Selection signatures in Apis mellifera jemenitica suggest candidate genes potentially involved in energy metabolism, proteostasis, reproduction, and cellular regulation

Honey bees (Apis mellifera) help pollinate plants, support biodiversity, and make a significant contribution to food production. Among their subspecies, A. m. jemenitica (JEM) inhabits desert and semi-desert regions, representing a valuable model for understanding genomic adaptation to extreme environmental conditions. We performed a comparative whole-genome resequencing analysis between JEM and A. m. mellifera (MEL) to identify genetic variants and selection signatures underlying adaptation to arid environments. A total of more than 2.9 million single nucleotide polymorphisms (SNPs) were identified and analyzed for population structure, linkage disequilibrium (LD), and genome-wide scans for selection signals using FST, XP-EHH, and π-ratio approaches. Population analyses revealed distinct clustering patterns and clear genetic differentiation between JEM and MEL, accompanied by faster LD decay in JEM, which is consistent with the larger effective population size in JEM (Ne = 2523) compared to MEL (Ne = 952). Through the combined selection scans, we identified 222 overlapping candidate genes that appear to be under positive selection. Many of these genes are involved in diverse biological processes, including energy metabolism, cellular regulation, protein homeostasis, stress response, genome maintenance, and cellular communication, with several having documented roles in heat tolerance, oxidative stress response, circadian regulation, and reproduction. Notable examples include LpR , inositol monophosphatase 1 , AcCoAS , enolase , BAG6 , alpha-Man-Ia , JHE , nocte , CRH-BP , and Est-6 , highlighting potential roles in osmotic and thermal stress tolerance, energy hemostasis, protein quality control, circadian regulation, and reproductive biology. These findings enhance our understanding of the molecular mechanisms underlying environmental adaptation in honey bees. Nevertheless, further multi-omics investigations, including transcriptomics, proteomics, metabolomics, as well as functional assays are needed to validate the adaptive relevance of the candidate genes and pathways identified in this study.