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Chiao A, Ge J. Determining lineages between individuals with high-density mitochondrial and Y-chromosomal single-nucleotide polymorphisms. Electrophoresis 2024; 45:843-851. [PMID: 38010138 DOI: 10.1002/elps.202300142] [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: 06/29/2023] [Revised: 10/19/2023] [Accepted: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Genetic genealogy has been more frequently used in forensic investigations in identifying criminals. However, the current genetic genealogy applications usually do not consider lineage markers (including both Y and mitochondrial deoxyribonucleic acid (DNA)), which is probably because not all distant relatives share the same lineage markers. In addition, there is no study to show how to use lineage markers and what methods or thresholds should be applied in genetic genealogy. In this study, we developed a method to quickly determine if two single-nucleotide polymorphism (SNP) profiles are from the same paternal or material lineages by using a mismatch frequency of the SNPs in Y-chromosomal or mitochondrial DNA. For both Y and mitochondrial SNPs, profile pairs from the same or different lineages can be decided with high accuracies (i.e., 0.380% or 0.157% error rates with Y and mitochondrial DNA, respectively). With kinship coefficient filtering based on autosomal SNPs, the accuracies of determining maternal and paternal lineage can be further improved (i.e., 0.120% or 0.057% error rates with Y and mitochondrial DNA, respectively, using a threshold of kinship coefficient >0). This study shows that lineage markers can be very powerful tools with high accuracies to determine lineages, which could help solve cases and reduce costs for genetic genealogy investigations.
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Affiliation(s)
- Austin Chiao
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
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Kumar L, Rajpal R, Ahlawat B, Sehrawat JS, Spalzin S, Fonia RS, Thangaraj K, Rai N. The maternal genetic origin and diversity of the extant populations of the Ladakh region in India. Mitochondrion 2024; 75:101828. [PMID: 38128747 DOI: 10.1016/j.mito.2023.101828] [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: 10/12/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the "Land of high passes" one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.
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Affiliation(s)
- Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Department of Anthropology, Panjab University, Chandigarh 160014, India
| | | | - Sonam Spalzin
- Archaeological Survey of India, Mini Circle Leh, UT Ladakh, 180004, India
| | - Ramnath Singh Fonia
- Archaeological Survey of India, 144/1Kalidas Road, Dehradun, Uttrakhand, 248001, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Mut P, Bertoni B, Sapiro R, Hidalgo PC, Torres A, Azambuja C, Sans M. Insights into the Y chromosome human diversity in Uruguay. Am J Hum Biol 2023; 35:e23963. [PMID: 37493343 DOI: 10.1002/ajhb.23963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages. AIMS The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population. METHODS We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó. RESULTS Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations. DISCUSSION Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century. CONCLUSIONS The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.
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Affiliation(s)
- Patricia Mut
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario Noreste, Tacuarembó, Uruguay
| | | | | | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
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Wen Y, Liu J, Su Y, Chen X, Hou Y, Liao L, Wang Z. Forensic biogeographical ancestry inference: recent insights and current trends. Genes Genomics 2023; 45:1229-1238. [PMID: 37081293 DOI: 10.1007/s13258-023-01387-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.
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Affiliation(s)
- Yufeng Wen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu, 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Linchuan Liao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Zheng Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China.
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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Guo F, Liu Z, Long G, Zhang B, Dong X, Liu D, Yu S. High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System. Forensic Sci Int Genet 2023; 65:102879. [PMID: 37150076 DOI: 10.1016/j.fsigen.2023.102879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/16/2023] [Accepted: 04/22/2023] [Indexed: 05/09/2023]
Abstract
Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp - Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.
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Affiliation(s)
- Fei Guo
- School of Forensic Science and Technology, Criminal Investigation Police University of China, Shenyang, Liaoning 110854, PR China.
| | - Ze Liu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Guannan Long
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Biao Zhang
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China
| | - Xinyu Dong
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, PR China
| | - Dahua Liu
- Department of Forensic Medicine, Jinzhou Medical University, Jinzhou, Liaoning 121001, PR China
| | - Shaobo Yu
- DNA Laboratory of Forensic Science Center, Shenyang Public Security Bureau, Shenyang, Liaoning 110002, PR China.
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He G, Wang M, Miao L, Chen J, Zhao J, Sun Q, Duan S, Wang Z, Xu X, Sun Y, Liu Y, Liu J, Wang Z, Wei L, Liu C, Ye J, Wang L. Multiple founding paternal lineages inferred from the newly-developed 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people. Hum Genomics 2023; 17:29. [PMID: 36973821 PMCID: PMC10045532 DOI: 10.1186/s40246-023-00476-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Non-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity. RESULTS Here, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history. CONCLUSIONS Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Lei Miao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jing Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, Inner Mongolia, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
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Watherston J, McNevin D. Skull and long bones – Forensic DNA techniques for historic shipwreck human remains. AUST J FORENSIC SCI 2023. [DOI: 10.1080/00450618.2023.2181395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- J. Watherston
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
- Biology Unit, Forensic Science Branch, Nt Police, Fire and Emergency Services, Berrimah, NT, Australia
- College of Health & Human Sciences, Faculty of Science, Charles Darwin University, Casuarina, NT, Australia
| | - D. McNevin
- Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
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García-Fernández C, Lizano E, Telford M, Olalde Í, de Cid R, Larmuseau MHD, M. de Pancorbo M, Calafell F. Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition. Sci Rep 2022; 12:20708. [PMID: 36456614 PMCID: PMC9715704 DOI: 10.1038/s41598-022-25200-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019-2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.
