsig_vis.RData (modified from step 8)
10. Run introduced_v2.R in the data folder must include:
input:
##this is a compilation from https://doi.org/10.1098/rspb.2020.0447
/sources/Table_S8 - compilation.csv
output:
introduced.RData
11. Run spp_area_island_v2.R in same folder as bat_model_v10.Rdata and introduced.Rdata must include:
input:
bat_model_v10.Rdata
introduced.Rdata
key output:
bat_SARs.RData
12. Run descriptive_v2.R in same folder as bat_model_v10.Rdata must include:
input:
bat_model_v10.Rdata
key output:
##summary of descriptive statistics on populations extant and extinct on one vs. many islands
descriptive.txt
##chi squared test of extinction or extirpation for species with geo range of one or many islands
single_many_island.txt
13. Run descriptive_LGM_v2.R in same folder as bat_model_v10.Rdata must include:
input:
bat_model_v10.Rdata
key output:
##summary of descriptive statistics on populations extant and extinct on one vs. many islands at the Last Glacial Maximum (LGM)
descriptive_LGM.txt
##ignore chi squared test as too many unknowns at LGM
Files and variables
README
May 11, 2026
Interactions between Eltonian and Grinnellian niche factors in island bat survival and extirpation in a global extinction hotspot
0a. Run pruningCode_MamPhy-to-CaribbeanTaxa.R in the caribbeanBats_Nov2025 folder, must include:
input:
##sample from https://doi.org/10.1371/journal.pbio.3000494
/caribbeanBats_Nov2025/MamPhy_fullPosterior_BDvr_Completed_5911sp_topoCons_NDexp_v2_sample100_nexus.trees
##taxonomy from https://doi.org/10.1371/journal.pbio.3000494
/caribbeanBats_Nov2025/taxonomy_mamPhy_5911species_toPublish.csv
##Caribbean bat list
/caribbeanBats_Nov2025/Updated_Species_List_Bats.tsv
##full rows of MRCAs
/caribbeanBats_Nov2025/nameToAdd_mrca1_mrca2_caribbeanBATS.txt
##list of species to extract from trees
/caribbeanBats_Nov2025/MamPhy_CaribbeanTaxaToPruneOut_BATS.tsv
key output: CaribbeanBATS_76_taxa_MamPhy_added17taxa_random100trees_resolvedUltra_FINAL.nex
0b. This is code for an alternate tree that has monophyletic Mormoopidae. Run pruningCode_mamphy-to-CaribbeanTaxa.R in the caribbeanBats_May2026 folder, must include:
input:
/caribbeanBats_May2026/4705sp_mean.nwk
##Caribbean bat list
/caribbeanBats_May2026/Updated_Species_List_Bats.tsv
##full rows of MRCAs
/caribbeanBats_May2026/nameToAdd_mrca1_mrca2_caribbeanBATS.txt
##list of species to extract from trees
/caribbeanBats_May2026/mamphy_CaribbeanTaxaToPruneOut_Bats.tsv
key output (this is only one tree): CaribbeanBATS_76_taxa_MamPhy_added17taxa_resolvedUltra_FINAL.nex
1. Run bat_island_data_process.R in the data folder must include:
input:
##data from https://doi.org/10.7208/chicago/9780226649214.003.0009
/sources/appendix9_2.csv
##data from https://doi.org/10.1098/rspb.2020.2905
/sources/Final_WTWTW_dataset_July2020.csv
##new island data compiled for our analysis
/sources/Table_S6 - compilation.csv
##data from https://doi.org/10.1002/ece3.399 that was not published then
/sources/Table_S7 - compilation.csv
output:
bat_island_data.RData
2. Run bat_island_data_corr.R in same folder as bat_island_data.RData
input:
bat_island_data.RData
output:
bat_island_data.RData (modified from step 1)
3. Run bat_traits_data_process.R in the data folder must include:
input:
##compiled body mass data
/sources/Table_S2 - compilation.csv
##compiled greatest length of skull data
/sources/Table_S3 - compilation.csv
##compiled roost type data
/sources/Table_S4 - compilation.csv
##compile diet type data
/sources/Table_S5 - compilation.csv
output:
bat_traits.RData
4a. Run impute_vars_phyr_v2.R in same folder as bat_traits.RData and CaribbeanBATS_76_taxa_MamPhy_added17taxa_random100trees_resolvedUltra_FINAL.nex must include:
input:
bat_traits.RData
CaribbeanBATS_76_taxa_MamPhy_added17taxa_random100trees_resolvedUltra_FINAL.nex
output:
impute_traits_phyr_v2.RData
4b. This is code for an alternate tree that has monophyletic Mormoopidae. Run impute_vars_phyr_alt.R in same folder as bat_traits.RData and CaribbeanBATS_76_taxa_MamPhy_added17taxa_resolvedUltra_FINAL.nex must include:
input:
bat_traits.RData
CaribbeanBATS_76_taxa_MamPhy_added17taxa_resolvedUltra_FINAL.nex
output:
impute_traits_phyr_alt.Rdata.RData
5a. Run bat_model_v10.R in same folder as bat_island_data.RData and impute_traits_phyr_v2.RData
must include:
input:
bat_island_data.RData
impute_traits_phyr_v2.RData
output:
##this is the equivalent of WTWTW dataset from https://doi.org/10.1098/rspb.2020.2905
Caribbean_island_bat_Nov2025.csv
bat_model_v10.RData
5b. This is code for an alternate tree that has monophyletic Mormoopidae. Run bat_model_alt.R in same folder as bat_island_data.RData and impute_traits_phyr_alt.RData
must include:
input:
bat_island_data.RData
impute_traits_phyr_alt.RData
output:
##this is a summary of regressions with alternate tree that has monophyletic Mormoopidae. Subsequent runs do not apply as there is only one mean tree, not 100 as in the Upham tree sample.
