Believe it or not, samples occasionally get mixed up in studies. Zack A. of Harappa recently listed good examples of such cases in the Behar et al. dataset (see Behar Paniya). I believe I found a similar problem in the Rasmussen et al. collection, with at least two fully European Russians being passed off as native Siberians. The samples are Koryak GSM558848 and Chukchi GSM558866. Based on detailed analyses of this pair, I suspect that the first is of Western Russian origin, and the second from a different part of Russia, possibly further north. For instance, let's take a look at some Identical by State (IBS) Z scores, based on 238K SNPs, starting with the Koryak:
vs. Rasmussen Koryaks
Koryak GSM558852 -2.312
Koryak GSM558854 -3.164
Koryak GSM558845 -3.211
Koryak GSM558850 -3.281
Koryak GSM558849 -3.291
vs. Eurogenes and Behar Russians
RU12 RU12 0.6699
RU GSM536913 1.001
RU GSM536914 0.6719
RU18 RU18 0.9004
RU16 RU16 1
The putative Koryak sample is matching his top five Koryaks at 2 or 3 standard deviations below the Koryak mean. What this shows is that this individual is a genetic outlier from the group, and at the very least harbors significant non-Koryak ancestry. However, the same sample is also matching Russians better than the Russians are matching each other on average (note the positive Z scores). The alleged Chukchi sample shows similar behavior.
vs. Rasmussen Chukchi
Chukchi GSM558867 -2.716
Chukchi GSM558872 -2.583
Chukchi GSM558877 -2.557
Chukchi GSM558870 -2.981
Chukchi GSM558878 -2.978
vs. Eurogenes and Behar Russians
RU15 RU15 0.5433
RU17 RU17 0.9265
RU GSM536914 0.9759
RU11 RU11 0.6654
RU GSM536913 0.394
An MDS analysis of these individuals against French, Yakut and Buryat samples shows clearly that they're not of Siberian origin. They cluster with the French.
In other experiments using ADMIXTURE, I noticed that the Koryak showed considerable "Southern Baltic" influence, which is typical of Western Russians and Belorussians. Indeed, this sample even exhibited relatively high affinity to Northwestern Europe in some comparisons. I've co-opted both of the putative Siberians into my intra-North European analysis as RU21 and RU22 respectively (see here). Anyone looking for Russian samples significantly different from the Vologda set offered by the HGDP should also consider using these two. They're a valuable addition to any project focusing on genetic diversity in Eastern and Northern Europe.
What you are showing with those Siberian samples is also evident in other ethnic group samples: the Georgian and the Armenian samples. Some of the Circassian Adygei are also anomalous.
ReplyDeleteOn my IBS 238K scores I have a Syrian in the first 10 whereas the other Syrians are a long way down the list. That Syrian is obviously less Syrian than the others.
One good thing about these Admixture runs is that outliers and closely related folks can be easily discovered.
Apparently Ponto's examples are all from the Behar et al. paper. Also, one of the Chuvash of Behar et al. seems anomalous, looking like Russians rather than the rest of Chuvash.
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