The evolutionary history of brackish specialization from marine ancestry in the seagrass Ruppia sinensis

Ruppia sinensis, a unique seagrass species that originated in the marine environment yet successfully colonized extreme inland habitats, offers a rare window onto how plants cope with major habitat shifts and clarifies the mechanisms of adaptive evolution during marine-to-brackish transitions. We assembled a chromosome-level genome, conducted comparative phylogenomic analyses, assessed salinity tolerance through physiological experiments, and analyzed whole-genome resequencing data from 103 individuals representing 19 coastal and inland populations. R. sinensis falls in the core seagrass PRC (Posidoniaceae, Ruppiaceae, and Cymodoceaceae) clade with a Ruppiaceae-specific whole-genome duplication yet has lost tolerance to full-strength seawater and is an obligate brackish specialist. Coastal and inland lineages diverged c. 25 000 yr ago; dramatic sea-level fluctuations since the Last Glacial Period repeatedly displaced coastal populations, causing reductions in effective population size, loss of genetic diversity, and elevated genetic load. Inland populations persisted in saline-lake refugia and retain nearly twice the genetic diversity. The marine-to-brackish shift is an evolutionary trade-off rather than passive habitat tracking, with inland saline lakes serving as refugia that preserved diversity. Such shifts may be a recurrent adaptive strategy in seagrass evolution, and these diverse inland populations warrant conservation priority under climate change.