1
|
Wen J, Chen H, Pan Y, Yang Y, Mamatyusupu D, Maimaitiyiming D, Xu S. Sex-Biased Admixture Followed by Isolation and Adaptive Evolution Shaped the Genomic and Blood Pressure Diversity of the LopNur People. Mol Biol Evol 2025; 42:msaf091. [PMID: 40235149 PMCID: PMC12034462 DOI: 10.1093/molbev/msaf091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 12/28/2024] [Accepted: 04/01/2025] [Indexed: 04/17/2025] Open
Abstract
The LopNur people are an ethnic group living on the edge of the Taklamakan Desert, and they are believed to demonstrate a unique genetic makeup due to their isolation and limited contact with neighboring populations. However, a lack of genetic studies on the LopNur people has resulted in limited knowledge about their ancestral origins and demographic history. Here, we conducted the first whole-genome sequencing study of 164 LopNur individuals (LOP) to gain insight into their genetic history and adaptive evolution in an isolated desert area. Our analysis revealed that the present-day LOP have experienced a complex history of admixture followed by long-term isolation, with their ancestry derived from East Asia (∼41.46%), West Eurasia (∼26.43%), Siberia (∼24.27%), and South Asia (∼7.82%). Notably, a remarkable sex-biased admixture occurred between Western males and Eastern females. In addition to complex admixture followed by long-term geographic isolation and further recent migrations, adaptive evolution jointly formed the gene pool and phenotypic diversity of the present-day LOP. Intriguingly, our analysis suggests that the USP35-GAB2 region may be correlated with blood pressure in LOP, based on a joint analysis of genomics and blood pressure data. Moreover, we identified two variants, rs7387065, and rs2229437, located on CSMD1 and PRCP, respectively. These variants exhibited frequency differences between Asian and European populations and were reported to be associated with antihypertensive drug absorption. Our results provide new insight into the complex history of the LOP, an admixed and isolated ethnic group residing at the crossroads of East and West, a case with ancient admixture, long-term isolation, adaptive evolution, and sex-biased gene flow.
Collapse
Affiliation(s)
- Jia Wen
- State Key Laboratory of Genetics and Development of Complex Phenotypes, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hao Chen
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuwen Pan
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuhan Yang
- State Key Laboratory of Genetics and Development of Complex Phenotypes, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China
| | - Dilinuer Maimaitiyiming
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Shuhua Xu
- State Key Laboratory of Genetics and Development of Complex Phenotypes, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
2
|
Wen J, Liu J, Feng Q, Lu Y, Yuan K, Zhang X, Zhang C, Gao Y, Wang X, Mamatyusupu D, Xu S. Ancestral origins and post-admixture adaptive evolution of highland Tajiks. Natl Sci Rev 2024; 11:nwae284. [PMID: 40040643 PMCID: PMC11879426 DOI: 10.1093/nsr/nwae284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 08/04/2024] [Accepted: 08/04/2024] [Indexed: 03/06/2025] Open
Abstract
It remains debatable how many genes and how various the mechanisms are behind human adaptation to extreme environments, such as high altitudes. Despite extensive studies on Tibetans, Andeans and Ethiopians, new insights are expected to be provided with careful analysis of underrepresented highlanders living in a different geographical region, such as the Tajiks, who reside on the Pamir Plateau at an average altitude exceeding 4000 meters. Moreover, genetic admixture, as we observed in the current whole-genome deep-sequencing study of Xinjiang Tajiks (XJT), offers a unique opportunity to explore how admixture may facilitate adaptation to high-altitude environments. Compared with other extensively studied highlanders, XJT showed pronounced admixture patterns: most of their ancestry are derived from West Eurasians (34.5%-48.3%) and South Asians (21.4%-40.0%), and some minor ancestry from East Asians and Siberians (3.62%-17.5%). The greater genetic diversity in XJT than in their ancestral source populations provides a genetic basis for their adaptation to high-altitude environments. The admixture gain of functional adaptive components from ancestral populations could facilitate adaptation to high-altitude environments. Specifically, admixture-facilitated adaptation was strongly associated with skin-related candidate genes that respond to UV radiation (e.g. HERC2 and BNC2) and cardiovascular-system-related genes (e.g. MPI and BEST1). Notably, no adaptive variants of genes showing outstanding natural selection signatures in the Tibetan or Andean highlanders were identified in XJT, including EPAS1 and EGLN1, indicating that a different set of genes contributed to XJT's survival on the Pamir Plateau, although some genes underlying natural selection in XJT have been previously reported in other highlanders. Our results highlight the unique genetic adaptations in XJT and propose that admixture may play a vital role in facilitating high-altitude adaptation. By introducing and elevating diversity, admixture likely induces novel genetic factors that contribute to the survival of populations in extreme environments like the highlands.
