Chimpanzee Genome Project

The Chimpanzee Genome Project was an effort to determine the DNA sequence of the chimpanzee genome. Sequencing began in 2005 and by 2013 twenty-four individual chimpanzees had been sequenced. This project was folded into the Great Ape Genome Project.

In 2013 high resolution sequences were published from each of the four recognized chimpanzee subspecies: Central chimpanzee, ''Pan troglodytes troglodytes'', 10 sequences; Western chimpanzee, ''Pan troglodytes verus'', 6 sequences; Nigeria-Cameroon chimpanzee, ''Pan troglodytes ellioti'', 4 sequences; and Eastern chimpanzee, ''Pan troglodytes schweinfurthii'', 4 sequences. They were all sequenced to a mean of 25-fold coverage per individual.

The research showed considerable genome diversity in chimpanzees with many population-specific traits. The central chimpanzees retain the highest diversity in the chimpanzee lineage, whereas the other subspecies demonstrate signs of population bottlenecks.

Background

Human and chimpanzee chromosomes are very alike. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. Humans have 23 pairs of chromosomes and other great apes have 24 pairs of chromosomes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres, producing human chromosome 2. There are nine other major chromosomal differences between chimpanzees and humans: chromosome segment inversions on human chromosomes 1, 4, 5, 9, 12, 15, 16, 17, and 18. After the completion of the Human genome project, a common chimpanzee genome project was initiated. In December 2003, a preliminary analysis of 7600 genes shared between the two genomes confirmed that certain genes such as the forkhead-box P2 transcription factor, which is involved in speech development, are different in the human lineage. Several genes involved in hearing were also found to have changed during human evolution, suggesting selection involving human language-related behavior. Differences between individual humans and common chimpanzees are estimated to be about 10 times the typical difference between pairs of humans.

Another study showed that patterns of DNA methylation, which are a known regulation mechanism for gene expression, differ in the prefrontal cortex of humans versus chimpanzees, and implicated this difference in the evolutionary divergence of the two species.

Draft genome sequence of the common chimpanzee

An analysis of the chimpanzee genome sequence was published in ''Nature'' on September 1, 2005, in an article produced by the Chimpanzee Sequencing and Analysis Consortium, a group of scientists which is supported in part by the National Human Genome Research Institute, one of the National Institutes of Health. The article marked the completion of the draft genome sequence.

A database now exists containing the genetic differences between human and chimpanzee genes, with about thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. Gene duplications account for most of the sequence differences between humans and chimps. Single-base-pair substitutions account for about half as much genetic change as does gene duplication.

Typical human and chimpanzee homologs of proteins differ in only an average of two amino acids. About 30 percent of all human proteins are identical in sequence to the corresponding chimpanzee protein. As mentioned above, gene duplications are a major source of differences between human and chimpanzee genetic material, with about 2.7 percent of the genome now representing differences having been produced by gene duplications or deletions during approximately 6 million years since humans and chimpanzees diverged from their common evolutionary ancestor. The comparable variation within human populations is 0.5 percent.

About 600 genes were identified that may have been undergoing strong positive selection in the human and chimpanzee lineages; many of these genes are involved in immune system defense against microbial disease (example: granulysin is protective against '' Mycobacterium tuberculosis'' ) or are targeted receptors of pathogenic microorganisms (example: Glycophorin C and ''Plasmodium falciparum''). By comparing human and chimpanzee genes to the genes of other mammals, it has been found that genes coding for transcription factors, such as forkhead-box P2 (FOXP2), have often evolved faster in the human relative to chimpanzee; relatively small changes in these genes may account for the morphological differences between humans and chimpanzees. A set of 348 transcription factor genes code for proteins with an average of about 50 percent more amino acid changes in the human lineage than in the chimpanzee lineage.

Six human chromosomal regions were found that may have been under particularly strong and coordinated selection during the past 250,000 years. These regions contain at least one marker allele