Raw data Genotyping-by-sequencing (GBS) files of Petunia axillaris, P. exserta, P. secreta Raw sequence reads

Environments in constant change mainly due to land use are often threatened. The South American grasslands constitute ecosystems sensitive to climate changes and human actions that promote landscape fragmentation and habitat loss for several species. These open fields home many endemic and narrowly distributed species for which environmental shifts could be even worse due to the usual small effective population size and low genetic diversity. Here we describe the genetic diversity, population structure, and evolutionary history of a cryptic herbaceous lineage that inhabits a severely impacted environment. We based our work on a wide genomic coverage, analyzed under a population genomic approach to test different hypotheses for this lineage origin, comparing with related species from the same area. The lineage is not yet recognized as an independent taxon but constitutes a divergent genetic component that allowed the colonization of a new micro-environment during a period of high diversification to the genus. We found limited genetic diversity and a high level of inbreeding in this lineage. Strongly threatened because of its habitat management, this cryptic lineage can serve as a model to propose a conservation strategy based on genomic studies for South American grasslands.