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Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan
Open accessAbstract
Background: The Kazakhs are one of the biggest Turkic-speaking ethnic groups, controlling vast swaths of land from the Altai to the Caspian Sea. In terms of area, Kazakhstan is ranked ninth in the world. Northern, Eastern, and Western Kazakhstan have already been studied in relation to genetic polymorphism 27 Y-STR. However, current information on the genetic polymorphism of the Y-chromosome of Southern Kazakhstan is limited only by 17 Y-STR and no geographical study of other regions has been studied at this variation. Results: The Kazakhstan Y-chromosome Haplotype Reference Database was expanded with 468 Kazakh males from the Zhambyl and Turkestan regions of South Kazakhstan by having their 27 Y-STR loci and 23 Y-SNP markers analyzed. Discrimination capacity (DC = 91.23%), haplotype match probability (HPM = 0.0029) and haplotype diversity (HD = 0.9992) are defined. Most of this Y-chromosome variability is attributed to haplogroups C2a1a1b1-F1756 (2.1%), C2a1a2-M48 (7.3%), C2a1a3-F1918 (33.3%) and C2b1a1a1a-M407 (6%). Median-joining network analysis was applied to understand the relationship between the haplotypes of the three regions. In three genetic layer can be described the position of the populations of the Southern region of Kazakhstan—the geographic Kazakh populations of Kazakhstan, the Kazakh tribal groups, and the people of bordering Asia. Conclusion: The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan. The variability of the Y-chromosome of the Kazakhs in a geographical context can be divided into four main clusters—south, north, east, west. At the same time, in the genetic space of tribal groups, the population of southern Kazakhs clusters with tribes from the same region, and genetic proximity is determined with the populations of the Hazaras of Afghanistan and the Mongols of China.
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TL;DR
This study expands the Kazakhstan Y-chromosome haplotype reference database with 468 Kazakh males from Southern Kazakhstan, analyzing 27 Y-STR loci and 23 Y-SNP markers. It reports high haplotype diversity and regional/tribal genetic structure, with Southern Kazakhs clustering geographically and showing proximity to Hazaras of Afghanistan and Mongols of China.
Key findings
- Among 468 Southern Kazakh males, 427 distinct 27 Y-STR haplotypes were found; forensic parameters were discrimination capacity 91.23%, haplotype match probability 0.0029, and haplotype diversity 0.9992.
- The major Y-chromosome haplogroups were C2-M217 (48.7%), J1 (8.8%), R1a1a (6.4%), J2 (6%), N1a (5.8%), and G (5.6%); within C2, C2a1a3-F1918 was most common at 33.3%, followed by C2a1a2-M48 at 7.3%, C2b1a1a1a-M407 at 6%, and C2a1a1b1-F1756 at 2.1%.
- The Kazakhstan Y-chromosome Haplotype Reference Database was expanded to 1796 samples from 16 regions of Kazakhstan; geographic Y-chromosome variability was divided into four main clusters—south, north, east, and west.
- Median-joining network analysis identified C2a1a3-F1918 as the largest cluster, including 156 haplotypes, with high haplotype diversity in the Zhambyl region; Southern Kazakhs showed genetic proximity to Hazaras of Afghanistan and Mongols of China.
Methods
- The study analyzed 468 unrelated male Kazakh volunteers whose ancestors had resided in South Kazakhstan for at least three generations, sampled from the Almaty (N = 80), Zhambyl (N = 253), and Turkestan (N = 135) regions.
- DNA was extracted and quantified, then 27 Y-STR loci were typed by capillary electrophoresis; haplogroups were predicted with Nevgen and genotyped for 23 Y-SNP markers using TaqMan assays.
- Analyses included haplotype frequency and forensic parameter calculations in Arlequin and STRAF, pairwise genetic distances and MDS via YHRD, and median-joining networks in NETWORK.
Limitations
- The paper has no explicit limitations section.
- The text states that tribal-level comparison samples with known affiliations across 20 tribes were limited to 17 Y-STR sites, which are less informative than the 27 Y-STR loci used for the new Southern Kazakh samples.
- The background notes that prior information on Southern Kazakhstan Y-chromosome polymorphism was limited to 17 Y-STR and lacked geographical study at the 27 Y-STR variation.
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In the paper
“On average, the gene diversity of rapidly mutating 8 single-copy loci (GD = 0.728) is higher than that of the standard 15 single-copy loci (GD = 0.571).”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Results and discussion > Haplotype/allele frequencies and forensic parameters
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan.”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Abstract > Conclusion
plainn = 1,796- Asserted: passes — The authors put it forward as true.
