The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread overlap between humans and now-extinct native mammals. Humans arrived in four waves (Lithic, Archaic, Ceramic, and European), each associated with increased environmental impact. Large-bodied mammals and several bats were extinct by the Archaic, following protracted extinction dynamics perhaps reflecting habitat loss. Most small-bodied rodents and lipotyphlan insectivores survived the Ceramic, but extensive landscape transformation and the introduction of invasive mammals following European colonization caused further extinctions, leaving a threatened remnant fauna. Both large- and small-bodied nonvolant mammals disappeared, reflecting complex relationships between body size, ecology, and anthropogenic change. Extinct bats were generally larger species, paralleling declines from natural catastrophes.
Date model
Script for meta-analyses of West Indian extinct mammal dates .Files required in same folder
# data: fossil.csv archeo.csv
# jags models: model.txt model0.txt model2.txt model3.txt model4.txt
date_model_dryad.R
Clean list
Script for summarizing data on West Indian extinct mammal dates
# Files required in same folder
# data: fossil.csv archeo.csv list.csv short_list_edited.csv cuba_silva2007.csv
# data: hispaniola_sam.csv puerto_rico_sam.csv
clean_list_dryad.R
Plot models
Script to make plots from meta-analyses of West Indian extinct mammal dates
#
# Files required in same folder
# prior results: dates.Rdata
plots_dryad.R
List of dated fossils
Compiled from literature and calibrated.
fossil.csv
Edited short list
List of species, after manual correction, needed to run clean_list_dryad.R
short_list_edited.csv
List of dated archeological sites
Compiled from literature and calibrated.
archeo.csv
List of species from Hispaniola
Based on literature evaluation by Sam Turvey.
hispaniola_sam.csv
List of species from Cuba
Based on Compendio de los MamÍferos Terrestres Autóctonos de Cuba Vivientes y Extinguidos, by G. Silva Taboada, W. Suarez Duque, and S. Diaz Franco 2007. Compendio de los MamÍferos Terrestres Autóctonos de Cuba Vivientes y Extinguidos. Museo Nacional de Historia Natural. Habana, Cuba
cuba_silva2007.csv
Baseline species list
Based on Dávalos LM, Turvey S. 2012. West Indian Mammals: The Old, the New, and the Recently Extinct In Bones, Clones, and Biomes: An Extended History of Recent Neotropical Mammals, ed. BD Patterson, LP Acosta, pp. 157-202. Chicago: University of Chicago Press
list.csv
Script for making Figure 3
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# Scripts for Fig 3 in Cooke et al. 2017 AREES
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Fig3_phylo_bodyMass_scripts_final.R
Table of body masses
For figure 3
bmTable_withAgeCats.csv
Table of evolutionary distance
For figure 3
caribbeanMam_65sp_ESvalues.txt
Table of invasive species
For figure 3
Invasive_Caribbean_mamSp.txt
Table of evolutionary distance
For figure 3, includes all mammals
MamPhy_5911sp_tipES_NDexp.txt
Table of body missing species
For figure 3
MamPhy_FIN4_1813sp_missing_LIST.txt
Phylogeny used for figure 3
Dated phylogeny including extinct mammals
MamPhy_fullPosterior_BDvr_pcsFIXED_NDexp_MCC_target.tre
Functions called for figure 3
Needed to run Fig3_phylo_bodyMass_scripts_final.R
DR_circleTree_functions.R