--- title: Colonial legacies influence biodiversity lessons output: html_document: default pdf_document: default --- # Citation Mohammed, R.S., Kemp, M., LeFebvre, M. J., Mychajliw, A. M., Turner, G., Fowler, K., Pateman, M., Nieves-Colón, M. A., Fanovich, L., Cooke, S. B., Dávalos, L. M., Fitzpatrick, S. M., Giovas, C. M., Stokowski, M., Wrean, A. A. 2022. Colonial legacies influence biodiversity lessons: how past trade routes and power dynamics shape present day scientific research and professional opportunities for Caribbean scientists. American Naturalist ------------------------------------------------------------------------ - Ryan S. Mohammed, ([ryansmohammed2020\@gmail.com](mailto:ryansmohammed2020@gmail.com)) - Melissa Kemp, ([mkemp\@austin.utexas.edu](mailto:mkemp@austin.utexas.edu)) - Michelle J. LeFebvre, ([mlefebvre\@floridamuseum.ufl.edu](mailto:mlefebvre@floridamuseum.ufl.edu)) - Alexis M. Mychajliw, ([amychajliw\@middlebury.edu](mailto:amychajliw@middlebury.edu)) - Grace Turner, ([gturner2018\@ammcbahamas.com](mailto:gturner2018@ammcbahamas.com)) - Kelly Fowler, ([kfowler\@ammcbahamas.com](mailto:kfowler@ammcbahamas.com)) - Michael Pateman, ([bahamamike\@gmail.com](mailto:bahamamike@gmail.com)) - Maria A. Nieves-Colón, ([mnievesc\@umn.edu](mailto:mnievesc@umn.edu)) - Lanya Fanovich, ([ericecologist\@eric-tobago.org](mailto:ericecologist@eric-tobago.org)) - Siobhan B. Cooke, ([siobhancooke\@jhmi.edu](mailto:siobhancooke@jhmi.edu)) - Liliana M. Dávalos, ([liliana.davalos\@stonybrook.edu](mailto:liliana.davalos@stonybrook.edu)) - Scott M. Fitzpatrick, ([smfitzpa\@uoregon.edu](mailto:smfitzpa@uoregon.edu)) - Christina M. Giovas, ([cgiovas\@sfu.edu](mailto:cgiovas@sfu.edu)) - Myles Stokowski, ([mstokowski\@middlebury.edu](mailto:mstokowski@middlebury.edu)) - Ashley A. Wrean, ([awrean\@middlebury.edu](mailto:awrean@middlebury.edu)) ------------------------------------------------------------------------ # Article summary This repository contains analyses and code for generating figures to demonstrate how colonial history has influenced research trajectories and community engagement in the Caribbean. ------------------------------------------------------------------------ # Data ### GBIF Data on digitized natural history specimen comes from the GBIF database through the GBIF API using the R package `rgbif`. ### Institution locations Institution locations were gathered partially through the GBIF API, and partially manually. The compiled list of institutions and their locations is in the file `orgTibbleEdited.csv`, where each row is an institution, and columns represent: - `publishingOrgKey`: a unique key for identifying the institution that published a digital specimen record - `title`: institution name - `lat`: latitude of institution - `long`: longitude of institution - `nSpecimens`: number of specimens published by the institution ------------------------------------------------------------------------ # Code Code was written by Ashley A. Wrean and Myles Stokowski. Additional editing to figures was performed by Alexis M. Mychajliw in Adobe Illustrator after generating the figures using the code and data in this repository. ### Figure 1a `fig1a.R`: Code to generate Figure 1a, which is a map of the number of specimens from Trinidad & Tobago in digital natural history collections worldwide. This script queries GBIF for all preserved and fossil specimens collected in Trinidad & Tobago. It then queries GBIF for the location of institutions that own these specimens, and