Clusters where they "shouldn't be"....

Gene ExpressionBy Razib KhanFeb 14, 2012 10:25 AM


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Uyghur girls

A few people have pointed me to the paper, Implications for health and disease in the genetic signature of the Ashkenazi Jewish population

. You should check it out if you don't have academic access to papers, it's not gated. Rather, I want to focus on a methodological issue. In the genetics reader survey

only 20 percent of you agreed that you understood how to read an ADMIXTURE plot. After looking at some of the results in this paper I have a lot of sympathy. Understanding what's going on requires more prior information than is often present in the legends of the figures. It is known that to a first approximation Ashkenazi Jews, that is, the Jews of Europe, can be understood as an admixture between a European population and a Middle Eastern one. But Ashkenazi Jews also exhibit their own genetic distinctiveness, probably due to long term endogamy. This shows up in various genetic statistics. In this paper the authors show that Ashkenazi form their own cluster in both PCA and ADMIXTURE, two ways in which to ascertain population structure. Below I've reedited and highlighted some populations of note in one of their ADMIXTURE plots. It's rather informative of the bigger problem with interpreting these sorts of results in the absence of context.

As you can see there is an ancestral element which is predominant in the Ashkenazi. A individual analysis also implies that most of those with a lower fraction of this element who identify as Ashkenazi probably have recent admixture (e.g., only three out of four grandparents were Jewish). What I found striking is that the Uyghur and Hazara both also shook out as of a particular ancestral element. The reality is that we know this is a total artifact of the ADMIXTURE software; the Hazara have a historical narrative of being the product of intermarriage between Mongols and Persians. The historical evidence for the origin of the Uyghur is sketchier and more confused, but it can be reconstructed. And the genetics make it likely that both these groups emerged over the past 2,000 years, as an admixture between a Western and Eastern Eurasian set of populations. What does this have to do with Ashkenazi Jews? I think one should be skeptical of an "Ashkenazi Jewish" modal element when we already know that this plot has useless clusters. It does not seem like they included any "real" East Asian reference populations, so the Hazara and Uyghur stepped up and took that position, despite both populations having ~50 percent West Eurasian admixture. The ADMIXTURE software transformed a clearly hybridized population into its own 'ancestral' population. Something similar might be happening with the Jews, especially in light of the fact that the authors had a relatively large Jewish population their data, geared to exploring the nature of Jewish genetic relationships. This is a case where we know that we probably don't know that much. The moral: don't think you can read a scientific figure plainly without any context.

Image credit: Wikipedia

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