Population genomics indicates micro‐refuges and riverine barriers for a southern South American grassland nightshade

Abstract Aim Pleistocene climate oscillations influenced the species distribution and genetic diversity in grasslands, and such climatic changes promoted expansion and contraction cycles, leading to fragmentation and isolation of evolutionary lineages in refuges. This study aimed to infer the evolutionary processes that most influenced the genetic diversity of a South American nightshade Petunia inhabiting subtropical grasslands under the Pleistocene influence. Location Pampa and Chaco. Taxon The widely distributed herb Petunia axillaris subsp. parodii (Solanaceae). Methods We obtained high‐density genome coverage throughout the geographical distribution of Petunia axillaris subsp. parodii. 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 geographical distance and environmental differences between populations. Results There are 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 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.