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Affiliation(s)
- Carla García-Fernández
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Esther Lizano
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain ,grid.7080.f0000 0001 2296 0625Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marco Telford
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Íñigo Olalde
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain ,grid.424810.b0000 0004 0467 2314Ikerbasque—Basque Foundation of Science, Bilbao, Spain
| | - Rafael de Cid
- grid.429186.00000 0004 1756 6852Genomes for Life-GCAT Lab, Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Maarten H. D. Larmuseau
- grid.5596.f0000 0001 0668 7884Laboratory of Human Genetic Genealogy, Department of Human Genetics, KU Leuven, Leuven, Belgium ,grid.5284.b0000 0001 0790 3681ARCHES–Antwerp Cultural Heritage Sciences, Faculty of Design Sciences, University of Antwerp, Antwerp, Belgium ,Histories Vzw, Gent, Belgium
| | - Marian M. de Pancorbo
- grid.11480.3c0000000121671098BIOMICs Research Group, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- grid.5612.00000 0001 2172 2676Department of Medicine and Life Sciences, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
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Liu J, Jiang L, Zhao M, Du W, Wen Y, Li S, Zhang S, Fang F, Shen J, He G, Wang M, Dai H, Hou Y, Wang Z. Development and validation of a custom panel including 256 Y-SNPs for Chinese Y-chromosomal haplogroups dissection. Forensic Sci Int Genet 2022; 61:102786. [DOI: 10.1016/j.fsigen.2022.102786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/25/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
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10
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Song M, Wang Z, Lyu Q, Ying J, Wu Q, Jiang L, Wang F, Zhou Y, Song F, Luo H, Hou Y, Song X, Ying B. Paternal genetic structure of the Qiang ethnic group in China revealed by high-resolution Y-chromosome STRs and SNPs. Forensic Sci Int Genet 2022; 61:102774. [PMID: 36156385 DOI: 10.1016/j.fsigen.2022.102774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/02/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022]
Abstract
The Qiang population mainly lived in Beichuan Qiang Autonomous County of Sichuan Province. It is one of the nomads in China, distributed along the Minjiang River. The Qiang population was assumed to have great affinity with the Han, the largest ethnic group in China, when it refers to the genetic origin. Whereas, it is deeply understudied, especially from the Y chromosome. Here in this study, we used validated high-resolution Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) panels to study the Qiang ethnic group to unravel their paternal genetic, forensic and phylogenetic characteristics. A total of 422 male samples of the Qiang ethnic group were genotyped by 233 Y-SNPs and 29 Y-STRs. Haplogroup O-M175 (N = 312) was the most predominant haplogroup in the Qiang ethnic group, followed by D-M174 (N = 32) and C-M130 (N = 32), N-M231 (N = 27), and Q-M242 (N = 15). After further subdivision, O2a-M324 (N = 213) accounted for the majority of haplogroup O. Haplogroup C2b-Z1338 (N = 29), D1a-CTS11577 (N = 30). O2a2b1a1a1-F42 (N = 48), O2a1b1a1a1a-F11 (N = 35), and O2a2b1a1-M117 (N = 21) represented other large terminal haplogroups. The results unveiled that Qiang ethnic group was a population with a high percentage of haplogroup O2a2b1a1a1-F42 (48/422) and O2a1b1a1a1a-F11 (35/422), and O2a2b1a1-M117 (21/422), which has never been reported. Its haplogroup distribution pattern was different from any of the Han populations, implying that the Qiang ethnic group had its unique genetic pattern. Mismatch analysis indicated that the biggest mismatch number in haplogroup O2a2b1a1a1-F42 was 21, while that of haplogroup O2a1b1a1a1a-F11 was 20. The haplotype diversity of the Qiang ethnic group equaled 0.999788, with 392 haplotypes observed, of which 367 haplotypes were unique. The haplogroup diversity of the Qiang ethnic group reached 0.9767, and 53 terminal haplogroups were observed (The haplogroup diversity of the Qiang ethnic group was the highest among Qiang and all Han subgroups, indicating the larger genetic diversity of the Qiang ethnic group.). Haplogroup O2a2b1a1a1-F42 was the most predominant haplogroup, including 11.37 % of the Qiang individuals. Median-joining trees showed gene flow between the Qiang and Han individuals. Our results indicated that 1) the highest genetic diversity was observed in the Qiang ethnic group compared to any of the former studied Chinese population, suggesting that the Qiang might be an older paternal branch; 2) the haplogroup D-M174 individuals of Qiang, Tibetans and Japanese distributed in three different subclades, which was unable to identify through low-resolution Y-SNP panel; and 3) the Qiang had lower proportion of haplogroup D compared to Yi and Tibetan ethnic groups, showing that the Qiang had less genetic communication with them than with Han Chinese.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Qiang Lyu
- Department of Clinical Laboratory, People's Hospital of Beichuan Qiang Autonomous County, Beichuan 622750, Sichuan, China
| | - Jun Ying
- Department of Clinical Laboratory, Santai People's Hospital, Santai 621100, Sichuan, China
| | - Qian Wu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
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Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs. Genes (Basel) 2022; 13:genes13081363. [PMID: 36011274 PMCID: PMC9407086 DOI: 10.3390/genes13081363] [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: 04/17/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation.
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12
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Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. Forensic Sci Int Genet 2022; 59:102708. [DOI: 10.1016/j.fsigen.2022.102708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/18/2022]
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13
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Vaura F, Palmu J, Aittokallio J, Kauko A, Niiranen T. Genetic, Molecular, and Cellular Determinants of Sex-Specific Cardiovascular Traits. Circ Res 2022; 130:611-631. [PMID: 35175841 DOI: 10.1161/circresaha.121.319891] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the well-known sex dimorphism in cardiovascular disease traits, the exact genetic, molecular, and cellular underpinnings of these differences are not well understood. A growing body of evidence currently points at the links between cardiovascular disease traits and the genome, epigenome, transcriptome, and metabolome. However, the sex-specific differences in these links remain largely unstudied due to challenges in bioinformatic methods, inadequate statistical power, analytic costs, and paucity of valid experimental models. This review article provides an overview of the literature on sex differences in genetic architecture, heritability, epigenetic changes, transcriptomic signatures, and metabolomic profiles in relation to cardiovascular disease traits. We also review the literature on the associations between sex hormones and cardiovascular disease traits and discuss the potential mechanisms underlying these associations, focusing on human studies.
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Affiliation(s)
- Felix Vaura
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland
| | - Joonatan Palmu
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland
| | - Jenni Aittokallio
- Department of Anesthesiology and Intensive Care (J.A.), University of Turku, Finland.,Division of Perioperative Services, Intensive Care and Pain Medicine (J.A.), Turku University Hospital, Finland
| | - Anni Kauko
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland
| | - Teemu Niiranen
- Department of Internal Medicine (F.V., J.P., A.K., T.N.), University of Turku, Finland.,Division of Medicine (T.N.), Turku University Hospital, Finland.,Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland (T.N.)
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14
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Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel. PLoS One 2022; 17:e0264125. [PMID: 35176104 PMCID: PMC8853543 DOI: 10.1371/journal.pone.0264125] [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: 07/05/2021] [Accepted: 02/03/2022] [Indexed: 11/19/2022] Open
Abstract
Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.
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Abstract
Direct-to-consumer DNA testing is increasingly affordable and accessible, and the potential implications from these tests are becoming more important. As additional people partake in DNA testing, larger population groups and information will cause further refinement of results and more extensive databases, resulting in further potential opportunities to connect biological relatives and increased chances of testers potentially having their identities re-aligned, reinforced or solidified. The effects of DNA testing were explored through 16 semi-structured in-depth interviews conducted with participants who had received their DNA test results. These participants came from diverse groups, genders and ethnic backgrounds. A thematic analysis found that notions of family were frequently challenged with unexpected DNA test results causing shifts in personal and social identities, especially in their family and biological identities. Discrepancies in DNA test results prompted re-negotiation of these identities and affected their feelings of belonging to their perceived social groups. Participants’ identities were important to them in varying degrees, with some feeling stronger connections with specific identities, thus having significant re-alignment of these identities and feelings of belonging. This article discusses the thematic analysis’s findings and explores how identities of the participants, many of whom took the test for genealogical purposes, were affected by DNA test results. As more people undertake DNA testing, it is important to explore how it may change the notions of family in the future and how their biological and family identities are affected.
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16
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Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan. Sci Rep 2022; 12:1027. [PMID: 35046511 PMCID: PMC8770644 DOI: 10.1038/s41598-022-05076-3] [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: 04/01/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.