Collapse
Affiliation(s)
- Jia Wen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaojiao Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qidi Feng
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200438, China
| | - Kai Yuan
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chao Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaoji Wang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi 830046, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
3
|
Pilli E, Morelli S, Poggiali B, Alladio E. Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology. Forensic Sci Int Genet 2023; 62:102806. [PMID: 36399972 DOI: 10.1016/j.fsigen.2022.102806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022]
Abstract
As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.
Collapse
Affiliation(s)
- Elena Pilli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Stefania Morelli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Brando Poggiali
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | | |
Collapse
|
4
|
Dai SS, Sulaiman X, Isakova J, Xu WF, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Wang MS, Shen QK, Yang XY, Yao YG, Aldashev AA, Saidov A, Chen W, Cheng LF, Peng MS, Zhang YP. The genetic echo of the Tarim mummies in modern Central Asians. Mol Biol Evol 2022; 39:6675590. [PMID: 36006373 PMCID: PMC9469894 DOI: 10.1093/molbev/msac179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The diversity of Central Asians has been shaped by multiple migrations and cultural diffusion. Although ancient DNA studies have revealed the demographic changes of the Central Asian since the Bronze Age, the contribution of the ancient populations to the modern Central Asian remains opaque. Herein, we performed high-coverage sequencing of 131 whole genomes of Indo-European-speaking Tajik and Turkic-speaking Kyrgyz populations to explore their genomic diversity and admixture history. By integrating the ancient DNA data, we revealed more details of the origins and admixture history of Central Asians. We found that the major ancestry of present-day Tajik populations can be traced back to the admixture of the Bronze Age Bactria–Margiana Archaeological Complex and Andronovo-related populations. Highland Tajik populations further received additional gene flow from the Tarim mummies, an isolated ancient North Eurasian–related population. The West Eurasian ancestry of Kyrgyz is mainly derived from Historical Era populations in Xinjiang of China. Furthermore, the recent admixture signals detected in both Tajik and Kyrgyz are ascribed to the expansions of Eastern Steppe nomadic pastoralists during the Historical Era.
Collapse
Affiliation(s)
- Shan Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China
| | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Wei Fang Xu
- Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen 518034, China
| | - Najmudinov Tojiddin Abdulloevich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Khudoidodov Behruz Ibrohimovich
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi 830011, China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Wei Kang Yang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Ming Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Quan Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xing Yan Yang
- Key Laboratory of Chemistry in Ethnic Medicinal Resource, Yunnan Minzu University, Kunming 650504, China.,School of Chemistry and Environment, Yunnan Minzu University, Kunming 650504, China
| | - Yong Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Almaz A Aldashev
- Institute of Molecular Biology and Medicine, Bishkek 720040, Kyrgyzstan
| | - Abdusattor Saidov
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe 734025, Tajikistan
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650224, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650224, China
| | - Lu Feng Cheng
- Department of Pharmacology, School of Pharmacy, Xinjiang Medical University, Urumqi 830054, China
| | - Min Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ya Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,KIZ/CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China
| |
Collapse
|
5
|
Guarino-Vignon P, Marchi N, Chimènes A, Monnereau A, Kroll S, Mashkour M, Lhuillier J, Bendezu-Sarmiento J, Heyer E, Bon C. Genetic analysis of a bronze age individual from Ulug-depe (Turkmenistan). Front Genet 2022; 13:884612. [PMID: 36072661 PMCID: PMC9441711 DOI: 10.3389/fgene.2022.884612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.
