Aim: Pleistocene climate oscillations influenced the species distribution and genetic diversity in South American grasslands. Paleoclimate changes promoted expansion and contraction cycles that could lead to fragmentation and isolation of evolutionary lineages in refuges. Moreover, sea-level oscillations led to defrosting in some areas, affecting the river dynamics and influencing South American species' evolutionary history. This study aimed to infer which evolutionary processes most influenced the lineages differentiation in South American nightshade Petunia inhabiting subtropical grasslands in a phylogeographical context.
Location: Pampa and Chaco.
Taxon: The widely distributed herb Petunia axillaris subsp. parodii (Solanaceae)
Methods: We obtained a high-density genome coverage throughout Petunia axillaris subsp . parodii geographic distribution. We estimated the genetic diversity and structure to evaluate population differentiation and applied a model-based demographic analysis to investigate the scenarios that could have influenced the species evolutionary history. We evaluated the association between neutral and outlier polymorphisms with environmental variables to distinguish the influence of the geographic distance and environmental differences between populations.
Results: The results revealed three evolutionary lineages in P. axillaris subsp . parodii. The origin and differentiation of these lineages were related to the Pleistocene refuges and rivers acting as barriers to the gene flow. We also identified 496 outlier loci related to adaptation to environmental conditions.
Main conclusion: The Pleistocene climate changes drove lineage diversification isolated in micro-refugia. Rivers and changes in their courses may have also acted on the population divergence, serving as barriers to gene flow or even as corridors for species range expansion. These findings contribute to the knowledge of the evolutionary processes that influenced the lineage diversification of South American subtropical grassland species.

This VCF file contains the 16,128 identified polymorphic SNPs throughout the P. axillaris reference genome, with no missing data and 100% of the reads mapped, as reported at Giudicelli et al. (2021).