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Saturday, October 10, 2015

Eight thousand years of natural selection in Europe - take 2

Open access at bioRxiv [LINK]. Lots of new samples in this updated version. The Principal Component Analysis (PCA) below from the paper appears to be affected by projection bias or shrinkage, but it's more or less correct. Can't wait to get my hands on the genotype data.

Abstract: The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.

Mathieson et al., Eight thousand years of natural selection in Europe, bioRxiv revised preprint, posted October 10, 2015, doi:

See also...

Lactase persistence and ancient DNA


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Davidski said...

Yes, there's more ancient data on the way from the Near East and also from Central Asia.

capra internetensis said...


If you want to put pioneer Chalcolithic herders, who did not to our knowledge even occupy the whole steppe yet, in the same reference class as full-on Iron Age steppe nomad hordes, then the burden of proof is on you - I have no intention of trying to produce probability distributions based on inadequate data and highly contingent processes. You haven't proposed any mechanism at all. Furthermore, none of the steppe spreads extended beyond eastern Europe; most have left so little trace we cannot even classify their languages. Indo-European converted almost all of Europe; the Copper Age was not the Iron Age.

Your probabilistic argument compares the number of events that occurred over a long period of time in one regime, with unstable outcomes (steppe nomads in constant flux), to the number of events over a short period of time in another regime, with a stable outcome (Russian colonization of Siberia). They do not sum together.

All this is assuming the eastward spread of languages is even a legitimate rule, which hasn't really been demonstrated.

Simon_W said...

Nirjhar: „Autosomal Structure is a subject of massive change, i think we give too much credit to it... „

That's a strange way to put it. In fact, autosomal DNA is the only DNA that reliably reflects the overall ancestry of an individual. If you want to know where an individual (e.g. a Sintashta guy) draws the vast majority of his ancestors from, autosomal DNA is the thing to look at. YDNA represents just one single lineage out of hundreds and thousands of lineages of valid ancestors. What's true is that autosomal DNA and yDNA are not strictly connected, so strictly speaking the autosomal DNA of an individual cannot reliably predict his yDNA and vice versa.

The reason why many people are so obsessed with their yDNA is cultural: Patrilinearity is deeply seated in many cultures, notably the IE ones. But this exaggeration of the importance of one's yDNA has no biological basis. Even I myself do have an odd tendency to take pride in my Norse roots, having R1a-Z287, but then I tell myself that I'm much, much more Baltic Prussian than Norse, from my paternal grandmother, though even this is just a minor admixture in my ancestry...

Simon_W said...

This means that North Euro-like Sintashta people might have had their yDNA from S-C Asia forebears. But it also means that modern S Asians might well have got their yDNA from North Euro-like Sintashta folks. In principle the discrete inheritance of yDNA and autosomes allows for both possibilities. Further arguments are needed to prefer one explanation over the other, and preferably ancient DNA from S-C Asia to close the case once and forever.

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