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17
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Xu ZM, Rüeger S, Zwyer M, Brites D, Hiza H, Reinhard M, Rutaihwa L, Borrell S, Isihaka F, Temba H, Maroa T, Naftari R, Hella J, Sasamalo M, Reither K, Portevin D, Gagneux S, Fellay J. Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. PLoS Comput Biol 2022; 18:e1009628. [PMID: 35025869 PMCID: PMC8791479 DOI: 10.1371/journal.pcbi.1009628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 01/26/2022] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels and array designs, since the selected single nucleotide polymorphisms (SNPs) may fail to capture population-specific haplotype structures, hence the full extent of common genetic variation. Here, we propose to sequence the full genomes of a small subset of an underrepresented study cohort to inform the selection of population-specific add-on tag SNPs and to generate an internal population-specific imputation reference panel, such that the remaining array-genotyped cohort could be more accurately imputed. Using a Tanzania-based cohort as a proof-of-concept, we demonstrate the validity of our approach by showing improvements in imputation accuracy after the addition of our designed add-on tags to the base H3Africa array. Genome-wide association studies, which study the association between genetic variants and various phenotypes, typically rely on genotyping arrays. Only a small proportion of genetic variants within the genome are typed on genotyping arrays. Untyped variants are statistically inferred through a process known as genotype imputation, where correlations between variants (haplotypes) observed in external reference panels are leveraged to infer untyped variants in the study population. However, for study populations that are underrepresented in existing reference panels, the quality of imputation is often sub-optimal. This is because typed variants incorporated on existing genotyping arrays can be unsuitable for the study population, and haplotype structures can be different between the reference and the study population. Here, we illustrate an approach to select a custom set of population-specific typed variants to improve genotype imputation in such underrepresented populations.
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Affiliation(s)
- Zhi Ming Xu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sina Rüeger
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michaela Zwyer
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Hellen Hiza
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Liliana Rutaihwa
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | - Thomas Maroa
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Jerry Hella
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Klaus Reither
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 2021; 57:102646. [PMID: 34875492 DOI: 10.1016/j.fsigen.2021.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/31/2022]
Abstract
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases FST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10-70. In a population genetic analysis, El Salvador showed the lowest FST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.
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Affiliation(s)
- Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadísitca, Universitat de Barcelona, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Nury Rivas
- Instituto de Medicina Legal Dr. Roberto Masferrer, San Salvador, El Salvador
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, 27 calle Pnte. No.1329 Colonia Layco, San Salvador, El Salvador
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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Claerhout S, Verstraete P, Warnez L, Vanpaemel S, Larmuseau M, Decorte R. CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics. PLoS Genet 2021; 17:e1009758. [PMID: 34491993 PMCID: PMC8423258 DOI: 10.1371/journal.pgen.1009758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/05/2021] [Indexed: 11/26/2022] Open
Abstract
Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics. Around 95% of the male-specific Y-chromosome (chrY) is non-recombining and therefore inherited in a conserved manner from father to son. It can therefore serve as a powerful marker for interdisciplinary genetic-genealogical research as it provides a strong link between genetic information and a family tree or pedigree. While Y-chromosomal short tandem repeats (Y-STRs) discriminate close paternal kinships, single nucleotide polymorphisms (Y-SNPs) enables the identification of far evolutionary ancestry. Unfortunately, an extensive chrY-specific sequencing panel combining a large number of familial Y-STRs and evolutionary Y-SNPs was not yet available. Therefore, chrY is rarely included in research projects and not often linked to a genealogical, history-demographical or life science database. In this way, the importance of chrY still remains not yet fully understood. Massive parallel sequencing (MPS) allows the simultaneous analysis at sequence level of Y-SNPs and Y-STRs with variable mutation rates in a large number of males. However, up until today, no commercial kit is exploiting the full potential that MPS offers on chrY. Therefore, we developed the ‘CSYseq’, which is the first extensive chrY-specific sequencing panel. The CSYseq simultaneously identifies 9,014 slow mutating Y-SNPs to identify evolutionary ancestry, and 202 rapid mutating Y-STRs to investigate paternal relationships. We validated and optimized the panel through the analysis of 130 males distributed over 65 families. This novel MPS panel is useful for biogeographical identity and ancestry analysis, together with Y-chromosome profiling for the identification of patrilineages and discrimination of closely related males. As the CSYseq includes a very diverse set of markers that can be easily interpreted, it is interesting for different interdisciplinary applications within evolutionary, population, molecular, medical and forensic genetics.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Liesbeth Warnez
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Simon Vanpaemel
- KU Leuven, Department of Mechanical Engineering, Noise and Vibration Engineering, Leuven, Belgium
- DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Maarten Larmuseau
- Histories vzw, Mechelen, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
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Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
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21
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Parfenchyk MS, Kotava SA. The Theoretical Framework for the Panels of DNA Markers Formation in the Forensic Determination of an Individual Ancestral Origin. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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22
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Villaescusa P, Seidel M, Nothnagel M, Pinotti T, González-Andrade F, Alvarez-Gila O, M de Pancorbo M, Roewer L. A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373. Forensic Sci Int Genet 2020; 51:102427. [PMID: 33254102 DOI: 10.1016/j.fsigen.2020.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (RST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.
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Affiliation(s)
- Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Oscar Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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23
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Lall GM, Larmuseau MHD, Wetton JH, Batini C, Hallast P, Huszar TI, Zadik D, Aase S, Baker T, Balaresque P, Bodmer W, Børglum AD, de Knijff P, Dunn H, Harding SE, Løvvik H, Dupuy BM, Pamjav H, Tillmar AO, Tomaszewski M, Tyler-Smith C, Verdugo MP, Winney B, Vohra P, Story J, King TE, Jobling MA. Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain. Eur J Hum Genet 2020; 29:512-523. [PMID: 33139852 PMCID: PMC7940619 DOI: 10.1038/s41431-020-00747-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/08/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.
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Affiliation(s)
| | - Maarten H D Larmuseau
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.,Laboratory of Socioecology and Social Evolution, KU Leuven-University of Leuven, Leuven, Belgium.,Histories vzw, Zoutwerf 5, 2800, Mechelen, Belgium
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Pille Hallast
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Tunde I Huszar
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Daniel Zadik
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | | | - Tina Baker
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Patricia Balaresque
- UMR5288, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | - Walter Bodmer
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anders D Børglum
- Department of Biomedicine & Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hayley Dunn
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK.,Museum of Cultural History, University of Oslo, Oslo, Norway
| | | | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
| | - Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | | | - Marta Pereira Verdugo
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, UK
| | - Pragya Vohra
- School of History, Politics and International Relations, University of Leicester, Leicester, UK.,Department of History, University of York, Heslington, York, UK
| | - Joanna Story
- School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Turi E King
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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24
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"Distribution of paternal lineages in Mestizo populations throughout Mexico: an in silico study based on Y-STR haplotypes". J Hum Genet 2020; 66:327-332. [PMID: 32920600 DOI: 10.1038/s10038-020-00824-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/05/2020] [Accepted: 08/05/2020] [Indexed: 01/04/2023]
Abstract
The Mexican-Mestizo population arose following European contact with the Americas due to the admixture of principally Spaniards, Native Americans, and Africans around 500 years ago. Because the paternal lineage distribution of the Mexican population has been poorly investigated, this study inferred the haplogroups of ten populations based on 1859 haplotypes (Y-STR data) using two haplogroup predictor programs. In the Mexican population sample, we found predominantly European ancestry (50.1%), followed by Native American (32.5%), Eurasian (13.4%), African (2.1%), East African-South Eurasian (1.3%), and Asian (0.6%) ancestries. In general, our results support a contrary north-to-south gradient throughout the Mexican territory of European and Native-American ancestries, respectively. Moreover, the presence of West-European R1b and Sub-Saharan African E1b1a haplogroups agrees with historical and genetic data of gene flow during the European conquest. This study represents the effort to analyze these paternal lineages on a large scale by taking advantage of Y-STR haplotype data to determine the distribution and ancestry proportions in this country.
