Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia

Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populat...

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Bibliographic Details
Published in:PloS one 2020-02, Vol.15 (2), p.e0228778-e0228778
Main Authors: Khrunin, Andrey V, Khvorykh, Gennady V, Fedorov, Alexei N, Limborska, Svetlana A
Format: Article
Language:English
Subjects:
Adaptation
Addictions
Alcoholism
Biology and Life Sciences
Cell interactions
Chromosome 11
Chromosome 4
Chromosomes
Climate
Coding
Comparative analysis
DNA microarrays
Drug addiction
Environmental conditions
Environmental quality
Evolution (Biology)
Evolution, Molecular
Gene Frequency
Gene loci
Gene sequencing
Genes
Genetic aspects
Genetic diversity
Genetic variance
Genetics, Population
Genome, Human - genetics
Genomes
Genomics
Haplotypes
Homeobox
Humans
Loci
Minorities
Natural selection
Non-coding RNA
Novels
People and Places
Polymorphism, Single Nucleotide
Population
Population genetics
Populations
Positive selection
Research and Analysis Methods
Russia
Selection, Genetic
Single-nucleotide polymorphism
Target recognition
Time
Transcription (Genetics)
Vitamin D
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Summary:Natural selection of beneficial genetic variants played a critical role in human adaptation to a wide range of environmental conditions. Northern Eurasia, despite its severe climate, is home to lots of ethnically diverse populations. The genetic variants associated with the survival of these populations have hardly been analyzed. We searched for the genomic signatures of positive selection in (1) the genome-wide microarray data of 432 people from eight different northern Russian populations and (2) the whole-genome sequences of 250 people from Northern Eurasia from a public repository through testing the extended haplotype homozigosity (EHH) and direct comparison of allele frequency, respectively. The 20 loci with the strongest selection signals were characterized in detail. Among the top EHH hits were the NRG3 and NBEA genes, which are involved in the development and functioning of the neural system, the PTPRM gene, which mediates cell-cell interactions and adhesion, and a region on chromosome 4 (chr4:28.7-28.9 Mb) that contained several loci affiliated with different classes of non-coding RNAs (RN7SL101P, MIR4275, MESTP3, and LINC02364). NBEA and the region on chromosome 4 were novel selection targets that were identified for the first time in Western Siberian populations. Cross-population comparisons of EHH profiles suggested a particular role for the chr4:28.7-28.9 Mb region in the local adaptation of Western Siberians. The strongest selection signal identified in Siberian sequenced genomes was formed by six SNPs on chromosome 11 (chr11:124.9-125.2 Mb). This region included well-known genes SLC37A2 and PKNOX2. SLC37A2 is most-highly expressed in the gut. Its expression is regulated by vitamin D, which is often deficient in northern regions. The PKNOX2 gene is a transcription factor of the homeobox family that is expressed in the brain and many other tissues. This gene is associated with alcohol addiction, which is widespread in many Northern Eurasian populations.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0228778