Population genomics for biodiversity conservation: Insights from the Swiss pilot study for monitoring genetic diversity

Abstract

Genetic diversity is the raw material of evolution and is essential for adaptation and survival. Concerted efforts have been made under the Kunming-Montreal Global Biodiversity Framework (GBF) to incorporate intraspecific genetic diversity into national monitoring efforts. Much emphasis has been put on non-genetic proxies of genetic diversity, due to the limited amount of genetic data currently available on species and their populations globally. Genomic data, however, provide a much more detailed perspective on intraspecific genetic diversity, revealing the demographic history, genetic structure and vulnerability of populations. To build capacity, knowledge and experience on the use of genomic data in biodiversity monitoring, we conducted a population genomic pilot study in Switzerland. We assessed five animal and plant species that are associated with habitats of national importance and anthropogenically modified landscapes. To achieve a representative, unbiased sampling of populations, we developed a proportional stratified random sampling strategy. We de novo assembled the reference genome of each species and re-sequenced 1,200 individuals. For two species, we also sequenced 400 historical samples to retrospectively assess temporal changes in genetic diversity. The genomic data allowed for detailed inference on the extent and spatial distribution of genetic diversity, connectivity and adaptive genetic variation. Changes in population inbreeding and effective population size ( N e ) were inferred back in time for 100 generations, providing insights that would otherwise require long-term monitoring. The results were summarised into five intuitive population genomic diversity variables and indicators for reporting to national authorities and stakeholders. We discuss the feasibility, strengths and potential limitations of our population genomic monitoring approach and conclude that a national monitoring of genetic diversity using whole-genome re-sequencing is nowadays technically and bioinformatically achievable, especially in the Global North. The knowledge gained has high potential to contribute to conservation actions that support the GBF key action of maintaining within-species genetic diversity to safeguard the adaptive potential of species.

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