Plumbing for bottlenecks

My series on mutual information and tests of selection (which began with "Information theory: a short introduction") is at a branching point. One of the critical factors determining the power of such tests is the ancient rate of genetic drift. So it's important to come to some understanding of the archaeological record and our best estimates of ancient demography, so that we can independently test the hypothesis that genetic drift was very strong in recent human evolution. That's a long project, potentially the topic of several review papers. Since nobody else has put together these data in useful way for population genetics, I'm going to do it in one place. What you see in this series are my notes about this project. Being notes, they are not complete, but they may occasionally be better than any other sources. Where it's appropriate, I'll spin off the results for review and publication, and point to them here.

Many geneticists believe that there were massive population bottlenecks within the last 30,000 years, citing both genetic and archaeological evidence in support of this proposition. Some claim that there have been significant population bottlenecks in the last 5000 years.

Some archaeologists agree. However, I think this is one of those Inigo Montoya cases: “That word, I do not think it means what you think it means.” Archaeology and genetics have completely different interpretations of the words, “bottleneck,” “contraction,” and “expansion.” The result has been a lot of confusion about the relation of archaeological and genetic estimates of population size.

A population bottleneck impacts genetics by increasing the rate of inbreeding. This takes time to change gene frequencies, and does so in inverse proportion to population size. It may seem surprising that a truly massive die-off, on the scale of the Black Death, will have no measurable genetic impact. But cutting a population of millions down by half just doesn’t impact gene frequencies. That is, unless you are looking at genes that helped people to survive the plague, in which case you’re looking at natural selection, not a bottleneck.

A significant genetic bottleneck is not just any population contraction – it’s an event in which the population is cut by a large fraction for a long time. In paleontological terms, we’re usually considering cases where the ratio of the number of individuals and the number of generations is near one. In other words, if you cut the population down to a thousand individuals, and keep it there for a thousand generations, you’re going to have a large genetic impact. Likewise, you can have a significant bottleneck that’s ten generations long, but you need to cut the population down to around ten people.

You can do a bit better measuring inbreeding by looking at lots and lots of people to study very rare alleles, like a rare genetic disease in a founder population. There, you may spot changes that unfolded in ten generations, even in a relatively large population of a hundred people. Increasingly, as we develop larger and larger datasets of gene variations, we will add power to detect such events in human prehistory.

In archaeology, a significant event is one in which fewer sites were occupied by ancient people in a well-studied region. The length of such a contraction depends on the sampling intensity and dating methods available – it might be a hundred years or many thousands. Likewise, the magnitude of population contraction will be uncertain – you can get an accurate estimate, but with substantial sampling error. As in genetics, there are other possible explanations for an apparent contraction. We might lack geological exposures of the right age, or people may simply have moved from formerly favored locations to new ones. Worse, it might just be that archaeologists haven’t looked hard enough at a given time interval.

Archaeology is necessarily imprecise about the census population that existed at any given time. So is genetics. Both have their strengths and weaknesses. We want these different areas of evidence to bear on the same prehistoric events.

Too much, instead of testing hypotheses, people just line up chronologies and look for matches. A geologist may claim that African paleoclimate is important because it may explain modern human origins.'' An archaeologist may claim that a hiatus at a site is consistent withgenetic bottlenecks.’’ And the geneticist may claim that inbreeding in a modern-day genetic sample dates to a period of time corresponding to the replacement of one tool industry by another.

Any might be a valid hypothesis, but we need to take it further, to actually provide some tests. I believe we can do better now, because of the growing amount of genetic information. But we’re going to have to do away with the facile idea that we’re looking for massive bottlenecks, we need to introduce a recognition of the role of selection in human genetic variation, and we need to start addressing the archaeological record as it really exists.

That’s a forward to what follows. I’m going through regions of the world at different time intervals, to discuss what we know about population size from the archaeological record.

Next: No Late Pleistocene bottleneck in southern Africa