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Ancestry and different rates of suicide and homicide in European countries: A study with population-level data. J Affect Disord 2018; 232:152-162. [PMID: 29494899 DOI: 10.1016/j.jad.2018.02.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/02/2018] [Accepted: 02/16/2018] [Indexed: 01/28/2023]
Abstract
INTRODUCTION There are large differences in suicide rates across Europe. The current study investigated the relationship of suicide and homicide rates in different countries of Europe with ancestry as it is defined with the haplotype frequencies of Y-DNA and mtDNA. MATERIAL AND METHODS The mortality data were retrieved from the WHO online database. The genetic data were retrieved from http://www.eupedia.com. The statistical analysis included Forward Stepwise Multiple Linear Regression analysis and Pearson Correlation Coefficient (R). RESULTS In males, N and R1a Y-DNA haplotypes were positively related to both homicidal and suicidal behaviors while I1 was negatively related. The Q was positively related to the homicidal rate. Overall, 60-75% of the observed variance was explained. L, J and X mtDNA haplogroups were negatively related with suicide in females alone, with 82-85% of the observed variance described. DISCUSSION The current study should not be considered as a study of genetic markers but rather a study of human ancestry. Its results could mean that research on suicidality has a strong biological but locally restricted component and could be limited by the study population; generalizability of the results at an international level might not be possible. Further research with patient-level data are needed to verify whether these haplotypes could serve as biological markers to identify persons at risk to commit suicide or homicide and whether biologically-determined ancestry could serve as an intermediate grouping method or even as an endophenotype in suicide research.
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102
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Huszar TI, Jobling MA, Wetton JH. A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing. Forensic Sci Int Genet 2018; 35:97-106. [PMID: 29679929 PMCID: PMC6010625 DOI: 10.1016/j.fsigen.2018.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/14/2018] [Accepted: 03/28/2018] [Indexed: 12/09/2022]
Abstract
23 Y-chromosomal STRs (PPY23) reanalysed by massively parallel sequencing. Phylogeny-based approach captures wide range of sequence variants in 100 samples. STR variants described in phase with their flanking sequences. Phylogenetic framework clarifies allele nomenclature and mutation processes.
Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega’s prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing. Including allele duplications and alleles resulting from likely somatic mutation, we characterised 2311 alleles, demonstrating 99.83% concordance with capillary electrophoresis (CE) data on the same sample set. The set contains 267 distinct sequence-based alleles (an increase of 58% compared to the 169 detectable by CE), including 60 novel Y-STR variants phased with their flanking sequences which have not been reported previously to our knowledge. Variation includes 46 distinct alleles containing non-reference variants of SNPs/indels in both repeat and flanking regions, and 145 distinct alleles containing repeat pattern variants (RPV). For DYS385a,b, DYS481 and DYS390 we observed repeat count variation in short flanking segments previously considered invariable, and suggest new MPS-based structural designations based on these. We considered the observed variation in the context of the Y phylogeny: several specific haplogroup associations were observed for SNPs and indels, reflecting the low mutation rates of such variant types; however, RPVs showed less phylogenetic coherence and more recurrence, reflecting their relatively high mutation rates. In conclusion, our study reveals considerable additional diversity at the Y-STRs of the PPY23 set via MPS analysis, demonstrates high concordance with CE data, facilitates nomenclature standardisation, and places Y-STR sequence variants in their phylogenetic context.
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Affiliation(s)
- Tunde I Huszar
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH, UK.
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103
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104
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Gemeinsame Empfehlungen der Projektgruppe „Biostatistische
DNA-Berechnungen“ und der Spurenkommission zur biostatistischen Bewertung von Y‑chromosomalen DNA-Befunden. Rechtsmedizin (Berl) 2018. [DOI: 10.1007/s00194-018-0244-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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105
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Weight of the evidence of genetic investigations of ancestry informative markers. Theor Popul Biol 2018; 120:1-10. [DOI: 10.1016/j.tpb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/11/2017] [Accepted: 12/14/2017] [Indexed: 01/03/2023]
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106
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Ji J, Qin Y, Wang R, Huang Z, Zhang Y, Zhou R, Song L, Ling X, Hu Z, Miao D, Shen H, Xia Y, Wang X, Lu C. Copy number gain of VCX, X-linked multi-copy gene, leads to cell proliferation and apoptosis during spermatogenesis. Oncotarget 2018; 7:78532-78540. [PMID: 27705943 PMCID: PMC5340235 DOI: 10.18632/oncotarget.12397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/25/2016] [Indexed: 11/25/2022] Open
Abstract
Male factor infertility affects one-sixth of couples worldwide, and non-obstructive azoospermia (NOA) is one of the most severe forms. In recent years there has been increasing evidence to implicate the participation of X chromosome in the process of spermatogenesis. To uncover the roles of X-linked multi-copy genes in spermatogenesis, we performed systematic analysis of X-linked gene copy number variations (CNVs) and Y chromosome haplogrouping in 447 idiopathic NOA patients and 485 healthy controls. Interestingly, the frequency of individuals with abnormal level copy of Variable charge, X-linked (VCX) was significantly different between cases and controls after multiple test correction (p = 5.10 × 10−5). To discriminate the effect of gain/loss copies in these genes, we analyzed the frequency of X-linked multi-copy genes in subjects among subdivided groups. Our results demonstrated that individuals with increased copy numbers of Nuclear RNA export factor 2 (NXF2) (p = 9.21 × 10−8) and VCX (p = 1.97 × 10−4) conferred the risk of NOA. In vitro analysis demonstrated that increasing copy number of VCX could upregulate the gene expression and regulate cell proliferation and apoptosis. Our study establishes a robust association between the VCX CNVs and NOA risk.
