A Recent Lineage Split in <i>Cladium mariscus</i> Preceding the Disjunction of Two Biodiversity Hotspots: Evidence From Plastid Genomes

We report the complete chloroplast genomes of two geographically disjunct populations of <i>Cladium mariscus</i> from the Yaluzangbu Valley (Bomi) and the Hengduan Mountains (Ninglang). Phylogenomic analysis supports the basal position of <i>Cladium</i> within Cyperaceae. We identify a Late Pleistocene lineage split (~68 kya) coinciding with the MIS4 glaciation, likely facilitated by earlier northward expansion during a warm period followed by glacial isolation. The chloroplast genomes show a contracted IR region and expanded LSC region, and exhibit strong A/T bias in SSRs, indicating compositional constraints. Additionally, <i>C. mariscus</i> displays distinct genomic features, including structural variation, compared to other Cyperaceae. This study highlights the role of Quaternary climate changes in driving divergence in high-altitude wetlands and provides valuable genomic resources for further research.