Collapse
Affiliation(s)
- Perle Guarino-Vignon
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- CAGT, UMR 5288, CNRS, Université Paul Sabatier Toulouse III, Toulouse, France
- *Correspondence: Perle Guarino-Vignon, ; Céline Bon,
| | - Nina Marchi
- CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Amélie Chimènes
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Aurore Monnereau
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Sonja Kroll
- Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnements (AASPE), Muséum National D'Histoire Naturelle, CNRS, Paris, France
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnements (AASPE), Muséum National D'Histoire Naturelle, CNRS, Paris, France
| | - Johanna Lhuillier
- Archéorient, Environnements et Sociétés de L'Orient Ancien, CNRS/Université Lyon 2, Lyon, France
| | - Julio Bendezu-Sarmiento
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Evelyne Heyer
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Céline Bon
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- *Correspondence: Perle Guarino-Vignon, ; Céline Bon,
| |
Collapse
|
6
|
Alladio E, Poggiali B, Cosenza G, Pilli E. Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field. Sci Rep 2022; 12:8974. [PMID: 35643723 PMCID: PMC9148302 DOI: 10.1038/s41598-022-12903-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.
Collapse
Affiliation(s)
- Eugenio Alladio
- Department of Chemistry, University of Turin, Turin, Italy.,Centro Regionale Antidoping e di Tossicologia "A. Bertinaria", Orbassano, Torino, Italy
| | - Brando Poggiali
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Giulia Cosenza
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy
| | - Elena Pilli
- Department of Biology, Forensic Molecular Anthropology Laboratory, University of Florence, Florence, Italy.
| |
Collapse
|
7
|
Cardinali I, Bodner M, Capodiferro MR, Amory C, Rambaldi Migliore N, Gomez EJ, Myagmar E, Dashzeveg T, Carano F, Woodward SR, Parson W, Perego UA, Lancioni H, Achilli A. Mitochondrial DNA Footprints from Western Eurasia in Modern Mongolia. Front Genet 2022; 12:819337. [PMID: 35069708 PMCID: PMC8773455 DOI: 10.3389/fgene.2021.819337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 12/14/2021] [Indexed: 11/15/2022] Open
Abstract
Mongolia is located in a strategic position at the eastern edge of the Eurasian Steppe. Nomadic populations moved across this wide area for millennia before developing more sedentary communities, extended empires, and complex trading networks, which connected western Eurasia and eastern Asia until the late Medieval period. We provided a fine-grained portrait of the mitochondrial DNA (mtDNA) variation observed in present-day Mongolians and capable of revealing gene flows and other demographic processes that took place in Inner Asia, as well as in western Eurasia. The analyses of a novel dataset (N = 2,420) of mtDNAs highlighted a clear matrilineal differentiation within the country due to a mixture of haplotypes with eastern Asian (EAs) and western Eurasian (WEu) origins, which were differentially lost and preserved. In a wider genetic context, the prevalent EAs contribution, larger in eastern and central Mongolian regions, revealed continuous connections with neighboring Asian populations until recent times, as attested by the geographically restricted haplotype-sharing likely facilitated by the Genghis Khan’s so-called Pax Mongolica. The genetic history beyond the WEu haplogroups, notably detectable on both sides of Mongolia, was more difficult to explain. For this reason, we moved to the analysis of entire mitogenomes (N = 147). Although it was not completely possible to identify specific lineages that evolved in situ, two major changes in the effective (female) population size were reconstructed. The more recent one, which began during the late Pleistocene glacial period and became steeper in the early Holocene, was probably the outcome of demographic events connected to western Eurasia. The Neolithic growth could be easily explained by the diffusion of dairy pastoralism, as already proposed, while the late glacial increase indicates, for the first time, a genetic connection with western Eurasian refuges, as supported by the unusual high frequency and internal sub-structure in Mongolia of haplogroup H1, a well-known post-glacial marker in Europe. Bronze Age events, without a significant demographic impact, might explain the age of some mtDNA haplogroups. Finally, a diachronic comparison with available ancient mtDNAs made it possible to link six mitochondrial lineages of present-day Mongolians to the timeframe and geographic path of the Silk Route.
