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other·genetics, population genetics, evolutionary biology, medical genetics·PMC10009479

Blocks identical by descent in the genomes of the indigenous population of Siberia demonstrate genetic links between populations

Vavilov Journal of Genetics and Breeding · 5 authors, 5 centres

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TL;DR

This study analyzed genome-wide SNP data from 477 individuals across 20 indigenous Siberian populations to identify DNA segments identical by descent (IBD). The distribution of IBD blocks clustered populations by geographic proximity rather than linguistic affiliation, with Chukchi, Koryaks, and Nivkhs forming a distinct cluster. The findings reveal recent genetic history, including bottlenecks, isolation, and inbreeding patterns, and identify 5,358 genes enriched in IBD regions, many linked to fatty acid metabolism and olfactory transduction, suggesting possible adaptation to cold climates and dietary habits.

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**Background:** The indigenous populations of Siberia represent a unique system for studying population genetics due to their high ethnic diversity, vast geographic distribution, and small population sizes. Genetic and demographic processes such as population fluctuations, migrations, and natural selection leave signatures in the genome in the form of linkage blocks identical by descent (IBD) — DNA segments inherited without recombination from a common ancestor. IBD analysis can reveal demographic history, including bottlenecks and gene flow, and can help detect recent natural selection. This study aimed to analyze the structure of the gene pool of Siberian indigenous populations by identifying IBD blocks and examining their intra- and interpopulation distribution.

**Methods:** Genome-wide genotyping was performed using Infinium Multi-Ethnic Global-8 microarrays (Illumina) with over 1.7 million markers. After quality filtering (samples with >5% missing positions, SNPs with >10% missing genotypes, and MAF <0.01 excluded), 886,889 autosomal SNPs were retained. The study included 477 individuals from 20 populations: Altaians (two groups, N=24 and N=25), Buryats (two groups, N=23 and N=28), Kalmyks (N=29), Kets (N=15), Koryaks (N=20), Chukchi (N=25), Nivkhs (N=13), Tatars (Tomsk, N=20), Tuvans (N=28), Udeges (N=15), Khanty (two groups, N=30 and N=26), Khakas (two groups, N=29 and N=26), Chulyms (N=22), Evenks (two groups, N=25 and N=28), and Yakuts (N=26). Genotypes were phased using Beagle 4.1, and IBD segments were detected using the Refined IBD algorithm (refined-ibd.16May19.ad5.jar). Sums of average IBD segment lengths between pairs of individuals were calculated for length ranges: 1.5–2 cM, 2–4 cM, 4–8 cM, 8–16 cM, and >16 cM. A heat map with dendrogram was built using the logarithm of the sum of average IBD lengths. SNPs falling into IBD segments at a frequency above the 99th quantile were identified, mapped to genes, and analyzed for biological significance using WebGestalt (KEGG pathways and Gene Ontology over-representation analysis with Benjamini–Hochberg correction, FDR=0.05).

**Key Results:** The heat map and clustering analysis showed that Siberian populations cluster primarily by geographic proximity. Chukchi, Koryaks, and Nivkhs formed a separate cluster from the main Siberian group, with Chukchi and Koryaks being most closely related. Within the Siberian cluster, subclusters of Evenks and Yakuts, Kets and Chulyms, and Tuvans and Altaians were observed. For longer IBD segments (>8 cM), clusters aligned more closely with current geographic locations, reflecting recent admixture. For example, Yakut Evenks shared more IBD with Yakuts (252.7 cM total) than with Transbaikal Evenks (102.5 cM). Kets shared IBD blocks with Chulyms (18.7–27.2–7.7 cM across three length ranges) and Khanty (23.4–24.4–4.8 cM for Khanty (K); 25.9–30.1–7.9 cM for Khanty (R)). Intrapopulation analysis revealed that Far North and Far East populations (Koryaks, Chukchi, Nivkhs) shared more IBD within their groups than South Siberian populations (Altaians, Tuvans). In Chukchi, Koryaks, and Nivkhs, short IBD fragments of 1.5–4 cM made the largest contribution (55–59%), suggesting past bottlenecks or isolation. In Chulyms and Khanty (R), IBDs longer than 8 cM contributed 47–51%, indicating recent inbreeding. Buryats (K) had a significantly larger average total IBD length within the population (335.4 cM) compared to Buryats (A) (163.5 cM), with differences attributed to population history. A total of 189,314 SNPs falling into the highest frequency of IBD segments (above the 99th quantile) were identified, of which 88,530 were intergenic and the remainder mapped to 5,358 genes. KEGG pathway analysis (FDR=0.05) revealed enrichment in: linoleic acid metabolism (hsa00591, FDR=0.0051, 17 genes), arachidonic acid metabolism (hsa00590, FDR=0.0240, 27 genes), tyrosine metabolism (hsa00350, FDR=0.0240, 18 genes), and olfactory transduction (hsa04740, FDR=4.55E-08, 159 genes). Gene Ontology analysis identified nine statistically significant biological processes all related to sensory perception of smell. Literature analysis highlighted several genes (e.g., AAGAB, GSE1, IQCH-AS1, SMAD3, IQCH, CHRNA4, COL20A1) that may play roles in cancer, adaptation, or neurobiology.