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Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Rong Wang
- Research Center for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Zhenyao Huang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yan Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ran Zhou
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ling Song
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiufeng Ling
- Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dengshun Miao
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Research Center for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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107
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Genetic variation in populations from central Argentina based on mitochondrial and Y chromosome DNA evidence. J Hum Genet 2018; 63:493-507. [DOI: 10.1038/s10038-017-0406-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/06/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022]
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108
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Mahal DG, Matsoukas IG. The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups. Front Genet 2018; 9:4. [PMID: 29410676 PMCID: PMC5787057 DOI: 10.3389/fgene.2018.00004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 01/04/2018] [Indexed: 02/05/2023] Open
Abstract
Several studies have evaluated the movements of large populations to the Indian subcontinent; however, the ancient geographic origins of smaller ethnic communities are not clear. Although historians have attempted to identify the origins of some ethnic groups, the evidence is typically anecdotal and based upon what others have written before. In this study, recent developments in DNA science were assessed to provide a contemporary perspective by analyzing the Y chromosome haplogroups of some key ethnic groups and tracing their ancient geographical origins from genetic markers on the Y-DNA haplogroup tree. A total of 2,504 Y-DNA haplotypes, representing 50 different ethnic groups in the Indian subcontinent, were analyzed. The results identified 14 different haplogroups with 14 geographic origins for these people. Moreover, every ethnic group had representation in more than one haplogroup, indicating multiple geographic origins for these communities. The results also showed that despite their varied languages and cultural differences, most ethnic groups shared some common ancestors because of admixture in the past. These findings provide new insights into the ancient geographic origins of ethnic groups in the Indian subcontinent. With about 2,000 other ethnic groups and tribes in the region, it is expected that more scientific discoveries will follow, providing insights into how, from where, and when the ancestors of these people arrived in the subcontinent to create so many different communities.
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Affiliation(s)
- David G Mahal
- School of Sport and Biomedical Sciences, University of Bolton, Bolton, United Kingdom.,Extension Division, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ianis G Matsoukas
- School of Sport and Biomedical Sciences, University of Bolton, Bolton, United Kingdom
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109
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Erzurumluoglu AM, Baird D, Richardson TG, Timpson NJ, Rodriguez S. Using Y-Chromosomal Haplogroups in Genetic Association Studies and Suggested Implications. Genes (Basel) 2018; 9:E45. [PMID: 29361760 PMCID: PMC5793196 DOI: 10.3390/genes9010045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/16/2018] [Accepted: 01/16/2018] [Indexed: 11/16/2022] Open
Abstract
Y-chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits, including cardiometabolic traits, have been reported. In apparently homogeneous populations defined by principal component analyses, there is still Y-DNA haplogroup variation which will result from population history. Therefore, hidden stratification and/or differential phenotypic effects by Y-DNA haplogroups could exist. To test this, we hypothesised that stratifying individuals according to their Y-DNA haplogroups before testing for associations between autosomal single nucleotide polymorphisms (SNPs) and phenotypes will yield difference in association. For proof of concept, we derived Y-DNA haplogroups from 6537 males from two epidemiological cohorts, Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 5080; 816 Y-DNA SNPs) and the 1958 Birth Cohort (n = 1457; 1849 Y-DNA SNPs), and studied the robust associations between 32 SNPs and body mass index (BMI), including SNPs in or near Fat Mass and Obesity-associated protein (FTO) which yield the strongest effects. Overall, no association was replicated in both cohorts when Y-DNA haplogroups were considered and this suggests that, for BMI at least, there is little evidence of differences in phenotype or SNP association by Y-DNA structure. Further studies using other traits, phenome-wide association studies (PheWAS), other haplogroups and/or autosomal SNPs are required to test the generalisability and utility of this approach.
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Affiliation(s)
- A Mesut Erzurumluoglu
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
| | - Denis Baird
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
| | - Santiago Rodriguez
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.
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110
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Ocakoğlu FT, Köse S, Özbaran B, Onay H. The oxytocin receptor gene polymorphism -rs237902- is associated with the severity of autism spectrum disorder: A pilot study. Asian J Psychiatr 2018; 31:142-149. [PMID: 29428512 DOI: 10.1016/j.ajp.2018.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/09/2017] [Accepted: 01/15/2018] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Previous studies showed the association of Autism Spectrum Disorder (ASD) and oxytocin receptor (OXTR) gene. We aimed to explore the OXTR gene single nucleotide polymorphisms (SNPs) across the ASD severity categories based on DSM-5. METHOD The whole encoding regions of the human OXTR gene were sequenced to identify the SNPs in 100 Turkish children with ASD. Genotypes of detected SNPs were also compared with the Childhood Autism Rating Scale (CARS) scores. RESULTS Disease severity of the patients carrying GA and AA genotypes (GA/AA) of rs237902 were found more severe compared to those carrying GG genotype (χ2 = 6.456, df = 2, p = .040). This finding was more powerful in boys (χ2 = 9.288, df = 2, p = .010). Similarly, GA/AA genotypes of rs237902 were found associated with higher CARS scores in boys (U = 650.5, r = 0.24, p = .021). CONCLUSION Significant relationship between the ASD severity categories of DSM-5 and rs237902 was shown for the first time.
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Affiliation(s)
- Fevzi Tuna Ocakoğlu
- Batman District State Hospital, Child Psychiatry Outpatient Clinic, MA: 72070, Batman, Turkey.
| | - Sezen Köse
- Department of Child and Adolescent Psychiatry, Ege University School of Medicine, Bornova, Izmir, Turkey.
| | - Burcu Özbaran
- Department of Child and Adolescent Psychiatry, Ege University School of Medicine, Bornova, Izmir, Turkey.
| | - Hüseyin Onay
- Department of Medical Genetic, Ege University School of Medicine, Bornova, Izmir, Turkey.
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111
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Alhammadi S, Alghafri R, Almarzoqi A, Khajah A, Alhosani I, Amiri K. Y-chromosome polymorphisms in the United Arab Emirates population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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112
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Vidal O, Drögemüller C, Obexer-Ruff G, Reber I, Jordana J, Martínez A, Bâlteanu VA, Delgado JV, Eghbalsaied S, Landi V, Goyache F, Traoré A, Pazzola M, Vacca GM, Badaoui B, Pilla F, D'Andrea M, Álvarez I, Capote J, Sharaf A, Pons À, Amills M. Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds. Sci Rep 2017; 7:16161. [PMID: 29170508 PMCID: PMC5701018 DOI: 10.1038/s41598-017-15593-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/27/2017] [Indexed: 11/09/2022] Open
Abstract
The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation.
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Affiliation(s)
- Oriol Vidal
- Departament de Biologia, Universitat de Girona, 17003, Girona, Spain.
