Genomic identification of direct seeding and evolutionary lineages by combining heterogeneous genomic resources

Human-induced habitat changes threaten biodiversity, prompting major initiatives for its restoration and promotion. Revegetation through direct seeding is common in agricultural and infrastructure construction projects, yet the provenance of seed material and its genetic impacts on natural populations remain underexplored. Introducing foreign ecotypes can lead to unintended consequences, as they may be adapted to different environmental conditions or represent distinct evolutionary lineages. In Switzerland, direct seeding is widely used to promote dry meadows, often using seeds of the Carthusian pink (Dianthus carthusianorum), a key species. To assess the extent and genetic effects of direct seeding and infer seed provenances, we combined genomic data from 446 samples collected in independent smaller-scale studies. We assembled a chromosome-level reference genome to map reads and developed a SNP panel of 48,299 SNPs. We identified six evolutionary significant units (ESUs) within the European distribution range of D. carthusianorum. As biodiversity promotion efforts are often coordinated nationally, we focused on populations in Switzerland and identified five ESUs: four occur naturally, and one was introduced from Eastern Europe. Our combined genomic data revealed that 48.4% of the 31 randomly sampled populations across Switzerland were established through direct seeding, with four (12.9%) of these populations using non-autochthonous seeds. Seven (22.6%) of the 31 populations showed signs of genetic introgression by two to three different ESUs, with six cases being human-mediated. Our findings demonstrate the power of combining genomic resources to support decision-making for national revegetation projects, emphasising the importance of using autochthonous seed sources for direct seeding.