Admixture in the Chuvash and the Uygur

I took the Behar et al. (2010) sample of Chuvash, excluding GSM536731 which has atypical ancestry and merged it with the Li et al. HGDP French_Basque and Dai. The latter two populations don't show evidence of admixture according to both the f3-statistic and ALDER (Loh et al. 2012). (I used a --geno 0.03 flag in PLINK and extracted a subset of SNPs including in the Rutgers recombination map for Illumina chips).

The f3-statistic f3(Chuvashs_16; French_Basque, Dai) was equal to -0.011311 (Z=-31.308), indicative of admixture.

I then ran an ALDER analysis:


Test SUCCEEDS (z=4.85, p=1.2e-06) for Chuvashs_16 with {French_Basque, Dai} weights

DATA: success (warning: decay rates inconsistent) 1.2e-06 Chuvashs_16 French_Basque Dai 4.85 3.78 5.18 50% 40.27 +/- 5.80 0.00032377 +/- 0.00006676 28.21 +/- 7.47 0.00004231 +/- 0.00000962 47.08 +/- 4.53 0.00016628 +/- 0.00003212

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B

This indicates that the Chuvash can be seen as admixed, but with inconsistent decays: the one with the French Basque (=28.21) is younger than the one with the Dai (=47.08). I think this makes fairly good sense, because the Chuvash are descended from people who came to Europe during the 1st millennium AD and must have later mixed with Europeans, perhaps with eastern Slavs as these made their way eastward during the 2nd millennium AD.

I then carried out similar analyses on the HGDP Uygur. As expected f3(Uygur; French_Basque, Dai) = -0.023917 (Z = -60.362), indicative of admixture. The ALDER analysis:


Test SUCCEEDS (z=6.85, p=7.4e-12) for Uygur with {French_Basque, Dai} weights

DATA: success 7.4e-12 Uygur French_Basque Dai 6.85 4.47 7.39 15% 20.56 +/- 3.00 0.00036760 +/- 0.00003660 22.59 +/- 5.06 0.00010920 +/- 0.00002025 19.46 +/- 2.64 0.00007864 +/- 0.00000710

DATA: test status p-value test pop ref A ref B 2-ref z-score 1-ref z-score A 1-ref z-score B max decay diff % 2-ref decay 2-ref amp_exp 1-ref decay A 1-ref amp_exp A 1-ref decay B 1-ref amp_exp B

suggests a very recent admixture on both the European and East Asian side. It seems fairly clear that whatever admixture was taking place in Central Asia, perhaps for thousands of years, the present-day Ugyur were formed, at least in part, by a fairly recent, perhaps post-Mongol admixture event.