Metric-dependent genomic diversity reveals phylogenetic and ecological structure in saproxylic beetles

Abstract 1. Comparative studies can reach different conclusions when genomic-diversity metrics use different denominators. 2. We analysed standardized ddRAD-seq data from 759 individuals, 149 species-by-site population records and 26 saproxylic beetle species across eight Polish forest complexes. 3. Species identity and sampling hierarchy explained most population-level variation. Deciduous-associated species had higher variant-site expected heterozygosity than conifer-associated species. 4. All-position nucleotide diversity showed stable phylogenetic signal, whereas occurrence tier and exploratory forest-management and protection contrasts showed no consistent associations. 5. Genomic-diversity metrics are not interchangeable; comparative assessments should report their denominator and test lineage sensitivity.