**Clinical Implications:** This study provides foundational population genetic data for indigenous Siberian groups, which is important for understanding human genetic diversity and demographic history. The identification of genes under recent selection related to fatty acid metabolism (linoleic and arachidonic acid pathways) may have implications for understanding metabolic adaptation to cold climates and dietary patterns. The enrichment of olfactory transduction genes suggests possible social or environmental selective pressures. Several genes identified in IBD blocks (e.g., AAGAB, GSE1, IQCH-AS1) are implicated in cancer biology and treatment response, though their roles require further study. These findings may inform future research on population-specific disease susceptibilities and pharmacogenomics, though direct clinical applications are not yet established.

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other

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genetics

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ORIGINAL PAPER

PMC10009479

Blocks identical by descent in the genomes of the indigenous population of Siberia demonstrate genetic links between populations

Vavilov Journal of Genetics and Breeding

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ABSTRACT

The gene pool of the indigenous population of Siberia is a unique system for studying population and evolutionary genetic processes, analyzing genetic diversity, and reconstructing the genetic history of populations. High ethnic diversity is a feature of Siberia, as one of the regions of the peripheral settlement of modern human. The vast expanses of this region and the small number of aboriginal populations contributed to the formation of significant territorial and genetic subdivision. About 40 indigenous peoples are settled on the territory of the Siberian historical and ethnographic province. Within the framework of this work, a large-scale population study of the gene pool of the indigenous peoples of Siberia was carried out for the first time at the level of high-density biochips. This makes it possible to fill in a significant gap in the genogeographic picture of the Eurasian population. For this, DNA fragments were analyzed, which had been inherited without recombination by each pair of individuals from their recent common ancestor, that is, segments (blocks) identical by descent (IBD). The distribution of IBD blocks in the populations of Siberia is in good agreement with the geographical proximity of the populations and their linguistic affiliation. Among the Siberian populations, the Chukchi, Koryaks, and Nivkhs form a separate cluster from the main Siberian group, with the Chukchi and Koryaks being more closely related. Separate subclusters of Evenks and Yakuts, Kets and Chulyms are formed within the Siberian cluster. Analysis of SNPs that fell into more IBD segments of the analyzed populations made it possible to compile a list of 5358 genes. According to the calculation results, biological processes enriched with these genes are associated with the detection of a chemical stimulus involved in the sensory perception of smell. Enriched for the genes found, molecular pathways are associated with the metabolism of linoleic, arachidonic, tyrosic acids and by olfactory transduction. At the same time, an analysis of the literature data showed that some of the selected genes, which were found in a larger number of IBD blocks in several populations at once, can play a role in genetic adaptation to environmental factors.

CITATION EXPORT

N.A. Kolesnikov, V.N. Kharkov, K.V. Vagaitseva et al.. Blocks identical by descent in the genomes
of the indigenous population of Siberia
demonstrate genetic links between populations. Vavilov Journal of Genetics and Breeding. (2023). https://doi.org/10.18699/VJGB-23-08

AUTHORS

5 · 5 CENTRES

N.A. Kolesnikov, V.N. Kharkov, K.V. Vagaitseva, A.A. Zarubin, V.A. Stepanov

Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia