journal article·2026-07-07Open access

Whole‐Genome Sequencing Pilot of the Central Asian Genomic Diversity Project Reveals Distinct Histories, Adaptation, and Introgression

Mengge Wang, Shuhan Duan, Qiuxia Sun, Renkuan Tang, Lintao Luo, Jie Zhong, Zhaxylyk Sabitov, CAGDP Consortium, Lan‐Hai Wei, Chao Liu, Maxat Zhabagin, Guanglin He

Abstract

ABSTRACT Central Asians are underrepresented in genomic research, limiting insights into their genetic history and disease risk. We established the Central Asian Genomic Diversity Project and sequenced whole genomes from 166 individuals across 20 Central Asian and Afghan Hazara groups. We identify marked differentiation driven by varying West/East Eurasian ancestry; Tajiks align with West Eurasians, Dungans with East Asians, and we report four geographically structured Turkic‐related clusters, two Indo‐European clines, and long‐range migration events, including Siberian links in Hazaras and Sino‐Tibetan ties in Dungans. Admixture dates cluster ∼650–1000 years ago, coinciding with the Song–Yuan era and Mongol expansion. We characterize distinct distributions of medically relevant variants and population‐specific adaptation signatures across metabolic, immune, and neurological pathways, and illuminate shifts in subsistence practices correlated with trait‐associated variation. We also detect Neanderthal‐like and Denisovan‐like segments that show group‐specific associations with immunity, psychiatric risk, drug metabolism, and diabetes, underscoring the scientific imperative for a broader characterization of Central Asian evolutionary history and informing precision medicine.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Forensic and Genetic Research · Genetic Associations and Epidemiology · Forensic Anthropology and Bioarchaeology Studies

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Department of Forensic Medicine College of Basic Medicine Chongqing Medical University Chongqing China

Institute of Rare Diseases West China Hospital of Sichuan University Sichuan University Chengdu China

Center For Archaeological Science Sichuan University Chengdu China

Western China Forensic Medicine Center College of Basic Medicine Chongqing Medical University Chongqing China

Chongqing Key Laboratory of Forensic Science & Chongqing Engineering Research Center of Criminal Investigation Technology College of Basic Medicine Chongqing Medical University Chongqing China

Research Institute for Jochi Ulus Studies Astana Kazakhstan

Kazakh Historical Society Astana Kazakhstan

School of Ethnology and Anthropology Inner Mongolia Normal University Hohhot China

State Key Laboratory of Bioactive Molecules and Druggability Assessment Guangdong Basic Research Center of Excellence for Natural Bioactive Molecules and Discovery of Innovative Drugs Jinan University Guangzhou China

National Center for Biotechnology Astana Republic of Kazakhstan

Nazarbayev University Astana Republic of Kazakhstan

Funding

National Natural Science Foundation of China · West China Hospital, Sichuan University

References (100+)

