This document discusses comparative genomics and the evolution of genes using Drosophila species as a model. It summarizes that 12 Drosophila genomes were compared phylogenetically and this comparison revealed patterns of gene family expansion and contraction over time as well as structural changes and rearrangements like in the Hox cluster. The multi-species comparisons provided strong evidence for gene models and functions are conserved despite sequence divergence across the Drosophila phylogeny.