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Zhou Z, Li Z, Yao Y, Qian J, Ji Q, Shao C, Xie J. Validation of phylogenetic informative Y-InDels in Y-chromosomal haplogroup O-M175. Front Genet 2023; 14:1182028. [PMID: 37205119 PMCID: PMC10185902 DOI: 10.3389/fgene.2023.1182028] [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: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
The Y-chromosomal haplogroup tree, which consists of a group of Y-chromosomal loci with phylogenetic information, has been widely applied in anthropology, archaeology and population genetics. With the continuous updating of the phylogenetic structure, Y-chromosomal haplogroup tree provides more information for recalling the biogeographical origin of Y chromosomes. Generally, Y-chromosomal insertion-deletion polymorphisms (Y-InDels) are genetically stable as Y-chromosomal single nucleotide polymorphisms (Y-SNPs), and therefore carry mutations that can accumulate over generations. In this study, potential phylogenetic informative Y-InDels were filtered out in haplogroup O-M175, which is dominant in East Asia, based on population data retrieved from the 1000 Genomes Project. A group of 22 phylogenetic informative Y-InDels were identified and then assigned to their corresponding subclades of haplogroup O-M175, which provided a supplement for the update and application of Y-chromosomal markers. Especially, four Y-InDels were introduced to define subclades determined using a single Y-SNP.
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Tao R, Li M, Chai S, Xia R, Qu Y, Yuan C, Yang G, Dong X, Bian Y, Zhang S, Li C. Developmental validation of a 381 Y-chromosome SNP panel for haplogroup analysis in the Chinese populations. Forensic Sci Int Genet 2023; 62:102803. [PMID: 36368220 DOI: 10.1016/j.fsigen.2022.102803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 09/19/2022] [Accepted: 10/26/2022] [Indexed: 01/15/2023]
Abstract
Y-chromosome single nucleotide polymorphism (Y-SNP) shows great variation in geographical distribution and population heterogeneity and can be used to map population genetics around the world. Massive parallel sequencing (MPS) methodology enables high-resolution Y-SNP haplogrouping for a certain male and is widely used in forensic genetics and evolutionary studies. In this present study, we used MPS to develop a customized 381 Y-SNP panel (SifaMPS 381 Y-SNP panel) to investigate the basic structure and subbranches of the haplogroup tree of the Chinese populations. The SifaMPS 381 Y-SNP panel covers all the Y-SNPs from our previously designed 183 Y-SNP panel and additional SNPs under the predominant haplogroups in the Chinese populations based on certain criteria. We also evaluated the sequencing matrix, concordance, sensitivity, repeatability of this panel and the ability to analyze mixed and case-type samples based on the Illumina MiSeq System. The results demonstrated that the novel MPS Y-SNP panel possessed good sequencing performance and generated accurate Y-SNP genotyping results. Although the recommended DNA input was greater than 1.25 ng, we observed that a lower DNA amount could still be used to analyze haplogroups correctly. In addition, this panel could handle mixed samples and common case-type samples and had higher resolution among Chinese Han males than previously reported. In conclusion, the SifaMPS 381 Y-SNP panel showed an overall good performance and offers a better choice for Y-SNP haplogrouping of the Chinese population, thereby facilitating paternal lineage classification, familial searching and other forensic applications.
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Affiliation(s)
- Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Min Li
- School of Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Siyu Chai
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Zunyi Medical University, Zunyi 563099, Guizhou, China
| | - Ruocheng Xia
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Yiling Qu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Science, Medical School of Soochow University, Suzhou 215123, China
| | - Chunyan Yuan
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Guangyuan Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; Department of Forensic Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Xinyu Dong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China; School of Forensic Medicine, Shanxi Medical University, Jinzhong 030619, Shanxi, China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China.
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P.R. China, Shanghai 200063, China.
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Li M, Zhang Y, Luo L, Bian Y, Li C. Development and validation of a custom panel including 183 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using a MALDI-TOF MS system. Electrophoresis 2020; 41:2047-2054. [PMID: 32854146 DOI: 10.1002/elps.202000145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 11/12/2022]
Abstract
Y-chromosome SNP haplogroups exhibit geographic structuring in many populations around the world. Therefore, Y-chromosome haplogroups have been widely used to infer paternal biogeographical ancestry and high-resolution paternal lineage classification. In the present study, we designed a customized panel containing 183 Y-SNPs based on previous studies and evaluated the genotyping performance and repeatability, concordance, sensitivity, and ability of analysing case-type samples using a MALDI-TOF MS platform. The average call rate for duplicate typing of any one SNP in the panel was 97.0%. In the concordance and accuracy study, the results of haplogroup designation obtained from MALDI-TOF MS platform were fully consistent with those obtained from the next-generation sequencing (NGS) platform. The optimal amount of template DNA in the PCR seemed to be 10 ng. However, if less DNA (≥156.25 pg) was available, it was still possible to obtain meaningful haplogroup information. For the application part, this panel could be applied for the detection of blood, semen, and buccal swabs samples. Particularly, blood stain on FTA card samples could be dissected by direct PCR amplification on the MALDI-TOF MS platform. Besides, 371 unrelated male individuals from four Chinese ethnic groups (Han, Hui, Mongolian, and Kazak) were detected using this panel. Total 78 terminal haplogroups were found and the haplogroup diversity was 0.933576. The results demonstrate that this panel could be an accurate, fast, and cost-effective method for database construction where the amount of sample material is less of a concern and when the cost of the assay is taken into consideration.
