Glaciation history and geographic barriers shape population genetic structure and diversity of Lewis flax across western North America

Understanding the forces that structure genetic variation within species is an essential goal of population genetics. Species with large distributions are useful for studying how and why genetic diversity is structured at continental scales. Here, we used whole genome sequencing to describe population genetic structure, genetic diversity, and demographic history of Linum lewisii (Lewis flax, prairie flax), a perennial forb native across most of western North America. Our dataset comprises 168 genomes sampled from public seed repositories, herbarium collections, and new field collections from Alaska and the Hudson Bay to Mexico, and from California to the Great Plains. We examined how historical processes, geographic features, and mating system traits have shaped the evolution of Lewis flax. We found that Lewis flax consists of four main genetic clusters and that this structuring occurred within the last 100,000 years, during the Last Glacial Period, with the Rocky Mountains as a likely geographic barrier. We also show evidence suggesting that current northern populations of Lewis flax are the result of a range expansion following the Last Glacial Maximum, accompanied by a shift towards increased selfing. We discuss how these continental-scale phylogeographic trends can inform Lewis flax domestication efforts and its continued use in ecological restoration. This work illustrates the value of broadly distributed museum collections combined with whole genome sequencing for studying evolutionary processes and natural history.