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | | | - Irene Reber
- Institute of Genetics, University of Bern, Bern, 3001, Switzerland
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Valentin Adrian Bâlteanu
- Institute of Life Sciences, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj-Napoca, Romania
| | | | - Shahin Eghbalsaied
- Transgenesis Center of Excellence, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Felix Goyache
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Amadou Traoré
- Institut de l'Environnement et Recherches Agricoles, 04 BP 8645, Ouagadougou, 04, Burkina Faso
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Bouabid Badaoui
- University Mohammed V, Agdal, Faculty of Sciences, 4 Av. Ibn Battota, Rabat, Morocco
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti, Università Degli Studi Del Molise, Campobasso, Italy
| | - Mariasilvia D'Andrea
- Dipartimento Agricoltura, Ambiente e Alimenti, Università Degli Studi Del Molise, Campobasso, Italy
| | - Isabel Álvarez
- Área de Genética y Reproducción Animal, SERIDA-Deva, Camino de Rioseco 1225, Gijón, 33394, Spain
| | - Juan Capote
- Instituto Canario de Investigaciones Agrarias, Canary Islands, Tenerife, La Laguna 38108, Spain
| | - Abdoallah Sharaf
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, České Budějovice, Czechia.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Àgueda Pons
- Unitat de Races Autòctones, Servei de Millora Agrària, (SEMILLA-SAU), Son Ferriol, 07198, Spain
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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113
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Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81). Sci Rep 2017; 7:15941. [PMID: 29162904 PMCID: PMC5698413 DOI: 10.1038/s41598-017-16271-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/09/2017] [Indexed: 12/30/2022] Open
Abstract
E-M183 (E-M81) is the most frequent paternal lineage in North Africa and thus it must be considered to explore past historical and demographical processes. Here, by using whole Y chromosome sequences from 32 North African individuals, we have identified five new branches within E-M183. The validation of these variants in more than 200 North African samples, from which we also have information of 13 Y-STRs, has revealed a strong resemblance among E-M183 Y-STR haplotypes that pointed to a rapid expansion of this haplogroup. Moreover, for the first time, by using both SNP and STR data, we have provided updated estimates of the times-to-the-most-recent-common-ancestor (TMRCA) for E-M183, which evidenced an extremely recent origin of this haplogroup (2,000-3,000 ya). Our results also showed a lack of population structure within the E-M183 branch, which could be explained by the recent and rapid expansion of this haplogroup. In spite of a reduction in STR heterozygosity towards the West, which would point to an origin in the Near East, ancient DNA evidence together with our TMRCA estimates point to a local origin of E-M183 in NW Africa.
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114
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Behar DM, Saag L, Karmin M, Gover MG, Wexler JD, Sanchez LF, Greenspan E, Kushniarevich A, Davydenko O, Sahakyan H, Yepiskoposyan L, Boattini A, Sarno S, Pagani L, Carmi S, Tzur S, Metspalu E, Bormans C, Skorecki K, Metspalu M, Rootsi S, Villems R. The genetic variation in the R1a clade among the Ashkenazi Levites' Y chromosome. Sci Rep 2017; 7:14969. [PMID: 29097670 PMCID: PMC5668307 DOI: 10.1038/s41598-017-14761-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/13/2017] [Indexed: 11/09/2022] Open
Abstract
Approximately 300,000 men around the globe self-identify as Ashkenazi Levites, of whom two thirds were previously shown to descend from a single male. The paucity of whole Y-chromosome sequences precluded conclusive identification of this ancestor's age, geographic origin and migration patterns. Here, we report the variation of 486 Y-chromosomes within the Ashkenazi and non-Ashkenazi Levite R1a clade, other Ashkenazi Jewish paternal lineages, as well as non-Levite Jewish and non-Jewish R1a samples. Cumulatively, the emerging profile is of a Middle Eastern ancestor, self-affiliating as Levite, and carrying the highly resolved R1a-Y2619 lineage, which was likely a minor haplogroup among the Hebrews. A star-like phylogeny, coalescing similarly to other Ashkenazi paternal lineages, ~1,743 ybp, suggests it to be one of the Ashkenazi paternal founders; to have expanded as part of the overall Ashkenazi demographic expansion, without special relation to the Levite affiliation; and to have subsequently spread to non-Ashkenazi Levites.
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Affiliation(s)
- Doron M Behar
- Estonian Biocentre, Tartu, 51010, Estonia. .,Genomic Research Center, Gene by Gene, Houston, 77008, Texas, USA.
| | - Lauri Saag
- Estonian Biocentre, Tartu, 51010, Estonia
| | | | - Meir G Gover
- Independent Genetic Genealogy Researcher, Savyon, 5690500, Israel
| | | | | | | | - Alena Kushniarevich
- Estonian Biocentre, Tartu, 51010, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072, Minsk, Belarus
| | - Oleg Davydenko
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072, Minsk, Belarus
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, 51010, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology of National Academy of Sciences, Yerevan, 0014, Armenia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology of National Academy of Sciences, Yerevan, 0014, Armenia
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Luca Pagani
- Estonian Biocentre, Tartu, 51010, Estonia.,APE Lab, Dept. of Biology, University of Padova, 35121, Padova, Italy
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Shay Tzur
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel.,Rambam Health Care Campus, Haifa, 3109601, Israel
| | - Ene Metspalu
- Estonian Biocentre, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology University of Tartu, Tartu, 51010, Estonia
| | - Concetta Bormans
- Genomic Research Center, Gene by Gene, Houston, 77008, Texas, USA
| | - Karl Skorecki
- Rambam Health Care Campus, Haifa, 3109601, Israel.,Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | | | | | - Richard Villems
- Estonian Biocentre, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology University of Tartu, Tartu, 51010, Estonia
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115
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Yang C, Ba H, Cao Y, Dong G, Zhang S, Gao Z, Zhao H, Zhou X. Linking Y-chromosomal short tandem repeat loci to human male impulsive aggression. Brain Behav 2017; 7:e00855. [PMID: 29201554 PMCID: PMC5698871 DOI: 10.1002/brb3.855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 04/13/2017] [Accepted: 09/17/2017] [Indexed: 11/08/2022] Open
Abstract
INTRODUCTION Men are more susceptible to impulsive behavior than women. Epidemiological studies revealed that the impulsive aggressive behavior is affected by genetic factors, and the male-specific Y chromosome plays an important role in this behavior. In this study, we investigated the association between the impulsive aggressive behavior and Y-chromosomal short tandem repeats (Y-STRs) loci. METHODS The collected biologic samples from 271 offenders with impulsive aggressive behavior and 492 healthy individuals without impulsive aggressive behavior were amplified by PowerPlexRY23 PCR System and the resultant products were separated by electrophoresis and further genotyped. Then, comparisons in allele and haplotype frequencies of the selected 22 Y-STRs were made in the two groups. RESULTS Our results showed that there were significant differences in allele frequencies at DYS448 and DYS456 between offenders and controls (p < .05). Univariate analysis further revealed significant frequency differences for alleles 18 and 22 at DYS448 (0.18 vs 0.27, compared to the controls, p = .003, OR=0.57,95% CI=0.39-0.82; 0.03 vs 0.01, compared to the controls, p = .003, OR=7.45, 95% CI=1.57-35.35, respectively) and for allele 17 at DYS456 (0.07 vs 0.14, compared to the controls, p = .006, OR=0.48, 95% CI =0.28-0.82) between two groups. Interestingly, the frequency of haploid haplotype 22-15 on the DYS448-DYS456 (DYS448-DYS456-22-15) was significantly higher in offenders than in controls (0.033 vs 0.004, compared to the control, p = .001, OR = 8.42, 95%CI =1.81-39.24). Moreover, there were no significant differences in allele frequencies of other Y-STRs loci between two groups. Furthermore, the unconditional logistic regression analysis confirmed that alleles 18 and 22 at DYS448 and allele 17 at DYS456 are associated with male impulsive aggression. However, the DYS448-DYS456-22-15 is less related to impulsive aggression. CONCLUSION Our results suggest a link between Y-chromosomal allele types and male impulsive aggression.
