The Eastern Asia (EA) – North America (NA) disjunction is a well-known biogeographic pattern of the Tertiary relict flora; however, few studies have investigated the evolutionary history of this disjunction using a phylogenomic approach. Here, we used 2369 single copy nuclear genes and nearly full plastomes to reconstruct the evolutionary history of the small Tertiary relict genus Thuja, which consists of five disjunctly distributed species. The nuclear species tree strongly supported an EA clade Thuja standishii–Thuja sutchuenensis and a “disjunct clade”, where western NA species T. plicata is sister to an EA-eastern NA disjunct Thuja occidentalis–Thuja koraiensis group. Our results suggested that the observed topological discordance among the gene trees as well as the cytonuclear discordance is mainly due to incomplete lineage sorting, probably facilitated by the fast diversification of Thuja around the Early Miocene and the large effective population sizes of ancestral lineages. Furthermore, approximately 20% of the T. sutchuenensis nuclear genome is derived from an unknown ancestral lineage of Thuja, which might explain the close resemblance of its cone morphology to that of an ancient fossil species. Overall, our study demonstrates that single genes may not resolve interspecific relationships for disjunct taxa, and that more reliable results will come from hundreds or thousands of loci, revealing a more complex evolutionary history. This will steadily improve our understanding of their origin and evolution.

中文翻译：

---

看穿树篱：侧柏（柏科）的系统基因组学揭示了第三纪孑遗植物群的显着不完整谱系分类和古代渗入

东亚（EA）-北美（NA）分离是第三纪孑遗植物群的著名生物地理格局；然而，很少有研究使用系统基因组学方法研究这种分离的进化历史。在这里，我们使用了 2369 个单拷贝核基因和几乎完整的质体来重建小型第三纪孑遗属 Thuja的进化历史，该属由五个分散分布的物种组成。核物种树强烈支持 EA 进化枝Thuja standishii-Thuja sutchuenensis和“分离进化枝”，其中西部 NA 物种T。 plicata是 EA 的姐妹-东部 NA 分离的 Thuja occidentalis–Thuja koraiensis团体。我们的研究结果表明，观察到的基因树之间的拓扑不一致以及细胞核不一致主要是由于不完全的谱系分类，这可能是由于早中新世前后金钟柏的快速多样化和祖先谱系的大量有效种群规模所促成的。此外，大约 20% 的T。 sutchuenensis核基因组来自一个未知的崖柏祖先谱系，这可能解释了它的锥体形态与古代化石物种的高度相似。总体而言，我们的研究表明，单个基因可能无法解决分离类群的种间关系，更可靠的结果将来自数百或数千个基因座，揭示了更复杂的进化历史。这将稳步提高我们对它们的起源和进化的理解。