A living document representing all mammal species that have been screened for Pneumocystis fungi.
This Excel database lists every mammal species screened for colonization by Pneumocystis based on a literature review as described in Babb-Biernacki et al. 2022. We intend for this database to serve as a living document and to grow as sampled Pneumocystis diversity increases. Researchers may download the database and commit changes to this GitHub repository, subject to the approval of the authors.
The database consists of several sheets, one for all mammal diversity as well as individual sheets representing mammal orders. Each sheet contains the names of sampled mammal genera, followed by species within that genus that have been sampled. In the row of each sampled mammal, cells represent whether or not the taxon was positive for Pneumocystis, whether there is genetic data available that represents that Pneumocystis lineage, whether the presence of Pneumocystis was assessed through microscopy alone, what genetic sequences (if any) were collected from the Pneumocystis lineage, and a citation for the source of the screening result (if any). Please include all of this information (in a "Yes/No" format for the first three categories) when entering new species.
In order to keep the math formulas in the Excel spreadsheet functional, some formatting quirks should be adhered to. Genera and species are listed in alphabetical order. When entering a new genus into the spreadheet, please preface it with a dollar sign ($) symbol, and when entering a new species, please preface it with a carrot (^) symbol. As states above, several categories must be represented by either a "Yes" or a "No"; capitalization does matter. Incorrectly inputting these things will lead to inaccurate calculations of total species sampled, etc.
It is helpful if you manually increase the column "Species Sampled in Genus" when inputting new species, as well as the "Total Species in Genus" when inputting new genera. The number of extant species in any given mammal genus can be found on the Mammal Diversity Database: https://www.mammaldiversity.org/ These values will be periodically checked and updated by the authors.
Please also include any new sampled species or genera in their respective order sheet in addition to the total species sheet.
Pull requests will be reviewed by the author and merged if they fulfill these requirements
Contact Spenser Babb-Biernacki (sbiern1@lsu.edu) if you have any questions.