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Affiliation(s)
- Chun Yang
- Department of Psychiatry Psychiatry Center of Chinese People's Liberation Army No.102 Hospital of People's Liberation Army Changzhou China
| | - Huajie Ba
- DNA Laboratory Public Security Bureau of Changzhou Changzhou China
| | - Yin Cao
- Department of Neurology Laboratory of Neurological Diseases Changzhou No.2 People's Hospital The Affiliated Hospital of Nanjing Medical University Changzhou China
| | - Guoying Dong
- Department of Neurology Laboratory of Neurological Diseases Changzhou No.2 People's Hospital The Affiliated Hospital of Nanjing Medical University Changzhou China
| | - Shuyou Zhang
- Department of Psychiatry Psychiatry Center of Chinese People's Liberation Army No.102 Hospital of People's Liberation Army Changzhou China
| | - Zhiqin Gao
- Department of Psychiatry Psychiatry Center of Chinese People's Liberation Army No.102 Hospital of People's Liberation Army Changzhou China
| | - Hanqing Zhao
- Department of Psychiatry Psychiatry Center of Chinese People's Liberation Army No.102 Hospital of People's Liberation Army Changzhou China
| | - Xianju Zhou
- Department of Neurology Laboratory of Neurological Diseases Changzhou No.2 People's Hospital The Affiliated Hospital of Nanjing Medical University Changzhou China
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116
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Wang M, Wang Z, Zhang Y, He G, Liu J, Hou Y. Forensic characteristics and phylogenetic analysis of two Han populations from the southern coastal regions of China using 27 Y-STR loci. Forensic Sci Int Genet 2017; 31:e17-e23. [DOI: 10.1016/j.fsigen.2017.10.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 11/30/2022]
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117
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Dzhaubermezov MA, Ekomasova NV, Litvinov SS, Khusainova RI, Akhmetova VL, Balinova NV, Khusnutdinova EK. Genetic characterization of Balkars and Karachays according to the variability of the Y chromosome. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417100039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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118
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Hu W, Chen M, Ji J, Qin Y, Zhang F, Xu M, Wu W, Du G, Wu D, Han X, Jin L, Xia Y, Lu C, Wang X. Interaction between Y chromosome haplogroup O3 * and 4-n-octylphenol exposure reduces the susceptibility to spermatogenic impairment in Han Chinese. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 144:450-455. [PMID: 28667856 DOI: 10.1016/j.ecoenv.2017.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
Certain genetic background (mainly Y chromosome haplogroups, Y-hg) may modify the susceptibility of certain environmental exposure to some diseases. Compared with respective main effects of genetic background or environmental exposure, interactions between them reflect more realistic combined effects on the susceptibility to a disease. To identify the interactions on spermatogenic impairment, we performed Y chromosome haplotyping and measurement of 9 urinary phenols concentrations in 774 infertile males and 520 healthy controls in a Han Chinese population, and likelihood ratio tests were used to examine the interactions between Y-hgs and phenols. Originally, we observed that Y-hg C and Y-hg F* might modify the susceptibility to male infertility with urinary 4-n-octylphenol (4-n-OP) level (Pinter = 0.005 and 0.019, respectively). Subsequently, based on our results, two panels were tested to identify the possible protective sub-branches of Y-hg F* to 4-n-OP exposure, and Y-hg O3* was uncovered to interact with 4-n-OP (Pinter = 0.019). In conclusion, while 4-n-OP shows an adverse effect on spermatogenesis, Y-hg O3* makes individuals more adaptive to such an effect for maintaining basic reproductive capacity.
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Affiliation(s)
- Weiyue Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Minjian Chen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juan Ji
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feng Zhang
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Miaofei Xu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Wu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guizhen Du
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Di Wu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiumei Han
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
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119
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Mahal DG, Matsoukas IG. Y-STR Haplogroup Diversity in the Jat Population Reveals Several Different Ancient Origins. Front Genet 2017; 8:121. [PMID: 28979290 PMCID: PMC5611447 DOI: 10.3389/fgene.2017.00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/30/2017] [Indexed: 11/19/2022] Open
Abstract
The Jats represent a large ethnic community that has inhabited the northwest region of India and Pakistan for several thousand years. It is estimated the community has a population of over 123 million people. Many historians and academics have asserted that the Jats are descendants of Aryans, Scythians, or other ancient people that arrived and lived in northern India at one time. Essentially, the specific origin of these people has remained a matter of contention for a long time. This study demonstrated that the origins of Jats can be clarified by identifying their Y-chromosome haplogroups and tracing their genetic markers on the Y-DNA haplogroup tree. A sample of 302 Y-chromosome haplotypes of Jats in India and Pakistan was analyzed. The results showed that the sample population had several different lines of ancestry and emerged from at least nine different geographical regions of the world. It also became evident that the Jats did not have a unique set of genes, but shared an underlying genetic unity with several other ethnic communities in the Indian subcontinent. A startling new assessment of the genetic ancient origins of these people was revealed with DNA science.
