The Pith: You’re Asian. Yes, you!
A conclusion to an important paper, Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich:
In particular, we have presented evidence suggesting that the genetic history of Europe from around 5000 B.C. includes:
1. The arrival of Neolithic farmers probably from the Middle East.
2. Nearly complete replacement of the indigenous Mesolithic southern European populations by Neolithic migrants, and admixture between the Neolithic farmers and the indigenous Europeans in the north.
3. Substantial population movement into Spain occurring around the same time as the archaeologically attested Bell-Beaker phenomenon (HARRISON, 1980).
4. Subsequent mating between peoples of neighboring regions, resulting in isolation-by-distance (LAO et al., 2008; NOVEMBRE et al., 2008). This tended to smooth out population structure that existed 4,000 years ago.
Further, the populations of Sardinia and the Basque country today have been substantially less influenced by these events.
It’s in Genetics, Ancient Admixture in Human History. Reading through it I can see why it wasn’t published in Nature or Science: methods are of the essence. The authors review five population genetic statistics of phylogenetic and evolutionary genetic import, before moving onto the novel results. These statistics, which measure the possibility of admixture, the extent of admixture, and the date of admixture, are often presented, but nested into supplements, in previous papers by the same group. On the one hand this removes from view the engines which are driving the science. On the other hand I have always appreciated that a benefit of this injustice to the methods which make insight possible is that those without academic access can actually bite into the meat of the researcher’s mode of thought.
I did read through the methods. Twice. I’ve encountered all the statistics before, and I’ve read how they were generated, but I’ll be honest and admit that I haven’t internalized them. That has to end now, because the authors have finally released a software package which implements the statistics, ADMIXTOOLS. I plan to use it in the near future, and it is generally best if you understand the underlying mechanisms of a software package if you are at the bleeding end of analytics. I will review the technical points in more detail in future posts, more for my own edification than yours. But for the moment I’ll be a bit more cursory. Four of the tests use comparisons of allele frequencies along explicit phylogenetic trees. That’s so general as to be uninformative as a description, but I think it’s accurate to the best of my knowledge. In the basics the tests are seeing if a model fits the data (as opposed to TreeMix, which finds the best model out of a range to fit the data). The last method, rolloff, infers the timing of an admixture event based upon the decay of linkage disequilibrium. In short, admixture between two very distinct populations has the concrete result of producing striking genomic correlations. Over time these correlations dissipate due to recombination. The magnitude of dissipation can allow one to gauge the time in the past when the original admixture occurred.