generates the map. Since location is not available for all institutions, we manually added locations for some institutions. The manually edited list of institution locations is available in the file `orgTibbleEdited.csv` ### Figure 1c `fig1c.R`: Code to generate Figure 1c, which is a histogram of specimen accessioning patterns within The University of the West Indies Zoology Museum (UWIZM) collection location in Trinidad & Tobago across select animal taxa through time. The script queries GBIF for specimens published by UWIZM and collected in Trinidad & Tobago, reorganizes taxonomic groupings, and generates the histogram. ### Figure 2 `fig2.R`: Code to generate Figure 2, which is a histogram of the number of digitized fossil and preserved specimens from The Bahamas published by the Florida Museum during each decade from 1930s to 2010s. ### Figure 3 `Todies.R`: Code to generate Figure 3. This includes a histogram showing the temporal distribution of occurrence data by source (iNaturalist, eBird, Preserved specimen) for the family Todidae, genus Todus, in the Greater Antilles. It also includes a map with the locations of occurrences and pie charts showing the proportions of occurrences per country that come from each data source. The GBIF API has a `taxonKey` associated with each species and level of taxonomic specificity: - `taxonKey == 2475383` is for all occurrences in the genus Todus The GBIF API uses `country` to locate occurrences with a location from the specified country: - Haiti: `country == "HT"` - Dominican Republic: `country == "DO"` - Cuba: `country == "CU"` - Puerto Rico: `country == "PR"` - Jamaica: `country == "JM"` The GBIF API uses `datasetKey` to access data from specific data sets within GBIF: - iNaturalist: `datasetKey == "50c9509d-22c7-4a22-a47d-8c48425ef4a7"` - eBird: `datasetKey == "4fa7b334-ce0d-4e88-aaae-2e0c138d049e"` The GBIF API uses `basisOfRecord` to access data from a certain type of occurrence record: - `basisOfRecord == "PESERVED_SPECIMEN"`: all preserved specimen occurrence records ------------------------------------------------------------------------ # Version information ``` R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Monterey 12.0.1 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mapdata_2.3.0 maps_3.4.0 viridis_0.6.2 viridisLite_0.4.0 [5] rnaturalearth_0.1.0 sf_1.0-3 ggimage_0.3.0 rgbif_3.6.0 [9] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 [13] readr_2.0.2 tidyr_1.1.4 tibble_3.1.5 ggplot2_3.3.5 [17] tidyverse_1.3.1 loaded via a namespace (and not attached): [1] httr_1.4.2 jsonlite_1.7.2 modelr_0.1.8 assertthat_0.2.1 [5] sp_1.4-5 wellknown_0.7.4 yulab.utils_0.0.4 cellranger_1.1.0 [9] pillar_1.6.4 backports_1.3.0 lattice_0.20-44 glue_1.4.2 [13] uuid_1.0-2 rvest_1.0.2 colorspace_2.0-2 ggfun_0.0.4 [17] plyr_1.8.6 pkgconfig_2.0.3 oai_0.3.2 broom_0.7.9 [21] haven_2.4.3 magick_2.7.3 scales_1.1.1 ggplotify_0.1.0 [25] whisker_0.4 tzdb_0.2.0 proxy_0.4-26 generics_0.1.1 [29] ellipsis_0.3.2 withr_2.4.2 lazyeval_0.2.2 cli_3.1.0 [33] magrittr_2.0.1 crayon_1.4.1 readxl_1.3.1 fs_1.5.0 [37] fansi_0.5.0 xml2_1.3.2 class_7.3-19 tools_4.1.1 [41] data.table_1.14.2 hms_1.1.1 lifecycle_1.0.1 munsell_0.5.0 [45] reprex_2.0.1 compiler_4.1.1 e1071_1.7-9 gridGraphics_0.5-1 [49] rlang_0.4.12 classInt_0.4-3 units_0.7-2 grid_4.1.1 [53] conditionz_0.1.0 rstudioapi_0.13 wk_0.5.0 gtable_0.3.0 [57] DBI_1.1.1 R6_2.5.1 gridExtra_2.3 lubridate_1.8.0 [61] utf8_1.2.2 KernSmooth_2.23-20 stringi_1.7.5 Rcpp_1.0.7 [65] vctrs_0.3.8 dbplyr_2.1.1 tidyselect_1.1.1 ```