A single nucleotide polymorphism is a nucleotide that is variable – not everyone has the same one at that site. To be more precise, it’s one that has significant variation – at least a few percent of people (in the population you’re studying) have something other than the most common nucleotide at that site. Generally, the most common nucleotide is the ancestral one.
You see such a variable site every few hundred nucleotides. Checking out the SNPs is less informative than sequencing the whole genome, but it’s much easier.
Most of these SNPs are in neutral parts of the genome and don’t do anything, one way or the other. If you’re investigating ancient population splits and such, this is useful, easier to analyze: neutral means unloaded dice, adaptive evolution means dice loaded in unpredictable ways.
In order to pick a set of SNPs, you look at members of some population and see which sites in the genome are sufficiently variable. They may still be good SNPs in another population, as long as that population is sufficiently similar – that is, shares most of the same drift history.
On the other hand, if the two populations have been separated for a long, long time, they won’t have the same SNPS, at least not entirely: sites that are variable in population 1, the population you used to pick your SNPS, may be fixed in the second population, while sites that are essentially fixed in the first population may be SNPs in population 2. The longer the separation, the more this happens.
Some years ago, some friends of mine looked at how ancestral (on average) SNPs were in different populations.
The average degree of ancestralness was almost exactly the same in Eurasian populations, but was noticeably higher in typical farming populations of sub-Saharan Africa such as the Yoruba, and was higher still in African hunter-gatherers such as the Pygmies and Bushmen.
We found this puzzling, and it took a while to figure it out. The root cause turned out to be that the drift histories of Eurasians were pretty much all the same, but the drift history of the Yoruba was different enough that they had somewhat different SNPs than Eurasians, while the Bushmen & Pygmies had split off even earlier and had an even more different drift history.
This point is technical, even boring once you figure out the answer, but add some misunderstanding&ideology and the story gets hilarious.
Now this following story I mostly got second hand, so take it with a grain of salt. But I think it’s basically accurate.
You see, somewhat earlier, people working with the same datasets noticed the same phenomenon, and instead of puzzling through it, they panicked. They thought that those higher levels of ancestrality in Africans meant that Africans were genetically closer to chimpanzees than other humans – which is not the case. One of them came up with the memorable phrase ‘chimp index‘ for average ancestrality.
Around the same time, there was a lot of odd activity at NIH, and I strongly suspect that activity was connected to the chimp index crisis. Even at the time, before we looked at this problem, I thought that something strange was going on. They called a special meeting, where those receiving NIH grants in human genetics were told to be careful to make sure that reporters didn’t get the wrong idea about genetic differences between populations. Marc Feldman proposed organizing ‘flying squads’ to rush out and counteract such misunderstandings – which inspired me to design a shoulder patch for those flying squads:
Eventually someone who knew some theory must have figured it out and explained it, which would have calmed things down. But for a while, the powers that be at NIH must have been shitting in their pants. How awful.