Multiple glacial refugia during Pleistocene climatic oscillations shape the genetic pattern of Machilus thunbergii across East Asia.

The article investigates the genetic structure and demographic history of Machilus thunbergii, an evergreen broad-leaved tree widespread in the Sino-Japanese Floristic Region (SJFR) of East Asia, focusing on the role of island glacial refugia during Pleistocene climatic oscillations. By analyzing chloroplast DNA and nuclear microsatellite markers from 1,378 samples across 64 locations, the study reveals pronounced genetic differentiation between mainland and island populations, with multiple distinct genetic groups corresponding to mainland China, Taiwan–Ryukyu Islands, Honshu, and other island units. The findings indicate that these islands, including Taiwan, the Ryukyu Archipelago, and parts of the East China Sea land bridge, served as important glacial refugia, preserving unique haplotypes and alleles with limited gene flow between mainland and island populations since their separation approximately 14,000 years ago. Postglacial expansions occurred within island refugia, shaping current genetic diversity and distribution patterns, while oceanic barriers and limited dispersal of pollen and seeds contributed to the observed genetic structure. This study enhances understanding of how continental shelf islands influenced plant phylogeography and the distribution of evergreen broad-leaved forests in East Asia during glacial cycles.