The Phylogeography of Selfing Caulokaempferia coenobialis Responded to Pleistocene Karst Development and Transgressions‐Regressions in Southern China

Aim Southern China was not directly affected by large continuous ice sheets during the late Pliocene to the Quaternary period, thus playing a central role in shaping the biodiversity distribution patterns of species globally. While numerous phylogeographical studies have focused on three subkingdoms: the Qinghai‐Tibetan Plateau (QTP), the Sino‐Himalayan Forest and the Sino‐Japanese Forest, research on the formation of plant diversity in South China is limited. This study aims to investigate the drivers of plant diversification in southern China by elucidating the evolutionary history of the endemic selfing herb Caulokaempferia coenobialis . Location Southern China. Taxon Caulokaempferia coenobialis (Zingiberaceae). Methods We analysed the evolutionary history of C. coenobialis by sequencing 11 chloroplast regions and three nuclear genes from 145 individuals across 15 populations, as well as assembling 29 plastid genomes. Results C. coenobialis exhibits high genetic diversity at the species and regional levels, with low population genetic diversity and significant inter‐population differentiation. All populations diverged into two major lineages located in Southwest and South China approximately 2.75 Ma, after which the South China lineage diverged into two sublineages in Southern and Northern South China approximately 1.21 Ma. These two divergences coincided with the Karst development between Southwest and South China and the transgressions and regressions in South China during the Pleistocene. Main Conclusions The Pleistocene monsoonal climatic fluctuations, the tectonic activity of the southeastern boundary fault of the QTP, the resulting development of Karst landforms and the transgressions and regressions in South China shaped the phylogeographical pattern of C. coenobialis . The study offers new insights into the effect of Pleistocene climatic fluctuations and neotectonic movement on the genetic isolation and population differentiation of plant species in southern China. It also offers practical implications for achieving the ‘30 × 30’ target of the Kunming‐Montreal Biodiversity Framework.