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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [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: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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Janho dit Hreich S, Juhel T, Leroy S, Ghinet A, Brau F, Hofman V, Hofman P, Vouret-Craviari V. Activation of the P2RX7/IL-18 pathway in immune cells attenuates lung fibrosis. eLife 2024; 12:RP88138. [PMID: 38300690 PMCID: PMC10945561 DOI: 10.7554/elife.88138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an aggressive interstitial lung disease associated with progressive and irreversible deterioration of respiratory functions that lacks curative therapies. Despite IPF being associated with a dysregulated immune response, current antifibrotics aim only at limiting fibroproliferation. Transcriptomic analyses show that the P2RX7/IL18/IFNG axis is downregulated in IPF patients and that P2RX7 has immunoregulatory functions. Using our positive modulator of P2RX7, we show that activation of the P2RX7/IL-18 axis in immune cells limits lung fibrosis progression in a mouse model by favoring an antifibrotic immune environment, with notably an enhanced IL-18-dependent IFN-γ production by lung T cells leading to a decreased production of IL-17 and TGFβ. Overall, we show the ability of the immune system to limit lung fibrosis progression by targeting the immunomodulator P2RX7. Hence, treatment with a small activator of P2RX7 may represent a promising strategy to help patients with lung fibrosis.
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Affiliation(s)
| | - Thierry Juhel
- Université Côte d’Azur, CNRS, INSERM, IRCANNiceFrance
| | - Sylvie Leroy
- FHU OncoAgeNiceFrance
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et CellulaireSophia-AntipolisFrance
- Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Pneumology DepartmentNiceFrance
| | - Alina Ghinet
- Inserm U995, LIRIC, Université de Lille, CHRU de Lille, Faculté de médecine – Pôle recherche, Place VerdunLilleFrance
- Hautes Etudes d’Ingénieur (HEI), JUNIA Hauts-de-France, UCLille, Laboratoire de chimie durable et santéLilleFrance
- ‘Al. I. Cuza’ University of Iasi, Faculty of ChemistryIasiRomania
| | - Frederic Brau
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et CellulaireSophia-AntipolisFrance
| | - Veronique Hofman
- Université Côte d’Azur, CNRS, INSERM, IRCANNiceFrance
- FHU OncoAgeNiceFrance
- Laboratory of Clinical and Experimental Pathology and Biobank, Pasteur HospitalNiceFrance
- Hospital-Related Biobank (BB-0033-00025), Pasteur HospitalNiceFrance
| | - Paul Hofman
- Université Côte d’Azur, CNRS, INSERM, IRCANNiceFrance
- FHU OncoAgeNiceFrance
- Laboratory of Clinical and Experimental Pathology and Biobank, Pasteur HospitalNiceFrance
- Hospital-Related Biobank (BB-0033-00025), Pasteur HospitalNiceFrance
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Zhang H, Huang X, Jin X, Ren Z, Wang Q, Yang M, Xu R, Yuan X, Yang D, Liu H, Shen W, Zhang H, Que Y, Huang J. Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 2023; 11:e16183. [PMID: 37780380 PMCID: PMC10538297 DOI: 10.7717/peerj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
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Affiliation(s)
- Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronglan Xu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Yuan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daiquan Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongyan Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wanyi Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Huiying Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangjie Que
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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Wagner JK, Yu JH, Fullwiley D, Moore C, Wilson JF, Bamshad MJ, Royal CD. Guidelines for genetic ancestry inference created through roundtable discussions. HGG ADVANCES 2023; 4:100178. [PMID: 36798092 PMCID: PMC9926022 DOI: 10.1016/j.xhgg.2023.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
The use of genetic and genomic technology to infer ancestry is commonplace in a variety of contexts, particularly in biomedical research and for direct-to-consumer genetic testing. In 2013 and 2015, two roundtables engaged a diverse group of stakeholders toward the development of guidelines for inferring genetic ancestry in academia and industry. This report shares the stakeholder groups' work and provides an analysis of, commentary on, and views from the groundbreaking and sustained dialogue. We describe the engagement processes and the stakeholder groups' resulting statements and proposed guidelines. The guidelines focus on five key areas: application of genetic ancestry inference, assumptions and confidence/laboratory and statistical methods, terminology and population identifiers, impact on individuals and groups, and communication or translation of genetic ancestry inferences. We delineate the terms and limitations of the guidelines and discuss their critical role in advancing the development and implementation of best practices for inferring genetic ancestry and reporting the results. These efforts should inform both governmental regulation and self-regulation.
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Affiliation(s)
- Jennifer K. Wagner
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joon-Ho Yu
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
| | - Duana Fullwiley
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
| | | | - James F. Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
| | - Michael J. Bamshad
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
| | - Charmaine D. Royal
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
| | - Genetic Ancestry Inference Roundtable Participants
- School of Engineering Design and Innovation, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Science, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA
- Rock Ethics Institute, Pennsylvania State University, University Park, PA 16802, USA
- Penn State Law, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Pediatrics and Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, USA
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
- Department of Anthropology, Stanford University, Stanford, CA 94305, USA
- The DNA Detectives, Dana Point, CA, USA
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, Scotland
- Department of Pediatrics and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA 98101, USA
- Departments of African and African American Studies, Biology, Global Health, and Family Medicine and Community Health, Duke University, Durham, NC 27708, USA
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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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Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet 2021; 57:102659. [PMID: 35007855 DOI: 10.1016/j.fsigen.2021.102659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
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Genealogy: The Tree Where History Meets Genetics. GENEALOGY 2021. [DOI: 10.3390/genealogy5040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although biological relationships are a universal reality for all human beings, the concepts of “family” and “family bond” depend on both the geographic region and the historical moment to which they refer. However, the concept of “family” can be determinant in a large variety of societies, since it can influence the lines of succession, inheritances and social relationships, as well as where and with whom an individual is buried. The relation between a deceased person and other members of a community, other individuals of the same necropolis, or even with those who are buried in the same tomb can be analysed from the genetic point of view, considering different perspectives: archaeological, historical, and forensic. In the present work, the concepts of “family” and “kinship” are discussed, explaining the relevance of genetic analysis, such as nuclear and lineage markers, and their contribution to genealogical research, for example in the heritage of surnames and Y-chromosome, as well as those cases where some discrepancies with historical record are detected, such as cases of adoption. Finally, we explain how genetic genealogical analyses can help to solve some cold cases, through the analysis of biologically related relatives.
