Repository with data and code for the paper evaluating IBA efficiency using Swedish Lepidoptera, titled "High-throughput biodiversity surveying sheds new light on the brightest of insect taxa"
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Repository with data and code for the paper evaluating IBA efficiency using Swedish Lepidoptera, titled "High-throughput biodiversity surveying sheds new light on the brightest of insect taxa". Authors: Ela Iwaszkiewicz-Eggebrecht, Robert M. Goodsell, Bengt-Åke Bengsson, Marko Mutanen, Mårten Klinth, Laura van Dijk, Piotr Lukasik, Andreia Miraldo, Anders F. Andresson, Ayco J. M. Tack, Tomas Roslin, Fredrik Ronquist Published in Proceedings of the Royal Society B. DOI: https://doi.org/10.1098/rspb.2024-2974 Correspondence: ela.iwaszkiewicz@nrm.se ##Folder structure The 'data' directory contains the DynTaxa Lepidoptera data used in the analyses, as well as the taxonomic annotations for Lepidoptera resulting from the application of v1 of the IBA bioinformatics pipeline (see the IBA data paper for more information on this). The 'code' directory contains the R scripts needed to regenerate the tables underlying the analysis of the metabarcoding data for Lepidoptera. Some tables rely on manual online searches using DynTaxa or NCBI's online nucleotide blast functionality. For these steps, the response files are stored in the 'dyntaxa_searches' and 'blast_searches' directories. There are R scripts that generate the relevant input files (species lists or fasta files) for these online searches. The 'dyntaxa_searches' and 'bast_searches' directories contain information about the online settings that were used. The table 'blast_search_files.tsv' contains an index of the blast search response files and how they match to ASV ids. The 'output_tables' directory contains the tables generated by the R scripts.
