Wednesday, December 07, 2005

"...But They are Still Dogs..."

Added Later: Here is a link to the NIH press release and, for those with Real Player, here is a link to a webcast about it. Concerning the 5% issue this is the only further info I have - in case it gives a clue to those who know a lot more about genetics than I do:

While dogs occupy a special place in human hearts, they also sit at a key branch point, relative to humans, in the evolutionary tree. It was already known that humans share more of their ancestral DNA with dogs than with mice; the availability of the dog genome sequence has allowed researchers to describe a common set of genetic elements - representing about 5 percent of the human genome - that are preferentially preserved among human, dog and mouse. Rather than being evenly distributed, some of these elements are crowded around just a small fraction of the genes in the genome. Future studies of these clusters may give scientists the critical insight needed to unravel how genomes work.

Those so inclined can also go to NCBI Dog Genome Resources.

National Geographic News and New Scientist have both done stories on the sequencing of the dog genome.

Meet Tasha. Tasha is the boxer who supplied the DNA for the study. Researchers used the shotgun sequencing technique to map her genome. This is how it works:

With this technique the genome is first broken into fragments and the DNA sequence of each determined. Then a computer stitches the fragments back together.

The process must be repeated several times to ensure accuracy, and the new draft is the product of 7.5 repetitions. The genome of Shadow, the poodle owned by gene-entrepreneur Craig Venter, had only 1.5 times coverage. The boxer was chosen as it is highly inbred. That means the difference between its paired chromosomes are smaller, making sequencing easier.

Researchers examined the sequences of 2.4 billion bases - equivalent to 39 pairs of chromosomes. Several interesting findings stand out. First, domestic dogs genomes are 99.85% similar:

The boxer and the poodle, for example, differ by about a single nucleotide change in every 900 bases. “A dog is a dog in a genomic sense,” says Lindblad-Toh.

Researchers also sequenced smaller parts from 10 other breeds of dog (such as german shephards, beagles and italian greyhounds) as well as coyotes and grey wolves:

The greater than 99% coverage of the 2.4 billion letters of Tasha’s genome has also revealed an important twist in our understanding of how natural selection works on DNA. Much of the non-coding DNA in dogs is the same as that in humans, indicating that it is under strong natural selection.

“Hence, non-coding DNA is not just ‘junk’,” says Hans Ellegren, of the department of evolutionary biology at Uppsala University, Sweden. Instead, he says that such sequences may constitute non-coding RNA or may have a regulatory function.

Even more interesting:

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 is interesting because dogs split off from the common ancestor before mice did, but the shared sequences are virtually the same:

"For genes this is not unexpected, since most mammals share a rather similar set of genes," said Hans Ellegren, an evolutionary biologist at Uppsala University in Sweden.

"However … this indicates that there is a core set of noncoding sequences needed to make a mammal."

The researchers have also found that many of the conserved sequences are clustered around developmental genes.

The most interesting aspect, to me was the genetic history. The research indicated a genetic bottleneck sometime around 10,000-15,000 years ago - roughly the time when dogs were first domesticated. Withing some of the breeds there are genetic bottlenecks ranging from 50-200 years ago which suggests that some breeds have a recent origin.