Monitoring genetic diversity: A genomics-based pilot study for Switzerland

Dr. Martin C. Fischer
Institute of Integrative Biology, ETH Zürich

Human exploitation of nature poses a major threat to biodiversity, through factors such as land use and climate change, as well as pollution and overexploitation or the spread of invasive species. This loss manifests itself at all three levels of biodiversity, species and ecosystem diversity, as well as at the most fundamental level, genetic diversity within species. The decline in genetic diversity has significant consequences, it reduces the ability of species to adapt to changing environments and general reduces the adaptive potential. In the past, efforts to conserve genetic diversity were neglected due to technical constraints. However, the genomic revolution has changed this, necessitating the development of capacity, knowledge, and experience. We initiated a pilot study on how genetic diversity can be monitored using a genomic-based approaches, with the aim of assessing genetic diversity indicators, thereby gaining the practical experience necessary for setting up a monitoring programme. We selected five focal animal and plant species based on criteria such as their presence in nationally important habitats or anthropogenically modified landscapes. We developed a tailored sampling strategy and sampled over 1,200 individuals across all biogeographic regions in Switzerland. For each species, we de novo assembled a reference genome and re-sequenced the genomes of all sampled individuals. Additionally, we used a museomics approach to assess temporal changes in genetic diversity over the past 200 years for two species. The data from our pilot study allow detailed conservation-relevant analyses of not only the current and historic spatial distribution of genetic diversity, but also of other genetic indicators such as genetic connectivity, inbreeding (FROH), adaptive genetic variation, and estimates of effective population size (Ne). With the experience gained, we are creating a framework for monitoring genetic diversity that can serve as an example for other national initiatives.