Genomic adaptation of the water flea Daphnia to elevated temperatures: Insights from power plant-heated lakes

Global warming increasingly threatens freshwater biodiversity, highlighting the need to understand how key ecological interactors, such as the zooplankton water flea Daphnia, genetically adapt to rising temperatures. Although local thermal adaptation has been documented in Daphnia, the underlying genomic changes remain poorly resolved. Here, we examined genomes of Daphnia cucullata (a member of the D. longispina complex) from five lakes artificially warmed for six decades by cooling water from power plant (increase of about 2 – 4 °C), and from seven adjacent, unheated/control lakes. Heated-lake and unheated-lake populations showed pronounced genomic divergence. Using a Hidden Markov Model framework, we identified genomic intervals showing high differentiation between the two population groups. These intervals were significantly enriched near thermal-adaptation candidate genes, with 188 thermal candidate genes located within or near highly differentiated regions, supporting a polygenic basis of thermal adaptation. Contrary to previous studies on the D. longispina complex that identified hybridization as a key driver of local adaptation, we found no evidence for adaptive introgression in the heated lakes, despite the presence of D. cucullata × D. galeata hybrids. Adaptive potential, measured as allelic richness at differentiated loci overlapping or located near thermal adaptation candidate genes, was high across all populations. Strikingly, genetic diversity at adaptive loci was higher in heated-lake than in unheated-lake populations. Taking advantage of this unique long-term warming system, our results identify specific loci associated with thermal adaptation in D. cucullata, demonstrate that adaptation has occurred independently of hybridization, and underscore the importance of standing genetic variation in local populations for adaptive evolution to warming.