Collapse
Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Edgar J Gomez
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States.,FamilySearch Int., Salt Lake City, UT, United States
| | - Erdene Myagmar
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Tumen Dashzeveg
- Department of Anthropology and Archaeology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Francesco Carano
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Scott R Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, State College, PA, United States
| | - Ugo A Perego
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.,Sorenson Molecular Genealogy Foundation, Salt Lake City, UT, United States.,Department of Math and Science, Southeastern Community College, Burlington, IA, United States
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| |
Collapse
|
8
|
Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia. Sci Rep 2022; 12:733. [PMID: 35031610 PMCID: PMC8760286 DOI: 10.1038/s41598-021-04144-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations — Yaghnobis and Tajiks — with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.
Collapse
|
9
|
Mahmood HK, Salman NF, Salih KM, Hasan DH, Al-Zubaidi MM. Frequency of Y-chromosome STRs using PowerPlex® Y23 System in Iraqi population. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2020. [DOI: 10.1186/s41935-020-00186-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Y-chromosome STRs are valuable in the forensic identification of male DNA from sexual assault cases, and they are used to link families through genetic genealogy.
Materials and methods
For Y-STR analysis, 1032 male blood samples were used in this study, direct PCR technique was used for DNA amplification using the PowerPlex® Y23 System, and then PCR product was run with Genetic Analyzer, and the data were analyzed with the Gene Mapper ID Analysis Software. Frequency-based statistical analysis was calculated with GenAlEx 6.5-Genetic Analysis.
Results
One hundred and eighty-five alleles were detected at the 23 Y-STR loci in 1032 samples. Alleles frequency ranged from 0.002 to 0.813 and the highest allele frequency registered (0.813) for allele 11 at locus DYS392, and the mean haplotype diversity was 0.616 ± 0.027. New variants were registered for DYS458 locus.
Conclusion
The present study established the genetic information obtained by using the PowerPlex® Y23 System for the Iraqi population and also created a database of 23 Y STR markers in this population.
Collapse
|
10
|
Wang Y, Jin X, Zhang W, Cui W, Kong T, Chen C, Guo Y, Meng H, Zhu B. Comprehensive analyses for genetic diversities of 19 autosomal STRs in Chinese Kazak group and its phylogenetic relationships with other continental populations. Forensic Sci Res 2020; 7:163-171. [PMID: 35784425 PMCID: PMC9245996 DOI: 10.1080/20961790.2020.1751379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Short tandem repeats (STRs) play an essential role in forensic genetics due to their high degree of polymorphisms, wide distributions and easy detection method. In this study, allelic frequencies and forensic statistical parameters of the 19 autosomal STR loci in a Kazak ethnic group were calculated, and its genetic relationships with reference populations were assessed in order to understand population structure better and enrich population genetic data for forensic practice in Chinese Kazak ethnic group. There were 226 identified alleles with the corresponding allelic frequencies ranging from 0.0008 to 0.5295 in the 628 unrelated healthy Kazak individuals in Xinjiang Uygur Autonomous Region. All autosomal STRs were conformed to the Hardy-Weinberg equilibrium after Bonferroni’s correction. The cumulative power of discrimination and the combined probability of exclusion of all the 19 autosomal STRs were 0.999 999 999 999 999 999 999 997 162 and 0.999 999 994 484, respectively. Furthermore, the DA distances and Fixation index values of pairwise populations, principal component analysis, multidimensional scaling analysis, phylogenetic tree analysis and structure analysis were conducted to probe the genetic relationships between the Kazak group and other reference populations. The population genetic results showed that these 19 autosomal STR loci were characterised by high genetic diversities in the Kazak group. Furthermore, the studied Kazak group had close genetic relationships with the Uyghur group and the Uzbek group. The present results may facilitate understanding the genetic background of the Chinese Xinjiang Kazak group.
