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Background Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. Results We sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping. Conclusions A. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1378-9) contains supplementary material, which is available to authorized users.

In Northeast China, large volumes of Mesozoic–Cenozoic igneous rocks have developed as a result of long-lasting subduction of the palaeo-Pacific and Pacific plates beneath the eastern Eurasian continent. Previous studies have convincingly confirmed the presence of depleted mantle (DM), FOcal ZOne (FOZO) mantle and enriched mantle 1 (EM1) end-members; the enriched mantle 2 (EM2) end-member is probably present but it has been poorly constrained. The Late Cretaceous Shuangyashan suite, comprising a monzogabbro and diorite–porphyrite stocks and their cumulate hornblendite enclaves, from the Shuangyashan coal basin, Northeast China, is characterized by high initial87Sr/86Sr (0.70922–0.71095) and low initial143Nd/144Nd ratios (0.51221–0.51238) at 98 Ma. Their occurrence demonstrates that EM2 is present in the lithospheric mantle of Northeast China and its formation may be related to recycled continental material in a subduction setting.