Although the statistical signals are relatively weak, a few classes of genes appear to be evolving more rapidly in humans than in chimps. The single strongest outlier involves genes that code for transcription factors, which are molecules that regulate the activity of other genes and that play key roles in embryonic development.

A small number of other genes have undergone even more dramatic changes. More than 50 genes present in the human genome are missing or partially deleted from the chimp genome. The corresponding number of gene deletions in the human genome is not yet precisely known. For genes with known functions, potential implications of these changes can already be discerned.

For example, the researchers found that three key genes involved in inflammation appear to be deleted in the chimp genome, possibly explaining some of the known differences between chimps and humans in respect to immune and inflammatory response. On the other hand, humans appear to have lost the function of the caspase-12 gene, which produces an enzyme that may help protect other animals against Alzheimer’s disease.

“This represents just the tip of the iceberg when it comes to exploring the genomic roots of our biological differences,” said one of the study’s co-authors LaDeana W. Hillier of the Genome Sequencing Center at Washington University School of Medicine. “As more is learned about other functional elements of the genome, we anticipate that other important differences outside of the protein-coding genes will emerge.”

Armed with the chimp sequence, researchers also scanned the entire human genome for deviations from normal mutation patterns. Such deviations may reveal regions of “selective sweeps,” which occur when a mutation arises in a population and is so advantageous that it spreads throughout the population within a few hundred generations and eventually becomes “normal.”

The researchers found six regions in the human genome that have strong signatures of selective sweeps over the past 250,000 years. One region contains more than 50 genes, while another contains no known genes and lies in an area that scientists refer to as a “gene desert.” Intriguingly, this gene desert may contain elements regulating the expression of a nearby protocadherin gene, which has been implicated in patterning of the nervous system. A seventh region with moderately strong signals contains the FOXP2 and CFTR genes. FOXP2 has been implicated in the acquisition of speech in humans. CFTR, which codes for a protein involved in ion transport and, if mutated, can cause the fatal disease cystic fibrosis, is thought to be the target of positive selection in European populations.

The chimp and human genome sequences, along with those of a wide range of other organisms such as mouse, honey bee, roundworm and yeast, can be accessed through the following public genome browsers: GenBank (www.ncbi.nih.gov/Genbank) at NIH's National Center for Biotechnology Information (NCBI); the UCSC Genome Browser (www.genome.ucsc.edu) at the University of California at Santa Cruz; the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute; the DNA Data Bank of Japan (http://www.ddbj.nig.ac.jp/); and EMBL-Bank (www.ebi.ac.uk/embl/index.html) at the European Molecular Biology Laboratory's Nucleotide Sequence Database.