Collapse
Affiliation(s)
- Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Tingting Kong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Haotian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Forensic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
11
|
Jay F, Boitard S, Austerlitz F. An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. Mol Biol Evol 2020; 36:1565-1579. [PMID: 30785202 DOI: 10.1093/molbev/msz038] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Species generally undergo a complex demographic history consisting, in particular, of multiple changes in population size. Genome-wide sequencing data are potentially highly informative for reconstructing this demographic history. A crucial point is to extract the relevant information from these very large data sets. Here, we design an approach for inferring past demographic events from a moderate number of fully sequenced genomes. Our new approach uses Approximate Bayesian Computation, a simulation-based statistical framework that allows 1) identifying the best demographic scenario among several competing scenarios and 2) estimating the best-fitting parameters under the chosen scenario. Approximate Bayesian Computation relies on the computation of summary statistics. Using a cross-validation approach, we show that statistics such as the lengths of haplotypes shared between individuals, or the decay of linkage disequilibrium with distance, can be combined with classical statistics (e.g., heterozygosity and Tajima's D) to accurately infer complex demographic scenarios including bottlenecks and expansion periods. We also demonstrate the importance of simultaneously estimating the genotyping error rate. Applying our method on genome-wide human-sequence databases, we finally show that a model consisting in a bottleneck followed by a Paleolithic and a Neolithic expansion is the most relevant for Eurasian populations.
Collapse
Affiliation(s)
- Flora Jay
- Laboratoire EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France.,Laboratoire de Recherche en Informatique, CNRS/Université Paris-Sud/Université Paris-Saclay, Orsay, France
| | - Simon Boitard
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France
| | - Frédéric Austerlitz
- Laboratoire EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France
| |
Collapse
|
12
|
Cilli E, Sarno S, Gnecchi Ruscone GA, Serventi P, De Fanti S, Delaini P, Ognibene P, Basello GP, Ravegnini G, Angelini S, Ferri G, Gentilini D, Di Blasio AM, Pelotti S, Pettener D, Sazzini M, Panaino A, Luiselli D, Gruppioni G. The genetic legacy of the Yaghnobis: A witness of an ancient Eurasian ancestry in the historically reshuffled central Asian gene pool. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 168:717-728. [PMID: 30693949 DOI: 10.1002/ajpa.23789] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 11/11/2022]
Abstract
OBJECTIVES The Yaghnobis are an ethno-linguistic minority historically settled along the Yaghnob River in the Upper-Zarafshan Valley in Tajikistan. They speak a language of Old Sogdian origin, which is the only present-day witness of the Lingua Franca used along the Silk Road in Late Antiquity. The aim of this study was to reconstruct the genetic history of this community in order to shed light on its isolation and genetic ancestry within the Euro-Asiatic context. MATERIALS AND METHODS A total of 100 DNA samples were collected in the Yaghnob and Matcha Valleys during several expeditions and their mitochondrial, Y-chromosome and autosomal genome-wide variation were compared with that from a large set of modern and ancient Euro-Asiatic samples. RESULTS Findings from uniparental markers highlighted the long-term isolation of the Yaghnobis. Mitochondrial DNA ancestry traced an ancient link with Middle Eastern populations, whereas Y-chromosome legacy showed more tight relationships with Central Asians. Admixture, outgroup-f3, and D-statistics computed on autosomal variation corroborated Y-chromosome evidence, pointing respectively to low Anatolian Neolithic and high Steppe ancestry proportions in Yaghnobis, and to their closer affinity with Tajiks than to Iranians. DISCUSSION Although the Yaghnobis do not show evident signs of recent admixture, they could be considered a modern proxy for the source of gene flow for many Central Asian and Middle Eastern groups. Accordingly, they seem to retain a peculiar genomic ancestry probably ascribable to an ancient gene pool originally wide spread across a vast area and subsequently reshuffled by distinct demographic events occurred in Middle East and Central Asia.
