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

Abstract

Genetic diversity is the raw material of evolution and is essential for species to adapt to changing environments. To date, systematic monitoring of genetic diversity on a national scale has rarely been undertaken. We have initiated a pilot study on genetic diversity monitoring in Switzerland, with the aim of assessing genetic diversity indicators for five animal and plant species, thereby gaining the practical experience necessary for setting up a genomics-based monitoring programme. The five selected species occur in habitats of national importance or in anthropogenically modified landscapes. We de novo assembled their reference genomes, sampled >1,200 individuals across all biogeographic regions in Switzerland, and re-sequenced their full genomes. For two species, we used a museomic approach to go back up to 200 years into the past. Together, these data enable detailed conservation-relevant analyses, not only of genetic diversity, but also of runs of homozygosity (ROH) and estimates of effective population size (Ne), and provide unprecedented insights into temporal changes in genetic diversity in natural populations. With the experience gained, it is now possible to monitor genetic diversity at a national scale. An ongoing challenge is to develop scientifically sound but intuitive indicators, which can be effectively communicated to relevant authorities and stakeholders for implementation in conservation management.