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25
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D’Atanasio E, Trionfetti F, Bonito M, Sellitto D, Coppa A, Berti A, Trombetta B, Cruciani F. Y Haplogroup Diversity of the Dominican Republic: Reconstructing the Effect of the European Colonization and the Trans-Atlantic Slave Trades. Genome Biol Evol 2020; 12:1579-1590. [PMID: 32835369 PMCID: PMC7523727 DOI: 10.1093/gbe/evaa176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2020] [Indexed: 12/12/2022] Open
Abstract
The Dominican Republic is one of the two countries on the Hispaniola island, which is part of the Antilles. Hispaniola was affected by the European colonization and massive deportation of African slaves since the XVI century and these events heavily shaped the genetic composition of the present-day population. To shed light about the effect of the European rules, we analyzed 92 single nucleotide polymorphisms on the Y chromosome in 182 Dominican individuals from three different locations. The Dominican Y haplogroup composition was characterized by an excess of northern African/European lineages (59%), followed by the African clades (38%), whereas the Native-American lineages were rare (3%). The comparison with the mitochondrial DNA variability, dominated by African clades, revealed a sex-biased admixture pattern, in line with the colonial society dominated by European men. When other Caribbean and non-Caribbean former colonies were also considered, we noted a difference between territories under a Spanish rule (like the Dominican Republic) and British/French rule, with the former characterized by an excess of European Y lineages reflecting the more permissive Iberian legislation about mixed people and slavery. Finally, we analyzed the distribution in Africa of the Dominican lineages with a putative African origin, mainly focusing on central and western Africa, which were the main sources of African slaves. We found that most (83%) of the African lineages observed in Santo Domingo have a central African ancestry, suggesting that most of the slaves were deported from regions.
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Affiliation(s)
- Eugenia D’Atanasio
- Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Flavia Trionfetti
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Andrea Berti
- Reparto CC Investigazioni Scientifiche di Roma, Sezione di Biologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Istituto di Biologia e Patologia Molecolari, CNR, Roma, Italy
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
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26
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Della Rocca C, Cannone F, D'Atanasio E, Bonito M, Anagnostou P, Russo G, Barni F, Alladio E, Destro-Bisol G, Trombetta B, Berti A, Cruciani F. Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel. Forensic Sci Int Genet 2020; 49:102374. [PMID: 32890883 DOI: 10.1016/j.fsigen.2020.102374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/06/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022]
Abstract
Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (ΦST = 0.14) largely exceeded that found among countries (ΦST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches.
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Affiliation(s)
- Chiara Della Rocca
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Cannone
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | | | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 - Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Filippo Barni
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Eugenio Alladio
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Giovanni Destro-Bisol
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 - Rome, Italy; Istituto Italiano di Antropologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma - Sezione di Biologia, Viale Tor di Quinto 119, 00191, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy; Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy.
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27
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Zieger M, Utz S. The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration. Forensic Sci Int Genet 2020; 48:102345. [PMID: 32622325 DOI: 10.1016/j.fsigen.2020.102345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 12/09/2022]
Abstract
A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.
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Affiliation(s)
- Martin Zieger
- Institute of Forensic Medicine, Forensic Molecular BiologyDpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
| | - Silvia Utz
- Institute of Forensic Medicine, Forensic Molecular BiologyDpt., University of Bern, Sulgenauweg 40, 3007, Bern, Switzerland.
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28
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Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs. Genes (Basel) 2020; 11:genes11070743. [PMID: 32635262 PMCID: PMC7397191 DOI: 10.3390/genes11070743] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022] Open
Abstract
Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.
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Naidoo T, Xu J, Vicente M, Malmström H, Soodyall H, Jakobsson M, Schlebusch CM. Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences. Genome Biol Evol 2020; 12:1031-1039. [PMID: 32697300 PMCID: PMC7375190 DOI: 10.1093/gbe/evaa098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/30/2022] Open
Abstract
Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.
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Affiliation(s)
- Thijessen Naidoo
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Jingzi Xu
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
- Academy of Science of South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
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30
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [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: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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Coutinho A, Günther T, Munters AR, Svensson EM, Götherström A, Storå J, Malmström H, Jakobsson M. The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:638-649. [PMID: 32497286 DOI: 10.1002/ajpa.24079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/26/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. METHODS We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. RESULTS The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style. CONCLUSION We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.
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Affiliation(s)
- Alexandra Coutinho
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
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González-Fortes G, Tassi F, Trucchi E, Henneberger K, Paijmans JLA, Díez-Del-Molino D, Schroeder H, Susca RR, Barroso-Ruíz C, Bermudez FJ, Barroso-Medina C, Bettencourt AMS, Sampaio HA, Grandal-d'Anglade A, Salas A, de Lombera-Hermida A, Fabregas Valcarce R, Vaquero M, Alonso S, Lozano M, Rodríguez-Alvarez XP, Fernández-Rodríguez C, Manica A, Hofreiter M, Barbujani G. A western route of prehistoric human migration from Africa into the Iberian Peninsula. Proc Biol Sci 2020; 286:20182288. [PMID: 30963949 DOI: 10.1098/rspb.2018.2288] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar.