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Affiliation(s)
- David G Mahal
- School of Sport and Biomedical Sciences, University of BoltonBolton, United Kingdom.,Extension Division, University of California, Los AngelesLos Angeles, CA, United States
| | - Ianis G Matsoukas
- School of Sport and Biomedical Sciences, University of BoltonBolton, United Kingdom
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120
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121
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Maan AA, Eales J, Akbarov A, Rowland J, Xu X, Jobling MA, Charchar FJ, Tomaszewski M. The Y chromosome: a blueprint for men's health? Eur J Hum Genet 2017; 25:1181-1188. [PMID: 28853720 PMCID: PMC5643963 DOI: 10.1038/ejhg.2017.128] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/16/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
The Y chromosome has long been considered a 'genetic wasteland' on a trajectory to completely disappear from the human genome. The perception of its physiological function was restricted to sex determination and spermatogenesis. These views have been challenged in recent times with the identification of multiple ubiquitously expressed Y-chromosome genes and the discovery of several unexpected associations between the Y chromosome, immune system and complex polygenic traits. The collected evidence suggests that the Y chromosome influences immune and inflammatory responses in men, translating into genetically programmed susceptibility to diseases with a strong immune component. Phylogenetic studies reveal that carriers of a common European lineage of the Y chromosome (haplogroup I) possess increased risk of coronary artery disease. This occurs amidst upregulation of inflammation and suppression of adaptive immunity in this Y lineage, as well as inferior outcomes in human immunodeficiency virus infection. From structural analysis and experimental data, the UTY (Ubiquitously Transcribed Tetratricopeptide Repeat Containing, Y-Linked) gene is emerging as a promising candidate underlying the associations between Y-chromosome variants and the immunity-driven susceptibility to complex disease. This review synthesises the recent structural, experimental and clinical insights into the human Y chromosome in the context of men's susceptibility to disease (with a particular emphasis on cardiovascular disease) and provides an overview of the paradigm shift in the perception of the Y chromosome.
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Affiliation(s)
- Akhlaq A Maan
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Joshua Rowland
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
| | - Fadi J Charchar
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University, Mount Helen Campus, Ballarat, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Division of Medicine, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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122
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Ullah I, Olofsson JK, Margaryan A, Ilardo M, Ahmad H, Sikora M, Hansen AJ, Shahid Nadeem M, Fazal N, Ali M, Buchard A, Hemphill BE, Willerslev E, Allentoft ME. High Y-chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan. Ann Hum Genet 2017; 81:234-248. [PMID: 28771684 DOI: 10.1111/ahg.12204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/26/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
The ethnic groups that inhabit the mountainous Dir and Swat districts of northern Pakistan are marked by high levels of cultural and phenotypic diversity. To obtain knowledge of the extent of genetic diversity in this region, we investigated Y-chromosomal diversity in five population samples representing the three main ethnic groups residing within these districts, including Gujars, Pashtuns and Kohistanis. A total of 27 Y-chromosomal short tandem repeats (Y-STRs) and 331 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) were investigated. In the Y-STRs, we observed very high and significant levels of genetic differentiation in nine of the 10 pairwise between-group comparisons (RST 0.179-0.746), and the differences were mirrored in the Y-SNP haplogroup frequency distribution. No genetic differences were found between the two Pashtun subethnic groups Tarklanis and Yusafzais (RST = 0.000). Utmankhels, also considered Pashtuns culturally, were not closely related to any of the other population samples (RST 0.451-0.746). Thus, our findings provide examples of both associations and dissociations between cultural and genetic legacies. When analyzed within a larger continental-scale context, these five ethnic groups fall mostly outside the previously characterized Y-chromosomal gene pools of the Indo-Pakistani subcontinent. Male founder effects, coupled with culturally and topographically based constraints upon marriage and movement, are likely responsible for the high degree of genetic structure in this region.
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Affiliation(s)
- Inam Ullah
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan.,Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, United Kingdom
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Habib Ahmad
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan.,Islamia University, Peshawar, Pakistan
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Numan Fazal
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Murad Ali
- Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan
| | - Anders Buchard
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, USA
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum, University of Copenhagen, Copenhagen, Denmark
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123
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Nath Choudhury M, Uddin A, Chakraborty S. Codon usage bias and its influencing factors for Y-linked genes in human. Comput Biol Chem 2017; 69:77-86. [DOI: 10.1016/j.compbiolchem.2017.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/30/2022]
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124
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Skowronek MF, Velazquez T, Mut P, Figueiro G, Sans M, Bertoni B, Sapiro R. Associations between male infertility and ancestry in South Americans: a case control study. BMC MEDICAL GENETICS 2017; 18:78. [PMID: 28747152 PMCID: PMC5530489 DOI: 10.1186/s12881-017-0438-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/13/2017] [Indexed: 01/20/2023]
Affiliation(s)
| | - Tatiana Velazquez
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Patricia Mut
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Gonzalo Figueiro
- Departamento de Antropología, Facultad de Humanidades y Ciencias de la Educación, UDELAR, Montevideo, Uruguay
| | - Monica Sans
- Departamento de Antropología, Facultad de Humanidades y Ciencias de la Educación, UDELAR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina UDELAR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina UDELAR, Montevideo, Uruguay.
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125
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Liu YS, Chen JG, Mei T, Guo YX, Meng HT, Li JF, Wei YY, Jin XY, Zhu BF, Zhang LP. Genetic variation and forensic characteristic analysis of 25 STRs of a novel fluorescence co-amplification system in Chinese Southern Shaanxi Han population. Oncotarget 2017; 8:55443-55452. [PMID: 28903432 PMCID: PMC5589671 DOI: 10.18632/oncotarget.19317] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 06/05/2017] [Indexed: 11/25/2022] Open
Abstract
We analyzed the genetic polymorphisms of 15 autosomal and 10 Y-chromosomal STR loci in 214 individuals of Han population from Southern Shaanxi of China and studied the genetic relationships between Southern Shaanxi Han and other populations. We observed a total of 150 alleles at 15 autosomal STR loci with the corresponding allelic frequencies ranging from 0.0023 to 0.5210, and the combined power of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999999999998866 and 0.999998491, respectively. For the 10 Y-STR loci, totally 100 different haplotypes were obtained, of which 94 were unique. The discriminatory capacity and haplotype diversity values of the 10 Y-STR loci were 0.9259 and 0.998269, respectively. The results demonstrated high genetic diversities of the 25 STR loci in the population for forensic applications. We constructed neighbor-joining tree and conducted principal component analysis based on 15 autosomal STR loci and conducted multidimensional scaling analysis and constructed neighbor-joining tree based on 10 Y-STR loci. The results of population genetic analyses based on both autosomal and Y-chromosome STRs indicated that the studied Southern Shaanxi Han population had relatively closer genetic relationship with Eastern Han population, and distant relationships with Croatian, Serbian and Moroccan populations.
