RAD-seq reveals Cenozoic shifts in the palaeogeographic distribution of Trigonobalanus verticillata across the Indochina Peninsula and Malay Archipelago

The complex geological history and rich biodiversity of Southeast Asia have long fascinated biologists, ecologists, and biogeographers. In this paper, we address the spatiotemporal patterns of genetic diversity and dispersal dynamics of Trigonobalanus verticillata across the Indochina Peninsula and Malay Archipelago since the early Cenozoic and project distribution range shifts into the future. Our work is based on the integration of RAD-seq data with ecological niche modeling, to assess genetic diversity, genetic structure, divergence timing, and demographic dynamics. The key findings are as follows: (1) the species originated in north Sundaland, i.e., Indochina Peninsula, in the late Eocene, followed by Oligocene-Miocene stepwise south and northward dispersal events, establishing allopatric lineages via the Indochina Peninsula to the Yunnan and Hainan Island, while also expanding across Borneo to other regions of the Malay Archipelago. (2) Tectonically-driven habitat heterogeneity and inter-refugial gene flow promoted high genetic diversity in the Indochina Peninsula, whereas historical bottlenecks reduced genetic diversity in the Malay Archipelago. (3) Borneo served as a persistent region of refugial suitability from the Last Glacial Maximum to the present and is expected to retain its refugial function in the future. Our findings elucidate how Neogene-Quaternary environmental changes shaped contemporary biodiversity patterns in Southeast Asia, underscoring Borneo's critical role in conservation being a long-term refuge that has sustained the evolutionary potential of the species. Our integrative approach also provides a framework for understanding regional biogeographic dynamics through the genomic-level history of T. verticillata.