Data from: Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation biogeography and reticulate evolution

Background The taxonomy and systematics of Salix subgenus Salix s.l. is difficult. The reliability and evolutionary implications of two important morphological characters (number of stamens, and morphology of bud scales) used in subgeneric classification within Salix remain untested, and a disjunct Old–New World distribution pattern of a main clade of subgenus Salix s.l., revealed by a previous study, lacks a reasonable explanation. To study these questions, we conducted phylogenetic analyses based on 4,688 bp of sequence data from four plastid (rbcL, trnD–T, matK, and atpB–rbcL) and two nuclear markers (ETS and ITS) covering all subgenera of Salix, and all sections of subgenus Salix s.l. Results Subgenus Salix came out as para- or polyphyletic in both nrDNA and plastid trees. The plastid phylogeny successfully resolved relationships among the major clades of Salix, but resolution within subgenus Salix s.l. remained low. Nevertheless, three monophyletic groups were identifiable in subgenus Salix s.l.: the ‘main clade’ of subgenus Salix s.l., with New and Old World species being reciprocally monophyletic; the section Triandroides clade; and the subgenus Pleuradenia clade. While nrDNA regions showed higher resolution within subgenus Salix s.l., they failed to resolve subgeneric relationships. Extensive, statistically significant gene-tree incongruence was detected across nrDNA–plastid as well as nrDNA ETS–ITS phylogenies, suggesting reticulate evolution or hybridization within the group. The results were supported by network analyses. Ancestral-state reconstructions indicated that multiple stamens and free bud scales represent the plesiomorphic states within Salix, and that several significant shifts in stamen number and bud scale morphology have occurred. Conclusions Subgenus Salix s.l. is not monophyletic, and the evolutionary history of the subgenus has involved multiple reticulation events that may mainly be due to hybridization. The delimitation of subgenus Salix s.l. should be redefined by excluding section Triandrae and subgenus Pleuradenia from it. The evolutionary lability of bud-scale morphology and stamen number means that these characters are unreliable bases for classification. The disjunct Old–New World distribution of subgenus Salix s.l. appears to be linked to the profound climatic cooling during the Tertiary, which cut off gene exchange between New and Old World lineages.研究背景 广义柳亚属（Salix subgenus Salix s.l.）的分类学与系统学研究长期面临诸多难点。目前，柳属亚属分类中广泛使用的两个关键形态性状——雄蕊数目与芽鳞形态——其分类可靠性及进化意义尚未得到实证验证；此前研究揭示的广义柳亚属主要分支的新旧世界间断分布格局，至今仍缺乏合理解释。为解答上述科学问题，本研究基于覆盖柳属所有亚属及广义柳亚属所有组的4个质体基因区域（rbcL、trnD–T、matK及atpB–rbcL）与2个核标记（ETS、ITS）的总计4688 bp序列数据，开展了系统发育分析。 研究结果 无论是核核糖体DNA（nrDNA）还是质体系统发育树，均显示广义柳亚属为并系或多系类群。质体系统发育树成功解析了柳属主要分支间的系统发育关系，但广义柳亚属内部的节点分辨率仍较低。不过，广义柳亚属内仍可分辨出3个单系类群：分别为广义柳亚属的"主分支"（其新旧世界物种互为单系）、Triandroides组分支以及Pleuradenia亚属分支。尽管核核糖体DNA区域在广义柳亚属内部具有更高的节点分辨率，却无法解析亚属间的系统发育关系。本研究在核核糖体DNA-质体以及核核糖体DNA ETS-ITS的系统发育树中，均检测到大量具有统计学显著性的基因树拓扑冲突现象，表明该类群内部存在网状演化或杂交事件，该结果得到了网络分析的支持验证。祖先性状重建结果显示，多雄蕊与离生芽鳞为柳属的祖征，且该类群在雄蕊数目与芽鳞形态上已发生多次显著的性状转变。 研究结论 广义柳亚属并非单系类群，其演化历史包含多次网状演化事件，此类事件主要由杂交介导。广义柳亚属的分类界定需进行修订，应将Triandrae组与Pleuradenia亚属从中移除。芽鳞形态与雄蕊数目的演化可塑性表明，这两个性状并不适合作为分类依据。广义柳亚属的新旧世界间断分布格局，可能与第三纪时期的大规模气候降温事件相关——该事件阻断了新旧世界支系间的基因交流。