Categories
agriculture Genetics Plants

Domestication Bottlenecks

Driveway tomato garden. How much diversity do these plants contain?
Driveway tomato garden. How much diversity do these plants contain?

Crops like tomatoes, even heirloom tomatoes, aren’t found in the wild. Domestication of crops usually involves only a relative handful of individual plants. Narrowing the species down to a few hundred (or possibly even a few dozen plants) means only a limited number of copies of each gene will be carried through and many of the variant copies of the genes present in the wild population won’t be included in that number. Keeping the population small for multiple generation reduces variability even more as by chance some rare version of genes in one generation won’t be passed to any of the offspring in the next.

Genetic bottlenecks happen in the animal world as well. Skin grafts between unrelated Cheetahs aren’t rejected because the animals are so genetically similar their immune system can’t distinguish the grafted skin as being different from its own skin. Even less fortunate are the tasmanian devils who have so little genetic diversity that they are being decimated by a transmissible cancer. After fighting with an infected devil, which has tumors on its face and neck, tiny bits of the cancer will get into an uninfected devil’s wounds, and since the immune system can’t distinguish the foreign cancer cells from the devil’s own cells, the cancer cells reproduce unchecked, the trait that makes normal cancers, produced by mutated versions of our own cells, so deadly. And the solution mentioned in the article, to save the species by protecting 200 individuals, while better than letting them all die, will sacrifice even more genetic variability by subjecting the already inbred devils to a new population (and genetic) bottleneck.

Categories
research stories

Of Genetics and Bears

One of John McCain’s signature issues is the wastefulness of government spending and one of the issues he’s getting a lot of play with is a government funded study of the genetics of bears in Montana. A description like “the genetics of bears” leaves a lot to the imagination so I looked up what the study actually entailed. They’re using wire traps to collect hair from grizzly and black bears in the wild and then using the samples to study the population structure. From the article I found in scientific American, it looks like they’re only looking at species (grizzly vs. black), gender, and number of individuals in the population. I can see why this is interesting from an ecological perspective, but I thought they were going to be doing deeper genetic analysis. 

Congress gave 4.8 million dollars to the bear genetics study, though McCain says 3 million in his speeches. With that much money, and the rapidly dropping cost of 454 and solexa technologies, a grant that size should have made it possible to shotgun sequence DNA from a number of individuals generating gigabases of data. Assembling the genome of the grizzly bear probably wouldn’t have been feasible within the 4.8 million dollar budget budget, but the data set generated could have been used for all sorts of studies. Looking at how much genetic diversity is present in different sub-populations. Looking for previous bottlenecks in grizzly bear populations. Identifying alleles of genes under positive selective pressure in the population. Testing if one set of alleles has been under selective pressure in the time frame since humans crossed the land bridge into the Americas, and a different set was under selective pressure previously. Alternatively, after mapping a number of single nucleotide polymorphisms (Spots in the genetic code occupied by different genetic bases (A, T, C and G) in different individuals, it should have been possible to develop a quick and (relatively) cheap test to identify different individuals. All the estimates I was able to find put the grizzly bear population in Montana at 1000 or less, meaning the cost per individual of this population count was over 5,000 dollars. My girlfriend informs me there are several ways to estimate a population cheaply and efficiently, such as recapture percentage.

My point here is that 4.8 million to study the population genetics and genomics of bears is completely justified, but there are probably cheaper ways to do a simple population census. Just to be clear, given that bears are an endangered species in Montana, there’s no question that a good population census was needed. McCain, however, sounds like he doesn’t think any study of bears is worthwhile. “I don’t know if it was a paternity issue or criminal, but it was a waste of money.” I guess funding genetic research into wildlife is wasteful by definition? Or maybe he means any genetic research except human genetics?

McCain seems opposed to basic research, and Hillary Clinton and Obama mention science as little as possible one way or the other. I’ve decided the reason I like Al Gore is that he actually comes across as smart and interested in research, but interestingly enough he only let that aspect of his personality emerge after he gave up on being president. What it comes down to is that the sort of person I wish was running this country is by definition unelectable.