The Drosophila 12 Genomes Consortium has sequenced and analyzed the genomes of 12 Drosophila species, including ten newly sequenced species, to enhance our understanding of evolutionary processes on a genomic scale. These genomes, which span a wide range of global distributions and ecological niches, reveal both conserved and divergent features. Despite significant phenotypic diversity, the species share a common body plan and life cycle, with many protein-coding genes, non-coding RNA genes, and cis-regulatory regions showing putatively non-neutral changes. The consortium used various assembly and annotation methods to improve the quality of the genomes, and they found that the majority of gene models are reliable, with high expression levels in adult flies. The study also identified abundant genome rearrangements, transposable element evolution, and lineage-specific gene expansions and contractions. Positive selection and selective constraints were analyzed using different methods, revealing that many genes are strongly constrained, while others show evidence of positive selection, particularly in functional categories such as defense response, proteolysis, and odorant binding. The analysis of codon bias and the impact of chromosomal location on protein evolution further highlights the complex dynamics of gene evolution in Drosophila.The Drosophila 12 Genomes Consortium has sequenced and analyzed the genomes of 12 Drosophila species, including ten newly sequenced species, to enhance our understanding of evolutionary processes on a genomic scale. These genomes, which span a wide range of global distributions and ecological niches, reveal both conserved and divergent features. Despite significant phenotypic diversity, the species share a common body plan and life cycle, with many protein-coding genes, non-coding RNA genes, and cis-regulatory regions showing putatively non-neutral changes. The consortium used various assembly and annotation methods to improve the quality of the genomes, and they found that the majority of gene models are reliable, with high expression levels in adult flies. The study also identified abundant genome rearrangements, transposable element evolution, and lineage-specific gene expansions and contractions. Positive selection and selective constraints were analyzed using different methods, revealing that many genes are strongly constrained, while others show evidence of positive selection, particularly in functional categories such as defense response, proteolysis, and odorant binding. The analysis of codon bias and the impact of chromosomal location on protein evolution further highlights the complex dynamics of gene evolution in Drosophila.