bat_binomial_models_alt.txt
bats_model_alt.Rdata
6. Requires multi-core system. Run phylo_phyr_binomial_bat_v10.R in same folder as bat_model_v10.RData must include:
input:
bats_v10.Rdata
output:
bats_impu_mods_v10.RData
7. Run summarize_phyr_binomial_fbat_v10.R in same folder as bats_impu_mods_v10.RData must include:
input:
bats_impu_mods_v10.RData
key output:
bats_fbat_vis.RData
8. Run summarize_phyr_binomial_fsig_v10.R in same folder as bats_impu_mods_v10.RData must include:
input:
bats_impu_mods_v10.RData
key output:
bats_fsig_vis.RData
9. Run plot_phyr_binomial_fbat_v10.R in same folder as bats_fbat_vis.RData must include:
input:
bats_fbat_vis.RData
key output:
bats_fsig_vis.RData (modified from step 8)
10. Run introduced_v2.R in the data folder must include:
input:
##this is a compilation from https://doi.org/10.1098/rspb.2020.0447
/sources/Table_S8 - compilation.csv
output:
introduced.RData
11. Run spp_area_island_v2.R in same folder as bat_model_v10.Rdata and introduced.Rdata must include:
input:
bat_model_v10.Rdata
introduced.Rdata
key output:
bat_SARs.RData
12. Run descriptive_v2.R in same folder as bat_model_v10.Rdata must include:
input:
bat_model_v10.Rdata
key output:
##summary of descriptive statistics on populations extant and extinct on one vs. many islands
descriptive.txt
##chi squared test of extinction or extirpation for species with geo range of one or many islands
single_many_island.txt
13. Run descriptive_LGM_v2.R in same folder as bat_model_v10.Rdata must include:
input:
bat_model_v10.Rdata
key output:
##summary of descriptive statistics on populations extant and extinct on one vs. many islands at the LGM
descriptive_LGM.txt
##ignore chi squared test as too many unknowns at LGM
Code/software
R code for Interactions between Eltonian and Grinnellian niche factors in bat survival and extirpation in the Caribbean
0a. pruningCode_MamPhy-to-CaribbeanTaxa.R
generates phylogenies including extinct species
0b. pruningCode_mamphy-to-CaribbeanTaxa.R
generates single phylogeny including extinct species
1. bat_island_data_process.R
generates first pass bat-island distribution
2. bat_island_data_corr.R
analyzes island variable correlations and modifies bat-island distribution data
3. bat_traits_data_process.R
compiles bat trait data
4a. impute_vars_phyr_v2.R
imputes bat traits for missing species
4b. impute_vars_phyr_alt.R
imputes bat traits for missing species using tree with monophyletic Mormoopidae
5a. bat_model_v10.R
generates first-pass, single-tree phylogenetic models of extirpation
5b. bat_model_alt.R
generates first-pass, single-tree phylogenetic models of extirpation using tree with monophyletic Mormoopidae
6. phylo_phyr_binomial_bat_v10.R
generates models across 100 phylogenies
7. summarize_phyr_binomial_fbat_v10.R
summarizes the 100 models for bat model (all variables)
8. summarize_phyr_binomial_fsig_v10.R
summarizes the 100 models for significant model (only significant variables)
9. plot_phyr_binomial_fbat_v10.R
generates plots for bat models
10. introduced_v2.R
organizes data for species-area relationship of introduced species data
11. spp_area_island_v2.R
generates SARs for bats, extinct bats, and introduced species
12. descriptive_v2.R
generates contingency table and chi squared test of species on one vs many islands an extinction/extirpation
13. descriptive_LGM_v2.R
generates contingency table of species putatively on one vs many islands an extinction/extirpation at the LGM