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Affiliation(s)
- Min Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China
| | - Yilun Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China.,School of Basic Medicine, Inner Mongolia Autonomous Region, Baotou Medical College, Baotou, P. R. China
| | - Li Luo
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China.,Department of Forensic Medicine, Zunyi Medical University, Zunyi, Guizhou, P. R. China
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, P.R. China, Ministry of Justice, Shanghai, P. R. China
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Sun J, Wei LH, Wang LX, Huang YZ, Yan S, Cheng HZ, Ong RTH, Saw WY, Fan ZQ, Deng XH, Lu Y, Zhang C, Xu SH, Jin L, Teo YY, Li H. Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians. Am J Hum Biol 2020; 33:e23486. [PMID: 32851723 DOI: 10.1002/ajhb.23486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/16/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians. MATERIALS AND METHODS We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation. RESULTS We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia. CONCLUSION Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | | | - Yun-Zhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China
| | - Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Hui Li
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
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Li M, Zhou W, Zhang Y, Huang L, Wang X, Wu J, Meng M, Wang H, Li C, Bian Y. Development and validation of a novel 29-plex Y-STR typing system for forensic application. Forensic Sci Int Genet 2020; 44:102169. [DOI: 10.1016/j.fsigen.2019.102169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 11/29/2022]
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A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups. ANTHROPOLOGICAL REVIEW 2018. [DOI: 10.2478/anre-2018-0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this study is to provide an insight into Balkan populations’ genetic relations utilizing in silico analysis of Y-STR haplotypes and performing haplogroup predictions together with network analysis of the same haplotypes for visualization of the relations between chosen haplotypes and Balkan populations in general. The population dataset used in this study was obtained using 23, 17, 12, 9 and 7 Y-STR loci for 13 populations. The 13 populations include: Bosnia and Herzegovina (B&H), Croatia, Macedonia, Slovenia, Greece, Romany (Hungary), Hungary, Serbia, Montenegro, Albania, Kosovo, Romania and Bulgaria. The overall dataset contains a total of 2179 samples with 1878 different haplotypes.
I2a was detected as the major haplogroup in four out of thirteen analysed Balkan populations. The four populations (B&H, Croatia, Montenegro and Serbia) which had I2a as the most prevalent haplogroup were all from the former Yugoslavian republic. The remaining two major populations from former Yugoslavia, Macedonia and Slovenia, had E1b1b and R1a haplogroups as the most prevalent, respectively.
The populations with E1b1b haplogroup as the most prevalent one are Macedonian, Romanian, as well as Albanian populations from Kosovo and Albania. The I2a haplogroup cluster is more compact when compared to E1b1b and R1b haplogroup clusters, indicating a larger degree of homogeneity within the haplotypes that belong to the I2a haplogroup. Our study demonstrates that a combination of haplogroup prediction and network analysis represents an effective approach to utilize publicly available Y-STR datasets for population genetics.
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Convergence of Y Chromosome STR Haplotypes from Different SNP Haplogroups Compromises Accuracy of Haplogroup Prediction. J Genet Genomics 2015; 42:403-7. [DOI: 10.1016/j.jgg.2015.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/21/2015] [Accepted: 03/24/2015] [Indexed: 11/20/2022]
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Wang CC, Gilbert MTP, Jin L, Li H. Evaluating the Y chromosomal timescale in human demographic and lineage dating. INVESTIGATIVE GENETICS 2014; 5:12. [PMID: 25215184 PMCID: PMC4160915 DOI: 10.1186/2041-2223-5-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/31/2014] [Indexed: 11/10/2022]
Abstract
Y chromosome is a superb tool for inferring human evolution and recent demographic history from a paternal perspective. However, Y chromosomal substitution rates obtained using different modes of calibration vary considerably, and have produced disparate reconstructions of human history. Here, we discuss how substitution rate and date estimates are affected by the choice of different calibration points. We argue that most Y chromosomal substitution rates calculated to date have shortcomings, including a reliance on the ambiguous human-chimpanzee divergence time, insufficient sampling of deep-rooting pedigrees, and using inappropriate founding migrations, although the rates obtained from a single pedigree or calibrated with the peopling of the Americas seem plausible. We highlight the need for using more deep-rooting pedigrees and ancient genomes with reliable dates to improve the rate estimation.
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Affiliation(s)
- Chuan-Chao Wang
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Li Jin
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China ; Department of Computational Genetics, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
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