Data from: Recent non-hybrid origin of sunflower ecotypes in a novel habitat

AbstractThe genomics of local adaptation is an increasingly active field, providing insights into the forces driving ecological speciation and the repeatability of evolution. Demography and gene flow play an important role in determining the paths by which parallel evolution occurs and the genomic signatures of adaptation. In the annual sunflowers, hybridization between species has repeatedly led to the colonization of extreme habitats, such as sand dunes. In a new case of adaptation to sand dunes that occurs in populations of H. petiolaris growing at Great Sand Dunes National Park and Preserve (Colorado), we wished to determine the age and long-term migration patterns of the system, as well as its ancestry. We addressed these questions with restriction-associated DNA (RAD) sequence data, aligned to a reference transcriptome. In an isolation with migration model using RAD sequences, coalescent analysis showed that the dune ecotype originated since the last ice age, which is very recent compared with the hybrid dune species, H. anomalus. Large effective population sizes and substantial numbers of gene migrants per generation between dune and nondune ecotypes explained the highly heterogeneous divergence observed among loci. Analysis of RAD-derived SNPs identified heterogeneous divergence between the dune and nondune ecotypes, as well as identifying its nearest relative. Our results did not support the hypothesis that the dune ecotype has hybrid ancestry, suggesting that adaptation of sunflowers to dunes has occurred by multiple mechanisms. The ancestry and long-term history of gene flow between incipient sunflower species provides valuable context for our understanding of ecological speciation and parallel adaptation.

摘要 本地适应基因组学是当前愈发活跃的研究领域，可为解析驱动生态物种形成的演化动力以及演化的可重复性提供重要见解。种群历史动态与基因流在决定平行演化的发生路径以及适应的基因组特征方面发挥关键作用。在一年生向日葵类群中，物种间杂交反复促成了极端生境（如沙丘）的定植与拓殖。针对科罗拉多大沙丘国家公园及保护区内的细叶向日葵（*Helianthus petiolaris*）种群所形成的沙丘适应新类群，本研究旨在解析该系统的起源时间、长期迁徙模式及其遗传祖先背景。本研究采用限制性酶切位点相关DNA（RAD）测序数据，并将其比对至参考转录组开展分析。基于RAD序列构建的迁徙隔离（IM）模型的溯祖分析结果显示，该沙丘生态型起源于末次冰期之后，相较于杂交起源的沙丘物种异常向日葵（*H. anomalus*）而言，其起源时间极晚。沙丘与非沙丘生态型间存在较大的有效种群大小以及每代可观的基因流个体数，这解释了不同位点间高度异质的分化水平。对RAD测序得到的单核苷酸多态性（SNPs）进行分析，不仅鉴定出沙丘与非沙丘生态型间的异质分化信号，还明确了该类群的近缘物种。本研究结果不支持该沙丘生态型具有杂交祖先的假说，表明向日葵对沙丘生境的适应可通过多种演化机制实现。初期向日葵物种间的遗传祖先关系与长期基因流历史，可为我们理解生态物种形成与平行适应提供极具价值的研究参考。