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Background  Long-term survival in isolated marginal seas of the China coast during the late Pleistocene ice ages is widely believed to be an important historical factor contributing to population genetic structure in coastal marine species. Whether or not contemporary factors (e.g. long-distance dispersal via coastal currents) continue to shape diversity gradients in marine organisms with high dispersal capability remains poorly understood. Our aim was to explore how historical and contemporary factors influenced the genetic diversity and distribution of the brown alga  Sargassum thunbergii , which can drift on surface water, leading to long-distance dispersal.    Results  We used 11 microsatellites and the plastid RuBisCo spacer to evaluate the genetic diversity of 22  Sargassum thunbergii  populations sampled along the China coast. Population structure and differentiation was inferred based on genotype clustering and pairwise  F   ST  and allele-frequency analyses. Integrated genetic analyses revealed two genetic clusters in  S. thunbergii  that dominated in the Yellow-Bohai Sea (YBS) and East China Sea (ECS) respectively. Higher levels of genetic diversity and variation were detected among populations in the YBS than in the ECS. Bayesian coalescent theory was used to estimate contemporary and historical gene flow. High levels of contemporary gene flow were detected from the YBS (north) to the ECS (south), whereas low levels of historical gene flow occurred between the two regions.    Conclusions  Our results suggest that the deep genetic divergence in  S. thunbergii  along the China coast may result from long-term geographic isolation during glacial periods. The dispersal of  S. thunbergii  driven by coastal currents may facilitate the admixture between southern and northern regimes. Our findings exemplify how both historical and contemporary forces are needed to understand phylogeographical patterns in coastal marine species with long-distance dispersal.    Electronic supplementary material  The online version of this article (10.1186/s12862-017-1089-6) contains supplementary material, which is available to authorized users.

Historical isolation and contemporary gene flow drive population diversity of the brown alga Sargassum thunbergii along the coast of China