###### Abstract
Previous molecular phylogenetic studies, based on the plastid genome (or plastid regions) and the nuclear ribosomal DNA (nrDNA) data, had solved some of the phylogenetic problems in _Clematis_, including genus delineation and determination of the sister group of _Clematis_[42; 43; 48; 49; 50]. However, those studies failed to yield a robust phylogenetic framework for _Clematis_ due to its complex evolutionary history and insufficient phylogenetic signal present in limited DNA regions. With the advances in molecular biology techniques and bioinformatics, genomic data have been widely applied to plant systematics [51; 52; 53; 54]. Genomic data have greatly improved our understanding of plant evolution and diversification compared to the traditional Sanger sequencing method [55; 56]. For phylogenomic analysis, one of the most applied data partitioning methods is genome skimming [15; 57; 58], which randomly captures a certain percentage of total genomic DNA. This method is simple and cost-effective, with high reproducibility compared with other genome partitioning strategies, such as RNA-seq  
Figure 1: Distributions of the _Clematis_ sect. _Tubulosae_ (with the exclusion of known hybrid taxa), according to the specimen records. and target enrichment methods [53; 54]. Cytoplasmic genome and tandemly repeated sequences, such as nrDNA, can be easily assembled from the genome skimming data. Recent studies have shown that genome skimming data with high sequencing depth (at least 10\(\times\)) can be used for assembling single-copy nuclear genes for phylogenomic analysis [15]. If the sequencing depth is low (even less than 1\(\times\)), genome skimming data can be used to obtain single nucleotide polymorphisms (SNPs) from the nuclear genome for phylogenetic reconstruction [59; 60]. _Clematis_ species have a considerably large genome size (more than 7 Gbp, [[https://cvalues.science.kew.org/search](https://cvalues.science.kew.org/search)]([https://cvalues.science.kew.org/search](https://cvalues.science.kew.org/search)), accessed on 1 May 2022), and up to now, no information about high-quality whole genome sequences has been published. High-depth sequencing data to assemble nuclear genes is too expensive to be extensively applied to _Clematis_. Using genome skimming (approximately 1\(\times\)) and transcriptome data, our recently published study [60] generated a robust phylogenetic framework of _Clematis_. [PERSON] et al. [60] revealed that the nuclear genome phylogeny was better resolved and better corresponded to the morphological classifications of _Clematis_ than the plastome phylogeny. A high degree of incomplete lineage sorting (ILS) and frequent interspecific hybridization events may have been responsible for widespread cytonuclear discordance in the genus. For sect. _Tubulose_ phylogenetic studies have shown that this section is closely related to the sect. _Clematis_[42; 43; 49], and these two sections may have been frequently hybridized with each other in their evolutionary history [60]. Until now, there are also natural intersectional hybrid taxa in both China and Japan [45; 46], and plants of the two sections can be hybridized easily in gardens [61]. With the exclusion of the hybrid taxa, nuclear genome data analyses have shown that sect. _Tubulose_ is a monophyletic group [60]. However, the incomplete sampling of sect. _Tubulose_ has prevented us from understanding its origin, evolution, and formation of its distribution range. In this study, we comprehensively sampled the sect. _Tubulose_ and aimed to reveal its origin and diversification history in SJFR by using phylogenomic analysis. The purposes of this study are as follows: (1) to reconstruct the phylogeny of sect. _Tubulose_ with a sampling of all the recognized taxa and elucidate the relationship between sect.