A Recent Lineage Split in Cladium mariscus Preceding the Disjunction of Two Biodiversity Hotspots: Evidence From Plastid Genomes.

We report the complete chloroplast genomes of two geographically disjunct populations of Cladium mariscus from the Yaluzangbu Valley (Bomi) and the Hengduan Mountains (Ninglang). Phylogenomic analysis supports the basal position of Cladium 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, C. mariscus 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.