Show source-provided references
1. 10.1093/molbev/msac17910.1093/molbev/msac179 ↗
2. 10.1126/sciadv.abe441410.1126/sciadv.abe4414 ↗
3. 10.1126/science.aat748710.1126/science.aat7487 ↗
4. 10.1038/s41559‐019‐0878‐210.1038/s41559‐019‐0878‐2 ↗
5. 10.1126/science.aar771110.1126/science.aar7711 ↗
6. 10.1038/s41586‐018‐0094‐210.1038/s41586‐018‐0094‐2 ↗
7. 10.1093/molbev/msab21610.1093/molbev/msab216 ↗
8. 10.1093/molbev/msaf22510.1093/molbev/msaf225 ↗
9. 10.1016/j.cell.2020.10.01510.1016/j.cell.2020.10.015 ↗
10. 10.1371/journal.pgen.100506810.1371/journal.pgen.1005068 ↗
11. 10.1126/science.115371710.1126/science.1153717 ↗
12. 10.1038/s41586‐018‐0579‐z10.1038/s41586‐018‐0579‐z ↗
13. 10.1038/nature1896410.1038/nature18964 ↗
14. 10.1038/s41576‐020‐0275‐310.1038/s41576‐020‐0275‐3 ↗
15. 10.1016/j.cell.2019.10.00410.1016/j.cell.2019.10.004 ↗
16. 10.1016/j.cell.2019.09.01910.1016/j.cell.2019.09.019 ↗
17. 10.1038/s41586‐019‐1793‐z10.1038/s41586‐019‐1793‐z ↗
18. 10.1126/science.aay501210.1126/science.aay5012 ↗
19. 10.1126/science.abj698710.1126/science.abj6987 ↗
20. 10.1007/s11427‐024‐2748‐410.1007/s11427‐024‐2748‐4 ↗
21. 10.1016/j.hlife.2024.04.00510.1016/j.hlife.2024.04.005 ↗
22. 10.1007/s11427‐024‐2736‐710.1007/s11427‐024‐2736‐7 ↗
23. 10.1038/s41591‐021‐01672‐410.1038/s41591‐021‐01672‐4 ↗
24. 10.1016/j.hlife.2024.06.00610.1016/j.hlife.2024.06.006 ↗
25. 10.59717/j.xinn‐life.2025.10013110.59717/j.xinn‐life.2025.100131 ↗
26. 10.1146/annurev‐biodatasci‐122220‐11255010.1146/annurev‐biodatasci‐122220‐112550 ↗
27. 10.1016/j.cell.2019.02.04810.1016/j.cell.2019.02.048 ↗
28. 10.1038/s41586‐025‐09272‐910.1038/s41586‐025‐09272‐9 ↗
29. 10.1038/s41586‐021‐03205‐y10.1038/s41586‐021‐03205‐y ↗
30. 10.1038/s41586‐020‐2859‐710.1038/s41586‐020‐2859‐7 ↗
31. 10.1126/science.adk508110.1126/science.adk5081 ↗
32. 10.1038/s41586‐023‐06560‐010.1038/s41586‐023‐06560‐0 ↗
33. 10.1126/sciadv.adi841910.1126/sciadv.adi8419 ↗
34. 10.1016/j.xgen.2023.10036110.1016/j.xgen.2023.100361 ↗
35. 10.1093/gpbjnl/qzaf04910.1093/gpbjnl/qzaf049 ↗
36. 10.1126/sciadv.adu793510.1126/sciadv.adu7935 ↗
37. 10.1126/sciadv.ady159710.1126/sciadv.ady1597 ↗
38. 10.1002/advs.20251593010.1002/advs.202515930 ↗
39. 10.1038/s41467‐022‐30526‐x10.1038/s41467‐022‐30526‐x ↗
40. 10.1016/j.celrep.2021.11001710.1016/j.celrep.2021.110017 ↗
41. 10.1038/s41422‐020‐0322‐910.1038/s41422‐020‐0322‐9 ↗
42. 10.1093/molbev/msaf25810.1093/molbev/msaf258 ↗
43. 10.1111/jse.1293810.1111/jse.12938 ↗
44. 10.1038/ejhg.2010.15310.1038/ejhg.2010.153 ↗
45. 10.1126/science.124351810.1126/science.1243518 ↗
46. 10.1093/molbev/msx17710.1093/molbev/msx177 ↗
47. 10.1093/molbev/msaf22510.1093/molbev/msaf225 ↗
48. 10.1186/s13059‐025‐03859‐110.1186/s13059‐025‐03859‐1 ↗
49. 10.1186/s13059‐023‐02912‐110.1186/s13059‐023‐02912‐1 ↗
50. 10.1038/s41597‐024‐03031‐710.1038/s41597‐024‐03031‐7 ↗