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Affiliation(s)
- Yao-Shun Liu
- Department of Biochemistry and Molecular Biology, Basic Medicine College of Xinjiang Medical University, Urumqi, Xinjiang 830011, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Jian-Gang Chen
- Department of Biochemistry and Molecular Biology, Basic Medicine College of Xinjiang Medical University, Urumqi, Xinjiang 830011, P. R. China.,Science and Technology Institute, Xinjiang Public Security Department, Urumqi, Xinjiang 830006, P.R. China
| | - Ting Mei
- Department of Biochemistry and Molecular Biology, Basic Medicine College of Xinjiang Medical University, Urumqi, Xinjiang 830011, P. R. China.,Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Yu-Xin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Hao-Tian Meng
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Jian-Fei Li
- School of Marxism, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P.R. China
| | - Yuan-Yuan Wei
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Xiao-Ye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P. R. China.,Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Li-Ping Zhang
- Department of Biochemistry and Molecular Biology, Basic Medicine College of Xinjiang Medical University, Urumqi, Xinjiang 830011, P. R. China
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126
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Loftus A, Murphy G, Brown H, Montgomery A, Tabak J, Baus J, Carroll M, Green A, Sikka S, Sinha S. Development and validation of InnoQuant® HY, a system for quantitation and quality assessment of total human and male DNA using high copy targets. Forensic Sci Int Genet 2017; 29:205-217. [DOI: 10.1016/j.fsigen.2017.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/26/2017] [Accepted: 04/14/2017] [Indexed: 11/27/2022]
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127
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Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer R, McCue M, Neuditschko M, Rieder S, Schlötterer C, Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Curr Biol 2017; 27:2029-2035.e5. [PMID: 28669755 DOI: 10.1016/j.cub.2017.05.086] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/19/2017] [Accepted: 05/26/2017] [Indexed: 11/25/2022]
Abstract
The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern European haplotypes, all modern horse breeds clustered together in a roughly 700-year-old haplogroup that was transmitted to Europe by the import of Oriental stallions. The Oriental horse group consisted of two major subclades: the Original Arabian lineage and the Turkoman horse lineage. We show that the English Thoroughbred MSY was derived from the Turkoman lineage and that English Thoroughbred sires are largely responsible for the predominance of this haplotype in modern horses.
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Affiliation(s)
- Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria.
| | - Nicola Palmieri
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Thomas Druml
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising 85354, Germany
| | - Jens Tetens
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany; Functional Breeding Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen 37077, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, University of Kiel, Kiel 24098, Germany
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden
| | - Leif Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 75007, Sweden; Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala 75123, Sweden; Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4461, USA
| | - Robert Schaefer
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | - Molly McCue
- Veterinary Population Medicine Department, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, Avenches 1580, Switzerland
| | - Christian Schlötterer
- Institut für Populationsgenetik, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
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Primativo G, Ottoni C, Biondi G, Serafino S, Martínez-Labarga C, Larmuseau MHD, Scardi M, Decorte R, Rickards O. Bight of Benin: a Maternal Perspective of Four Beninese Populations and their Genetic Implications on the American Populations of African Ancestry. Ann Hum Genet 2017; 81:78-90. [PMID: 28205221 DOI: 10.1111/ahg.12186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/03/2017] [Indexed: 12/01/2022]
Abstract
The understanding of the first movements of the ancestral populations within the African continent is still unclear, particularly in West Africa, due to several factors that have shaped the African genetic pool across time. To improve the genetic representativeness of the Beninese population and to better understand the patterns of human settlement inside West Africa and the dynamics of peopling of the Democratic Republic of Benin, we analyzed the maternal genetic variation of 193 Beninese individuals belonging to Bariba, Berba, Dendi, and Fon populations. Results support the oral traditions indicating that the western neighbouring populations have been the ancestors of the first Beninese populations, and the extant genetic structure of the Beninese populations is most likely the result of admixture between populations from neighbouring countries and native people. The present findings highlight how the Beninese populations contributed to the gene pool of the extant populations of some American populations of African ancestry. This strengthens the hypothesis that the Bight of Benin was not only an assembly point for the slave trade during the Trans-Atlantic Slave Trade but also an important slave trapping area.
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Affiliation(s)
| | - Claudio Ottoni
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Gianfranco Biondi
- Department of Clinical Medicine, Public Health, Life and Environment, University of L'Aquila, L'Aquila, Italy
| | - Sara Serafino
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Department of Public Health and Infectious Diseases, University of Rome Sapienza, Rome, Italy
| | | | - Maarten H D Larmuseau
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Department of Biology, Laboratory of Socioecology and Social Evolution, KU Leuven - University of Leuven, Leuven, Belgium
| | - Michele Scardi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Ronny Decorte
- Department of Imaging and Pathology, Center for Archaeological Sciences, KU Leuven - University of Leuven, Leuven, Belgium.,Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, Leuven, Belgium
| | - Olga Rickards
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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129
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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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130
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Groeger J, Opler M, Kleinhaus K, Perrin MC, Calderon-Margalit R, Manor O, Paltiel O, Conley D, Harlap S, Malaspina D. Live birth sex ratios and father's geographic origins in Jerusalem, 1964-1976. Am J Hum Biol 2017; 29. [PMID: 27901293 DOI: 10.1002/ajhb.22945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/15/2016] [Accepted: 11/06/2016] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE To examine whether ancestry influenced sex ratios of offspring in a birth cohort before parental antenatal sex selection influenced offspring sex. METHODS We measured the sex ratio as the percent of males according to countries of birth of paternal and maternal grandfathers in 91,459 live births from 1964 to 1976 in the Jerusalem Perinatal Study. Confidence limits (CI) were computed based on an expected sex ratio of 1.05, which is 51.4% male. RESULTS Of all live births recorded, 51.4% were male. Relative to Jewish ancestry (51.4% males), significantly more males (1,761) were born to Muslim ancestry (54.5, 95% CI = 52.1-56.8, P = 0.01). Among the former, sex ratios were not significantly associated with paternal or maternal age, education, or offspring's birth order. Consistent with a preference for male offspring, the sex ratio decreased despite increasing numbers of births over the 13-year period. Sex ratios were not affected by maternal or paternal origins in North Africa or Europe. However, the offspring whose paternal grandfathers were born in Western Asia included fewer males than expected (50.7, 50.1-51.3, P = 0.02), whether the father was born abroad (50.7) or in Israel (50.8). This was observed for descendents of paternal grandfathers born in Lebanon (47.6), Turkey (49.9), Yemen & Aden (50.2), Iraq (50.5), Afghanistan (50.5), Syria (50.6), and Cyprus (50.7); but not for those from India (51.5) or Iran (51.9). The West Asian group showed the strongest decline in sex ratios with increasing paternal family size. CONCLUSIONS A decreased sex ratio associated with ancestry in Western Asia is consistent with reduced ability to bear sons by a subset of Jewish men in the Jerusalem cohort. Lower sex ratios may be because of pregnancy stress, which may be higher in this subgroup. Alternatively, a degrading Y chromosome haplogroup or other genetic or epigenetic differences on male germ lines could affect birth ratios, such as differential exposure to an environmental agent, dietary differences, or stress. Differential stopping behaviors that favor additional pregnancies following the birth of a daughter might exacerbate these lower sex ratios.
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Affiliation(s)
- J Groeger
- College of Medicine, SUNY Downstate, Brooklyn, New York, 11203
| | - M Opler
- Department of Psychiatry, New York University School of Medicine, 1 Park Avenue, Floor 8, New York, New York, 10016, USA.,Prophase, 3 Park Avenue, New York, New York, 10016
| | - K Kleinhaus
- Department of Psychiatry, New York University School of Medicine, 1 Park Avenue, Floor 8, New York, New York, 10016, USA
| | - M C Perrin
- Department of Psychiatry, New York University School of Medicine, 1 Park Avenue, Floor 8, New York, New York, 10016, USA
| | - R Calderon-Margalit
- Braun School of Public Health, Hebrew University-Hadassah School of Public Health, Jerusalem, 91120, Israel.,Department of Sociology, Princeton University, Princeton, New Jersey, 08544
| | - O Manor
- Braun School of Public Health, Hebrew University-Hadassah School of Public Health, Jerusalem, 91120, Israel.,Department of Sociology, Princeton University, Princeton, New Jersey, 08544
| | - O Paltiel
- Braun School of Public Health, Hebrew University-Hadassah School of Public Health, Jerusalem, 91120, Israel.,Department of Sociology, Princeton University, Princeton, New Jersey, 08544
| | - D Conley
- Department of Sociology, Princeton University, Princeton, New Jersey, 08544
| | - S Harlap
- Department of Psychiatry, New York University School of Medicine, 1 Park Avenue, Floor 8, New York, New York, 10016, USA
| | - D Malaspina
- Department of Psychiatry, New York University School of Medicine, 1 Park Avenue, Floor 8, New York, New York, 10016, USA
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131
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Trombetta B, D'Atanasio E, Cruciani F. Patterns of Inter-Chromosomal Gene Conversion on the Male-Specific Region of the Human Y Chromosome. Front Genet 2017; 8:54. [PMID: 28515739 PMCID: PMC5413550 DOI: 10.3389/fgene.2017.00054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/18/2017] [Indexed: 12/31/2022] Open
Abstract
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized. The main effect of ICGC is to increase the allelic diversity of MSY by generating a significant excess of clustered single nucleotide polymorphisms (SNPs) (defined as groups of two or more SNPs occurring in close proximity and on the same branch of the Y phylogeny). On the human MSY, 13 inter-chromosomal gene conversion hotspots (GCHs) have been identified so far, involving donor sequences mainly from the X-chromosome and, to a lesser extent, from autosomes. Most of the GCHs are evolutionary conserved and overlap with regions involved in aberrant X–Y crossing-over. This review mainly focuses on the dynamics and the current knowledge concerning the recombinational landscape of the human MSY in the form of ICGC, on how this molecular mechanism may influence the evolution of the MSY, and on how it could affect the information enclosed within a genomic region which, until recently, appeared to be an evolutionary independent unit.
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Affiliation(s)
- Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di RomaRome, Italy
| | - Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di RomaRome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di RomaRome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche (CNR),Rome, Italy
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132
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Spermatogenic failure and the Y chromosome. Hum Genet 2017; 136:637-655. [PMID: 28456834 DOI: 10.1007/s00439-017-1793-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/30/2017] [Indexed: 12/29/2022]
Abstract
The Y chromosome harbors a number of genes essential for testis development and function. Its highly repetitive structure predisposes this chromosome to deletion/duplication events and is responsible for Y-linked copy-number variations (CNVs) with clinical relevance. The AZF deletions remove genes with predicted spermatogenic function en block and are the most frequent known molecular causes of impaired spermatogenesis (5-10% of azoospermic and 2-5% of severe oligozoospermic men). Testing for this deletion has both diagnostic and prognostic value for testicular sperm retrieval in azoospermic men. The most dynamic region on the Yq is the AZFc region, presenting numerous NAHR hotspots leading to partial losses or gains of the AZFc genes. The gr/gr deletion (a partial AZFc deletion) negatively affects spermatogenic efficiency and it is a validated, population-dependent risk factor for oligozoospermia. In certain populations, the Y background may play a role in the phenotypic expression of partial AZFc rearrangements and similarly it may affect the predisposition to specific deletions/duplication events. Also, the Yp contains a gene array, TSPY1, with potential effect on germ cell proliferation. Despite intensive investigations during the last 20 years on the role of this sex chromosome in spermatogenesis, a number of clinical and basic questions remain to be answered. This review is aimed at providing an overview of the role of Y chromosome-linked genes, CNVs, and Y background in spermatogenesis.
