Supplementary files of The origin and evolution of shrubby xerophyte species in Clematis
Creators: name: He, Jian
Publisher: name: Zenodo
Year: 2022
Subjects: xerophytic adaptation, phylogenomic, shrubby habit, convergent evolution, homoploid hybridization, methodology

description: The drylands have the most special ecosystems on earth. Its natural environment is drastic, but hosts a surprisingly rich biodiversity. Xerophytes are one of the most important parts of dryland ecosystems, and how these taxa originated has always been of great interest to researchers. Clematis is one of the cosmopolitan genera of the buttercup family (Ranunculaceae), and is well known for its climbing habit. However, there are also several erect shrubby species (<em>C</em>. sect. <em>Fruticella</em> <em>s.l.</em>, with about 8–9 species) widely distributed in the Central Asian dryland ecosystems and adjacent dry areas. These species not only have well-branched woody stems, but also have simple or rarely very reduced compound leaves, which are specialized adaptations that minimize water loss. How, when and where the shrubby habit and xerophytes of <em>Clematis</em> originated, and its relationship with geological history and past environmental changes are issues worthy of attention. Therefore, in this study, we try to explore the origin and evolution of those taxa with a combined multidisciplinary approach. Firstly, we used genome skimming data to assemble the whole chloroplast genome and nrDNA sequences of 56 <em>Clematis</em> species (representing 8 species of <em>C</em>. sect <em>Fruticella s.l.</em>). The phylogenetic relationships were generated. The taxa of shrubby species of<em> Clematis</em> are not monophyletic, and are embedded in three major clades. Then, the molecular dating, historical range reconstruction, and character optimization analyses were conducted. The results clearly showed that the three lineages originated from vine plants independently and have different ancestral distribution areas. All of three lineages diverged from its sister after the late Miocene. The drought in Central Asia since the late Miocene may be the major driver for the convergence of these taxa. In addition, the strong cyto–nuclear discordance of the phylogenetic relationships within <em>C.</em> sect. <em>Fruticella</em> <em>s.l</em>. were observed, and it implies some hybridization events in those taxa. To test the above hypothesis, all species of <em>C.</em> sect. <em>Fruticella</em> <em>s.l.</em> (covering 28 populations) and its related taxa (covering 34 species) was sampled in the field. After transcriptome sequencing and filtering, we obtained a total of 8147 single-copy orthologs. Using this data, we reconstructed a high-resolution phylogenetic relationship. The multi-species coalescent model simulation was conducted and it show that the cyto–nuclear discordance of these taxa is mainly caused by interspecific hybridization events. Therefore, we used a variety of methods to perform detailed detection of hybridization events, and combined with multi-disciplinary data such as cytology and ecology. The hypothesis of convergent evolution of <em>C.</em> sect. <em>Fruticella s.l.</em> was verified. And it was revealed that the homoploid hybridization also played an important role in the origin of some lineages of shrubby species of <em>Clematis</em>. The aridity of Central Asian after the Late Miocene and glacial period fluctuation in the Pleistocene may be the driving forces for the origin and diversification of the shrubby <em>Clematis</em>. This study also clarifies an important mechanism for the hybridization events in the evolution of new adaptations. The hybridization between ancestral lineages can provide more genetic variation and evolutionary potential to adapt new niche and fuel high diversification rates and it led the shrubby species of <em>Clematis</em> adapted to the extremely vast and diverse dryland environment in Central Asia. In addition, we also made several attempts at methodology. At first, we verified that silica gel-dried plant tissues can be used for phylotranscriptomic studies. Then we developed a pipeline for rapid detection of hybridization in large-scale phylogenetic relationships. In summary, this study not only provide important evidence for the origin and evolution of species in drylands, but also can be used as a methodology reference for other studies.