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

BACKGROUND: Human-induced habitat changes threaten biodiversity, prompting large-scale restoration initiatives. 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). RESULTS: 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 panel of 48,299 representative single nucleotide polymorphisms (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, where we found five ESUs: four occur naturally, and one was introduced from Eastern Europe. Our combined genomic data revealed that 15 of 31 randomly sampled populations across Switzerland (48.4%) originated from direct seeding. Allochthonous seed material was detected in eight populations (25.8%), with six of these showing admixture involving two to three ESUs. CONCLUSIONS: Our results demonstrate the effectiveness of genomic approaches for identifying direct seeding and clarifying seed provenance, thereby supporting decision-making in national revegetation projects and emphasising the importance of using autochthonous seed sources.