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In the paper
“Figure 9 visualizes the strong founder effect of this cluster, which includes 156 haplotypes and shows that derived haplotypes from the founder haplotype are mainly represented by individuals from the Zhambyl region.”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Results and discussion > Median-joining network for Southern Kazakhs
boostedstates an association- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Figure 9 visualizes the strong founder effect of this cluster, which includes 156 haplotypes and shows that derived haplotypes from the founder haplotype are mainly represented by individuals from the Zhambyl region.”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Results and discussion > Median-joining network for Southern Kazakhs
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There are no differences in terms of population between Kazakhs living in Kazakhstan’s southern area and those living in Kazakhstan generally.”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Results and discussion > Population comparison analysis
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In the paper
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Methods > Sample collection
“In three regions of southern Kazakhstan, blood samples were taken from 468 Kazakh men.”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Methods > DNA extraction and quantification
“DNA was extracted from saliva samples of participants using the Wizard(R) Genomic DNA Purification Kit (Promega, USA).”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Methods > Data analysis
“the haplotype and haplogroup data in the present study (N = 184) have been submitted to the YHRD”
§ Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan > Results and discussion > Haplotype/allele frequencies and forensic parameters
“27 Y-STR haplotype distribution in the Kazakh population of the Southern region of Kazakhstan (N = 468) are presented in Additional file 1.”
Citations
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The Genetic Legacy of the Mongols
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A recent bottleneck of Y chromosome diversity coincides with a global change in culture
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Cited by
Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Central Kazakhstan
Ashirbekov, Y., Zhunussova, A., Abaildayev, A., Mailenova, A., Sabitov, Z. M., & Zhabagin, M. K. (2024) · Annals of Human Biology · doi:10.1080/03014460.2024.2377571 · Cited by 6
Self-citationGenomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire
Askapuli, A., Kanzawa-Kiriyama, H., Kakuda, T., Kassenali, A., Yessen, S., Schamiloglu, U., Schrodi, S. J., Hawks, J., & Saitou, N. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2531003123 · Cited by 5
Zhabagin, M., Bukayev, A., Dyussenova, Z., Zhuraliyeva, A., Tashkarayeva, A., Zhunussova, A., Aidarov, B., Darmenov, A., Akilzhanova, A., Schamiloglu, U., et al. (2024) · PLOS ONE · doi:10.1371/journal.pone.0309080 · Cited by 5
Self-citationA Review of Genetic Diversity Based on the Y Chromosome in the Romanian Population
Hodișan, R., Zaha, D. C., Jurcă, M. C., Petcheși, C. D., & Bembea, M. (2024) · Cureus · doi:10.7759/cureus.67593 · Cited by 1
Artifacts of analysis in cell line identification by short tandem repeat profiling
Malchenkova, A. A., & Kosobokova, E. N. (2024) · CARDIOVASCULAR THERAPY AND PREVENTION · doi:10.15829/1728-8800-2024-4121 · Cited by 1
Metadata
- Authors
- Ashirbekov, Y., Seidualy, M., Abaildayev, A., Maxutova, A., Zhunussova, A., Akilzhanova, A., Sharipov, K., Sabitov, Z., & Zhabagin, M.
- Affiliations
- National Center for Biotechnology (KZ)
- Astana International University (KZ)
- L. N. Gumilyov Eurasian National University (KZ)
- Corresponding author
- Zhabagin, Maxat
- ORCID
- Venue
- BMC Genomics
- Published
- 2023-10-27
- Volume
- 24
- Issue
- 1
- Pages
- 649-649
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC10612363
- OpenAlex
- W4387971097
- Semantic Scholar
- f09596c02d052886ce39a02cc84ac6863313aa69
- Cited by
- 12
- References
- 39
- Citations by year
- 2026: 7 · 2025: 1 · 2024: 4
- FWCI
- 1.46
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Nazarbayev University Repository (Nazarbayev University) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Science Committee of the Ministry of Science and Higer Education of the Republic of Kazakhstan (AP09259560, BR18574101)
- Collaborative Research Program of Nazarbayev University (091019CRP2119)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Y chromosome, Kazakhs, Y-chromosome short tandem repeats, Y-SNPs, haplogroups, discrimination capacity, median-joining network, population structure, southern Kazakhstan, Zhambyl region, Turkestan region, tribal population, Hazara, Mongols
- MeSH terms
- Genetics, Population, Haplotypes, Humans, Kazakhstan, Male, Polymorphism, Genetic, Genetic Variation, Microsatellite Repeats, Chromosomes, Human, Y
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