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Aaspõllu A, Allmäe R, Puss F, Parson W, Pihkva K, Kriiska-Maiväli K, Unt A. The Unique Identification of an Unknown Soldier from the Estonian War of Independence. Genes (Basel) 2021; 12:1722. [PMID: 34828329 PMCID: PMC8624759 DOI: 10.3390/genes12111722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
The identification of human remains is challenging mostly due to the bad condition of the remains and the available background information that is sometimes limited. The current case report is related to the identification of an unknown soldier from the Estonian War of Independence (1918-1920). The case includes an anthropological study of the remains, examinations of documents found with the exhumed remains, and kinship estimations based on archival documents, and DNA analyses. As the preliminary data pointed to remains of male origin, Y-chromosomal STR (short tandem repeat) analyses of 22 Y-STR loci were used to analyze the exhumed teeth. Reference samples from individuals from two paternal lineages were collected based on archival documents. Y-chromosomal STR results for the tooth samples were consistent with a patrilineal relationship to only one reference sample out of two proposed paternal lineages. Based on the provided pedigrees in the consistent case, the Y-STR results are approximately four million times more likely if the tooth sample originated from an individual related along the paternal line to the matching reference sample, than if the tooth sample originated from another person in the general population. Special considerations have to be met when limited evidence is available.
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Affiliation(s)
- Anu Aaspõllu
- Department of Nutrition Research, National Institute for Health Development, 11619 Tallinn, Estonia
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, 10130 Tallinn, Estonia;
| | - Fred Puss
- Faculty of Arts and Humanities, University of Tartu, 50090 Tartu, Estonia;
- Department on Language History, Dialects, and Finno-Ugric Languages, Institute of the Estonian Language, 10119 Tallinn, Estonia
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria;
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Küllike Pihkva
- Preservation Department in Tartu, National Archives of Estonia, 50411 Tartu, Estonia;
| | | | - Arnold Unt
- Estonian War Museum-General Laidoner Museum, 74001 Tallinn, Estonia;
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10
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Boattini A, Bortolini E, Bauer R, Ottone M, Miglio R, Gueresi P, Pettener D. The surname structure of Trentino (Italy) and its relationship with dialects and genes. Ann Hum Biol 2021; 48:260-269. [PMID: 34459343 DOI: 10.1080/03014460.2021.1936635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Thanks to the availability of rich surname, linguistic and genetic information, together with its geographic and cultural complexity, Trentino (North-Eastern Italy) is an ideal place to test the relationships between genetic and cultural traits. AIM We provide a comprehensive study of population structures based on surname and dialect variability and evaluate their relationships with genetic diversity in Trentino. SUBJECTS AND METHODS Surname data were collected for 363 parishes, linguistic data for 57 dialects and genetic data for different sets of molecular markers (Y-chromosome, mtDNA, autosomal) in 10 populations. Analyses relied on different multivariate methods and correlation tests. RESULTS Besides the expected isolation-by-distance-like patterns (with few local exceptions, likely related to sociocultural instances), we detected a significant and geography-independent association between dialects and surnames. As for molecular markers, only Y-chromosomal STRs seem to be associated with the dialects, although no significant result was obtained. No evidence for correlation between molecular markers and surnames was observed. CONCLUSION Surnames act as cultural markers as do other words, although in this context they cannot be used as reliable proxies for genetic variability at a local scale.
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Affiliation(s)
- Alessio Boattini
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Bologna, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Roland Bauer
- Fachbereich Romanistik, Universität Salzburg, Austria
| | - Marta Ottone
- Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Rossella Miglio
- Department of Statistical Sciences, University of Bologna, Italy
| | - Paola Gueresi
- Department of Statistical Sciences, University of Bologna, Italy
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, Bologna, Italy
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11
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Y chromosome analysis for common surnames in the Japanese male population. J Hum Genet 2021; 66:731-738. [PMID: 33526818 DOI: 10.1038/s10038-020-00884-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/06/2020] [Accepted: 11/23/2020] [Indexed: 11/08/2022]
Abstract
For many years of Japan's long history, Japanese surnames have been handed down patrilineally. This study investigated relations between major surnames and Y chromosomal polymorphism among the Japanese male population. To analyze genetic phylogeny in namesakes, the Y-single nucleotide polymorphism (SNP) plus Y-short tandem repeat (STR) approach was employed. A haplogroup based on SNPs and haplotypes at 17 STR loci were typed in 567 unrelated volunteers recruited in Kanagawa, Japan. Samples covered 27 common surnames such as Satoh and Suzuki, each name having 10-55 bearers. Significant difference was found for SNP haplogroup compositions and a multidimensional scaling plot using STR haplotypes in several surname groups. By contrast, these common surnames displayed wide diversity with phylogenetic networks, suggesting that no genetic drift event has occurred in their history. In all, 22 descent clusters were found, as judgcriteria ed by ad hoc of groups within five mutational steps in the 15 STR loci with the same haplogroup. The times of the most recent common ancestor ranged from 279 to over 2577 years. According to the approximate millennium span of Japanese surname history, descent criteria are expected to be reasonable for grouping within four step-neighbors. High heterogeneity of common surnames resembles that observed for England and Spain, but not for Ireland. Our results highlight that common Japanese surnames consist of descent clusters and many singletons, reflecting a mixture of long-term bearers and short-term bearers among the population. The genetic study of this population revealed characteristic features of Japanese surnames.
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12
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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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13
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Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, Balaresque P. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters. Forensic Sci Int Genet 2020; 48:102342. [PMID: 32818722 DOI: 10.1016/j.fsigen.2020.102342] [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: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022]
Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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Affiliation(s)
- Caroline Bouakaze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Franklin Delehelle
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; REVA Unit, UMR 5505 - CNRS & Université de Toulouse, Institut de Recherche en Informatique de Toulouse, 31400 Toulouse, France
| | - Nancy Saenz-Oyhéréguy
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Andreia Moreira
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Stéphanie Schiavinato
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Solène Delon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Cesar Fortes-Lima
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Morgane Gibert
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Louis Bujan
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Eric Huyghe
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Gil Bellis
- INED Institut National d'Etudes Démographiques, 133 Boulevard Davout, 75980 Paris cedex 20, France
| | - Rosario Calderon
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Candela Lucia Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Efren Avendaño-Tamayo
- Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia, Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Instituto de Biología, Universidad de Antioquia Medellín Colombia, Colombia
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, GenPoB Research Group, Instituto de Investigaciones, Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | | | - Jacques Charioni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Andres Ruiz-Linares
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jean-Michel Dugoujon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Thèves
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Mollereau-Manaute
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Camille Noûs
- Laboratoire Cogitamous, CNRS & Université Toulouse III, 31000 Toulouse, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400 Toulouse, France
| | - Turi King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of Western Cape, Cape Town, South Africa
| | - Patricia Balaresque
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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14
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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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15
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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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16
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DNA Testing Reveals the Putative Identity of JB55, a 19th Century Vampire Buried in Griswold, Connecticut. Genes (Basel) 2019; 10:genes10090636. [PMID: 31443502 PMCID: PMC6769528 DOI: 10.3390/genes10090636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/22/2019] [Accepted: 08/20/2019] [Indexed: 11/25/2022] Open
Abstract
In 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a “skull and crossbones” orientation. The lid of the 19th century coffin had brass tacks that spelled “JB55”, the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be “killed” by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname “Barber”. A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of “NB13,” found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.
