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. 2020 May;139(5):557-568.
doi: 10.1007/s00439-020-02132-8. Epub 2020 Feb 19.

Decoding a highly mixed Kazakh genome

Madina Seidualy  1 , Asta Blazyte  1 , Sungwon Jeon  1   2 , Youngjune Bhak  1   2 , Yeonsu Jeon  1   2 , Jungeun Kim  3 , Anders Eriksson  4   5 , Dan Bolser  6 , Changhan Yoon  1   2 , Andrea Manica  7 , Semin Lee  1   2 , Jong Bhak  8   9   10   11
Affiliations

Decoding a highly mixed Kazakh genome

Madina Seidualy et al. Hum Genet. 2020 May.

Abstract

We provide a Kazakh whole genome sequence (MJS) and analyses with the largest comparative Kazakh genomic data available to date. We found 102,240 novel SNVs and a high level of heterozygosity. ADMIXTURE analysis confirmed a significant proportion of variations in this individual coming from all continents except Africa and Oceania. A principal component analysis showed neighboring Kalmyk, Uzbek, and Kyrgyz populations to have the strongest resemblance to the MJS genome which reflects fairly recent Kazakh history. MJS's mitochondrial haplogroup, J1c2, probably represents an early European and Near Eastern influence to Central Asia. This was also supported by the heterozygous SNPs associated with European phenotypic features and strikingly similar Kazakh ancestral composition inferred by ADMIXTURE. Admixture (f3) analysis showed that MJS's genomic signature is best described as a cross between the Neolithic East Asian (Devil's Gate1) and the Bronze Age European (Halberstadt_LBA1) components rather than a contemporary admixture.

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Conflict of interest statement

The authors declare they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Classification of short variants found in the MJS genome
Fig. 2
Fig. 2
ADMIXTURE plot showing the MJS genome originating from multiple different artificial ancestral populations. Each modern population is represented by genomes which are depicted as colored bars. Each color indicates a different ancestral group and proportion of possibly shared ancestry within larger subgroups.
Fig. 3
Fig. 3
Plot of the first two principal components with the modern Eurasian populations. Dots represent genomes color-coded by the continental groups: Europe (EUR)—dark green, West Asia (WA)—light green, Central Asia (CA)—blue, North Asia (NA)—peach, South Asia (SA)—grey, Southeast Asia (SEA) and East Asia (EA)—brown, and America (AM)—yellow, Oceania (OC)—coral, serving as outgroups. Separate populations are visualized as different shades and the MJS sample is visualized as a purple dot
Fig. 4
Fig. 4
The Admixture f3 analysis representing MJS genome as a mixture of genomes A and B. The genomes are color-coded by regions; yellow representing ancient genomes found in Europe, red—ancient genomes from Northeast Asia and indigenous (present-day) genomes from Russian Far East, blue—present-day East Asian populations, and green—present-day West Asian populations. Thirty pairs with the lowest f3 score for the Kazakh (MJS) are presented
See this image and copyright information in PMC

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