Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals

Cooke SB, Dávalos LM, Mychajliw AM, Turvey ST, Upham NS

Date Published: July 14, 2017

DOI: https://doi.org/10.5061/dryad.tj4p5

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Title Date model
Downloaded 1 time
Description 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
Download date_model_dryad.R (9.682 Kb)
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Title Clean list
Downloaded 2 times
Description 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
Download clean_list_dryad.R (12.13 Kb)
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Title Plot models
Downloaded 1 time
Description Script to make plots from meta-analyses of West Indian extinct mammal dates # # Files required in same folder # prior results: dates.Rdata
Download plots_dryad.R (9.802 Kb)
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Title List of dated fossils
Downloaded 1 time
Description Compiled from literature and calibrated.
Download fossil.csv (38.53 Kb)
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Title Jags model 3
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Download model3.txt (2.353 Kb)
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Title Jags model 4
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Download model4.txt (2.41 Kb)
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Title Edited short list
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Description List of species, after manual correction, needed to run clean_list_dryad.R
Download short_list_edited.csv (27.01 Kb)
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Title Jags model 2
Downloaded 1 time
Download model2.txt (900 bytes)
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Title List of dated archeological sites
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Description Compiled from literature and calibrated.
Download archeo.csv (7.692 Kb)
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Title List of species from Hispaniola
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Description Based on literature evaluation by Sam Turvey.
Download hispaniola_sam.csv (545 bytes)
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Title List of species from Cuba
Downloaded 1 time
Description 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
Download cuba_silva2007.csv (496 bytes)
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Title Baseline species list
Downloaded 1 time
Description 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
Download list.csv (35.60 Kb)
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Title Jags model 0
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Download model0.txt (665 bytes)
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Title Jags model 1
Downloaded 1 time
Download model.txt (776 bytes)
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Title Script for making Figure 3
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Description ### # Scripts for Fig 3 in Cooke et al. 2017 AREES ###
Download Fig3_phylo_bodyMass_scripts_final.R (9.235 Kb)
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Title Table of body masses
Downloaded 1 time
Description For figure 3
Download bmTable_withAgeCats.csv (16.58 Kb)
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Title Table of evolutionary distance
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Description For figure 3
Download caribbeanMam_65sp_ESvalues.txt (4.128 Kb)
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Title Table of invasive species
Downloaded 1 time
Description For figure 3
Download Invasive_Caribbean_mamSp.txt (736 bytes)
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Title Table of evolutionary distance
Downloaded 1 time
Description For figure 3, includes all mammals
Download MamPhy_5911sp_tipES_NDexp.txt (397.9 Kb)
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Title Table of body missing species
Downloaded 1 time
Description For figure 3
Download MamPhy_FIN4_1813sp_missing_LIST.txt (78.53 Kb)
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Title Phylogeny used for figure 3
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Description Dated phylogeny including extinct mammals
Download MamPhy_fullPosterior_BDvr_pcsFIXED_NDexp_...et.tre (4.430 Mb)
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Title Functions called for figure 3
Downloaded 1 time
Description Needed to run Fig3_phylo_bodyMass_scripts_final.R
Download DR_circleTree_functions.R (8.82 Kb)
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When using this data, please cite the original publication:

Cooke SB, Dávalos LM, Mychajliw AM, Turvey ST, Upham NS (2017) Anthropogenic extinction dominates Holocene declines of West Indian mammals. Annual Review of Ecology, Evolution, and Systematics 48(1): 301-327. https://doi.org/10.1146/annurev-ecolsys-110316-022754

Additionally, please cite the Dryad data package:

Cooke SB, Dávalos LM, Mychajliw AM, Turvey ST, Upham NS (2017) Data from: Anthropogenic extinction dominates Holocene declines of West Indian mammals. Dryad Digital Repository. https://doi.org/10.5061/dryad.tj4p5
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