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17
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Wang CZ, Wei LH, Wang LX, Wen SQ, Yu XE, Shi MS, Li H. Relating Clans Ao and Aisin Gioro from northeast China by whole Y-chromosome sequencing. J Hum Genet 2019; 64:775-780. [PMID: 31148597 DOI: 10.1038/s10038-019-0622-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/09/2022]
Abstract
The Y-chromosome haplogroup C2b1a3a2-F8951 is the paternal lineage of the Aisin Gioro clan, the most important brother branch of the famous Mongolic-speaking population characteristic haplogroup C2*-Star Cluster (C2b1a3a1-F3796). However, investigations on its internal phylogeny are still limited. In this study, we used whole Y-chromosome sequencing to update its phylogenetic tree. In the revised tree, C2b1a3a2-F8951 and C2*-Star Cluster differentiated 3852 years ago (95% CI = 3295-4497). Approximately 3558 years ago (95% CI = 3013-4144), C2b1a3a2-F8951 was divided into two main subclades, C2b1a3a2a-F14753 and C2b1a3a2b-F5483. Currently, samples of C2b1a3a2-F8951 were mainly from the House of Aisin Gioro clan, the Ao family from Daur and some individuals mainly from northeast China. Although other haplogroups are also found in the Ao family, including C2b1a2-M48, C2b1a3a1-F3796, C2a1b-F845, and N1c-M178, the haplogroup C2b1a3a2-F8951 is still the most distinct genetic component. For haplogroup C2b1a3a2-F8951, the time of the most recent common ancestor of the House of Aisin Gioro clan and the Ao family were both very late, just a few hundred years ago. Some family-specific Y-SNPs of the House of Aisin Gioro and the Ao family were also discovered. This revision evidently improved the resolving power of Y-chromosome phylogeny in northeast Asia, deepening our understanding of the origin of these two families, even the Mongolic-speaking population.
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Affiliation(s)
- Chi-Zao Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Xiamen University, 361005, Xiamen, China
| | - Ling-Xiang Wang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Shao-Qing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Xue-Er Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Mei-Sen Shi
- Institute of the Investigation, School of Criminal Justice, China University of Political Science and Law, 100088, Beijing, China.
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 200438, Shanghai, China. .,Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, 037006, Datong, China.
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18
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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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19
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Genetic structure in the paternal lineages of South East Spain revealed by the analysis of 17 Y-STRs. Sci Rep 2019; 9:5234. [PMID: 30914710 PMCID: PMC6435739 DOI: 10.1038/s41598-019-41580-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/08/2019] [Indexed: 11/09/2022] Open
Abstract
The genetic data of 17 Y chromosome short tandem repeats in 146 unrelated donor residents in the provinces of Granada, Málaga, and Almería (GMA) were analyzed to determine the genetic legacy of the male inhabitants of the former Kingdom of Granada. A total of 139 unique haplotypes were identified. Observed allele frequencies and haplogroup frequencies were also analyzed. By AMOVA and STRUCTURE analysis, the populations of the 3 provinces could be treated genetically as a single population. The most frequent haplogroup was R1b1b2 (58.22%). By network analysis of all individuals, we observed a distribution according to haplogroup assignment. To improve the characterization of GMA population, it was compared with those of North Africa, the Iberian Peninsula, and southern Europe. In our analysis of allele frequencies and genetic distances, the GMA population lay within the Spanish population group. Further, in the STRUCTURE analysis, there was no African component in the GMA population, confirming that, based on our genetic markers, the GMA population does not reflect any male genetic influence of the North African people. The presence of African haplogroups in the GMA population is irrelevant when their frequency is compared with those in other European populations.
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20
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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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21
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Zhabagin MK, Balanovsky ОЕ, Sabitov ZM, Temirgaliyev AZ, Agdzhoyan AT, Koshel SM, Ramankulov ЕМ, Balanovska EV. Reconstructing the genetic structure of the Kazakh from clan distribution data. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Applying quasigenetic markers - non-biological traits which are nevertheless inherited in generations - is one of the research fields within human population genetics. For the West European, East European, and Caucasus populations, surnames are typical quasigenetic markers. For Central Asian populations, particularly Kazakh, the clan affiliation serves as a good marker: a set of papers demonstrated that many clans include mainly persons which biologically descent from a recent common ancestor. In this study, we analyzed a large (~4.2 million persons) dataset on quasigenetic markers - the geographic distribution of 50 Kazakh clans at the beginning of the 20th century, and compared the dataset with the direct data of the Y-chro-mosomal diversity in modern Kazakh populations. The analysis included three steps: the isonymy method, which is standard for quasigenetic markers, comparing frequencies of quasigenetic markers, and comparing the quasigenetic and genetic datasets. We constructed 50 maps of frequency of the distribution of each clan and revealed that these maps correlate with the maps of genetic distances. The Mantel test also demonstrated a significant correlation between geographic and quasigenetic distances (г = 0.60; p < 0.05). The analysis of inter-population variability revealed the largest diversity between geographic territories corresponding to the social-territorial groups of the Kazakh Khanate (zhuzes) rather than to other historical groups that existed on the territory of Kazakhstan in preceding and modern epochs. The same is evidenced by the principal components and multidimensional scaling plots, which grouped geographic populations into three clusters corresponding to three zhuzes. This indicates that the final structuring of the Kazakh gene pool might have occurred during the Kazakh Khanate period.
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Affiliation(s)
- M. K. Zhabagin
- National Center for Biotechnology; National Laboratory Astana, Nazarbayev University
| | - О. Е. Balanovsky
- Vavilov Institute of General Genetics, RAS; Research Centre for Medical Genetics; Biobank of North Eurasia
| | | | | | - A. T. Agdzhoyan
- Vavilov Institute of General Genetics, RAS; Research Centre for Medical Genetics
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22
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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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23
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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24
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Boattini A, Sarno S, Fiorani O, Lisa A, Luiselli D, Pettener D. Ripples on the surface. Surnames and genes in Sicily and Southern Italy. Ann Hum Biol 2018; 45:57-65. [PMID: 29183201 DOI: 10.1080/03014460.2017.1411525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Southern Italy and Sicily played a key role in the peopling history of the Mediterranean. While genetic research showed the remarkable homogeneity of these regions, surname-based studies instead suggested low population mobility, hence potential structuring. AIM In order to better understand these different patterns, this study (1) thoroughly analysed the surname structure of Sicily and Southern Italy and (2) tested its relationships with a wide set of molecular markers. SUBJECTS AND METHODS Surname data were collected from 1213 municipalities and compared to uniparental and autosomal genetic markers typed in ∼300 individuals from 8-10 populations. Surname analyses were performed using different multivariate methods, while comparisons with genetic data relied on correlation tests. RESULTS Surnames were clearly structured according to regional geographic patterns, which likely emerged because of recent isolation-by-distance-like population dynamics. In general, genetic markers, hinting at a pervasive homogeneity, did not correlate with surname distribution. However, long autosomal haplotypes (>5 cM) that compared to genotypic (SNPs) data identify more "recent" relatedness, showing a clear association with surname patterns. CONCLUSION The apparent contradiction between surname structure and genetic homogeneity was resolved by figuring surnames as recent "ripples" deposited on a vast and ancient homogeneous genetic "surface".
