New Featured Software: geographic coverage of DNA barcodes

New Featured Software: Geographic Coverage of DNA Barcodes

Featured Software from the Kartzinel Lab: Geographic Coverage of DNA Barcodes. The inaugural code repository to be highlighted in our Featured Software section of the Software & Data page presents the Quarto Code Book published in association with our Molecular Ecology Review Paper, "Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research" can be easily modified to evaluate the geographic coverage of other data sets. Although the featured code emphasizes geographic coverage from our work in Yellowstone National Park...

The codebook itself is readily customizable for a wide variety of uses. To facilitate re-use, we have divided it into four parts that follow the Methods section of the publication and includes eight code notebooks that we used in the analyses for this publication. Source code is available in a GitHub repository

To see how data are formatted and work through the Yellowstone example as a vignette, supplementary data sets (S1-S4) can be downloaded from the supplement available with the published paper. Move those four files into the /data folder in the GitHub repository when running the code notebooks. If running notebooks from the repository, headers in the data retrieved may differ than headers in the datasets provided in the Supplemental Materials.

The sections documenting the workflow are as follows: 
Building global BOLD data

1. Building the BOLD dataset

Geographic coverage

1. Coverage by climatic zones
2. Coverage by country

Taxonomic coverage

1. Fetching data from ITIS
2. Correlations – plant species and available barcodes

Case-study Yellowstone National Park

1. Continent-scale barcode coverage of lodgepole pine and big sagebrush
2. Fetching data from GBIF
3. Case-study in geographic coverage of site-based reference data