Friday Peer Reviewed Cat Blogging

A paper just out in Genomics presents a very thorough study of cat genetics. Cat as is in kitty cat. The findings are expected, yet surprising in a few areas. The conclusion the authors draw about cat origins is very weak, in my view, but the information this study provides about cat breed genetics is excellent and will be of value to cats around the world.


ResearchBlogging.orgWild cats (Felis silvestris) are or were found in a roughly continuous distribution across much of Africa (not restricted only to savannas, as is often stated), the Middle East, and Europe, and possibly disjunct in Southeast Asia (though I suspect that wild populations were continuous across southern Asia). The most "wild" (not admixed with domestic kitties) and well studied population is in the Kalahari (see photo above), where it is actually fairly easy to see them in the wild. They are quite common there. In fact, you can't swing a dead cat without hitting one....

Domestic cats have generally been thought of as having been bred from the African variety, unless you are an archaeologist, then one uses the term "Middle East" instead of "Africa," owing to the usual Eurocentric/Holyland Centric biases.

The present study investigated a large sample of domestic breeds of cats, and used previously collected data from some wild cats. It should be noted that there are not too many breeds of cats, compared, say, to dogs. There are perhaps around 700 breeds of dogs, but fewer than 100 breeds of cats.

The graphic and very cute phylogeny derived from this study is reproduced here:

Fig. 2. Neighbor-joining tree of cat breeds and populations. The phylogenetic tree was constructed using Cavalli-Sforza's chord distance. Bootstrap values above 50% are presented on relationship nodes. Asian (green), Western European (red), East African (purple), Mediterranean basin (blue), and wildcat (black) populations form strongly supported monophyletic branches. European and African wildcats are closely related, whereas short branches of most all other populations indicate close relationships of these breeds and populations. Random-bred populations are indicated in italics, breeds are in standard font. Cat photographs courtesy of Royal Canin and Richard Katris of Chanan Photography.

While the authors conclude that their study verifies the previously estimated "Middle Eastern" origin of cats, this is not entirely clear from their data. I would rather put it another way: Breeds found across Europe and Asia appear to be clustered geographically (with a few odd exceptions) and root nicely in a cluster that includes their sample of wild cats, indicating that cat domestication happened more or less once, in a restricted zone, and all breeds were transported (along with humans, presumably) from that core area.

The Africa wild cat data they used were from southern Africa (I suspect the Kalahari, because that is where you can easily find samples). This is very far from the origin of cats, and this shows, in the great genetic distance between that sample and all the other samples. The non-African samples must be considered likely admixed with domestic cats. So, in distinguishing between an origin, say, in the Levant vs. Northeast Africa, the present study must remain mute.

American cats cluster fully with the European cats. This means that if you own a Maine Coon Cat, sorry, you have neither a primordial cat or a cross breed between a cat and a raccoon!

An important finding of this study is that many cat breeds are genetically a little thin on variation, and thus at risk for genetic diseases. There are, indeed, numerous such diseases found among cat breeds.

The study falls to explain LOL cats, or the cat obsession with World Domination.


Thanks very much to John Lynch, who also blogged this story, for turning me on to this research.

LIPINSKI, M., FROENICKE, L., BAYSAC, K., BILLINGS, N., LEUTENEGGER, C., LEVY, A., LONGERI, M., NIINI, T., OZPINAR, H., SLATER, M. (2008). The ascent of cat breeds: Genetic evaluations of breeds and worldwide random-bred populations. Genomics, 91(1), 12-21. DOI: 10.1016/j.ygeno.2007.10.009

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That tree looks a little too neat. Given that cats don't care about keeping bloodlines pure (or to put it more crudely: they'll happily fuck anything that goes "meow"), I have to suspect there's a bit more cross-over between branches than is shown (at least until you enter the modern era of "cat fanciers" who make an effort to sequester their queens from random toms).


That is a good point. I can explain.

First, I went back and stuck the figure caption in, which might help (or maybe not, it does not really add too much).

The problem is that all trees look like this. Tree drawing does not show bleeding between lineages, really. One can read bleeding between lineages only by knowing some independent expectation of how the tree should look and then finding branches that are either the "wrong" length or in the "wrong" place.

A person might look, say, at a tree of human populations and, figuring that human races are real, deep, biological, genetic phenomena such that pretty large genetic distances between groups and true boundaries between groups exist and matter, and not question the tree at all. Or a person (such as yourself) might look at a tree of cats and, believing (probably correctly) that cat populations should have a lot of gene flow between their groups, and wonder "hey, can this tree be right"?

The tree probably is right, but it is a genetic distance map of averages, not a story about cat (or if this were people, people) populations are distinct and do not overlap.

I could have also said this: Many of the cats on this tree are purebreds, so no, they are not interbreeding. But many are "random bred" (their term) as well.

