An Automated Bioinformatic Pipeline to Analyze Biodiversity Data for Conservation Purposes: A Test Case for Colorado Macrofungi

Fungi are of critical importance in supporting biodiversity and the world’s ecosystems, yet their conservation status has only been assessed relatively recently as part of the IUCN’s Red List of threatened species. While there are several challenges to evaluating fungi for conservation purposes, there is an urgent need to bring fungi more broadly into the conservation framework. Here, we present an automated bioinformatic pipeline for processing data from one of the largest fungal biodiversity datasets to assess species conservation status using a test case of conspicuous macrofungi from the state of Colorado. This pipeline can rapidly process existing data from both specimen- and observation-based records available through MyCoPortal for making conservation status assessments, and the approach presented employs ‘fuzzy matching’ techniques for correcting commonly encountered misspelled taxonomic names in the data. Such assessments are required for integrating fungi into the NatureServe conservation status framework. The pipeline can easily be scaled to produce robust assessments, even at the national level, which can be valuable in focusing field activity for verification purposes. Of the available 117,006 biodiversity data records from Colorado, our processing test case produced a final processed dataset of 36,637 macrofungal records from the state. From this, a focus list of 1613 rarely documented Colorado species was produced for consideration, with 30 of these also being found on the Red List. A more comprehensive conservation status assessment based on scoring in the NatureServe framework was then produced that provided status ranking for 2438 unique, valid, and current taxonomic names for Colorado macrofungi in the processed dataset.