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5.11: The Human and Chimpanzee Genomes

Now that the genomes of both the human and the chimpanzee have been determined, it is possible to make more direct comparisons between the two species.

Comparison results

Their genomes are 98.8% identical (between any two humans — picked at random — the figure is closer to 99.5%).

  • Comparing over 7,000 genes that occur in both species (as well as in the mouse), it turns out that slightly over 1,500 of these have evolved quite differently in the two species.
    • In humans, genes for hearing, speech, olfaction — among others — have evolved rapidly since the two species diverged, while
    • in chimps, genes involved in formation of muscle and skeleton have evolved more rapidly.
  • In addition to the differences in the proteins these genes encode, differences between chimps and humans also involve changes in regulatory sequences — promoters and enhancers — of their genes. This is especially evident for genes encoding transcription factors. So even if a gene product is quite similar in the two species, how strongly, where, and when its gene is expressed might be quite different.
  • One gene product that is different between the two species is a protein designated myosin heavy chain16 (MYH16). In the 25 March 2004 issue of Nature, Stedman et al report that
  • in chimpanzees (as well as pigmy chimps, gorillas, orangutans, and Old World monkeys), the MYH16 gene is expressed almost exclusively in their jaw muscles where it transcribed and translated to produce one form of myosin that is used in the thick filaments of their jaw muscle fibers.
  • In all humans, the MYH16 gene has a deletion producing a frameshift that results in a premature STOP codon (a nonsense mutation), and thus the myosin molecule is too short to make effective thick filaments.
  • The result in humans is jaw muscles that must rely on other myosins which produce fibers much thinner than those of the other hominoids and a much smaller muscle.
  • From these data, the authors speculate that
    • because smaller — and thus weaker — jaw muscles would exert less force on their bony attachment (the cranium),
    • this would allow more flexibility and the potential for greater growth of the cranium during childhood and thus allow for the larger brain found in humans and their Homo ancestors (e.g. Homo erectus).
  • The authors date the origin of the mutation to approximately 2.5 million years ago, when fossil evidence indicates that the line leading to the genus Homo — with brain cases growing from 0.75 to 1.4 liters — split from the Australopithecus line with its brain case of less than half a liter.
  • Another gene product that differs between the two species is the protein FoxP2. FoxP2 is a transcription factor. Rare humans with only one copy of the gene (FOXP2) have severe language defects.

    The human FOXP2 gene differs from that of the chimp by 5 nucleotides, 2 of which result in non-synonymous codons encoding 2 different amino acids in the protein. The human protein differs from that in the mouse by only 3 amino acids. When you consider that we shared a common ancestor with mice over 60 million years ago but with the champanzee only about 6 million years ago, it is tempting to think that these recent changes in the human gene are related to the acquisition of language.

  • While there are only small (~1%) coding differences in their genes, their genomes differ in other ways.
    • Many insertions and deletions ("indels") and
    • many gene duplications
    are found in one species but not the other. Later work has revealed that of 510 chimpanzee sequences that are deleted in the human genome, only one occurs in the coding region of a gene. The others are found in introns or between genes, and at least some of these occur in gene-regulatory regions like enhancers.
  • Many single-nucleotide differences create different splicing sites so alternative splicing can produce substantial differences in the proteins of two species.