The biogeography and genetic structure of aquatic zooplankton populations remains understudied in the Eastern Palearctic, especially the Qinghai-Tibetan Plateau. Here, we explored the population-genetic diversity and structure of the cladoceran waterflea Daphnia magna found in eight (out of 303 investigated) waterbodies across China. The three Tibetan D. magna populations were detected within a small geographical area, suggesting these populations have expanded from refugia. We detected two divergent mitochondrial lineages of D. magna in China: one was restricted to the Qinghai-Tibetan Plateau and the other was present in lowland China. Several different haplotypes in the Qinghai-Tibetan Plateau were most similar to those from various parts of Siberia, suggesting that as a source region. We also found substantial genetic differentiation between D. magna populations from the Qinghai-Tibetan Plateau and those from lowland China. Moreover, significant morphological differences were identified: D. magna from the Qinghai-Tibetan Plateau had a larger head length, body length and body width than did those from lowland China. Geographical and environmental factors were correlated with the observed morphological variation and genetic divergence of D. magna in China. Our data offer an insight into the divergence of freshwater zooplankton due to the uplift of the Qinghai-Tibetan Plateau.
