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.