MDDv2_ms

Codebase for Journal of Mammalogy ms documenting changes to the Mammal Diversity Database from v1.0 to v2.0

• Citation: Burgin, C. J., Zijlstra, J. S., Becker, M. C., Handika, H., Alston, J., Widness, J., Liphardt, S. W., Huckaby, D. G., & Upham, N. S. (2025). How many mammal species are there now? Updates and trends in taxonomic, nomenclatural, and geographic knowledge. Journal of Mammalogy.
• Live site: https://mammaldiversity.org/
• Versioning of taxonomy: https://doi.org/10.5281/zenodo.4139722
• Zenodo mirror:

Contents

inputs

• MDD_v2.0: full taxonomy files for the v2.0 release of the MDD, including the Species_Syn_v2.0.csv file
• MDD_versions: CSV formatted versions for all releases between v1.0 and v2.0 MDD taxonomy
• Diff_files: Tracked differences between adjacent versions of the MDD, from v1.0 to v2.0
• Metadata_files: Versions of the field definitions for each versions of the MDD, from v1.2 to v2.0

scripts

• mdd2_manuscript_code.R: all code for performing analyses and making figures in this paper.
• country_matrix_v2.R: script for parsing the 'countryDistribution' field of the MDD v2.0 database into a species-by-country matrix.

outputs

• eps_figures: EPS and PDF formatted versions of the final figures in the MDD v2.0 manuscript.

• graphs: non-map plotting of data for the MDD v2.0 manuscript.

• map_figures: map-based plotting of data for the MDD v2.0 manuscript.

• non_scripted_figures: Fig. 7, which was made in Whimsical online software.

• supplementary_files: additional files of relevance for analyses, including intermediary files.

  • Includes a parsing of the 'countryDistribution' field in the MDD v2.0 database into a species-by-country matrix; each country in which the species is extant or reintroduced into its native distribution is listed and separated by pipes (|); 0=absence, 1=presence, 2=potential presence. The script 'country_matrix_v2.R' is used to create the files 'v2_country_matrix.txt' and 'v2_country_totals.txt'

• tables: HTML output of tables from the paper.

mdd2_supplemental_data

• SD1 to SD11 from the Journal of Mammalogy paper

  • SD1: MDD2 species list, plus associated metadata, in a zipped folder.
  • SD2: MDD2 synonym list, plus associated metadata, in a zipped folder.
  • SD3: All MDD version species lists, plus associated metadata, in a zipped folder.
  • SD4: All MDD ‘diff’ files, plus associated metadata, in a zipped folder.
  • SD5: ‘Diff’ file specifically between MDD1 and MDD2, plus associated metadata, in a zipped folder.
  • SD6: Summary of nomenclatural data and species totals by taxonomic group, plus associated metadata, in a zipped folder.
  • SD7: Summary of nomenclatural data and species totals by geographic region, plus associated metadata, in a zipped folder.
  • SD8: Summary of nomenclatural data totals by nomenclatural and validity status, plus associated metadata, in a zipped folder.
  • SD9: Total available and valid names described per year since 1758 and summary of 10-year running means used to create Figure 1, plus associated metadata, in a zipped folder.
  • SD10: Occurrence matrix for species country and offshore territory distribution data in a zipped folder.
  • SD11: Per country usage of the MDD website at mammaldiversity.org in a zipped folder.