Literature

The publication of genome sequences in recent years is providing a data-rich platform for research. In the paper cited below, the research team considered 110,000 genes in 9,990 gene families that are shared by humans, common chimpanzees, mice, rats and dogs. Of particular interest were examples of “gene gain” and “gene loss”, because these are regarded as providing “clues to the evolutionary forces that have shaped mammalian genomes”. One of the headline findings is that “humans and chimpanzees differ by at least 6% […] in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences.” The authors quote approvingly the words of King and Wilson in 1975 who said of the 1.5% result that “the genetic distance between humans and the chimpanzee is probably too small to account for their substantial organismal differences”.
What is obvious from the new research is that methodology is a critical factor in making comparisons. Change the criteria and you change the measured difference. In the past, acknowledgement of this simple point would have raised the quality of the debate over these issues.
It is worth noting that the authors adopt an evolutionary perspective in their research. Genes are gained or lost via “evolutionary forces”. This contrasts with a design perspective, where functionality is the key. The genetics of chimps and humans are similar, not because they necessarily share a common ancestor, but because they have similar functional needs. Common ancestry has to be justified by the evidence, not assumed to interpret the evidence. This design perspective offers numerous avenues of research to explore these issues further: looking at the non-coding DNA and considering biological information outside the genome, for example. As noted above, methodology is a critical factor.

The Evolution of Mammalian Gene Families
Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
PLoS ONE 1(1): e85. doi:10.1371/journal.pone.0000085

Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.