The Historical Biogeography of Divergence in the Relict Cypress Chamaecyparis obtusa, and the Implications for Conservation and Management in East Asia

East Asia provides long-term stable refugia for relict plant species and supports high species richness. Chamaecyparis obtusa is a typical relict species that is now restricted to particularly warm, humid areas in East Asia, mainland Japan, and Taiwan. It is widely used for timber, and understanding its genetic characteristics within its natural range is important for appropriate management and conservation. This study used genome-wide single nucleotide polymorphisms (SNPs) to examine the historical biogeography as well as genetic characteristics of C. obtusa populations across its distribution range. High levels of genetic divergence were found between mainland Japan and Taiwan (0.673–0.717 F_ST). The initial divergence occurred around 1 million years ago (Ma) based on a neighbor-joining tree and 1.32 Ma (with a 95% confidence interval of 0.20–2.54 Ma) based on a DIYABC analysis, during the early Pleistocene when the land bridge connecting mainland Japan and Taiwan collapsed. Populations in mainland Japan exhibited higher genetic diversity, suggesting frequent gene flow and past population expansions. Within mainland Japan, both northern and southern marginal populations exhibited high levels of genetic distinctness and are considered to represent past refugia from the last glacial period. The populations in Taiwan exhibited lower genetic differentiation, even though infrequent gene flow was seen between them. All the C. obtusa populations studied exhibited random mating based on F_IS values, and continuous conservation of restricted areas is indicated. The highly divergent populations emphasize the need for conservation, and seedling transfers between the different genetic clusters identified are not recommended.