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Climate is a fundamental abiotic factor that plays a key role in driving the evolution, distribution and population diversification of species. However, there have been few investigations of genomic signatures of adaptation to local climatic conditions in cladocerans. Here, we have provided the first high‐quality chromosome‐level genome assembly (~143 Mb, scaffold N50 12.6 Mb) of the waterflea, Daphnia galeata...