A short cut to sample coverage standardization in meta-barcoding data provides new insights into land use effects on insect diversity

The use of metabarcoding for insect species identification has grown rapidly, but the absence of abundance data hinders meaningful diversity metrics like sample coverage-standardized species richness. Additionally, the vast number of taxa often lacks a unified phylogeny or trait database. We present a framework for constructing a phylogenetic tree encompassing the majority of insect families, standardisation of sample coverage (an objective measure of sample completeness) and assessment of both taxonomic and phylogenetic diversity using the Hill series for metabarcoding data. Applied to central Europe, our framework analysed insect diversity from 400 families along a land-use gradient. Results revealed land-use intensity significantly affects sample coverage, emphasizing the need for biodiversity standardization. After standardization, taxonomic diversity declined by 27–44%, and phylogenetic diversity by 13–29% across 39,000 Operational Taxonomic Units, from forests to agricultural areas. Rare species exhibited greater phylogenetic diversity loss than taxonomic, while dominant species showed smaller phylogenetic losses but stronger declines in taxonomic diversity. Our findings underscore agriculture’s detrimental effects on specific insect taxa, even after adjusting for sample coverage, and provide new insights into the loss of functional diversity, as represented by phylogeny.