John was kind enough to send me the paper as well, and I read it with interest. But as so often with these genetic studies, it operates on a scale level so high that it makes it almost useless to archaeologists. What care I, when I find Iron Age cat bones in Sweden, about the Maglemosian-era Near Eastern origins of the domesticated cat? I want to know from what area that individual cat or his great-grandma was obtained.

I went over this with Razib recently, and it took a while to convince him that I am not a nat-sci-hating humanities scholar. It's just that the humanities don't give a damn about global generalities. We want to know what happened in Mucketymorton parish in the late 5th century.

I find the chart confusing and contradictory. It says that random-bred cats are shown in italics, and then has American shorthair in roman font. I'm fairly certain that "American shorthair" is basically a bucket for any short-haired cat found in America that is not pure-bred. At least, "domestic shorthair" is what my vet has put on the medical record of each of my cats (provenance: trailer park, redneck family who don't get their animals neutered, barn, and stray, respectively).

Likewise, I read elsewhere that the paper showed that the Japanese bobtail was more closely related to European than Asian lineages, but the chart shows J. Bobtail right there in the same branch with the other Asian cats.

Many years ago, I read that it was believed that "temple cats" were domesticated independently of other cats. That would be the applehead* Siamese (not shown!), Siamese, Burmese, etc. The abstract would seem to imply that this is not the case, but again, the chart shows all the temple breeds clustered on a single branch at some distance from other breeds.

I'm just a layperson and cat-owner, but I'm not getting any kind of clear sense of just what this study is actually trying to say.

* My sister, who is not a cat person and has never owned a cat before, recently rescued an applehead. What a magnificent animal she is. Supposedly, applehead Siamese are the "original" southeast Asian temple cat, with the modern Siamese being backbred with the more typical Egyptian/Middle-Eastern cats.

HP: American Shorthair and Domestic Shorthair are synonyms, but American Shorthair is the preferred, current term, the name officially changed some time ago. It is a pure breed. Lots of "regular" (random-bred, which is a technical cat breed term) cats tend to look like the AS. This is probably not entirely a coincidence. Random bred cats in central Africa tend to look like a certain breed as well, but not American shorthair ... they actually look kind of Abyssinian.

Your cat may be a member of the new breed, "Trailer Park Blue Point." Does it have a mullet?

On the "Temple breeds" ... That is a term I've never heard. I understood the Temple to be the BIrman. But whatever, yes, this one set of cats including those you mention are said in some of the old cat literature to have been bred from a wild oriental cat. But there are two or three other stories as well, that are totally different.

I'm sorry, I needed to pick and choose among many details to turn this peer reviewed piece inoto a blog post. Let me tell you what they say about "temple breeds":

Consider the following sets of breeds:
Singapura and Burmese
Havana Brown and Siamese
Korat and Birman
Exotic Shorthair and Persian.

If you look at all of these breeds together in the big picture, they all show up as the same breed. They are one stick on the chart, and you can't separate out different samples or breeds when looking at cats as a whole. The specific allelic differences betweeen, say, a Birman and a Burmese, are too sall.

If you look at just these breeds alone, they divide out as shown in the list above: You can tell a Korat/Birman from an Exotic Shorthair/Persian, but not a Korat from a Birman.

On the tree (see my comment above) Persian ends up way over in the wrong place because the Exotic is bred from the Persion, so the computer software throws them together and then joins them with the western european breeds. This is one example of why one needs not see trees as truth, bur rather, as tools.

The takehome message is that cat breeds are way more similar to each other than, say, dog breeds, and cats seem to have all been bred from a domestic stock that has more or less a single origin.

The "New York" is a sample of random bred cats from New York City.

To depict crossover "bleeding", how about having a breed represented by a thin line drawn in a certain color, then have it flanked by outside bands of a much lighter shade, perhaps with a slight bit of the colors of the breeds most likely to interbreed with said breed?

I don't really know much about cats. All I know are the "pusang gala" (roaming cats)in our community. These are cats owned by nobody but feed by anybody who cares to feed them. So I find it interesting that someone was able to come up with a "cat-breeds tree". It seems like the cat will just be identified depending on the resulting looks.

Perhaps ours will just be the New York kind. Random.

The way I understand it about the domestic and American short hairs is that the domestic shorthair was the moggie that developed in its own pace with no control. And then, as people love to breed cats to get specific looks, they started doing just that to the moggie - and now there are about 80 different color variations in the breeding program. The American shorthair was a term that appeared in the 60's and because of their systematic breeding are now considered a purebred cat breed.

The ordinary domestic short hairs keep of breeding on their own (and occasionally producing a domestic longhair - the gene is recessive so for a kitten to be long haired it needs to get that gene from both its parents).

Leena :)