DOI: 10.5061/dryad.tj4p5
title: Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals

description: 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.
description: Date
 modelScript 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.txtdate_model_dryad.RClean listScript 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.csvclean_list_dryad.RPlot modelsScript to make plots from meta-analyses of West Indian extinct mammal dates # # Files required in same folder # prior results: dates.Rdataplots_dryad.RList of dated fossilsCompiled from literature and calibrated.fossil.csvJags model 3model3.txtJags model 4model4.txtEdited short listList of species, after manual correction, needed to run clean_list_dryad.Rshort_list_edited.csvJags model 2model2.txtList of dated archeological sitesCompiled from literature and calibrated.archeo.csvList of species from HispaniolaBased on literature evaluation by Sam Turvey.hispaniola_sam.csvList of species from CubaBased 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, Cubacuba_silva2007.csvBaseline species listBased 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 Presslist.csvJags model 0model0.txtJags model 1model.txtScript for making Figure 3### # Scripts for Fig 3 in Cooke et al. 2017 AREES ###Fig3_phylo_bodyMass_scripts_final.RTable of body massesFor figure 3bmTable_withAgeCats.csvTable of evolutionary distanceFor figure 3caribbeanMam_65sp_ESvalues.txtTable of invasive speciesFor figure 3Invasive_Caribbean_mamSp.txtTable of evolutionary distanceFor figure 3, includes all mammalsMamPhy_5911sp_tipES_NDexp.txtTable of body missing speciesFor figure 3MamPhy_FIN4_1813sp_missing_LIST.txtPhylogeny used for figure 3Dated phylogeny including extinct mammalsMamPhy_fullPosterior_BDvr_pcsFIXED_NDexp_MCC_target.treFunctions called for figure 3Needed to run Fig3_phylo_bodyMass_scripts_final.RDR_circleTree_functions.R