Sunday, July 13, 2008

Doggie ancestry

I heard about this, but never saw the details:

From the website of Doggie DNAPrint:
For example, in 2004 Parker et al. sequenced 75 SNP and 96 microsatellite loci in 85 dog breeds and showed that modern dog breeds are distinct genetic units and that breed can be accurately determined from dog DNA. Looking back relatively far in the dog family tree, Parker et al. noted that there appear to be 4 main dog breed types:
  1. The wolf-like (yellow in the K=4 part of Figure 1)
  2. The Herders (green in the K=4 part of Figure 1)
  3. The Hunters (red in the K=4 part of Figure 1), and
  4. The Mastiff (blue in the K=4 part of Figure 1)

Figure 1 (above) shows some of their data (Figure 3 of Parker et al., 2004), where dog breeds are clustered based on their affinity with the founders or parental dog populations for each of these 3 ancestral groups. Dog breeds such as the Akita, Chow Chow and Siberian Husky fall into the Wolf-Like group, Collies, Greyhounds, Borzoi etc. fall into the Herder group, Beagles, Pointers and Terriers (etc.) fall into the Hunter group and Bulldogs, Mastiffs, Boxers (etc.) fall into the Mastiff group.You will note that, due to the history of their origins, each breed is characterized by a unique ratio of admixture among these families.


Maju said...

There's surely much more to know. I mean that K=4 looks like a rather shallow depth for such a widespread and variegated species. I'm quite sure that K=5, K=6, etc. should show new clusters. Often populations that look monocolored or mixed at shallow levels end up showing a very distinctive group of their own when greater depth is achieved. You can see that already in the German Sepherd and the Belgian Sheepdog, for example, that in K=2 are almost only red and in K=4 are almost only anything but that.

IMO K-means clustring is the best that can be done with autosomal DNA but much greater depth should be achieved before a clear picture appears.

Yann Klimentidis said...

yeah, and that was only 75 SNPs and about 100 microsatellites, and this was in 2004. The company uses 204 "especially informative SNPs", but "More recently, a US company has developed DNA chips containing large numbers of dog SNPs (two types, one with 26,000 SNPs and another with 125,000 SNPs)" There's some more info on the website.
I wonder what best explains the diversity: behavior (herding, hunting), or geographical "origin"? ... probably depends..

Maju said...

There was an article in PLOS genetics this month (Ke Hao et al) that strongly suggested than larger samples were much more informative than larger SNP arrays. Apaprently the info provided by larger arrays tends to be redundant.

I wonder what best explains the diversity: behavior (herding, hunting), or geographical "origin"? ... probably depends..

Probably both but certainly for the "wolf-like" yellow cluster I could actually detect more a "Siberian" (or East Asian) geographical area than anything clearly "wolf-like" among most of the breeds. I would not dare to claim that the Chow-chow is more "wolf-like" than, say, a German Sepherd.

Anonymous said...

I also thought it was odd that the ultimate herding dog, the Border Collie, contains almost zero 'herding' type, and is nearly fully 'hunting' type.

My border collie has no hunting instinct whatsoever, but is a keen herder.

Yann Klimentidis said...

yeah, that's true...weird.

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