Collapse
Affiliation(s)
- Elisabetta Cilli
- Laboratories of Physical Anthropology and Ancient DNA, Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Guido Alberto Gnecchi Ruscone
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Patrizia Serventi
- Laboratories of Physical Anthropology and Ancient DNA, Department of Cultural Heritage, University of Bologna, Ravenna, Italy.,Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paolo Delaini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Paolo Ognibene
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Gian Pietro Basello
- Department of Asian, African and Mediterranean Studies, University of Naples "L'Orientale", Naples, Italy
| | - Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Gianmarco Ferri
- Department of Diagnostic and Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy
| | - Davide Gentilini
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - Anna Maria Di Blasio
- Centre for Biomedical Research and Technologies, Italian Auxologic Institute, IRCCS, Milan, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Davide Pettener
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Antonio Panaino
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Donata Luiselli
- Laboratories of Physical Anthropology and Ancient DNA, Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Giorgio Gruppioni
- Laboratories of Physical Anthropology and Ancient DNA, Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| |
Collapse
|
13
|
Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff S, Sousa VC, Wang Y. Phylogeny Estimation by Integration over Isolation with Migration Models. Mol Biol Evol 2018; 35:2805-2818. [PMID: 30137463 PMCID: PMC6231491 DOI: 10.1093/molbev/msy162] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
Collapse
Affiliation(s)
- Jody Hey
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | - Yujin Chung
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
- The Department of Applied Statistics, Kyonggi University, Suwon, South Korea
| | - Arun Sethuraman
- Department of Biology, Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA
| | - Joseph Lachance
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Georgia Institute of Technology, Atlanta, GA
| | - Sarah Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Vitor C Sousa
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ
- University of Lisbon, Lisboa, Portugal
| | - Yong Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ
- Ancestry, San Francisco, CA
| |
Collapse
|
14
|
Genetic diversity of 21 forensic autosomal STRs and DYS391 in the Han population from Shanghai, Eastern China. Forensic Sci Int Genet 2018; 37:e23-e25. [PMID: 30181102 DOI: 10.1016/j.fsigen.2018.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/26/2018] [Indexed: 01/11/2023]
|
15
|
Cooke NP, Nakagome S. Fine-tuning of Approximate Bayesian Computation for human population genomics. Curr Opin Genet Dev 2018; 53:60-69. [PMID: 30029009 DOI: 10.1016/j.gde.2018.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/30/2018] [Indexed: 12/13/2022]
Abstract
Approximate Bayesian Computation (ABC) is a flexible statistical tool widely applied to addressing a variety of questions regarding the origin and evolution of humans. The significant growth of genomic scale data from diverse geographic populations has facilitated the use of ABC in modelling the complex processes that underlie human demography and local adaptation. However, a fundamental issue still remains in how to efficiently capture patterns of genetic variation with a set of summary statistics in order to achieve better approximation of Bayesian inference. Here, we review recent advances in ABC methodology and its applications for human population genomics, with a particular focus on optimal tuning of ABC approaches for different types of genetic data and different sets of evolutionary parameters.
Collapse
Affiliation(s)
- Niall P Cooke
- Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- Trinity Translational Medicine Institute, School of Medicine, Trinity College Dublin, Dublin, Ireland.
| |
Collapse
|
16
|
Marchi N, Mennecier P, Georges M, Lafosse S, Hegay T, Dorzhu C, Chichlo B, Ségurel L, Heyer E. Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy. Sci Rep 2018; 8:9397. [PMID: 29925873 PMCID: PMC6010435 DOI: 10.1038/s41598-018-27047-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 04/13/2018] [Indexed: 01/12/2023] Open
Abstract
When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.
Collapse
Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.,LM2E-UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, Plouzane, 29280, France
| | - Sophie Lafosse
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Tatyana Hegay
- Republican Scientific Center of Immunology, Ministry of Public Health, Tashkent, 100060, Uzbekistan
| | - Choduraa Dorzhu
- Department of biology and ecology, Tuvan State University, Kyzyl, 667000, Russia
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.
| |
Collapse
|
17
|
Austerlitz F, Heyer E. Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations. Mol Biol Evol 2018; 35:1304-1307. [PMID: 29659992 DOI: 10.1093/molbev/msy067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.
Collapse
Affiliation(s)
- Frédéric Austerlitz
- UMR 7206 Eco-Anthropologie et Ethnobiologie, CNRS, MNHN, Université Paris Diderot, Paris, France
| | - Evelyne Heyer
- UMR 7206 Eco-Anthropologie et Ethnobiologie, CNRS, MNHN, Université Paris Diderot, Paris, France
| |
Collapse
|
18
|
Thouzeau V, Mennecier P, Verdu P, Austerlitz F. Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations. Proc Biol Sci 2018; 284:rspb.2017.0706. [PMID: 28835553 DOI: 10.1098/rspb.2017.0706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/17/2017] [Indexed: 11/12/2022] Open
Abstract
Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer program PopLingSim that simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.
