Most theories used to explain the evolution of eusociality rest upon two key assumptions: mutations affecting the phenotype of sterile workers evolve by positive selection if the resulting traits benefit fertile kin, and that worker traits provide the primary mechanism allowing social insects to adapt to their environment. Despite the common view that positive selection drives phenotypic evolution of workers, we know very little about the prevalence of positive selection acting on the genomes of eusocial insects. We mapped the footprints of positive selection in Apis mellifera through analysis of 40 individual genomes, allowing us to identify thousands of genes and regulatory sequences with signatures of adaptive evolution over multiple timescales. We found Apoidea-and Apis-specific genes to be enriched for signatures of positive selection, indicating that novel genes play a disproportionately large role in adaptive evolution of eusocial insects. Worker-biased proteins have higher signatures of adaptive evolution relative to queen-biased proteins, supporting the view that worker traits are key to adaptation. We also found genes regulating worker division of labor to be enriched for signs of positive selection. Finally, genes associated with worker behavior based on analysis of brain gene expression were highly enriched for adaptive protein and cis-regulatory evolution. Our study highlights the significant contribution of worker phenotypes to adaptive evolution in social insects, and provides a wealth of knowledge on the loci that influence fitness in honey bees.natural selection | kin selection | social evolution | taxonomically restricted genes E usocial behavior evolved multiple times in insects and is characterized in part by extreme asymmetries in the reproductive potential of individuals (1). This asymmetry is most pronounced in advanced eusocial insects, with their fertile queen and sterile worker castes. Darwin first recognized that natural selection cannot directly optimize worker phenotypes because workers are usually sterile (2). Hamilton (3, 4) developed kinselection theory to describe the conditions that allow natural selection to indirectly optimize worker phenotypes if such phenotypes benefit their fertile kin. It is commonly believed that worker traits, such as sib-care, foraging, and colony defense, play important roles in allowing colonies to adapt to their environment (5-7). However, despite the central role of kin-selection and inclusive fitness theory in the field of Sociobiology (8, 9), we lack knowledge on the pattern and prevalence of positive selection acting on the genomes of eusocial insects.Population genomic studies provide unprecedented opportunities to detect signatures of selection on DNA sequences over different timescales (10). There are several tests of selection that can be applied to genome-wide datasets. The McDonald-Kreitman (MK) test is arguably the best method for detecting selection on protein coding sequences because of its robustness to changes in a species' demography,...