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Affiliation(s)
- Alessio Boattini
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Stefania Sarno
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Ornella Fiorani
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Antonella Lisa
- b Institute of Molecular Genetics (IGM) , Consiglio Nazionale delle Ricerche (CNR) , Pavia , Italy
| | - Donata Luiselli
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
| | - Davide Pettener
- a Department of Biological, Geological and Environmental Sciences , University of Bologna , Bologna , Italy
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25
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Orrù A, De Iasio S, Frederic P, Girotti M, Boano R, Sanna E. Spatial diffusion of surnames by long transhumance routes between highland and lowland: A study in Sardinia. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2018; 69:127-138. [PMID: 30017379 DOI: 10.1016/j.jchb.2018.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/26/2018] [Indexed: 11/24/2022]
Abstract
RIASSUNTO.
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Affiliation(s)
- A Orrù
- Department of Life Sciences and Systems Biology, University of Turin, Italy.
| | - S De Iasio
- Department of Biosciences, University of Parma, Italy
| | - P Frederic
- Department of Economics "Marco Biagi", RECent (Center for Economic Research), University of Modena, Italy
| | - M Girotti
- Department of Life Sciences and Systems Biology, University of Turin, Italy
| | - R Boano
- Department of Life Sciences and Systems Biology, University of Turin, Italy
| | - E Sanna
- Department of Environmental and Life Sciences, University of Cagliari, Italy
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26
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Mekonnen A, Rueness EK, Stenseth NC, Fashing PJ, Bekele A, Hernandez-Aguilar RA, Missbach R, Haus T, Zinner D, Roos C. Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands. BMC Evol Biol 2018; 18:106. [PMID: 29986642 PMCID: PMC6038355 DOI: 10.1186/s12862-018-1217-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia. Results We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines. Conclusions The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway. .,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia.
| | - Eli K Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - Peter J Fashing
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, CA, 92834, USA
| | - Afework Bekele
- Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - R Adriana Hernandez-Aguilar
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rose Missbach
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tanja Haus
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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27
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Zeng TC, Aw AJ, Feldman MW. Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck. Nat Commun 2018; 9:2077. [PMID: 29802241 PMCID: PMC5970157 DOI: 10.1038/s41467-018-04375-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/24/2018] [Indexed: 01/18/2023] Open
Abstract
In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory. A population bottleneck 5000-7000 years ago in human males, but not females, has been inferred across several African, European and Asian populations. Here, Zeng and colleagues synthesize theory and data to suggest that competition among patrilineal kin groups produced the bottleneck pattern.
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Affiliation(s)
- Tian Chen Zeng
- Department of Sociology, Stanford University, Stanford, CA, 94305, USA.,Mathematical and Computational Science Program, Stanford University, Stanford, CA, 94305, USA
| | - Alan J Aw
- Mathematical and Computational Science Program, Stanford University, Stanford, CA, 94305, USA.,Department of Biology, Stanford University, Stanford, CA, USA
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28
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Kaplanis J, Gordon A, Shor T, Weissbrod O, Geiger D, Wahl M, Gershovits M, Markus B, Sheikh M, Gymrek M, Bhatia G, MacArthur DG, Price AL, Erlich Y. Quantitative analysis of population-scale family trees with millions of relatives. Science 2018; 360:171-175. [PMID: 29496957 PMCID: PMC6593158 DOI: 10.1126/science.aam9309] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 02/07/2018] [Indexed: 12/12/2022]
Abstract
Family trees have vast applications in fields as diverse as genetics, anthropology, and economics. However, the collection of extended family trees is tedious and usually relies on resources with limited geographical scope and complex data usage restrictions. We collected 86 million profiles from publicly available online data shared by genealogy enthusiasts. After extensive cleaning and validation, we obtained population-scale family trees, including a single pedigree of 13 million individuals. We leveraged the data to partition the genetic architecture of human longevity and to provide insights into the geographical dispersion of families. We also report a simple digital procedure to overlay other data sets with our resource.
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Affiliation(s)
- Joanna Kaplanis
- New York Genome Center, New York, NY 10013, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Assaf Gordon
- New York Genome Center, New York, NY 10013, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tal Shor
- MyHeritage, Or Yehuda 6037606, Israel
- Computer Science Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Omer Weissbrod
- Computer Science Department, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dan Geiger
- Computer Science Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Mary Wahl
- New York Genome Center, New York, NY 10013, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Barak Markus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Mona Sheikh
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Melissa Gymrek
- New York Genome Center, New York, NY 10013, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gaurav Bhatia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Daniel G MacArthur
- Harvard Medical School, Boston, MA 02115, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Yaniv Erlich
- New York Genome Center, New York, NY 10013, USA.
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- MyHeritage, Or Yehuda 6037606, Israel
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY, USA
- Center for Computational Biology and Bioinformatics, Department of Systems Biology, Columbia University, New York, NY, USA
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Votrubova J, Saskova L, Frolik J, Vanek D. Linking the Y-chromosomal haplotype from a high medieval (1160–1421) skeleton from a Podlazice excavation site with living descendants. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Old RW, Bestwick JP, Wald NJ. Prenatal maternal plasma DNA screening for cystic fibrosis: A computer modelling study of screening performance. F1000Res 2017; 6:1896. [PMID: 29167740 PMCID: PMC5680537 DOI: 10.12688/f1000research.12849.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 12/27/2022] Open
Abstract
Background: Prenatal cystic fibrosis (CF) screening is currently based on determining the carrier status of both parents. We propose a new method based only on the analysis of DNA in maternal plasma. Methods: The method relies on the quantitative amplification of the CF gene to determine the percentage of DNA fragments in maternal plasma at targeted CF mutation sites that carry a CF mutation. Computer modelling was carried out to estimate the distributions of these percentages in pregnancies with and without a fetus affected with CF. This was done according to the number of DNA fragments counted and fetal fraction, using the 23 CF mutations recommended by the American College of Medical Genetics for parental carrier testing. Results: The estimated detection rate (sensitivity) is 70% (100% of those detected using the 23 mutations), the false-positive rate 0.002%, and the odds of being affected given a positive screening result 14:1, compared with 70%, 0.12%, and 1:3, respectively, with current prenatal screening based on parental carrier testing. Conclusions: Compared with current screening practice based on parental carrier testing, the proposed method would substantially reduce the number of invasive diagnostic procedures (amniocentesis or chorionic villus sampling) without reducing the CF detection rate. The expected advantages of the proposed method justify carrying out the necessary test development for use in a clinical validation study.