51. 10.1093/nsr/nwab12410.1093/nsr/nwab124 ↗
52. 10.1093/nsr/nwad07710.1093/nsr/nwad077 ↗
53. 10.1038/ncomms1013010.1038/ncomms10130 ↗
54. 10.1161/CIRCRESAHA.117.31208610.1161/CIRCRESAHA.117.312086 ↗
55. 10.1038/s41588‐020‐00757‐z10.1038/s41588‐020‐00757‐z ↗
56. 10.1038/s41588‐021‐00931‐x10.1038/s41588‐021‐00931‐x ↗
57. 10.1016/j.ajhg.2018.11.00810.1016/j.ajhg.2018.11.008 ↗
58. 10.1038/s41467‐020‐15649‐310.1038/s41467‐020‐15649‐3 ↗
59. 10.1136/annrheumdis‐2020‐21906510.1136/annrheumdis‐2020‐219065 ↗
60. 10.1093/hmg/ddz17510.1093/hmg/ddz175 ↗
61. 10.1038/s41586‐026‐10358‐110.1038/s41586‐026‐10358‐1 ↗
62. 10.1038/nature1158210.1038/nature11582 ↗
63. 10.1007/s10654‐019‐00598‐z10.1007/s10654‐019‐00598‐z ↗
64. 10.1016/j.neuroimage.2021.11860310.1016/j.neuroimage.2021.118603 ↗
65. 10.1165/rcmb.2018‐0384OC10.1165/rcmb.2018‐0384OC ↗
66. 10.1038/s41588‐018‐0307‐510.1038/s41588‐018‐0307‐5 ↗
67. 10.1126/science.aay669010.1126/science.aay6690 ↗
68. 10.1038/s41467‐020‐17368‐110.1038/s41467‐020‐17368‐1 ↗
69. 10.1038/s41467‐022‐30110‐310.1038/s41467‐022‐30110‐3 ↗
70. 10.1038/s41467‐018‐07862‐y10.1038/s41467‐018‐07862‐y ↗
71. 10.1007/s00439‐018‐1910‐310.1007/s00439‐018‐1910‐3 ↗
72. 10.1073/pnas.121620611010.1073/pnas.1216206110 ↗
73. 10.1038/s41588‐018‐0151‐710.1038/s41588‐018‐0151‐7 ↗
74. 10.1038/s41588‐018‐0309‐310.1038/s41588‐018‐0309‐3 ↗
75. 10.1371/journal.pgen.100816410.1371/journal.pgen.1008164 ↗
76. 10.1038/s41588‐022‐01124‐w10.1038/s41588‐022‐01124‐w ↗
77. 10.1371/journal.pgen.100659410.1371/journal.pgen.1006594 ↗
78. 10.1038/s41467‐019‐09117‐w10.1038/s41467‐019‐09117‐w ↗
79. 10.1038/s41576‐023‐00643‐410.1038/s41576‐023‐00643‐4 ↗
80. 10.1016/j.cell.2023.12.02910.1016/j.cell.2023.12.029 ↗
81. 10.1016/j.cell.2020.01.01210.1016/j.cell.2020.01.012 ↗
82. 10.1016/j.cell.2018.02.03110.1016/j.cell.2018.02.031 ↗
83. 10.1016/j.cub.2022.08.02710.1016/j.cub.2022.08.027 ↗
84. 10.1073/pnas.221830812010.1073/pnas.2218308120 ↗
85. 10.1093/molbev/msw21610.1093/molbev/msw216 ↗
86. 10.1038/s41586‐021‐03236‐510.1038/s41586‐021‐03236‐5 ↗
87. 10.1038/ng.371410.1038/ng.3714 ↗
88. 10.1038/s41588‐022‐01213‐w10.1038/s41588‐022‐01213‐w ↗
89. 10.1038/s41588‐018‐0302‐x10.1038/s41588‐018‐0302‐x ↗
90. 10.1038/s41586‐022‐04434‐510.1038/s41586‐022‐04434‐5 ↗
91. 10.1038/s41588‐019‐0378‐y10.1038/s41588‐019‐0378‐y ↗
92. 10.1038/s41588‐018‐0157‐110.1038/s41588‐018‐0157‐1 ↗
93. 10.1093/nar/gkae109010.1093/nar/gkae1090 ↗
94. 10.1016/j.gim.2023.10086610.1016/j.gim.2023.100866 ↗
95. 10.1038/s41588‐019‐0516‐610.1038/s41588‐019‐0516‐6 ↗
96. 10.1038/s41586‐021‐04108‐810.1038/s41586‐021‐04108‐8 ↗
97. Golden P. B. · 2011
98. 10.1016/j.fsigen.2019.06.01810.1016/j.fsigen.2019.06.018 ↗
99. 10.1093/molbev/msab15810.1093/molbev/msab158 ↗
100. 10.1038/s41586‐023‐06618‐z10.1038/s41586‐023‐06618‐z ↗