Collapse
Affiliation(s)
- Valentin Thouzeau
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Philippe Mennecier
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Paul Verdu
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Frédéric Austerlitz
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| |
Collapse
|
19
|
Zhao YX, Yang J, Lv FH, Hu XJ, Xie XL, Zhang M, Li WR, Liu MJ, Wang YT, Li JQ, Liu YG, Ren YL, Wang F, Hehua EE, Kantanen J, Arjen Lenstra J, Han JL, Li MH. Genomic Reconstruction of the History of Native Sheep Reveals the Peopling Patterns of Nomads and the Expansion of Early Pastoralism in East Asia. Mol Biol Evol 2017. [PMID: 28645168 PMCID: PMC5850515 DOI: 10.1093/molbev/msx181] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in > 1,000 modern samples. Population genomic analyses combined with archeological records and historical ethnic demographics data revealed genetic signatures of the origins, secondary expansions and admixtures, of Chinese sheep thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia. Originating from the Mongolian Plateau ∼5,000‒5,700 years ago, Chinese sheep were inferred to spread in the upper and middle reaches of the Yellow River ∼3,000‒5,000 years ago following the expansions of the Di-Qiang people. Afterwards, sheep were then inferred to reach the Qinghai-Tibetan and Yunnan-Kweichow plateaus ∼2,000‒2,600 years ago by following the north-to-southwest routes of the Di-Qiang migration. We also unveiled two subsequent waves of migrations of fat-tailed sheep into northern China, which were largely commensurate with the migrations of ancestors of Hui Muslims eastward and Mongols southward during the 12th‒13th centuries. Furthermore, we revealed signs of argali introgression into domestic sheep, extensive historical mixtures among domestic populations and strong artificial selection for tail type and other traits, reflecting various breeding strategies by nomadic societies in ancient China.
Collapse
Affiliation(s)
- Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiao-Ju Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China.,School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wen-Rong Li
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnological Research Center, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yu-Tao Wang
- College of Life and Geographic Sciences, Kashgar University, Kashgar, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yan-Ling Ren
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - EEr Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (Luke), Jokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| |
Collapse
|
20
|
The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana. Sci Rep 2017; 7:3085. [PMID: 28596519 PMCID: PMC5465200 DOI: 10.1038/s41598-017-03176-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
Collapse
|
21
|
Unterländer M, Palstra F, Lazaridis I, Pilipenko A, Hofmanová Z, Groß M, Sell C, Blöcher J, Kirsanow K, Rohland N, Rieger B, Kaiser E, Schier W, Pozdniakov D, Khokhlov A, Georges M, Wilde S, Powell A, Heyer E, Currat M, Reich D, Samashev Z, Parzinger H, Molodin VI, Burger J. Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe. Nat Commun 2017; 8:14615. [PMID: 28256537 PMCID: PMC5337992 DOI: 10.1038/ncomms14615] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/13/2017] [Indexed: 01/10/2023] Open
Abstract
During the 1st millennium before the Common Era (BCE), nomadic tribes associated with the Iron Age Scythian culture spread over the Eurasian Steppe, covering a territory of more than 3,500 km in breadth. To understand the demographic processes behind the spread of the Scythian culture, we analysed genomic data from eight individuals and a mitochondrial dataset of 96 individuals originating in eastern and western parts of the Eurasian Steppe. Genomic inference reveals that Scythians in the east and the west of the steppe zone can best be described as a mixture of Yamnaya-related ancestry and an East Asian component. Demographic modelling suggests independent origins for eastern and western groups with ongoing gene-flow between them, plausibly explaining the striking uniformity of their material culture. We also find evidence that significant gene-flow from east to west Eurasia must have occurred early during the Iron Age.
