The 6% Solution to Human-Chimpanzee Divergence

This past summer, Matt Hahn presented a talk at the Society for Molecular Biology Evolution meeting and Evolution 2006 entitled "The 17% Solution: Gene Family Divergence Between Human And Chimpanzee". The basic premise was that, even though humans and chimps are ~99% identical at the DNA sequence level, they differ substantially in copy number variants. That is, the two species have different amounts of genes from certain gene families, which Hahn estimated as a 17% difference in genes between them. Given the amount of copy number polymorphism within humans, it should come as no surprise that there exists substantial variation in copy number between species.

Hahn argued that this could play a role in the phenotypic differences between the two species -- an alternative to the King and Wilson view that changes in gene expression explain the morphological divergence of humans and chimps. He modestly pointed out that some simple back of the envelope calculations (and, really, are there any other back of the envelope calculations?) reveal that his result is consistent with that of Lynch and Conery from 2000. If only Lynch and Conery had extended their rate of duplication to the divergence between humans and chimps, they would have discovered Hahn's 17% solution.

Eurekalert is reporting that Hahn and colleagues will be publishing a similar result in the inaugural issue of PLoS One:

Hahn and his research partners examined 110,000 genes in 9,990 gene families that are shared by humans, common chimpanzees (Pan troglodytes), mice, rats and dogs. The scientists found that 5,622, or 56 percent, of the gene families they studied from these five species have grown or shrunk in the number of genes per gene family, suggesting changes in gene number have been so common as to constitute an evolutionary "revolving door."

The researchers paid special attention to gene number changes between humans and chimps. Using a statistical method they devised, the scientists inferred humans have gained 689 genes (through the duplication of existing genes) and lost 86 genes since diverging from their most recent common ancestor with chimps. Including the 729 genes chimps appear to have lost since their divergence, the total gene differences between humans and chimps was estimated to be about 6 percent.

Hahn said any serious measure of genetic difference between humans and chimps must incorporate both variation at the nucleotide level among coding genes and large-scale differences in the structure of human and chimp genomes. The real question biologists will face is not which measure is correct but rather which sets of differences have been more important in human evolution.

The press release reports, "Approximately 6 percent of human and chimp genes are unique to those species". The paper is currently not available online, so it's still unclear why Hahn's estimate has dropped from 17% to 6%, but I have some ideas. I'll hesitate on commenting any more until I have a chance to read the article.

(Via Lynch's Posse.)