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Affiliation(s)
- G González-Fortes
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - F Tassi
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - E Trucchi
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - K Henneberger
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - J L A Paijmans
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - D Díez-Del-Molino
- 3 Department of Bioinformatics and Genetics, Swedish Museum of Natural History , 104 05 Stockholm , Sweden
| | - H Schroeder
- 4 Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen , 1353 Copenhagen K , Denmark
| | - R R Susca
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - C Barroso-Ruíz
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - F J Bermudez
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - C Barroso-Medina
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - A M S Bettencourt
- 6 Landscape, Heritage and Territory Laboratory-Lab2PT, Department of History, University of Minho , 4700-057 Braga , Portugal
| | - H A Sampaio
- 7 Landscape, Heritage and Territory Laboratory-Lab2PT, Department of Hospitality and Tourism, Polytechnic Institute of Cávado and Ave , Barcelos , Portugal
| | - A Grandal-d'Anglade
- 8 Universitary Institute of Geology, University of Coruña , A Coruña 15081 , Spain
| | - A Salas
- 9 Unidade de Xenética, Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, and GenPoB (IDIS-SERGAS) , Galicia , Spain
| | - A de Lombera-Hermida
- 10 Department of History GEPN-AAT, University of Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - R Fabregas Valcarce
- 10 Department of History GEPN-AAT, University of Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - M Vaquero
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - S Alonso
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - M Lozano
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - X P Rodríguez-Alvarez
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | | | - A Manica
- 14 Department of Zoology, University of Cambridge , Cambridge CB2 3EJ , UK
| | - M Hofreiter
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - G Barbujani
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
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Petrovick MS, Boettcher T, Fremont-Smith P, Peragallo C, Ricke DO, Watkins J, Schwoebel E. Analysis of complex DNA mixtures using massively parallel sequencing of SNPs with low minor allele frequencies. Forensic Sci Int Genet 2020; 46:102234. [PMID: 32018060 DOI: 10.1016/j.fsigen.2020.102234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/05/2019] [Accepted: 01/02/2020] [Indexed: 11/18/2022]
Abstract
DNA mixtures from 3 or more contributors have proven difficult to analyze using the current state-of-the-art method of short-tandem repeat (STR) amplification followed by capillary electrophoresis (CE). Here we analyze samples from both laboratory-defined mixtures and complex multi-contributor touch samples using a single nucleotide polymorphism (SNP) panel comprised of 2311 low-minor-allele-frequency loci, combined with massively parallel sequencing (MPS). This approach demonstrates that as many as 10 people can be identified in touch samples using a threshold of -Log P(RMNE) of 6, and a detection rate of 18-94 % across 10 different materials using a threshold of -Log P(RMNE) of 2. Thirty-two false positives were observed in 100 touch samples.
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Affiliation(s)
- Martha S Petrovick
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States.
| | - Tara Boettcher
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Philip Fremont-Smith
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Chelsea Peragallo
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Darrell O Ricke
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - James Watkins
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
| | - Eric Schwoebel
- Massachusetts Institute of Technology, Lincoln Laboratory, 244 Wood St., Lexington, MA 02421, United States
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34
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Schaan AP, Gusmão L, Jannuzzi J, Modesto A, Amador M, Marques D, Rabenhorst SH, Montenegro R, Lopes T, Yoshioka FK, Pinto G, Santos S, Costa L, Silbiger V, Ribeiro-Dos-Santos Â. New insights on intercontinental origins of paternal lineages in Northeast Brazil. BMC Evol Biol 2020; 20:15. [PMID: 31996123 PMCID: PMC6990597 DOI: 10.1186/s12862-020-1579-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022] Open
Abstract
Background The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states. Results Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, FST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions. Conclusions We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.
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Affiliation(s)
- Ana Paula Schaan
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Juliana Jannuzzi
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Antonio Modesto
- Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil
| | - Marcos Amador
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Diego Marques
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Silvia Helena Rabenhorst
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Raquel Montenegro
- Pathology and Legal Medicine Department, Federal University of Ceará, Fortaleza, CE, 60020-181, Brazil
| | - Thayson Lopes
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - France Keiko Yoshioka
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Giovanny Pinto
- Genetics and Molecular Biology Laboratory, Federal University of Piauí, Parnaíba, PI, 64202-020, Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil
| | - Lorenna Costa
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Vivian Silbiger
- Clinical and Toxicological Analyses Department, Federal University of Rio Grande do Norte, Natal, RN, 59300-000, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Human and Medical Genetics Laboratory, Federal University of Pará, Av. Augusto Corrêa, 01 - Cidade Universitária Prof. José Silveira Netto - Guamá, Belém, PA, 66075-110, Brazil. .,Center for Oncology Research, Federal University of Pará, Belém, PA, 66073-005, Brazil.
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Larmuseau MH, van den Berg P, Claerhout S, Calafell F, Boattini A, Gruyters L, Vandenbosch M, Nivelle K, Decorte R, Wenseleers T. A Historical-Genetic Reconstruction of Human Extra-Pair Paternity. Curr Biol 2019; 29:4102-4107.e7. [DOI: 10.1016/j.cub.2019.09.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/12/2019] [Accepted: 09/30/2019] [Indexed: 11/25/2022]
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36
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Grugni V, Raveane A, Colombo G, Nici C, Crobu F, Ongaro L, Battaglia V, Sanna D, Al-Zahery N, Fiorani O, Lisa A, Ferretti L, Achilli A, Olivieri A, Francalacci P, Piazza A, Torroni A, Semino O. Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case. Int J Mol Sci 2019; 20:E5763. [PMID: 31744094 PMCID: PMC6888588 DOI: 10.3390/ijms20225763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 11/17/2022] Open
Abstract
Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Carmen Nici
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Francesca Crobu
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Daria Sanna
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Fiorani
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Antonella Lisa
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Paolo Francalacci
- Dipartimento di Scienza della Vita e dell’Ambiente, Università di Cagliari, 09123 Cagliari, Italy;
| | - Alberto Piazza
- Dipartimento di Scienze Mediche, Scuola di Medicina, Università di Torino, 10124 Torino, Italy;
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
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37
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Neparáczki E, Maróti Z, Kalmár T, Maár K, Nagy I, Latinovics D, Kustár Á, Pálfi G, Molnár E, Marcsik A, Balogh C, Lőrinczy G, Gál SS, Tomka P, Kovacsóczy B, Kovács L, Raskó I, Török T. Y-chromosome haplogroups from Hun, Avar and conquering Hungarian period nomadic people of the Carpathian Basin. Sci Rep 2019; 9:16569. [PMID: 31719606 PMCID: PMC6851379 DOI: 10.1038/s41598-019-53105-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/26/2019] [Indexed: 01/08/2023] Open
Abstract
Hun, Avar and conquering Hungarian nomadic groups arrived to the Carpathian Basin from the Eurasian Steppes and significantly influenced its political and ethnical landscape, however their origin remains largely unknown. In order to shed light on the genetic affinity of above groups we have determined Y chromosomal haplogroups and autosomal loci, suitable to predict biogeographic ancestry, from 49 individuals, supposed to represent the power/military elit. Haplogroups from the Hun-age are consistent with Xiongnu ancestry of European Huns. Most of the Avar-age individuals carry east Eurasian Y haplogroups typical for modern north-eastern Siberian and Buryat populations and their autosomal loci indicate mostly un-admixed Asian characteristics. In contrast the conquering Hungarians seem to be a recently assembled population incorporating un-admixed European, Asian as well as admixed components. Their heterogeneous paternal and maternal lineages indicate similar supposed phylogeographic origin of males and females, derived from Central-Inner Asian and European Pontic Steppe sources.
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Affiliation(s)
- Endre Neparáczki
- Department of Genetics, University of Szeged, Szeged, H-6726, Hungary
| | - Zoltán Maróti
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, H-6720, Hungary
| | - Tibor Kalmár
- Department of Pediatrics and Pediatric Health Center, University of Szeged, Szeged, H-6720, Hungary
| | - Kitti Maár
- Department of Genetics, University of Szeged, Szeged, H-6726, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, H-6782, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hun. Acad. Sci, Szeged, H-6726, Hungary
| | | | - Ágnes Kustár
- Department of Anthropology, Hungarian Natural History Museum, Budapest, H-1083, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, H-6726, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged, H-6726, Hungary
| | - Antónia Marcsik
- Department of Biological Anthropology, University of Szeged, Szeged, H-6726, Hungary
| | - Csilla Balogh
- Department of Art History, Istanbul Medeniyet University, Istanbul, 34700, Turkey
| | | | | | - Péter Tomka
- Department of Archaeology, Flóris Rómer Museum of Art and History, H-9024, Győr, Hungary
| | | | - László Kovács
- Institute of Archaeology of the Center for Humanities of the Hun. Acad. Sci, Budapest, Hungary
| | - István Raskó
- Institute of Genetics, Biological Research Centre of the Hun. Acad. Sci, Szeged, H-6726, Hungary
| | - Tibor Török
- Department of Genetics, University of Szeged, Szeged, H-6726, Hungary.
