The Japanese archipelago exhibits a notable difference in snow depth in winter, deep snow on the Sea of Japan side and low snow cover on the Pacific Ocean side. This contrasting pattern has shaped the distribution of infraspecific taxon pairs in a range of woody plants, with taxa found on the Sea of Japan side typically exhibiting a stunted shrub form with multiple decumbent stems. The phylogenetic origin of these taxon pairs is unknown, i.e., whether the two taxa diverged from the same species or if they have different origins. This study aimed to reveal the phylogenetic origin of two varieties of Torreya nucifera (Taxaceae); var. nucifera is a tree found on the Pacific Ocean side, whereas var. radicans is a shrub found on the Sea of Japan side. We examined the phylogenetic relationships of the two varieties and worldwide Torreya taxa using whole chloroplast genomes, chloroplast DNA fragments, and the nuclear ribosomal internal transcribed spacer (ITS). The whole chloroplast genome phylogeny indicated that T. nucifera var. radicans was a sister taxon to Chinese T. grandis, rather than to var. nucifera. In contrast, the nuclear ITS phylogeny indicated that while several haplotypes of T. nucifera var. radicans were closely related to T. grandis, most haplotypes of T. nucifera var. radicans formed a single clade with those of var. nucifera. This implies that the homogenization of the ITS has occurred between the two taxa, while taxon-specific chloroplast DNA haplotypes were retained. These discordant phylogenies suggested that the two taxa have different phylogenetic origins, but have an intricate evolutionary history, involving inter-taxa hybridization and gene flow, possibly when their distributions were confined to sympatric refugia. Given the genetic evidence and distinct difference in growth form, we propose that T. nucifera var. radicans should be taxonomically treated as a distinct species, T. fruticosa.

日本列岛冬季积雪深度差异显着，日本海一侧积雪较深，太平洋一侧积雪较少。这种对比模式塑造了一系列木本植物中种下分类群对的分布，在日本海一侧发现的分类群通常呈现出具有多个外倾茎的矮小灌木形式。这些分类群对的系统发育起源是未知的，即这两个分类群是否来自同一物种或它们是否具有不同的起源。本研究旨在揭示榧树（紫杉科）两个品种的系统发育起源；变种 nucifera是一种在太平洋一侧发现的树，而 var. 自由基是在日本海一侧发现的灌木。我们使用整个叶绿体基因组、叶绿体 DNA 片段和核核糖体内部转录间隔区 (ITS)检查了这两个品种和全球榧树分类群的系统发育关系。整个叶绿体基因组系统发育表明T . 纽西法拉变种 radicans是Chinese T的姊妹分类单元。Grandis，而不是 var。忍冬。相比之下，核 ITS 系统发育表明，虽然T 的几种单倍型。纽西法拉变种 radicans与T密切相关。Grandis，T 的大多数单倍型。纽西法拉变种 radicans与 var 的那些形成了一个单一的进化枝。忍冬。这意味着 ITS 的同质化发生在两个分类群之间，而分类群特异性叶绿体 DNA 单倍型被保留。这些不一致的系统发育表明这两个分类群具有不同的系统发育起源，但具有复杂的进化历史，涉及分类群间杂交和基因流动，可能当它们的分布仅限于同域避难所时。鉴于遗传证据和生长形式的明显差异，我们建议T。纽西法拉变种 自由基应该在分类学上被视为一个独特的物种，T。果果。