Data from: Population genomic variation reveals roles of history, adaptation, and ploidy in switchgrass

Geographic patterns of genetic variation are shaped by multiple
evolutionary processes, including genetic drift, migration, and natural
selection. Switchgrass (Panicum virgatum L.) has strong genetic and
adaptive differentiation despite life history characteristics that promote
high levels of gene flow and can homogenize intraspecific differences,
such as wind-pollination and self-incompatibility. To better understand
how historical and contemporary factors shape variation in switchgrass, we
use genotyping-by-sequencing to characterize switchgrass from across its
range at 98,042 SNPs. Population structuring reflects biogeographic and
ploidy differences within and between switchgrass ecotypes and indicates
that biogeographic history, ploidy incompatibilities, and differential
adaptation each have important roles in shaping ecotypic differentiation
in switchgrass. At one extreme, we determine that two Panicum taxa are not
separate species but are actually conspecific, ecologically divergent
types of switchgrass adapted to the extreme conditions of coastal sand
dune habitats. Conversely, we identify natural hybrids among lowland and
upland ecotypes and visualize their genome-wide patterns of admixture.
Furthermore, we determine that genetic differentiation between primarily
tetraploid and octoploid lineages is not caused solely by ploidy
differences. Rather, genetic diversity in primarily octoploid lineages is
consistent with a history of admixture. This suggests that polyploidy in
switchgrass is promoted by admixture of diverged lineages, which may be
important for maintaining genetic differentiation between switchgrass
ecotypes where they are sympatric. These results provide new insights into
the mechanisms shaping variation in widespread species and provide a
foundation for dissecting the genetic basis of adaptation in switchgrass.