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38
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Claerhout S, Roelens J, Van der Haegen M, Verstraete P, Larmuseau MHD, Decorte R. Ysurnames? The patrilineal Y-chromosome and surname correlation for DNA kinship research. Forensic Sci Int Genet 2019; 44:102204. [PMID: 31760354 DOI: 10.1016/j.fsigen.2019.102204] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 11/30/2022]
Abstract
The Y-chromosome is a widely studied and useful small part of the genome providing different applications for interdisciplinary research. In many (Western) societies, the Y-chromosome and surnames are paternally co-inherited, suggesting a corresponding Y-haplotype for every namesake. While it has already been observed that this correlation may be disrupted by a false-paternity event, adoption, anonymous sperm donor or the co-founding of surnames, extensive information on the strength of the surname match frequency (SMF) with the Y-chromosome remains rather unknown. For the first time in Belgium and the Netherlands, we were able to study this correlation using 2,401 males genotyped for 46 Y-STRs and 183 Y-SNPs. The SMF was observed to be dependent on the number of Y-STRs analyzed, their mutation rates and the number of Y-STR differences allowed for a kinship. For a perfect match, the Yfiler® Plus and our in-house YForGen kit gave a similar high SMF of 98%, but for non-perfect matches, the latter could overall be identified as the best kit. The SMF generally increased due to less mismatches when encountering [1] deep Y-subhaplogroups, [2] less frequently occurring surnames, and [3] small geographical distances between relatives. This novel information enabled the design of a surname prediction model based on genetic and geographical distances of a kinship. The prediction model has an area under the curve (AUC) of 0.9 and is therefore useable for DNA kinship priority listing in estimation applications like forensic familial searching.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium.
| | - Jennifer Roelens
- Department of Earth and Environmental Sciences, KU Leuven, Leuven 3000, Belgium
| | - Michiel Van der Haegen
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Maarten H D Larmuseau
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven 3000, Belgium; Histories vzw, Mechelen 2800, Belgium; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium; Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven 3000, Belgium
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39
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Anderson K, Cañadas-Garre M, Chambers R, Maxwell AP, McKnight AJ. The Challenges of Chromosome Y Analysis and the Implications for Chronic Kidney Disease. Front Genet 2019; 10:781. [PMID: 31552093 PMCID: PMC6737325 DOI: 10.3389/fgene.2019.00781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The role of chromosome Y in chronic kidney disease (CKD) remains unknown, as chromosome Y is typically excluded from genetic analysis in CKD. The complex, sex-specific presentation of CKD could be influenced by chromosome Y genetic variation, but there is limited published research available to confirm or reject this hypothesis. Although traditionally thought to be associated with male-specific disease, evidence linking chromosome Y genetic variation to common complex disorders highlights a potential gap in CKD research. Chromosome Y variation has been associated with cardiovascular disease, a condition closely linked to CKD and one with a very similar sexual dimorphism. Relatively few sources of genetic variation in chromosome Y have been examined in CKD. The association between chromosome Y aneuploidy and CKD has never been explored comprehensively, while analyses of microdeletions, copy number variation, and single-nucleotide polymorphisms in CKD have been largely limited to the autosomes or chromosome X. In many studies, it is unclear whether the analyses excluded chromosome Y or simply did not report negative results. Lack of imputation, poor cross-study comparability, and requirement for separate or additional analyses in comparison with autosomal chromosomes means that chromosome Y is under-investigated in the context of CKD. Limitations in genotyping arrays could be overcome through use of whole-chromosome sequencing of chromosome Y that may allow analysis of many different types of genetic variation across the chromosome to determine if chromosome Y genetic variation is associated with CKD.
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Affiliation(s)
- Kerry Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Marisa Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Robyn Chambers
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Alexander Peter Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
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40
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Jankova R, Seidel M, Videtič Paska A, Willuweit S, Roewer L. Y-chromosome diversity of the three major ethno-linguistic groups in the Republic of North Macedonia. Forensic Sci Int Genet 2019; 42:165-170. [PMID: 31351212 DOI: 10.1016/j.fsigen.2019.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/31/2019] [Accepted: 07/10/2019] [Indexed: 10/26/2022]
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41
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Lang M, Liu H, Song F, Qiao X, Ye Y, Ren H, Li J, Huang J, Xie M, Chen S, Song M, Zhang Y, Qian X, Yuan T, Wang Z, Liu Y, Wang M, Liu Y, Liu J, Hou Y. Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population. Forensic Sci Int Genet 2019; 42:e13-e20. [PMID: 31353318 DOI: 10.1016/j.fsigen.2019.07.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 07/20/2019] [Accepted: 07/20/2019] [Indexed: 12/11/2022]
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) frequency distributions provide resources for assessment of male population stratification among world-wide populations. Currently, the Y-STR Haplotype Reference Database (YHRD) contains numerous Y-chromosome haplotype profiles from various populations and countries around the world. However, for many of the recently discovered and already phylogenetically mapped Y-SNPs, the population data are scarce. Herein, the typing of 27 Y-STRs (Yfiler Plus) and 143 Y-SNPs (self-designed Y-SNP panel) was performed on 1269 unrelated males from 11 Han Chinese populations. Haplogroup O-M175 was the most predominant haplogroup in our Han Chinese data, ranging from 67.34% (Henan Han) to 93.16% (Guangdong Han). The highest haplogroup diversity (0.967056) was observed in Heilongjiang Han, with a discrimination capacity (DC) value of 0.3723. The number of alleles at single-copy loci varied from 2 for DYS391 (Guangdong Han) to 16 for DYS518 (Henan Han). For the majority of the populations (8/11), both the haplotype diversity and DC values are 1.0000. Furthermore, genetic differentiations were observed between Northern and Southern Han Chinese. These genetic differences were mainly reflected in haplogroup distribution and frequency, and they were confirmed by statistical analysis.
