Adaptation of a keystone aquatic crustacean to cold temperatures on the Qinghai–Tibetan Plateau

Understanding the genomic architecture of temperature adaptation is critical for characterizing and predicting the effects of temperature changes on natural populations. However, our understanding of these mechanisms is still limited, especially concerning adaptation to a cold climate. Here, we looked for adaptive phenotypic features that may help high‐elevation waterflea (Daphnia sinensis) clones to cope with the low temperatures of the Qinghai–Tibetan Plateau (QTP) and explored possible genomic signatures of adaptation to cold. We used an experimental approach to compare transcriptional responses, in high‐elevation and lowland D. sinensis ecotypes from China to different experimental temperatures (16°C vs. 20°C). We ran life table experiments and found that high‐elevation clones (from the QTP) produced more offspring in their 1st clutch (or over the 1st two clutches) than lowland clones when grown at a lower temperature. This temperature‐dependent life history difference was associated with strong genomic signatures of temperature adaptation: the gene SLC4A11 (encoding a transmembrane protein transporting Na+ and H+), together with its encompassing genomic island, might contribute to the adaptive evolution to the cold temperature experienced by high‐elevation clones. We noted that a set of candidate genes specific to the high‐elevation clones was associated with lipid metabolism, cuticle production, and cellular proliferation, possibly involved in the mechanism of temperature adaptation of these clones to the climate on the QTP. Our findings advance the understanding of how organisms have evolved to cope with cold environments.