Independent colonisations of serpentine habitats highlight species-specific evolutionary histories of lineage diversification

Serpentine soils are characterized by high levels of heavy metals, low nutrient availability, and water scarcity, presenting significant ecological challenges for plant species. Nonetheless, some species have adapted successfully to these conditions. We investigate the population genomic structure, evolutionary history and phenotypic differentiation of three diploid generalist plant species, Lavandula stoechas L., Halimium atriplicifolium (Lam) Spach. subsp. atriplicifolium, and Phlomis purpurea L., all of which inhabit adjacent serpentine and non-serpentine soils in the Malaga region in the southern Iberian Peninsula (Spain). We explore whether populations from serpentine and non-serpentine soils represent distinct evolutionary lineages and whether there is genomic and phenotypic differentiation associated with serpentine conditions. We measured plant height and specific leaf area (SLA) to detect potential ecotypic variation associated with soil type. A ddRADseq SNP dataset was generated for each species, representing 10 populations from serpentine and 10 from non-serpentine soils. We ordinated genotype data to assess genomic variation, conducted an ADMIXTURE analysis to infer ancestral groups, and used Treemix analyses to investigate phylogenetic relationships and gene flow events between populations. Isolation by distance (IBD) analyses evaluated the role of geographic separation in observed genomic differentiation. Our results reveal species-specific patterns of genomic, and to some extent phenotypic, differentiation between serpentine and non-serpentine populations, with evidence of multiple colonisations of serpentine sites in all three species. The study highlights the role of historical differentiation and subsequent gene flow in shaping the genomic structure of plant populations, alongside observed variation in phenotypic traits across environments.