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Affiliation(s)
- Robert W Old
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jonathan P Bestwick
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Nicholas J Wald
- Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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31
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Solé-Morata N, Villaescusa P, García-Fernández C, Font-Porterias N, Illescas MJ, Valverde L, Tassi F, Ghirotto S, Férec C, Rouault K, Jiménez-Moreno S, Martínez-Jarreta B, Pinheiro MF, Zarrabeitia MT, Carracedo Á, de Pancorbo MM, Calafell F. Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ. Sci Rep 2017; 7:7341. [PMID: 28779148 PMCID: PMC5544771 DOI: 10.1038/s41598-017-07710-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/28/2017] [Indexed: 11/28/2022] Open
Abstract
Haplogroup R1b-M269 comprises most Western European Y chromosomes; of its main branches, R1b-DF27 is by far the least known, and it appears to be highly prevalent only in Iberia. We have genotyped 1072 R1b-DF27 chromosomes for six additional SNPs and 17 Y-STRs in population samples from Spain, Portugal and France in order to further characterize this lineage and, in particular, to ascertain the time and place where it originated, as well as its subsequent dynamics. We found that R1b-DF27 is present in frequencies ~40% in Iberian populations and up to 70% in Basques, but it drops quickly to 6–20% in France. Overall, the age of R1b-DF27 is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of W Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates; NE Iberia is the most likely place of origin of DF27. Subhaplogroup frequencies within R1b-DF27 are geographically structured, and show domains that are reminiscent of the pre-Roman Celtic/Iberian division, or of the medieval Christian kingdoms.
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Affiliation(s)
- Neus Solé-Morata
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Carla García-Fernández
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Neus Font-Porterias
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - María José Illescas
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Laura Valverde
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, Ferrara, Italy
| | - Claude Férec
- Inserm, UMR 1078, Brest, France.,Laboratoire de Génétique Moléculaire, CHRU Brest, Hôpital Morvan, Brest, France.,Université de Bretagne Occidentale, Brest, France.,Etablissement Français du Sang-Bretagne, Brest, France
| | - Karen Rouault
- Inserm, UMR 1078, Brest, France.,Laboratoire de Génétique Moléculaire, CHRU Brest, Hôpital Morvan, Brest, France
| | - Susana Jiménez-Moreno
- Forensic and Legal Medicine Area, Department of Pathology and Surgery, University Miguel Hernández, Elche, Spain
| | | | - Maria Fátima Pinheiro
- Forensic Genetics Department, National Institute of Legal Medicine and Forensic Sciences, Porto, Portugal
| | | | - Ángel Carracedo
- Genomic Medicine Group, CIBERER- University of Santiago de Compostela, Galician Foundation of Genomic Medicine (SERGAS), Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
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32
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Paradoxical Impact of Ileal Pouch-Anal Anastomosis on Male and Female Fertility in Patients With Ulcerative Colitis. Dis Colon Rectum 2017; 60:603-607. [PMID: 28481854 DOI: 10.1097/dcr.0000000000000796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Birth rates in males with ulcerative colitis and ileal pouch-anal anastomosis have not been studied. OBJECTIVE This study aimed to estimate birth rates in males and females with ulcerative colitis and study the impact of ileal pouch-anal anastomosis. DESIGN This was a retrospective registry-based cohort study that was performed over a 30-year period. SETTINGS Records for parenting a child from the same period were cross-linked with patient records, and birth rates were calculated using 15 through 49 years as age limits. All data were prospectively registered. PATIENTS All patients with ulcerative colitis and ulcerative colitis with ileal pouch-anal anastomosis between 1980 and 2010 were identified in Danish national databases. MAIN OUTCOME MEASURES The primary outcomes measured were birth rates in females and males with ulcerative colitis and ulcerative colitis with ileal pouch-anal anastomosis. RESULTS We included 27,379 patients with ulcerative colitis (12,812 males and 14,567 females); 1544 had ileal pouch-anal anastomosis (792 males and 752 females). Patients with ulcerative colitis have slightly reduced birth rates (males at 40.8 children/1000 years, background population 43.2, females at 46.2 children/1000 years, background population 49.1). After ileal pouch-anal anastomosis, males had increased birth rates at 47.8 children/1000 years in comparison with males with ulcerative colitis without ileal pouch-anal anastomosis (40.5 children/1000 years), whereas females had reduced birth rates at 27.6 children/1000 years in comparison with females with ulcerative colitis without ileal pouch-anal anastomosis (46.8 children/1000 years). LIMITATIONS Only birth rates were investigated and not fecundability. Furthermore, there is a question about misattributed paternity, but this has previously been shown to be less than 5%. CONCLUSIONS Ulcerative colitis per se has little impact on birth rates in both sexes, but ileal pouch-anal anastomosis surgery leads to a reduction in birth rates in females and an increase in birth rates in males. This has clinical impact when counseling patients before ileal pouch-anal anastomosis surgery.
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Abstract
The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.
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34
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Khan K, Siddiqi MH, Abbas M, Almas M, Idrees M. Forensic applications of Y chromosomal properties. Leg Med (Tokyo) 2017; 26:86-91. [DOI: 10.1016/j.legalmed.2017.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 04/08/2017] [Accepted: 04/15/2017] [Indexed: 01/17/2023]
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35
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Ehler E, Vanek D. Forensic genetic analyses in isolated populations with examples of central European Valachs and Roma. J Forensic Leg Med 2017; 48:46-52. [PMID: 28454050 DOI: 10.1016/j.jflm.2017.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/22/2017] [Accepted: 04/09/2017] [Indexed: 01/27/2023]
Abstract
Isolated populations present a constant threat to the correctness of forensic genetic casework. In this review article we present several examples of how analyzing samples from isolated populations can bias the results of the forensic statistics and analyses. We select our examples from isolated populations from central and southeastern Europe, namely the Valachs and the European Roma. We also provide the reader with general strategies and principles to improve the laboratory practice (best practice) and reporting of samples from supposedly isolated populations. These include reporting the precise population data used for computing the forensic statistics, using the appropriate θ correction factor for calculating allele frequencies, typing ancestry informative markers in samples of unknown or uncertain ethnicity and establishing ethnic-specific forensic databases.