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Affiliation(s)
- Min Lang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hai Liu
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xianhua Qiao
- The Institute of Forensic Science and Technology, Henan Provincial Public Security Bureau, Zhengzhou 450003, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - He Ren
- Beijing Police College, Beijing 102202, China
| | - Jienan Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Huang
- Department of Forensic genetics, Brain Hospital of Hunan Province, Hunan University of Chinese Medicine, Changsha 410007, China
| | - Mingkun Xie
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shengjie Chen
- Criminal Detection Unit of Qingxiu District Public Security Sub-bureau in Nanning, Nanning 530000, China
| | - Mengyuan Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Youfang Zhang
- Department of Forensic Science, Zhejiang Police College, Hangzhou 310053, China
| | - Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Taoxiu Yuan
- Forensic Science Institute of Zhejiang Di'an Diagnosis Technology Co., Ltd, Hangzhou 310012, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yuming Liu
- Forensic Science Center Zhongding Guangdong, Zhanjiang 524000, China
| | - Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yacheng Liu
- Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100085, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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42
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Ralf A, van Oven M, Montiel González D, de Knijff P, van der Beek K, Wootton S, Lagacé R, Kayser M. Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing. Forensic Sci Int Genet 2019; 41:93-106. [PMID: 31063905 DOI: 10.1016/j.fsigen.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. However, most previously developed forensic Y-SNP tools did not provide Y haplogroup resolution on the high level needed in forensic applications, because the limited multiplex capacity of the DNA technologies used only allowed the inclusion of a relatively small number of Y-SNPs. In a proof-of-principle study, we recently demonstrated that high-resolution Y haplogrouping is feasible via two AmpliSeq PCR analyses and simultaneous massively parallel sequencing (MPS) of 530 Y-SNPs allowing the inference of 432 Y-haplogroups. With the current study, we present a largely improved Y-SNP MPS lab tool that we specifically designed for the analysis of low quality and quantity DNA often confronted with in forensic DNA analysis. Improvements include i) Y-SNP marker selection based on the "minimal reference phylogeny for the human Y chromosome" (PhyloTree Y), ii) strong increase of the number of targeted Y-SNPs allowing many more Y haplogroups to be inferred, iii) focus on short amplicon length enabling successful analysis of degraded DNA, and iv) combination of all amplicons in a single AmpliSeq PCR and simultaneous sequencing allowing single DNA aliquot use. This new MPS tool simultaneously analyses 859 Y-SNPs and allows inferring 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that this tool performs highly accurate, is sensitive and robust. We also provide a revised software tool for analysing the sequencing data produced by the new MPS lab tool including final Y haplogroup assignment. We envision the tools introduced here for high-resolution Y-chromosomal haplogrouping to determine a man's paternal lineage and/or paternal bio-geographic ancestry to become widely used in forensic Y-chromosome DNA analysis and other applications were Y haplogroup information from low quality / quantity DNA samples is required.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Kees van der Beek
- Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB, The Hague, the Netherlands
| | - Sharon Wootton
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Robert Lagacé
- Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands.
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43
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Roewer L. Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/wfs2.1336] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin and Berlin Institute of Health, Charité‐Universitätsmedizin Berlin 13353 Berlin Germany
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44
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Forensic characteristics and phylogenetic analysis of both Y-STR and Y-SNP in the Li and Han ethnic groups from Hainan Island of China. Forensic Sci Int Genet 2019; 39:e14-e20. [DOI: 10.1016/j.fsigen.2018.11.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/24/2018] [Accepted: 11/26/2018] [Indexed: 11/21/2022]
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45
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Wang M, Wang Z, He G, Liu J, Wang S, Qian X, Lang M, Li J, Xie M, Li C, Hou Y. Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system. Forensic Sci Int Genet 2019; 38:70-76. [DOI: 10.1016/j.fsigen.2018.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 09/18/2018] [Accepted: 10/09/2018] [Indexed: 02/03/2023]
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46
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Alonso Morales LA, Casas-Vargas A, Rojas Castro M, Resque R, Ribeiro-dos-Santos ÂK, Santos S, Gusmão L, Usaquén W. Paternal portrait of populations of the middle Magdalena River region (Tolima and Huila, Colombia): New insights on the peopling of Central America and northernmost South America. PLoS One 2018; 13:e0207130. [PMID: 30439976 PMCID: PMC6237345 DOI: 10.1371/journal.pone.0207130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/25/2018] [Indexed: 11/18/2022] Open
Abstract
The valley of the Magdalena River is one of the main population pathways in Colombia. The gene pool and spatial configuration of human groups in this territory have been outlined throughout three historical stages: the Native pre-Hispanic world, Spanish colonization, and XIX century migrations. This research was designed with the goal of characterizing the diversity and distribution pattern of Y-chromosome lineages that are currently present in the Tolima and Huila departments (middle Magdalena River region). Historic cartography was used to identify the main geographic sites where the paternal lineages belonging to this area have gathered. Twelve municipalities were chosen, and a survey that included genealogical information was administered. Samples collected from 83 male volunteers were analyzed for 48 Y-SNPs and 17 Y-STRs. The results showed a highly diverse region characterized by the presence of 16 sublineages within the major clades R, Q, J, G, T and E and revealed that 93% (n = 77) of haplotypes were different. Among these haplogroups, European-specific R1b-M269 lineages were the most representative (57.83%), with six different subhaplogroups and 43 unique haplotypes. Native American paternal ancestry was also detected based on the presence of the Q1a2-M3*(xM19, M194, M199) and Q1a2-M346*(xM3) lineages. Interestingly, all Q1a2-M346*(xM3) samples (n = 7, with five different haplotypes) carried allele six at the DYS391 locus. This allele has a worldwide frequency of 0.169% and was recently associated with a new Native subhaplogroup. An in-depth phylogenetic analysis of these samples suggests the Tolima and Huila region to be the principal area in all Central and South America where this particular Native lineage is found. This lineage has been present in the region for at least 1,809 (+/- 0,5345) years.
