Experimental evolution-induced transcriptome and phenotype responses of Drosophila melanogaster to novel thermal environments

Thermal stress imposes significant challenges on organisms, influencing cellular functions, morphology and survival. This study investigates the transcriptomic and phenotypic adaptations of Drosophila melanogaster populations subjected to constant high-temperature (HT) and fluctuating-temperature (FT) regimes over 80 generations in experimental evolution settings. RNA sequencing identified 1288 and 1152 differentially expressed genes in HT and FT populations, respectively, relative to the baseline population. Multiple gene ontology (GO) terms, including chromatin organization, nucleosome assembly, nucleic acid binding and polytene chromosome band formation, were enriched under both regimes, suggesting shared adaptive pathways. A weighted gene co-expression network analysis (WGCNA) revealed mitochondrial function and protein homeostasis as central to thermal adaptation, with HT populations showing enrichment of DNA repair and FT populations exhibiting enrichment of RNA processing and translation regulation-related terms. Phenotypic assays demonstrated increased heat tolerance, accelerated development and prolonged longevity in evolved populations, highlighting parallel as well as thermal regime-specific adaptive responses. This study emphasizes the complexity of transcriptomic–phenotypic adaptations to thermal stress in new environments.