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Affiliation(s)
- Edvard Ehler
- Department of Biology and Environmental Studies, Charles University in Prague, Faculty of Education, Magdaleny Rettigove 4, Prague, 116 39, Czech Republic; Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7, 170 00, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, V Uvalu 84, Prague, 150 06, Czech Republic; Nemocnice Na Bulovce, Institute of Legal Medicine, Budinova 2, Prague, 180 81, Czech Republic.
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36
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Batini C, Jobling MA. Detecting past male-mediated expansions using the Y chromosome. Hum Genet 2017; 136:547-557. [PMID: 28349239 DOI: 10.1007/s00439-017-1781-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/15/2017] [Indexed: 12/29/2022]
Abstract
Males and females display biological differences that lead to a higher variance of offspring number in males, and this is frequently exacerbated in human societies by mating practices, and possibly by past socio-cultural circumstances. This implies that the genetic record might contain the imprint of past male-mediated expansions, which can be investigated by analysing the male-specific region of the Y chromosome (MSY). Here, we review studies that have used MSY data to infer such expansions. Sets of short-tandem repeats define haplotypes of very low average frequencies, but in a few cases, high-frequency haplotypes are observed, forming the core of descent clusters. Estimates of the ages of such clusters, together with geographical information, have been used to propose powerful historical founders, including Genghis Khan, although without direct supporting evidence. Resequencing of multi-megabase segments of MSY has allowed the construction of detailed phylogenies in which branch lengths are proportional to time, leading to the identification of lineage expansions in the last few millennia as well as the more distant past. Comparisons with maternally-inherited mitochondrial DNA sequence data allow the male specificity of some of these expansions to be demonstrated. These include expansions in Europe in the last ~5000 years that may be associated with a cultural shift during the Bronze Age, as well as expansions elsewhere in the world for which explanations from archaeological evidence are not yet clear.
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Affiliation(s)
- Chiara Batini
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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37
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The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 2016; 136:559-573. [DOI: 10.1007/s00439-016-1740-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
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38
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Mutation Rates and Discriminating Power for 13 Rapidly-Mutating Y-STRs between Related and Unrelated Individuals. PLoS One 2016; 11:e0165678. [PMID: 27802306 PMCID: PMC5089551 DOI: 10.1371/journal.pone.0165678] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/14/2016] [Indexed: 11/29/2022] Open
Abstract
Rapidly Mutating Y-STRs (RM Y-STRs) were recently introduced in forensics in order to increase the differentiation of Y-chromosomal profiles even in case of close relatives. We estimate RM Y-STRs mutation rates and their power to discriminate between related individuals by using samples extracted from a wide set of paternal pedigrees and by comparing RM Y-STRs results with those obtained from the Y-filer set. In addition, we tested the ability of RM Y-STRs to discriminate between unrelated individuals carrying the same Y-filer haplotype, using the haplogroup R-M269 (reportedly characterised by a strong resemblance in Y-STR profiles) as a case study. Our results, despite confirming the high mutability of RM Y-STRs, show significantly lower mutation rates than reference germline ones. Consequently, their power to discriminate between related individuals, despite being higher than the one of Y-filer, does not seem to improve significantly the performance of the latter. On the contrary, when considering R-M269 unrelated individuals, RM Y-STRs reveal significant discriminatory power and retain some phylogenetic signal, allowing the correct classification of individuals for some R-M269-derived sub-lineages. These results have important implications not only for forensics, but also for molecular anthropology, suggesting that RM Y-STRs are useful tools for exploring subtle genetic variability within Y-chromosomal haplogroups.
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39
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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40
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Larmuseau MHD, Matthijs K, Wenseleers T. Cuckolded Fathers Rare in Human Populations. Trends Ecol Evol 2016; 31:327-329. [PMID: 27107336 DOI: 10.1016/j.tree.2016.03.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 11/27/2022]
Abstract
Contemporary data of extra-pair paternity (EPP) in human populations may be biased by the use of modern contraceptives. Studies have now estimated historical EPP rates in several human populations. The observed low EPP rates challenge the idea that women routinely 'shop around' for good genes by engaging in extra-pair copulations.
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Affiliation(s)
- Maarten H D Larmuseau
- Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium; Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium; Department of Genetics, University of Leicester, Leicester, UK.
| | - Koen Matthijs
- Faculty of Social Sciences, Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - Tom Wenseleers
- Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven, Leuven, Belgium
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41
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Montinaro F, Davies J, Capelli C. Group membership, geography and shared ancestry: Genetic variation in the Basotho of Lesotho. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:156-61. [PMID: 26779678 DOI: 10.1002/ajpa.22933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/16/2015] [Accepted: 12/14/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVES The investigation of the evolution of cultural and genetic traits and how they interact represents a vibrant area of research in evolutionary genetics, whose dynamics are particularly relevant for our species. One of the key assumptions of the "gene-culture coevolution" framework is the coinheritance of cultural and genetic traits. A corollary of the model is that culturally defined groups with a unique (or a limited number of) common origin(s) whose membership is inherited only through the male or female line are expected to show a relatively low intragroup variation for genetic markers similarly transmitted. Across human societies this is expected to be the case for cultural toponymies and family names within patrilineal and matrilineal groups considered in association with the nonrecombining region of the Y chromosome (NRY) and the mitochondrial DNA (mtDNA) portion of the genome, respectively. This study aims at exploring the degree of correlation between culture and genetics by investigating the genetic variation of culturally and geographically defined groups. METHODS We analyzed the genetic variation at NRY and mtDNA in 181 individuals from the Basotho, a Southern African patrilineal population from Lesotho, in combination with information about group membership and geographic origin. RESULTS Our results show that (a) the genetic distance between individuals belonging to the same culturally defined group is lower than the population as a whole when NRY markers are considered; (b) cultural traits have a bigger impact than geography for the within-group variation of Y chromosome, but not mtDNA; and (c) within-group genetic variation is compatible with a more homogeneous origin for less common groups. CONCLUSIONS Our results provided additional evidence for the relevance of the dual inheritance model (culture and genetics) in understanding the patterns of human genetic variation, as implied by gene-culture coevolution theory.
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Affiliation(s)
- Francesco Montinaro
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
| | - Joseph Davies
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
| | - Cristian Capelli
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
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42
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Risso D, Taglioli L, De Iasio S, Gueresi P, Alfani G, Nelli S, Rossi P, Paoli G, Tofanelli S. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach. PLoS One 2015; 10:e0140146. [PMID: 26452043 PMCID: PMC4599962 DOI: 10.1371/journal.pone.0140146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/21/2015] [Indexed: 11/18/2022] Open
Abstract
This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447-2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8-30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics.
