Multi-locus marker Swiss Orthoptera
Evaluating the conservation status of species is essential for effectively informing conservation actions. As the biodiversity loss accelerates, there is an urgent need to monitor not only interspecific diversity but also intraspecific diversity, a key factor in population and species viability. In insects a single mitochondrial gene, COI, has been classically used as a barcode to determine samples at the species level. However, intraspecific resolution of such a barcode is limited and applications are strongly impacted by several biases.The development of streamlined molecular tools based on nuclear orthologs for species delimitation and identification would enhance the integration of genomic information in diversity assessments, while capturing genetic diversity and population's structure. In this study, we present a new set of multi-locus markers applied to Orthoptera, including 290 UCEs, 108 USCOs, the mitogenome and the ribosomal DNA. This set was captured and sequenced in 645 samples including all Swiss Orthoptera species collected at the country-wide scale during the update of the Red List between 2018 and 2022. The application of this multi-locus marker has enabled the resolution of the phylogeny of Swiss species and the clarification of complex taxonomic questions with direct consequences in conservation practice. In addition, we validated the efficiency of the multi-locus marker in capturing country-wide population structure and investigated the correlation of intraspecific genetic diversity with species' ecology and conservation status. We identified a significant correlation with a single ecological factor, the species' association with floodplain and riparian habitats. The IUCN criteria failed to account for species' genetic diversity, whereas the genetic diversity measures produced by the multi-locus marker provided complementary and crucial perspective on conservation status. These results are included for the first time in the forthcoming Orthoptera Red List update, setting a precedent for subsequent integration of genetic monitoring programs resulting in future national conservation policies.