Friday, December 09, 2005

J'like dags?

Afarensis reported some of the popular press surrounding the publication of the dog genome. One item from National Geographic's coverage seemed a bit odd:
"Scientists had previously found that about 5 percent of the human genome sequence appears in the mouse genome. The new study shows that 5 percent of the human genome is also shared with dogs."
This made absolutely no sense to me. It sounds like they are saying that there is 5% sequence identity between humans, mice, and dogs -- this is totally erroneous considering the following quote from the mouse genome publication:
"At the nucleotide level, approximately 40% of the human genome can be aligned to the mouse genome. These sequences seem to represent most of the orthologous sequences that remain in both lineages from the common ancestor, with the rest likely to have been deleted in one or both genomes."
From reading the Nature report of the genome sequence, however, I have discovered the true meaning of the five percent:
"A comparative analysis of the human, mouse and dog by Lindblad-Toh et al. showed that about 5% of the human genome is being maintained by natural selection - suggesting that it has some essential function. Almost all of this sequence is also present in the dog genome. Only 1-2% of the genomes encodes proteins, so there would seem to be an additional common set (about 3%) of functional elements in mammalian non-coding DNA. These common sequences may constitute, for example, regulatory elements, structural elements or RNA genes. Notably, such regions are found mostly within the 0.8 Gbp of ancestral sequence common to human, mouse and dog."
I have not read the actual article (I plan to, and if it's interesting I'll blog on it), but it appears that 5% of the genome is more conserved that expected based on neutral evolution. As they mention, genes are expected to evolve slower (be more conserved), but there is also a substantial suite of regulatory elements that are also under strong purifying selection.


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