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.

遗传变异的地理格局由多种进化过程塑造，涵盖遗传漂变、种群迁移与自然选择。柳枝稷（Panicum virgatum L.）虽具备风媒传粉、自交不亲和等可促进高水平基因流、淡化种内差异的生活史特征，却仍存在显著的遗传与适应性分化。为深入厘清历史与当代因素如何塑造柳枝稷的遗传变异格局，本研究采用基于测序的基因分型（genotyping-by-sequencing）技术，对其分布范围内的种群进行遗传分型，共获取98042个单核苷酸多态性位点（SNPs）。种群结构分析结果反映了柳枝稷生态型内部及生态型间的生物地理与倍性差异，表明生物地理历史、倍性不亲和性以及适应性分化均在柳枝稷生态型分化过程中扮演关键角色。在极端生境类群的分析中，本研究证实两个黍属类群并非独立物种，实则为适应沿海沙丘极端生境的同种生态分化型柳枝稷。与之相反，本研究在低地与高地生态型间鉴定到天然杂交个体，并可视化了其全基因组的遗传混合模式。此外，研究发现四倍体与八倍体谱系间的遗传分化并非仅由倍性差异所致；八倍体谱系的遗传多样性特征符合遗传混合的演化历史。这表明柳枝稷的多倍化过程可由分化谱系的遗传混合所驱动，该机制或对维持同域分布的柳枝稷生态型间的遗传分化具有重要意义。本研究结果为解析广布物种的变异塑造机制提供了新认知，同时为解析柳枝稷适应性的遗传基础奠定了重要研究基础。