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Tracing the spread of agriculture with stone-age human DNA

This week's paper is "Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe" by M.L. Sampietro and others, published online in Proceedings of the Royal Society. The paper is interesting both for its findings and for its methods.

We know that agriculture spread from the Near East -- do people in Asia call this the Near West? -- to western Europe, starting around 10,000 years ago. But did this mostly involve farmers moving, or the spread of agriculture without major movement of people?

People have tried to figure out past population movements using genetic differences among modern populations, but it would help to have genetic information from people who lived thousands of years ago, as well. This is technically challenging, however...

It is possible to extract DNA from bones thousands of years old, but to get enough DNA to analyze (i.e., to determine its sequence), it needs to be amplified, using the polymerase chain reaction. PCR uses several enzymes that respond differently to temperature, and cycles through different temperatures, doubling the number of copies of DNA fragments containing the primer sequences, with each cycle. Most labs use a programmable "thermal cycler", but it can be done manually, using three different-temperature water baths.

Want to know if there are any bacteria that can oxidize ammonia to nitrate, in your soil sample? (You might, because nitrate is much more likely to leach into groundwater than ammonium is.) Use PCR with primers common to all ammonium-oxidizing bacteria. Want to know how many there are per gram of soil? Use quantitative PCR. Remember the old joke about counting cows by counting the number of legs and dividing by four? With quantitative PCR, you can count the number of copies of a gene, then divide by the number of copies of that gene per bacterial cell.

The problem, of course, is that PCR will amplify any DNA that contains a near-match to the target sequence. In particular, this includes DNA in skin cells of anyone who handled the 5000-year-old bones, as well as any contamination during sample preparation for PCR. (The problem of contamination is a concern for forensic uses as well. "If you aren't guilty, Detective, why was your DNA at the scene of the crime?")

It helps somewhat to use genes that were abundant in the original sample. This study, like other similar studies, analyzed DNA from mitochondria, distant descendants of bacteria, which are central to energy metabolism and present in multiple copies per cell. But even so, contamination was a serious concern.

An unusual strength of this study was that they had access to all six people who were known to have handled the bones and extracted the DNA samples, from the time the bones were dug up to when the PCR was run. So they could detect and correct for the 17% of DNA sequences in the samples that resulted from accidental contamination by these people. (In the future, maybe only Australian aborigines should be be allowed to work on archaeological digs in Europe, and vice versa. Or I guess they could wear gloves.)

There were still a number of complications, which experts in the field are probably discussing. But the data seem to show that the people who live in the Iberian Peninsula today are closely related to those who lived there 5000 years ago. This contrasts with a recent comparison showing that Stone Age people in Northern Europe were different from those who live there now. And the Stone Age people in Iberia were quite different from those in Northern Europe. At least the women were; mitochondria are inherited only from mothers.

Combining the genetic data with archaeological information on pottery etc. -- using multiple lines of evidence is always a good idea -- the authors concluded that migration of large numbers of people was probably important to the spread of agriculture through southern Europe, but it might have been introduced into northern Europe by only a few travelers.

I don't know enough to have an opinion about these conclusions, but I think it's cool that we can study the genetics of people who have been dead for thousands of years!

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