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Affiliation(s)
- Davide Risso
- National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20854, United States of America
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of BiGeA, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Luca Taglioli
- Dipartimento di Biologia, University of Pisa, Via Ghini 13, 56126 Pisa, Italy
| | - Sergio De Iasio
- Dipartimento di Genetica Biologia dei Microrganismi Antropologia Evoluzione, University of Parma, Parco Area delle Scienze 11/a, 43124 Parma, Italy
| | - Paola Gueresi
- Dipartimento di Scienze Statistiche, University of Bologna, Via Belle Arti 41, 40126 Bologna, Italy
| | - Guido Alfani
- Bocconi University, Dondena Centre and IGIER, Milan, Italy
| | | | - Paolo Rossi
- Dipartimento di Fisica, University of Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giorgio Paoli
- Dipartimento di Biologia, University of Pisa, Via Ghini 13, 56126 Pisa, Italy
| | - Sergio Tofanelli
- Dipartimento di Biologia, University of Pisa, Via Ghini 13, 56126 Pisa, Italy
- * E-mail:
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43
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Three hundred years of low non-paternity in a human population. Heredity (Edinb) 2015; 115:396-404. [PMID: 25944467 DOI: 10.1038/hdy.2015.36] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 01/21/2023] Open
Abstract
When cuckoldry is frequent we can expect fathers to withhold investment in offspring that may not be theirs. Human paternal investment can be substantial and is in line with observations from tens of thousands of conceptions that suggest that cuckoldry is rare in humans. The generality of this claim seems to be in question as the rate of cuckoldry varies across populations and studies have mostly been on Western populations. Two additional factors complicate our conclusions, (1) current estimates of the rate of cuckoldry in humans may not reflect our past behaviour as adultery can be concealed by the use of contraceptives; and (2) it is difficult to obtain samples that are random with respect to their paternity certainty. Studies that combine genealogies with Y-chromosome haplotyping are able to circumvent some of these problems by probing into humans' historical behaviour. Here we use this approach to investigate 1273 conceptions over a period of 330 years in 23 families of the Afrikaner population in South Africa. We use haplotype frequency and diversity and coalescent simulations to show that the male population did not undergo a severe bottleneck and that paternity exclusion rates are high for this population. The rate of cuckoldry in this Western population was 0.9% (95% confidence interval 0.4-1.5%), and we argue that given the current data on historical populations we have to conclude that, at least for Western human populations, cuckoldry rate is probably in the range of 1%.
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44
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Martinez-Cadenas C, Blanco-Verea A, Hernando B, Busby GBJ, Brion M, Carracedo A, Salas A, Capelli C. The relationship between surname frequency and Y chromosome variation in Spain. Eur J Hum Genet 2015; 24:120-8. [PMID: 25898922 DOI: 10.1038/ejhg.2015.75] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/28/2015] [Accepted: 03/17/2015] [Indexed: 11/09/2022] Open
Abstract
In most societies, surnames are passed down from fathers to sons, just like the Y chromosome. It follows that, theoretically, men sharing the same surnames would also be expected to share related Y chromosomes. Previous investigations have explored such relationships, but so far, the only detailed studies that have been conducted are on samples from the British Isles. In order to provide additional insights into the correlation between surnames and Y chromosomes, we focused on the Spanish population by analysing Y chromosomes from 2121 male volunteers representing 37 surnames. The results suggest that the degree of coancestry within Spanish surnames is highly dependent on surname frequency, in overall agreement with British but not Irish surname studies. Furthermore, a reanalysis of comparative data for all three populations showed that Irish surnames have much greater and older surname descent clusters than Spanish and British ones, suggesting that Irish surnames may have considerably earlier origins than Spanish or British ones. Overall, despite closer geographical ties between Ireland and Britain, our analysis points to substantial similarities in surname origin and development between Britain and Spain, while possibly hinting at unique demographic or social events shaping Irish surname foundation and development.
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Affiliation(s)
- Conrado Martinez-Cadenas
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain.,Human Evolutionary Genetics Group, Department of Zoology, University of Oxford, Oxford, UK
| | - Alejandro Blanco-Verea
- Instituto de Investigación Sanitaria de Santiago de Compostela, Grupo de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - George B J Busby
- Human Evolutionary Genetics Group, Department of Zoology, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Maria Brion
- Instituto de Investigación Sanitaria de Santiago de Compostela, Grupo de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Instituto de Investigación Sanitaria de Santiago de Compostela, Grupo de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristian Capelli
- Human Evolutionary Genetics Group, Department of Zoology, University of Oxford, Oxford, UK
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Larmuseau MHD, Boon N, Vanderheyden N, Van Geystelen A, Larmuseau HFM, Matthys K, De Clercq W, Decorte R. High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment. Heredity (Edinb) 2015; 115:3-12. [PMID: 25873146 DOI: 10.1038/hdy.2015.5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/20/2014] [Accepted: 12/23/2014] [Indexed: 01/02/2023] Open
Abstract
There is limited knowledge on the biological relatedness between citizens and on the demographical dynamics within villages, towns and cities in pre-17th century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it is possible to provide insights into the genetic diversity and the relatedness between indigenous paternal lineages within a particular community at the time of the surname adoption. To obtain these insights, six Flemish communities were selected in this study based on the differences in geography and historical development. After rigorous selection of appropriate DNA donors, low relatedness between Y chromosomes of different surnames was found within each community, although there is co-occurrence of these surnames in each community since the start of the surname adoption between the 14th and 15th century. Next, the high communal diversity in Y-chromosomal lineages was comparable with the regional diversity across Flanders at that time. Moreover, clinal distributions of particular Y-chromosomal lineages between the communities were observed according to the clinal distributions earlier observed across the Flemish regions and Western Europe. No significant indication for genetic differences between communities with distinct historical development was found in the analysis. These genetic results provide relevant information for studies in historical sciences, archaeology, forensic genetics and genealogy.
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Affiliation(s)
- M H D Larmuseau
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium [3] Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - N Boon
- 1] Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium [2] Institute of Tropical Medicine, Antwerp, Belgium
| | - N Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - A Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - H F M Larmuseau
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - K Matthys
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - W De Clercq
- Faculty of Arts and Philosophy, Department of Archaeology, Ghent University, Ghent, Belgium
| | - R Decorte
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
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46
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Prestes PR, Mitchell RJ, Daniel R, Sanchez JJ, van Oorschot RA. Predicting biogeographical ancestry in admixed individuals – values and limitations of using uniparental and autosomal markers. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1022600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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47
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Calderón R, Hernández CL, Cuesta P, Dugoujon JM. Surnames and Y-chromosomal markers reveal low relationships in Southern Spain. PLoS One 2015; 10:e0123098. [PMID: 25860017 PMCID: PMC4393112 DOI: 10.1371/journal.pone.0123098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/27/2015] [Indexed: 11/21/2022] Open
Abstract
A sample of 416 males from western and eastern Andalusia has been jointly analyzed for surnames and Y-chromosome haplogroups and haplotypes. The observed number of different surnames was 222 (353 when the second surname of the Spanish system of naming is considered). The great majority of recorded surnames have a Castilian-Leonese origin, while Catalan or Basque surnames have not been found. A few Arab-related surnames appear but none discernible of Sephardic-Jewish descent. Low correlation among surnames with different population frequencies and Y-chromosome markers, at different levels of genetic resolution, has been observed in Andalusia. This finding could be explained mainly by the very low rate of monophyletic surnames because of the historical process of surname ascription and the resulting high frequencies of the most common Spanish surnames. The introduction of surnames in Spain during the Middle Ages coincided with Reconquest of the territories under Islamic rule, and Muslims and Jews progressively adopted the present male line surname system. Sampled surnames and Y-chromosome lineages fit well a power-law distribution and observed isonymy is very close to that of the general population. Besides, our data and results show that the reliability of the isonymy method should be questioned because of the high rate of polyphyletic surnames, even in small geographic regions and autochthonous populations. Random isonymy would be consistently dependent of the most common surname frequencies in the population.
