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I don’t mean to be an Ewen Callaway clipping service (though there are worse things to be), but today he has a piece up on ancient feline DNA and what it might imply for the distribution and spread of cats, How cats conquered the world (and a few Viking ships). My dissertation project is no longer on felines, but I spent several years doing analysis and thinking deeply on the issue of how cats emerged, and what might account for their contemporary distribution and phylogeographic relationships.

There are a few things I can divulge without scooping any future researchers who might work the data I’ve seen. First, ships and cats seem to be very closely connected. That is, maritime trade routes turn out to be highly suggestive of many of the patterns you see. This goes to the distinction between cats and dogs: the former are definitely creatures whose coexistence with humanity is conditional on complex civilization. The “finer things” in life, as it were.

The “domestication” of the cat is probably hard to disentangle from the emergence of urban centers, and the vermin which they attracted. What humans term vermin, the cats would naturally consider prey. The selective pressures are easy to imagine. Cats and humans are now companions, but initially their interests were simply concurrent.

And just as cities emerged independently in several locales (as well as agriculture), it is not implausible that domestic felines emerged from different wild populations, though at this point I’m modestly skeptical of most claims. Though it is not unlikely that there is introgression or admixture from diverged wild lineages into many domestic cat populations, the evidence of independent domestications is weak in my judgment. In contrast, cattle seem to be derived from two very distinct groups.

Rather, these research point to deep ancient structure among Middle Eastern feline groups, and parallel possibilities of human-cat coexistence as farming communities emerged rapidly during the early Holocene, with exigencies of historical events leading to later phylogeographic patterns we see around. I think the above research is on the right path. There is definitely a connection between most European domestic cat lineages and the indigenous populations for Egyptian cat (for example).

 
• Category: Science • Tags: Cats 
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Best friends forever

As I mentioned yesterday I’m a contributor to a paper which made a big splash yesterday in PNAS, Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. It’s been pretty widely covered in the media. One thing that hasn’t gotten that much play because most people don’t work with whole genomes is that the feline reference genome needed some work, and the group at Washington Unviersity’s Genome Institute really pushed it much further along the way to being useful. Much respect to Wes Warren and his team. This is not an uncommon issue. We may live in the “post-genomic era,” but that really applies to humans and a few particular model organisms for now. For many lineages there is the requisite genome-of-the-week paper, a hastily assembled reference, and then the group goes onto greener pastures. To get a sense, the original “cat genome” paper had 1.9-fold coverage. That means you expect that each SNP will be sequenced ~2 times. The problem with this is that that’s an average, and with variation there will be lots of gaps (leaving aside repetitive regions which are hard to span normally). And, with a ~1% error rate it will be hard to be confident about whether the variation you see is “real” or just error. To get a sense of how much better this paper’s data is they got 58-fold coverage out of pooled samples (n=22) from a wide range of domestic cats from different lineages (as opposed to just Cinnamon the Abyssinian). They also got 7-fold coverage of the wildcat samples, essential for comparative purposes.

To get you some quick background, F. silvestris catus diverged from its wildcat ancestors 5,000 to 10,000 years ago. This is in contrast to the dog, which seems to have been domesticated at least 15,000 years ago. The mitochondrial profile of Egyptian cats ~2,500 years ago was already similar to what you see in Egypt today. Over the past few thousand years domestic cats have expanded across a wide range in Eurasia. Breeds are relatively new for domestic cats, and tend to be relatively inbred lineages developed over the past few hundred years at most. In contrast the feral cats exhibit population genetic diversity in the same range as humans.

Citation: Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Citation: Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

So what did this paper find? First, I think the biggest aspect, which has been picked up by the media, is that cats are subject to the “domestication syndrome” due to selection on development of neural crest cells. This is not entirely surprising. Domestic cats have a reputation as being marginally tame and lacking in the servile sycophantic affect of the dog. But in comparison to the wildcats F. silvestris catus is actually very tolerant of coexistence with humans. In addition, they exhibit behavioral patterns which are not found in wildcats, such as residing in colonies. The practical reason for this is pretty obvious, as cats residing within Neolithic villages would be living cheek-by-jowl in comparison with their ancestors.

In regards to selection, because there were numerous samples, comparisons could be made across lineages using a sliding window method. Areas with high F st and sharply reduced heterozygosity are tells for selection events. Everyone has their particular genes of interest. What always makes a mark for me is how often I recognize genes which are targets of selection in domestic mammals, considering that that there are ~20,000 genes (granted, some of these selection events sweep across many genes, and the ones listed are often selected based on functional considerations). Evolutionary processes are substrate-neutral, but across a particular phylogenetic depth they tend to rework the same ‘raw material’ over and over again. As we expand the post-genomic empire outward it seems likely that animals and plants closely associated with humans will get the earliest treatment. And I think that will yield some very definite insights into the nature of genomic constraint and convergence conditional on being wrapped up in the same ‘ecosystem’.

 
• Category: Science • Tags: Cats, Genomics 
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John Bradshaw, author of Cat Sense: How the New Feline Science Can Make You a Better Friend to Your Pet, has an intriguing observation:

GROSS: You know, so many people get their cats from shelters, and so many of the cats in shelters – well many of the cats in shelters are the offspring of feral cats. And so many housecats are neutered. Are we breeding cats who succeed on the streets, more so than we’re breeding cats who are successful domesticated pets?

BRADSHAW: Well, I think we are accidentally favoring the cat that lives on the street, because it’s the cat that lives on the street who produces offspring. Many of those, you know, do sadly die of injury or disease or whatever, but some of them end up in rescue, the lucky ones, and then become pets.

Now if we’re going to neuter a large majority of our pet cats, that means that the most successful cats, and the most successful cats that are best adapted to living in people’s houses, never leave any offspring. And so where the next generation of cats comes from is from cats that are – whose parents, anyway, were adapted to living on the street.

Now that’s OK for a while, and I’m not saying there’s an imminent crisis, you know. It’s over the horizon. But it’s going to be there. I think that cats are going to become very, very slightly less friendly with every generation. And eventually we’re going to come to the point where cats become less attractive, less appealing, because they’re much harder to socialize.

At the moment you can do a huge amount, probably everything you need to, by handling the kittens and treating them the right way. I’m just hopeful that we won’t ever get to the point where some kittens really just don’t respond to handling in the same way that wild kittens don’t. The kittens of wild cats don’t respond to handling. They just go wild again, eventually.

This is standard quantitative genetics logic. The devil here is in the details, though it’s not implausible on the face of it. But if true the solution is also available via evolutionary genetics: instead of selecting for salient aesthetic characteristics breeders should pick particular amiable individuals lacking in species typical ferocity.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Cats, Evolution 
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(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Cats, Culture 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"