Data from: Peripatric speciation in an endemic Macaronesian plant after recent divergence from a widespread relative

The Macaronesian Scrophularia lowei is hypothesized to have arisen from the widespread S. arguta on the basis of several phylogenetic studies of the genus, but sampling has been limited. Although these two annual species are morphologically distinct, the origin of S. lowei is unclear because genetic studies focused on this Macaronesian species are lacking. We studied 5 S. lowei and 25 S. arguta populations to determine the relationship of both species and to infer the geographical origin of S. lowei. The timing of S. lowei divergence and differentiation was inferred by dating analysis of the ITS region. A phylogenetic analysis of two nuclear (ITS and ETS) and two chloroplast (psbJ–petA and psbA–trnH) DNA regions was performed to study the relationship between the two species, and genetic differentiation was analysed by AMOVA. Haplotype network construction and Bayesian phylogeographic analysis were conducted using chloroplast DNA regions and a spatial clustering analysis was carried out on a combined dataset of all studied regions. Our results indicate that both species constitute a well-supported clade that diverged in the Miocene and differentiated in the Late Miocene-Pleistocene. Although S. lowei constitutes a well-supported clade according to nDNA, cpDNA revealed a close relationship between S. lowei and western Canarian S. arguta, a finding supported by the spatial clustering analysis. Both species have strong population structure, with most genetic variability explained by inter-population differences. Our study therefore supports a recent peripatric speciation of S. lowei—a taxon that differs morphologically and genetically at the nDNA level from its closest relative, S. arguta, but not according to cpDNA, from the closest Macaronesian populations of that species. In addition, a recent dispersal of S. arguta to Madeira from Canary Islands or Selvagens Islands and a rapid morphological differentiation after the colonization to generate S. lowei is the most likely hypothesis to explain the origin of the last taxon.学界基于对玄参属（Scrophularia）的多项系统发育研究，推测Lowei玄参（Macaronesian Scrophularia lowei）起源于广布的S. arguta，但相关采样范围有限。尽管这两个一年生物种在形态上存在显著差异，但由于缺乏针对该马卡罗尼群岛物种的遗传研究，Lowei玄参的起源仍不明确。本研究共采集5个Lowei玄参种群与25个S. arguta种群的样本，以明确二者的亲缘关系，并推断Lowei玄参的地理起源。通过对ITS（内部转录间隔区，Internal Transcribed Spacer）区域开展年代校准分析，我们推定了Lowei玄参的分化与演化时间节点。本研究针对两个核DNA区域（ITS，内部转录间隔区，Internal Transcribed Spacer，与ETS，外部转录间隔区，External Transcribed Spacer）以及两个叶绿体DNA区域（psbJ–petA与psbA–trnH）进行系统发育分析，以解析两物种的亲缘关系，并通过AMOVA（分子方差分析，Analysis of Molecular Variance）分析遗传分化水平。基于叶绿体DNA区域数据，我们构建了单倍型网络并开展贝叶斯系统地理学分析；同时针对所有研究区域的联合数据集进行空间聚类分析。研究结果表明，两物种共同构成一个支持度极高的演化支，其分化起始于中新世，并在晚中新世-更新世时期完成进一步演化分化。尽管基于核DNA（nDNA）分析，Lowei玄参自身构成一个支持度极高的演化支，但叶绿体DNA（cpDNA）分析显示，Lowei玄参与加那利群岛西部的S. arguta种群亲缘关系紧密，该结果得到空间聚类分析的佐证。两物种均表现出显著的种群遗传结构，绝大多数遗传变异源于种群间的差异。因此，本研究支持Lowei玄参为近期发生的边域成种（peripatric speciation）事件产物：该类群在形态与核DNA遗传层面均与其近缘类群S. arguta存在显著差异，但在叶绿体DNA层面，其与该物种的马卡罗尼群岛近缘种群并无明显分化。此外，最能解释Lowei玄参起源的假说是：S. arguta近期从加那利群岛或塞尔瓦任斯群岛（Selvagens Islands）扩散至马德拉群岛，并在定植后快速发生形态分化，最终演化形成Lowei玄参。