Genomic and Metagenomic Analyses Reveal Parallel Ecological Divergence in Heliosperma pusillum (Caryophyllaceae)

Cases of parallel ecological divergence in closely related taxa offer an invaluable material to study the processes of ecological speciation. Applying a combination of population genetic and metagenomic tools on a high-coverage RAD sequencing dataset, we test for parallel evolution across six population pairs of Heliosperma pusillum and H. veselskyi (Caryophyllaceae), two plant species found in the south-eastern Alps and characterized by clear morphological (glabrous vs. hairy) and ecological (alpine vs. montane, wet vs. dry) differentiation. Our analyses support a scenario of multiple independent instances of divergence between these species during the last 10,000 years. Structure analyses and simulations show that interspecific gene flow in each population pair is very low. A single locus, annotated as E3 ubiquitin ligase, an enzyme involved in plant innate immunity, shows a pattern of non-random segregation across populations of both species. A metagenomic analysis revealed information about contaminant exogenous DNA present in RAD sequencing libraries obtained from leaf material. Results of this analysis show clearly divergent bacterial and fungal phyllosphere communities between the species, but consistent communities across populations within each species. A similar set of biotic interactions is involved, together with abiotic factors, in shaping common selective regimes at different growing sites of each species. Different occurrences of H. veselskyi appear now genetically isolated from H. pusillum and from each other, and may independently proceed along the speciation continuum. Our work supports the hypothesis that repeated ecological divergence, observed here at an early stage, may be a common process of species diversification.