Genetic structure and diversity of the declining orchid <i>Gymnadenia conopsea</i> in Scandinavia: implications for conservation and management

Understanding how historical versus contemporary processes shape population genetic structure and diversity is important to design effective management actions for threatened species. We genotyped 1834 SNPs in 1120 individuals from 110 Scandinavian populations of the declining orchid Gymnadenia conopsea , in three different habitat types, to examine whether genetic structure was related to wind speed, terrain ruggedness, forest cover, and seasonality at the landscape scale, and whether genetic diversity increases with census population size and is higher in core habitats (fen and meadow) than in marginal, coastal habitats. We identified three genetic clusters and pronounced isolation by distance, consistent with two independent colonization routes after the last glacial maximum, followed by admixture. Effective population size was highest in the admixed cluster. Estimates of effective migration indicated reduced gene flow along the Atlantic coast, between coastal and inland populations, and among southern meadow populations. High landscape resistance to gene flow was associated with complex topography and pronounced seasonality. Genetic diversity increased with population size but did not vary among habitat types. Genetic diversity peaked in core habitats, i.e. southern meadows and inland fens along the Scandes Mountains. The lowest genetic diversity was found along the Atlantic coast and in a few scattered populations. Current genetic structure suggests a strong legacy of historical events, and the high genetic diversity documented in the main Scandinavian range indicates that current viability and future adaptation potential are high. To maintain genetic diversity and connectivity between genetic groups, it is particularly important to preserve southern meadow populations, which are currently in strong decline. Overall, our results illustrate how a declining species can help us understand the impact of historical and current processes, how landscape genetic data can inform proactive conservation, and how a slow genetic response to fragmentation can allow time to maintain genetic diversity through habitat restoration and management.