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Affiliation(s)
- Luz Angela Alonso Morales
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail: (LAAM); (WU)
| | - Andrea Casas-Vargas
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Madelyn Rojas Castro
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Rafael Resque
- Laboratório de Toxicologia e Química Farmacêutica, Departamento de Ciências da Saúde e Biológicas, Universidade Federal do Amapá, Macapá, Brazil
| | - Ândrea Kelly Ribeiro-dos-Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará - UFPA), Belém, state of Pará (PA), Brazil
| | - Sidney Santos
- Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará - UFPA), Belém, state of Pará (PA), Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), Institute of Biology, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - William Usaquén
- Populations Genetics and Identification Group, Institute of Genetics, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail: (LAAM); (WU)
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47
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Poriswanish N, Neumann R, Wetton JH, Wagstaff J, Larmuseau MHD, Jobling MA, May CA. Recombination hotspots in an extended human pseudoautosomal domain predicted from double-strand break maps and characterized by sperm-based crossover analysis. PLoS Genet 2018; 14:e1007680. [PMID: 30296256 PMCID: PMC6193736 DOI: 10.1371/journal.pgen.1007680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/18/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023] Open
Abstract
The human X and Y chromosomes are heteromorphic but share a region of homology at the tips of their short arms, pseudoautosomal region 1 (PAR1), that supports obligate crossover in male meiosis. Although the boundary between pseudoautosomal and sex-specific DNA has traditionally been regarded as conserved among primates, it was recently discovered that the boundary position varies among human males, due to a translocation of ~110 kb from the X to the Y chromosome that creates an extended PAR1 (ePAR). This event has occurred at least twice in human evolution. So far, only limited evidence has been presented to suggest this extension is recombinationally active. Here, we sought direct proof by examining thousands of gametes from each of two ePAR-carrying men, for two subregions chosen on the basis of previously published male X-chromosomal meiotic double-strand break (DSB) maps. Crossover activity comparable to that seen at autosomal hotspots was observed between the X and the ePAR borne on the Y chromosome both at a distal and a proximal site within the 110-kb extension. Other hallmarks of classic recombination hotspots included evidence of transmission distortion and GC-biased gene conversion. We observed good correspondence between the male DSB clusters and historical recombination activity of this region in the X chromosomes of females, as ascertained from linkage disequilibrium analysis; this suggests that this region is similarly primed for crossover in both male and female germlines, although sex-specific differences may also exist. Extensive resequencing and inference of ePAR haplotypes, placed in the framework of the Y phylogeny as ascertained by both Y microsatellites and single nucleotide polymorphisms, allowed us to estimate a minimum rate of crossover over the entire ePAR region of 6-fold greater than genome average, comparable with pedigree estimates of PAR1 activity generally. We conclude ePAR very likely contributes to the critical crossover function of PAR1. 95% of our genome is contained in 22 pairs of chromosomes shared by all humans. However, women and men differ in their sex chromosomes: while women have two X chromosomes, men have an X and a smaller, sex-determining Y chromosome. To ensure correct partition of X and Y into sperm, genetic exchange (crossover) must occur between these very different chromosomes in a short, shared region. The location of the boundary of this region was thought to have been conserved since before the divergence from old world monkeys at least 27 million years ago, but recently it has been shown that some human males carry an extended version on their Y chromosomes, thanks to the transposition of a piece of DNA from the X chromosome. Here, we asked if genetic exchange occurs in this newly extended region. To do this, we used previously published information that signposted the positions within the X chromosome segment which exhibit the hallmarks of crossover initiation. We then sought direct evidence of crossover in the sperm of men carrying the extension. This work showed that the signposts were accurate, pointing to frequent crossover in this novel shared sex-chromosomal domain.
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Affiliation(s)
- Nitikorn Poriswanish
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Forensic Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jon H. Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - John Wagstaff
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Imaging and Pathology, KU Leuven, Belgium
| | - Mark A. Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Celia A. May
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Krzewińska M, Kılınç GM, Juras A, Koptekin D, Chyleński M, Nikitin AG, Shcherbakov N, Shuteleva I, Leonova T, Kraeva L, Sungatov FA, Sultanova AN, Potekhina I, Łukasik S, Krenz-Niedbała M, Dalén L, Sinika V, Jakobsson M, Storå J, Götherström A. Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads. SCIENCE ADVANCES 2018; 4:eaat4457. [PMID: 30417088 PMCID: PMC6223350 DOI: 10.1126/sciadv.aat4457] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/23/2018] [Indexed: 05/25/2023]
Abstract
For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
| | - Gülşah Merve Kılınç
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614 Poznań, Poland
| | - Alexey G. Nikitin
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, MI 49401, USA
| | - Nikolai Shcherbakov
- Laboratory of Methodology and Methods of Humanitarian Research, Bashkir State Pedagogical University, Octyabrskoy Revolutsii, 3A, 450007 Ufa, Russia
| | - Iia Shuteleva
- Laboratory of Methodology and Methods of Humanitarian Research, Bashkir State Pedagogical University, Octyabrskoy Revolutsii, 3A, 450007 Ufa, Russia
- Institute of History and State Management, Bashkir State University, Zaki Validy Street 32, 450076 Ufa, Russia
| | - Tatiana Leonova
- Laboratory of Methodology and Methods of Humanitarian Research, Bashkir State Pedagogical University, Octyabrskoy Revolutsii, 3A, 450007 Ufa, Russia
| | - Liudmila Kraeva
- Archaeological Laboratory, Orenburg State Pedagogical University, Orenburg, Russia
| | - Flarit A. Sungatov
- Archaeological Laboratory, Bashkir State University, Str. Validi Z. 32, Ufa, Russia
| | - Alfija N. Sultanova
- Archaeological Laboratory, Bashkir State University, Str. Validi Z. 32, Ufa, Russia
| | - Inna Potekhina
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Sylwia Łukasik
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Marta Krenz-Niedbała
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614 Poznań, Poland
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Post Office Box 50007, 10405 Stockholm, Sweden
| | - Vitaly Sinika
- Taras Shevchenko University in Tiraspol, October Street 25, 33-00 Tiraspol, Moldova
- Nizhnevartovsk State University, Lenin Street, 56, Nizhnevartovsk, 628605, Khanty-Mansi Autonomous District, Yugra, Russia
| | - Mattias Jakobsson
- Subdepartment of Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18 C, SE-752 36 Uppsala, Sweden
- Science for Life Laboratory, Norbyvägen 18 C, SE-752 36 Uppsala, Sweden
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park 2006, South Africa
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91 Stockholm, Sweden
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Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 2018; 19:139. [PMID: 30241495 PMCID: PMC6151024 DOI: 10.1186/s13059-018-1522-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively. RESULTS Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours. CONCLUSIONS We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.
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Affiliation(s)
- Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Anne-Mai Ilumäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Terhi Honkola
- Department of Biology, University of Turku, 20014, Turku, Finland
- Institute of Estonian and General Linguistics, University of Tartu, 51014, Tartu, Estonia
| | - Outi Vesakoski
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Quentin Atkinson
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Sergey Litvinov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Timo Rantanen
- Department of Geography and Geology, University of Turku, 20014, Turku, Finland
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Sergey I Zhadanov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Radiology, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Marina Gubina
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Larisa D Damba
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Institute of Medical and Social Problems and Control of the Healthcare Department of Tuva Republic, Kyzyl, 667003, Russia
| | - Marina Bermisheva
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Khadizhat Dibirova
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia
- Anthony Nolan, London, NW3 2NU, UK
| | - Mari Nelis
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Andres Metspalu
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Tõnu Esko
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, 119991, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450054, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, 630090, Russia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Department of Archaeology, University of Cambridge, Cambridge, CB2 1QH, UK
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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50
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Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes. Int J Legal Med 2018; 133:17-23. [PMID: 30229332 DOI: 10.1007/s00414-018-1936-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) found within the non-recombining region of the Y chromosome (NRY) represent a powerful tool in forensic genetics for inferring the paternal ancestry of a vestige and complement the determination of biogeographical origin in combination with other markers like AIMs. In the present study, we introduce a panel of 15 Y-SNPs for a fine-resolution subtyping of the haplogroup R1b-DF27, in a single minisequencing reaction. This is the first minisequencing panel that allows a fine subtyping of R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. This panel includes subhaplogroups of DF27 that display moderate geographical differentiation, of interest to link a sample with a specific location of the Iberian Peninsula or with Iberian ancestry. Conversely, part of the intricacy of a new minisequencing panel is to have all the included variants available to test the effectiveness of the analysis method. We have overcome the absence of the least common variants through site-directed mutagenesis. Overall, the results show that our panel is a robust and effective method for subtyping R1b-DF27 lineages from a minimal amount of DNA, and its high resolution enables to improve male lineage discrimination in Iberian and Southwest European descent individuals. The small length of the amplicons and its reproducibility makes this assay suitable for forensic and population genetics purposes.
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