The hypothesis that adaptive evolution in cities can occur on both contemporary and microgeographic scales was tested by investigating morphological, genetic and life history traits of waterflea Ceriodaphnia cornuta in an urbanized river. After the partial isolation from the Yingtao River by urban construction 16 years ago, the population of C. cornuta in the Shangyi Pond showed a different pattern of genotypic composition. Nuclear microsatellite markers revealed significant population genetic structure of C. cornuta among the Shangyi Pond, the Yingtao River and the Dianshan Lake in the upstream area. Migration analyses demonstrated little gene flow among different waters. In a common garden experiment, the changes in multivariate reaction norms provided evidence of local adaptation to dietary cyanobacteria in the river and lake populations. The results indicated that fragmenting river landscapes with urbanization resulted in the significant genetic differentiation and subsequent adaptive evolution in zooplankton populations on a short temporal and geographical scale.

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