Data from: Phylogeny and evolutionary history of Pinaceae updated by transcriptomic analysis

Pinaceae comprises 11 genera, and represents the largest family of conifers with an extensive wild distribution in the Northern Hemisphere. Intergeneric relationships of Pinaceae have been investigated using many morphological characters and molecular markers, but phylogenetic positions of four genera, including Cathaya, Cedrus, Nothotsuga and Pseudolarix, remain controversial or have not been completely resolved. To completely resolve the intergeneric relationships of Pinaceae, we conducted a comparative transcriptomic study of 14 species representing all Pinaceae genera. Multiple data sets, containing up to 6,369,681 sites across 4676 loci, were analyzed using concatenation and coalescent methods. Our study generated a robust topology, which divides Pinaceae into two clades, one (pinoid) including Cathaya, Larix, Picea, Pinus, and Pseudotsuga, and the other (abietoid) including Abies, Cedrus, Keteleeria, Nothotsuga, Pseudolarix, and Tsuga. Cathaya and Pinus form a clade sister to Picea; Cedrus is sister to the remaining abietoid genera, and the two genera Nothotsuga and Tsuga form a clade sister to Pseudolarix. The discordant positions of Cathaya, Cedrus and Pseudolarix in different gene trees could be explained by ancient radiation and/or molecular homoplastic evolution. The hybrid origin hypothesis of Nothotsuga is not supported. Based on molecular dating, extant Pinaceae genera diverged since about 206 Mya, earlier than the break-up of Pangea, and the divergence among the pinoid genera occurred earlier than the split among the abietoid genera. Moreover, our study indicates that two radiation events occurred in the evolution of Pinaceae genera, and some important morphological characters evolved multiple times based on ancestral state reconstruction.

松科（Pinaceae）包含11个属，是北半球野生分布范围最广、规模最大的针叶树科类群。此前已有诸多研究借助形态性状与分子标记对松科的属间亲缘关系展开探究，但银杉属（Cathaya）、雪松属（Cedrus）、长苞铁杉属（Nothotsuga）以及金钱松属（Pseudolarix）在内的4个属的系统发育位置仍存在争议，尚未完全解决。为彻底厘清松科的属间亲缘关系，本研究针对代表松科全部11个属的14个物种开展了比较转录组学研究。构建了涵盖4676个基因位点、总计最多达6369681个碱基位点的多套数据集，分别采用串联法与溯祖法进行分析。本研究得到了稳健的系统发育拓扑结构，将松科划分为两个演化支：其一为松支系（pinoid），包含银杉属、落叶松属、云杉属、松属与黄杉属；其二为冷杉支系（abietoid），包含冷杉属、雪松属、油杉属、长苞铁杉属、金钱松属与铁杉属。其中银杉属与松属构成一个演化支，作为云杉属的姊妹群；雪松属为其余冷杉支系类群的姊妹群，而长苞铁杉属与铁杉属共同形成一个演化支，作为金钱松属的姊妹群。不同基因树中银杉属、雪松属与金钱松属的位置冲突现象，可通过古老辐射演化或/和分子同塑进化予以解释。长苞铁杉属的杂交起源假说未获得本研究支持。基于分子定年分析结果，现存松科各属的分化始于约2.06亿年前（Mya），早于泛大陆（Pangea）的裂解时期；且松支系各属的分化时间早于冷杉支系类群的分化时间。此外，本研究表明松科各属的演化历程中曾发生两次辐射演化事件，结合祖先状态重建结果可知，部分重要的形态性状曾多次独立演化。