Comments on: Evolutionary Genetics of Canine Population Structure

By: Frank

Frank — Sat, 07 Jun 2008 18:47:36 +0000

For those interested, here’s a link to another paper on this issue. We actually point out the difficulties in inferring the dog breed phylogeny in the paper.http://www.biomedcentral.com/1471-2148/8/28

By: Greg Laden

Greg Laden — Wed, 07 May 2008 10:24:28 +0000

I do not dispute this paper and the reseach it represents overall, but I absolutely do not agree that these clusters are accurate at any level of detail whatsoever. The primary reason for this is that the model assumes divergence of lineages. However, what has really happened with dog breeds is a steady flow of divergence (espeically earlier in history, most likely) followed by frequent cross-breeding. For instance, there is a pile of evidence linking the Newfoundland and the Pyrenees. That may be wrong, but it is reasonable. But these two dogs do not show up in the same cluster. Why? Because the Newfie was bred from the Pyr by adding alleles from other breeds. Depending on what part of the genome is driving the phylogeny, this could cause the Newfy and the Pyr to remain identical, or it could cause the Neuwfy to float off to some other cluster.In this case the Newfoundland is linked with the corgi and a bunch of terriers. DNA is not truth!Why is the African Basenju linked only with Asian breeds?The St Bernard is linked with spaniels and the greyhound, etc. I don’t think so….Fortunately, this is not a study of dog phylogeny.By the way, the mastiffs on this chart are not the southern (i.e. Tibetan) mastiffs. They are English.

By: John

John — Wed, 07 May 2008 09:53:33 +0000

Per the Dog Genome Project:http://www.genome.org/cgi/content/full/17/11/1562————————————————————The new “mountain” cluster, shown in purple in the structure graph on the left side of Figure 1, is anchored by the Bernese Mountain Dog and Greater Swiss Mountain Dog and includes other large dogs such as the German Shepherd and Saint Bernard (Fig. 1)….The other two clusters are the mastiff/terrier cluster, which first becomes apparent at K = 3, and the herding/sighthound cluster (Supplemental Fig. 5).————————————————————So it sounds like you’re saying the Tibetan Mastiff falls into the Mountain Dog Cluster? In fact if what you say is correct it should anchor it.Or possibly you dispute their findings (or their analysis) in which case I freely admit it’s likely to go over my head pretty fast.It doesn’t look like the Great Pyrenees falls into that group. They’re grouping it between Irish Wolfhound and Airedale Terrier.

By: Greg Laden

Greg Laden — Wed, 07 May 2008 09:39:48 +0000

John,This is a major research project of mine that I have put aside, but when I lay my hands on some materials I’ll pass it on.

By: John

John — Wed, 07 May 2008 09:18:18 +0000

Exactly.I would say that if all you have to go on is what the locals think is the history of the breed than that’s all you have to go on. If there’s more solid evidence then that is what you rely on. I don’t see this as a life or death or even an ego thing. I just want to know more.So to sum it up, I was hoping you’d cough up a couple of quick references to save me the trouble of looking for the papers myself. I guess I’ll have to go do the work myself then.Sigh…Love the topic, btw. When I was a kid I had a chart of about 200 or so dog breeds and how it was thought they were related stuck to my wall. That and a map of Middle Earth.

By: Mary

Mary — Tue, 06 May 2008 17:15:16 +0000

I just remembered Susie, though--too: the orangutan genome sequence (you can see the orangutan data in the UCSC Genome Browser here) came from Susie in the Gladys Porter Zoo; check the "assembly details" section on this page.

By: Mary

Mary — Tue, 06 May 2008 16:04:25 +0000

http://www.genome.gov/11006943 Frequently asked questions about the genome project from that link. Check out the “Whose DNA was sequenced for the Human Genome Project?” section.The “official” or “reference” genome sequence that we usually refer to is a composite of different people. But there are individual genomes you can look at. For example, Jim Watson’s genome can be viewed here: http://jimwatsonsequence.cshl.edu/

By: Greg Laden

Greg Laden — Tue, 06 May 2008 13:11:22 +0000

John, I don’t have time to lay out the argument for you here. I’ve read every word written on the dogs, and this is what I think is most likely, and it accords with the genetic evidence. Not necessarily the tibent mastiff, but some mountain dog form the Atlas-Nepalewse axis. The TM is considered by most to be the most like the “aboriginal” mountain dog in the region.This applies to the G.P. The BMD is a bit more obscure but it is probably derived from one of these mountain dogs.(Oh: And public opinion and dogs… that’s not a good source of information about dog history OR behavior!)Gort: Good question. I think both have been true, usually the latter but sometimes the former. Maybe someone who knows will chime in here.

By: gort

gort — Tue, 06 May 2008 13:00:15 +0000

Nice post. This seems like a good thread for this question: When a genome for a species, like humans, is said to be completely sequenced, does this mean that the genome for a single individual has been mapped or is the result more of a composite sketch built from a number of individuals?

By: John

John — Tue, 06 May 2008 12:57:19 +0000

Just out of curiosity, do you have any evidence of your claims of the ancestry of the Great Pyrenees and the Bernese Mountain Dog? A link to the Tibetan Mastiff certainly does not seem to be the consensus of public opinion. For both breeds the histories record them as having been bred from local farm dogs.