The genome sequence of the Brown Norway rat (Rattus norvegicus) has provided new insights into mammalian evolution. This is the third complete mammalian genome sequenced, and comparisons with the human and mouse genomes reveal details of mammalian evolution. The rat genome is smaller than the human genome but larger than the mouse genome. Both species have similar numbers of genes, with most genes persisting since the last common ancestor. Some genes in the rat but not the mouse arose through gene family expansion, including those involved in pheromones, immunity, chemosensation, detoxification, and proteolysis. Most human disease-associated genes have orthologs in the rat genome, but their rates of synonymous substitution differ. About 3% of the rat genome is in large segmental duplications, a fraction between mouse and human. The eutherian core of the rat genome, which aligns orthologously to mouse and human, comprises a billion nucleotides and contains most exons and regulatory elements. A portion of this core is under selective constraint in rodents and primates. Approximately 30% of the rat genome aligns only with the mouse, a considerable portion of which is rodent-specific repeats. More genomic changes occurred in the rodent lineage than in the primate lineage. The rat genome has a higher rate of base substitution in neutral DNA compared to the human lineage. A strong correlation exists between microinsertions, microdeletions, transposable element insertions, and nucleotide substitutions since the divergence of rat and mouse. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a male mutation bias, with small indels and nucleotide substitutions being more common in males. The G+C content of the rat genome varies across the genome, and the distribution of CpG islands is similar to the mouse genome but different from the human genome. The rat genome has a higher number of CpG islands per Mb than the human genome. The substitution spectra between mouse and rat show a shift in G+C content, with the rat genome being enriched in G+C content relative to the mouse genome. This shift may be due to differences in mutation events that have accumulated in the mouse and rat lineages. The rat genome has a higher rate of point substitutions than the mouse genome. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome hasThe genome sequence of the Brown Norway rat (Rattus norvegicus) has provided new insights into mammalian evolution. This is the third complete mammalian genome sequenced, and comparisons with the human and mouse genomes reveal details of mammalian evolution. The rat genome is smaller than the human genome but larger than the mouse genome. Both species have similar numbers of genes, with most genes persisting since the last common ancestor. Some genes in the rat but not the mouse arose through gene family expansion, including those involved in pheromones, immunity, chemosensation, detoxification, and proteolysis. Most human disease-associated genes have orthologs in the rat genome, but their rates of synonymous substitution differ. About 3% of the rat genome is in large segmental duplications, a fraction between mouse and human. The eutherian core of the rat genome, which aligns orthologously to mouse and human, comprises a billion nucleotides and contains most exons and regulatory elements. A portion of this core is under selective constraint in rodents and primates. Approximately 30% of the rat genome aligns only with the mouse, a considerable portion of which is rodent-specific repeats. More genomic changes occurred in the rodent lineage than in the primate lineage. The rat genome has a higher rate of base substitution in neutral DNA compared to the human lineage. A strong correlation exists between microinsertions, microdeletions, transposable element insertions, and nucleotide substitutions since the divergence of rat and mouse. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a male mutation bias, with small indels and nucleotide substitutions being more common in males. The G+C content of the rat genome varies across the genome, and the distribution of CpG islands is similar to the mouse genome but different from the human genome. The rat genome has a higher number of CpG islands per Mb than the human genome. The substitution spectra between mouse and rat show a shift in G+C content, with the rat genome being enriched in G+C content relative to the mouse genome. This shift may be due to differences in mutation events that have accumulated in the mouse and rat lineages. The rat genome has a higher rate of point substitutions than the mouse genome. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has a higher rate of microdeletions than microinsertions. The rat genome has