An automated decision-making procedure for ranking and selecting species in biodiversity projects

In large-scale biodiversity genomics projects, the number of species that could be sequenced exceeds the resources available. Species selection is therefore a crucial component, requiring clear criteria and procedures. In a bottom-up approach, the Biodiversity Genomics Europe project implemented an Automated Decision-Making (ADM) process for species selection based on objective criteria and tested it on simulated and empirical data. Here, we present our species ranking ADM process. It includes three stages: exclusion, ranking, and feasibility-check. The composition of selected species retained the diversity of the community-nominated species pool for key taxonomic, geographic, and demographic assessment criteria while reducing bias. Feasibility and funding limits influenced the final selection more than other factors, indicating that investments in these areas would improve available reference genome diversity. The ADM achieved species selection for genome sequencing in a large-scale biodiversity project in a relatively objective manner consistent with the broader European biodiversity genomic community’s priorities.