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Affiliation(s)
- Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
- * E-mail:
| | - Candela L. Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Pedro Cuesta
- Centro de Proceso de Datos, Universidad Complutense, Madrid, Spain
| | - Jean Michel Dugoujon
- CNRS UMR 5288 Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
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48
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Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency. Eur J Hum Genet 2015; 23:1549-57. [PMID: 25689924 DOI: 10.1038/ejhg.2015.14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/26/2014] [Accepted: 01/13/2015] [Indexed: 01/03/2023] Open
Abstract
The biological behavior of the Y chromosome, which is paternally inherited, implies that males sharing the same surname may also share a similar Y chromosome. However, socio-cultural factors, such as polyphyletism, non-paternity, adoption, or matrilineal surname transmission, may prevent the joint transmission of the surname and the Y chromosome. By genotyping 17 Y-STRs and 68 SNPs in ~2500 male samples that each carried one of the 50 selected Catalan surnames, we could determine sets of descendants of a common ancestor, the population of origin of the common ancestor, and the date when such a common ancestor lived. Haplotype diversity was positively correlated with surname frequency, that is, rarer surnames showed the strongest signals of coancestry. Introgression rates of Y chromosomes into a surname by non-paternity, adoption, and transmission of the maternal surname were estimated at 1.5-2.6% per generation, with some local variation. Average ages for the founders of the surnames were estimated at ~500 years, suggesting a delay between the origin of surnames (twelfth and thirteenth centuries) and the systematization of their paternal transmission. We have found that, in general, a foreign etymology for a surname does not often result in a non-indigenous origin of surname founders; however, bearers of some surnames with an Arabic etymology show an excess of North African haplotypes. Finally, we estimate that surname prediction from a Y-chromosome haplotype, which may have interesting forensic applications, has a ~60% sensitivity but a 17% false discovery rate.
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49
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Balaresque P, Poulet N, Cussat-Blanc S, Gerard P, Quintana-Murci L, Heyer E, Jobling MA. Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations. Eur J Hum Genet 2015; 23:1413-22. [PMID: 25585703 DOI: 10.1038/ejhg.2014.285] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/25/2014] [Accepted: 11/28/2014] [Indexed: 11/09/2022] Open
Abstract
High-frequency microsatellite haplotypes of the male-specific Y-chromosome can signal past episodes of high reproductive success of particular men and their patrilineal descendants. Previously, two examples of such successful Y-lineages have been described in Asia, both associated with Altaic-speaking pastoral nomadic societies, and putatively linked to dynasties descending, respectively, from Genghis Khan and Giocangga. Here we surveyed a total of 5321 Y-chromosomes from 127 Asian populations, including novel Y-SNP and microsatellite data on 461 Central Asian males, to ask whether additional lineage expansions could be identified. Based on the most frequent eight-microsatellite haplotypes, we objectively defined 11 descent clusters (DCs), each within a specific haplogroup, that represent likely past instances of high male reproductive success, including the two previously identified cases. Analysis of the geographical patterns and ages of these DCs and their associated cultural characteristics showed that the most successful lineages are found both among sedentary agriculturalists and pastoral nomads, and expanded between 2100 BCE and 1100 CE. However, those with recent origins in the historical period are almost exclusively found in Altaic-speaking pastoral nomadic populations, which may reflect a shift in political organisation in pastoralist economies and a greater ease of transmission of Y-chromosomes through time and space facilitated by the use of horses.
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Affiliation(s)
- Patricia Balaresque
- UMR 5288, Faculté de Médecine Purpan, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), CNRS/Université Paul Sabatier, Toulouse, France.,Department of Genetics, University of Leicester, Leicester, UK
| | - Nicolas Poulet
- Onema, Direction de l'Action Scientifique et Technique, Toulouse, France
| | | | - Patrice Gerard
- UMR 5288, Faculté de Médecine Purpan, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), CNRS/Université Paul Sabatier, Toulouse, France
| | - Lluis Quintana-Murci
- CNRS URA3012, Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Evelyne Heyer
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, Paris, France
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
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50
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Balaresque P, King TE, Parkin EJ, Heyer E, Carvalho-Silva D, Kraaijenbrink T, de Knijff P, Tyler-Smith C, Jobling MA. Gene conversion violates the stepwise mutation model for microsatellites in y-chromosomal palindromic repeats. Hum Mutat 2014; 35:609-17. [PMID: 24610746 PMCID: PMC4233959 DOI: 10.1002/humu.22542] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/25/2014] [Indexed: 01/19/2023]
Abstract
The male-specific region of the human Y chromosome (MSY) contains eight large inverted repeats (palindromes), in which high-sequence similarity between repeat arms is maintained by gene conversion. These palindromes also harbor microsatellites, considered to evolve via a stepwise mutation model (SMM). Here, we ask whether gene conversion between palindrome microsatellites contributes to their mutational dynamics. First, we study the duplicated tetranucleotide microsatellite DYS385a,b lying in palindrome P4. We show, by comparing observed data with simulated data under a SMM within haplogroups, that observed heteroallelic combinations in which the modal repeat number difference between copies was large, can give rise to homoallelic combinations with zero-repeats difference, equivalent to many single-step mutations. These are unlikely to be generated under a strict SMM, suggesting the action of gene conversion. Second, we show that the intercopy repeat number difference for a large set of duplicated microsatellites in all palindromes in the MSY reference sequence is significantly reduced compared with that for nonpalindrome-duplicated microsatellites, suggesting that the former are characterized by unusual evolutionary dynamics. These observations indicate that gene conversion violates the SMM for microsatellites in palindromes, homogenizing copies within individual Y chromosomes, but increasing overall haplotype diversity among chromosomes within related groups.
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Affiliation(s)
- Patricia Balaresque
- UMR5288 CNRS/UPS-AMIS-Université Paul Sabatier, Toulouse, France; Department of Genetics, University of Leicester, Leicester, UK
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