Table_2_Molecular Phylogeny and Historical Biogeography of Goodyera R. Br. (Orchidaceae): A Case of the Vicariance Between East Asia and North America.XLSX

Understanding of intercontinental distribution in the Northern Hemisphere has attracted a lot of attention from botanists. However, although Orchidaceae is the largest group of angiosperms, biogeographical studies on the disjunctive pattern have not been sufficient for this family. Goodyera R. Br. (tribe Cranichideae, subfamily Orchidoideae, family Orchidaceae) is widely distributed in temperate and tropical regions. Although the phylogenetic relationship of Goodyera inferred from both morphological and molecular data has been conducted, the sampled taxa were mainly distributed in Asia regions that resulted in non-monophyly of this genus. In this study, the complete plastid genomes of Goodyera, generated by next-generation sequencing (NGS) technique and sampled in East Asia and North America, were used to reconstruct phylogeny and explore the historical biogeography. A total of 18 Goodyera species including seven newly sequenced species were analyzed. Based on 79 protein-coding genes, the phylogenetic analysis revealed that Goodyera could be subdivided into four subclades with high support values. The polyphyletic relationships among Goodyera taxa were confirmed, and the unclear position of G. foliosa was also resolved. The datasets that are composed of the 14 coding sequences (CDS) (matK, atpF, ndhK, accD, cemA, clpP, rpoA, rpl22, ndhF, ccsA, ndhD, ndhI, ndhA, and ycf 1) showed the same topology derived from 79 protein-coding genes. Molecular dating analyses revealed the origin of Goodyera in the mid-Miocene (15.75 Mya). Nearctic clade of Goodyera was diverged at 10.88 Mya from their most recent common ancestor (MRCA). The biogeographical reconstruction suggests that subtropical or tropical Asia is the origin of Goodyera and it has subsequently spread to temperate Asia during the Miocene. In addition, Nearctic clade is derived from East Asian species through Bering Land Bridge (BLB) during the Miocene. The speciation of Goodyera is most likely to have occurred during Miocene, and climatic and geological changes are thought to have had a part in this diversification. Our findings propose both origin and vicariance events of Goodyera for the first time and add an example for the biogeographical history of the Northern Hemisphere.

对北半球跨大陆分布的理解引起了植物学家们的广泛关注。然而，尽管兰科（Orchidaceae）是最大的被子植物类群，但针对其离散分布模式的生物地理学研究尚不充分。Goodyera R. Br.（属名，隶属于兰科兰舌子草族兰基属，亚科兰基亚科，兰科）在温带和热带地区广泛分布。尽管已从形态学和分子数据推断出Goodyera的进化关系，但样本税类主要分布在亚洲地区，导致该属缺乏单系性。在本研究中，利用下一代测序（NGS）技术生成并采集于东亚和北美的Goodyera完整叶绿体基因组被用于重建进化树和探索历史生物地理学。共分析了18种Goodyera，包括7种新测序物种。基于79个蛋白质编码基因，系统发育分析揭示了Goodyera可以被细分为四个亚系，且支持值较高。Goodyera税类之间的多系性关系得到了证实，G. foliosa的位置不明确问题也得到了解决。由14个编码序列（CDS）（matK、atpF、ndhK、accD、cemA、clpP、rpoA、rpl22、ndhF、ccsA、ndhD、ndhI、ndhA和ycf 1）组成的数据库显示了与79个蛋白质编码基因相同的拓扑结构。分子年代学分析揭示了Goodyera起源于中新世中期（约1.575亿年前）。Goodyera的近北类群在中新世（约1088万年前）从其最近共同祖先（MRCA）中分离。生物地理学重建表明，亚热带或热带亚洲是Goodyera的起源地，并在中新世期间传播到温带亚洲。此外，近北类群在中新世通过白令陆桥（BLB）从东亚物种衍生而来。Goodyera的物种形成最有可能发生在中新世，气候变化和地质变迁在此多样化过程中发挥了作用。我们的发现首次提出了Goodyera的起源和分歧事件，并为北半球生物地理史提供了实例。