Identification of lineage-specific adaptive changes in the genomes of 13 bee species

Adaptive evolution often leaves molecular traces in the genomes of organisms. These signatures of selection can be detected by comparing orthologous sequence data across a phylogeny of closely related species with diverse life histories and ecologies. We have searched for adaptive genetic changes associated with the evolution of different bee lineages, including all four corbiculate bee tribes (honey bees, orchid bees, bumble bees, and stingless bees). We created brain expressed sequence tag (EST) sets for 12 bee species, including multiple members of all four corbiculate tribes, to be used in combination with the sequenced honey bee (Apis mellifera) genome. Alignments made from orthologous coding regions were fitted by maximum likelihood to codon substitution models to identify genes that have undergone lineage-specific changes in selective regime. Here, we report the identification of adaptive changes in the genomes of each of these 13 species. Associations between gene functions and interesting ecological and life history traits are discussed, with a special focus on molecular changes associated with differences in behavior.