Wide-ranging changes to the coastline of East Asia during the glacial periods of the Quaternary might have significantly influenced the genetic structure of coastal plants. To verify its historical migration and potential breaks to gene flow, we investigated the genetic structure of the vulnerable halophyte Suaeda malacosperma, whose distribution is restricted to brackish tidal areas of Korea and Japan. Two chloroplast DNA (cpDNA) regions (rpl32-trnL, trnH-psbA) were used for five individuals each from 11 populations. SNP data obtained via multiplexed ISSR genotyping by sequencing (MIG-Seq) were used for 181 individuals from those populations. Ecological niche modeling (ENM) was combined with genetic analyses to compare current and past distributions. The cpDNA sequences and MIG-Seq data revealed largely congruent results indicating that S. malacosperma consists of three genetic clusters: western coast of Korea, southern coast of Korea, and Japan. The patterns produced through structure analysis and cpDNA haplotypes showed that the gene flow occurred at or after the last glaciation from Japan to the southern coast of Korea via the Korea/Tsushima Strait land bridge. Despite the coastal habitat of this species, ocean currents had less influence. Integrating genetic data with past distribution models by ENM provided insight into potential recolonization routes from refugia in each region. Those data suggested that, instead of contemporary gene flow, a historical range shift due to climate change affected the population structure. These results support the need for a conservation strategy and advance our understanding about the historical range dynamics of coastal plants in temperate East Asia.
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