Collapse
Affiliation(s)
- Martina Unterländer
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Friso Palstra
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Aleksandr Pilipenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Zuzana Hofmanová
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Melanie Groß
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Christian Sell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Karola Kirsanow
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin Rieger
- Molecular Genetics and Genome Analysis Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Elke Kaiser
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Wolfram Schier
- Department of History and Cultural Studies, Freie Universität Berlin, 14195 Berlin, Germany
| | - Dimitri Pozdniakov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara 443099, Russian Federation
| | - Myriam Georges
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Sandra Wilde
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Adam Powell
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany
| | - Evelyne Heyer
- CNRS UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, 75016 Paris, France
| | - Mathias Currat
- Dépt. de Génétique & Evolution, Unité d'anthropologie, Université de Genève, 1205 Genève, Suisse
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zainolla Samashev
- Branch of Margulan Institute of Archaeology, Astana 010000, Kazakhstan
| | | | - Vyacheslav I. Molodin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 10, Novosibirsk 630090, Russia
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Science, Akademika Lavrentieva 17, Novosibirsk 630090, Russia
| | - Joachim Burger
- Palaeogenetics Group, Institute of Evolutionary Biology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| |
Collapse
|
22
|
Marchi N, Hegay T, Mennecier P, Georges M, Laurent R, Whitten M, Endicott P, Aldashev A, Dorzhu C, Nasyrova F, Chichlo B, Ségurel L, Heyer E. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162:627-640. [PMID: 28158897 DOI: 10.1002/ajpa.23151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. METHODS We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. RESULTS Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. CONCLUSIONS This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
Collapse
Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Tatyana Hegay
- Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Romain Laurent
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Mark Whitten
- MPRG on Comparative Population Linguistics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Endicott
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Almaz Aldashev
- Institute molecular biology and medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Firuza Nasyrova
- Laboratory of Plant Genetics, Institute of Botany, Plant Physiology and Genetics, TAS, Dushanbe, 734063, Tajikistan
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| |
Collapse
|
23
|
Mei T, Shen CM, Liu YS, Meng HT, Zhang YD, Guo YX, Dong Q, Wang XX, Yan JW, Zhu BF, Zhang LP. Population genetic structure analysis and forensic evaluation of Xinjiang Uigur ethnic group on genomic deletion and insertion polymorphisms. SPRINGERPLUS 2016; 5:1087. [PMID: 27468387 PMCID: PMC4947079 DOI: 10.1186/s40064-016-2730-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023]
Abstract
Background The Uigur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and valuable resource for the study of ethnogeny. The objective of this study was to estimate the genetic diversities and forensic parameters of 30 insertion-deletion loci in Uigur ethnic group from Xinjiang Uigur Autonomous Region of China and to analyze the genetic relationships between Xinjiang Uigur group and other previously published groups based on population data of these loci. Results All the tested loci were conformed to Hardy–Weinberg equilibrium after Bonferroni correction. The observed and expected heterozygosity ranged from 0.3750 to 0.5515; and 0.4057 to 0.5037, respectively. The combined power of discrimination and probability of exclusion in the group were 0.99999999999940 and 0.9963, respectively. We analyzed the DA distance, interpopulation differentiations and population structure, conducted principal component analysis and neighbor-joining tree based on our studied group and 21 reference groups. The present results indicated that the studied Xinjiang Uigur group (represented our samples from the whole territory of Xinjiang Uigur Autonomous Region) had a close relationships with Urumchi Uigur (represented previously reported samples from Urumchi of Xinjiang) and Kazak groups. Conclusions The present study may provide novel biological information for the study of population genetics, and can also increase our understanding of the genetic relationships between Xinjiang Uigur group and other groups. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2730-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ting Mei
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Chun-Mei Shen
- Institute of Brain and Behavioral Sciences, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710062 China.,Blood Center of Shaanxi Province, Xi'an, 710061 People's Republic of China
| | - Yao-Shun Liu
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Yu-Dang Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Yu-Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Qian Dong
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Xin-Xin Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Jiang-Wei Yan
- Key Laboratory of Genome Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 People's Republic of China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China.,Clinical Reaserch Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004 People's Republic of China
| | - Li-Ping Zhang
- Department of Biochemistry and Molecular Biology, Basic Medicine College, Xinjiang Medical University, Urumqi, 830011 People's Republic of China
| |
Collapse
|