Multi-locus nuclear barcode assessment of genetic diversity in Swiss Orthoptera unveils conservation status limitations

With accelerating biodiversity loss, tracking both inter- and intraspecific diversity is critical, as within-species variation underpins population viability and adaptive potential. Traditional single-locus barcoding, targeting short mitochondrial or plastid fragments, generally provides reliable species-level resolution but poorly captures intraspecific variation. To address this, we developed an Orthoptera-specific marker panel targeting 398 nuclear loci plus the complete mitogenome and ribosomal DNA, sequencing these regions in 645 specimens representing every Swiss Orthoptera species sampled during the nationwide Red List update. This multilocus dataset produced a well-supported phylogeny and resolved several taxonomic ambiguities with direct conservation relevance. Genetic variation was further used to infer population structure and to test whether intraspecific diversity correlates with ecological traits and Red List status. While species’ IUCN threat levels were not correlated with genetic diversity, we found a significant negative association between genetic diversity and dependence on riparian habitats: river-bank specialists showed lower diversity, likely reflecting the severe fragmentation and alteration of these ecosystems. Our results demonstrate that genetic diversity measures from multilocus markers provide valuable, complementary insights into conservation status. However, the lack of correlation with IUCN threat levels highlights a challenge for integrating genetic data into Red List assessments: while low diversity often flags advanced decline and urgent action, high diversity does not necessarily signal low extinction risk, as it can persist for some time after population decline. Genomic data should therefore be incorporated cautiously alongside traditional criteria. These findings are being integrated into the upcoming Swiss Orthoptera Red List update. Metadata.xlsx Species, sampling locality and date, altitude, biogeographical region, legacy donor as well as extraction and library concentration per sample. Coordinates are provided in LV03+. Orthology_inference_results.xlsx Location of identified Ultra-Conserved Elements (UCEs) and Unique Single-Copy Orthologs (USCOs) in reference genomes. Loci_results_summary.xlsx Summary statistics of global multiple sequence alignments of COI barcodes, mitochondrial genes, ribosomal DNA, Ultra-Conserved Elements (UCEs), and Unique Single-Copy Orthologs (USCOs) per family. Sample_results_summary.xlsx Number of raw, clean, and mapped reads per sample, as well as the number and length of Ultra-Conserved Elements (UCEs) and Unique Single-Copy Orthologs (USCOs). The file also provides genetic diversity values, the number and length of mitochondrial genes, and the lengths of COI sequences and ribosomal DNA. Data_genetic_diversity_estimates. Percentage of polymorphic sites per species, calculated using UCEs and USCOs, ribosomal DNA, the entire mitogenome or the COI barcode. The dataset includes associated ecological and conservation factors for each species: IUCN Red List national threat status, Conservation priority designation at the Swiss level, Degree of habitat specificity, Indicator status for riparian habitats, Indicator status for dry meadow and pasture habitats, Estimated species mobility, Preference for warm habitats, Elevational range or preference. Folder MSA_Phylogenies Family-level phylogenetic tree inferred with IQ-TREE v2.0.5 using COI barcodes, mitochondrial genes, ribosomal DNA, Ultra-Conserved Elements (UCEs), and Unique Single-Copy Orthologs (USCOs).