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133
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Improved phylogenetic resolution for Y-chromosome Haplogroup O2a1c-002611. Sci Rep 2017; 7:1146. [PMID: 28442769 PMCID: PMC5430735 DOI: 10.1038/s41598-017-01340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/28/2017] [Indexed: 11/25/2022] Open
Abstract
Y-chromosome Haplogroup O2a1c-002611 is one of the dominant lineages of East Asians and Southeast Asians. However, its internal phylogeny remains insufficiently investigated. In this study, we genotyped 89 new highly informative single nucleotide polymorphisms (SNPs) in 305 individuals with Haplogroup O2a1c-002611 identified from 2139 Han Chinese males. Two major branches were identified, O2a1c1-F18 and O2a1c2-L133.2 and the first was further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11.13% and 2.20% of Han Chinese, respectively. In Haplogroup O2a1c1a-F11, we also determined seven sublineages with quite different frequency distributions in Han Chinese ranging from 0.187% to 3.553%, implying they might have different demographic history. The reconstructed haplogroup tree for all the major clades within Haplogroup O2a1c-002611 permits better resolution of male lineages in population studies of East Asia and Southeast Asia. The dataset generated in the present study are also valuable for forensic identification and paternity tests in China.
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134
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Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet 2017; 136:499-510. [PMID: 28444560 DOI: 10.1007/s00439-017-1800-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 01/25/2023]
Abstract
We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations. A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal populations, the Birhor (Austro-Asiatic-speaking) and Irula (Dravidian-speaking) are the nearest neighbours of South Asian non-tribal populations, with a common origin in the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population. This analysis suggests that Indian populations have complex ancestry which cannot be explained by a single expansion model.
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Affiliation(s)
- Mayukh Mondal
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK.
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain.
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135
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Pamjav H, Fóthi Á, Fehér T, Fóthi E. A study of the Bodrogköz population in north-eastern Hungary by Y chromosomal haplotypes and haplogroups. Mol Genet Genomics 2017; 292:883-894. [PMID: 28409264 DOI: 10.1007/s00438-017-1319-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/09/2017] [Indexed: 11/30/2022]
Abstract
We have determined the distribution of Y chromosomal haplotypes and haplogroups in population samples from one of the most important areas in north-eastern Hungary from many villages in the Bodrogköz. The Bodrogköz region was chosen due to its isolated nature, because this area was a moorland encircled by the Tisza, Bodrog, and Latorca Rivers and inhabitants of this part of Hungary escaped from both Tatar and Ottoman invasions, which decimated the post-Hungarian Conquest populations in many parts of the country. Furthermore, in the first half of the tenth century, this region served as the Palatial Centre and burial grounds of the Hungarian tribes. It has thus been assumed that the present population in this area is likely to be more similar to the population that lived in the Conquest period. We analysed male-specific markers, 23 Y-STRs and more than 30 Y-SNPs, that reflect the past and recent genetic history. We found that the general haplogroup distribution of the samples showed high genetic similarity to non-Bodrogköz Hungarians and neighbouring populations, despite its sheltered location and historical record. We were able to classify the Y-chromosomal haplogroups into four large groups based on STR mutation events: pre-Roman/Roman ancient lineage, Finno-Ugric speakers arriving into the Carpathian Basin, Migration period admixture, and post-Hungarian Conquest admixture. It is clear that a significantly larger database with deep haplogroup resolution, including ancient DNA data, is required to strengthen this research.
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Affiliation(s)
- Horolma Pamjav
- National Centre of Forensic Experts and Research, Budapest, Hungary.
| | - Á Fóthi
- Department of Genetics, Faculty of Sciences, Eötvös Loránd University, Budapest, Hungary
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - T Fehér
- The Hungarian Magyar Family Tree DNA Project, Budapest, Hungary
| | - Erzsébet Fóthi
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary.
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136
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Haitjema S, van Setten J, Eales J, van der Laan SW, Gandin I, de Vries JPPM, de Borst GJ, Pasterkamp G, Asselbergs FW, Charchar FJ, Wilson JF, de Jager SCA, Tomaszewski M, den Ruijter HM. Genetic variation within the Y chromosome is not associated with histological characteristics of the atherosclerotic carotid artery or aneurysmal wall. Atherosclerosis 2017; 259:114-119. [PMID: 28238413 DOI: 10.1016/j.atherosclerosis.2017.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 01/27/2023]
Abstract
BACKGROUND AND AIMS Haplogroup I, a common European paternal lineage of the Y chromosome, is associated with increased risk of coronary artery disease in British men. It is unclear whether this haplogroup or any other haplogroup on the Y chromosome is associated with histological characteristics of the diseased vessel wall in other vascular manifestations of cardiovascular diseases showing a male preponderance. METHODS We examined Dutch men undergoing either carotid endarterectomy from the Athero-Express biobank (AE, n = 1217) or open aneurysm repair from the Aneurysm-Express biobank (AAA, n = 393). Upon resolving the Y chromosome phylogeny, each man was assigned to one of the paternal lineages based on combinations of single nucleotide polymorphisms of the male-specific region of the Y chromosome. We examined the associations between the Y chromosome and the histological characteristics of the carotid plaque and aneurysm wall, including lipid content, leukocyte infiltration and intraplaque haemorrhage, in all men. RESULTS A majority of men were carriers of either haplogroup I (AE: 28% AAA: 24%) or haplogroup R (AE: 59% AAA: 61%). We found no association between Y chromosomal haplogroups and histological characteristics of plaque collected from carotid arteries or tissue specimens of aneurysms. Moreover, the distribution of frequency for all Y chromosomal haplogroups in both cohorts was similar to that of a general population of Dutch men. CONCLUSIONS Our data show that genetic variation on the Y chromosome is not associated with histological characteristics of the plaques from carotid arteries or specimens of aneurysms in men of Dutch origin.
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Affiliation(s)
- Saskia Haitjema
- Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jessica van Setten
- Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands; Netherlands Heart Institute, Utrecht, The Netherlands
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Sander W van der Laan
- Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ilaria Gandin
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Jean-Paul P M de Vries
- Department of Vascular Surgery, St. Antonius Hospital Nieuwegein, Nieuwegein, The Netherlands
| | - Gert J de Borst
- Department of Vascular Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerard Pasterkamp
- Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands; Laboratory of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands; Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom
| | - Fadi J Charchar
- Faculty of Science and Technology, Federation University Australia, Ballarat, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland, United Kingdom; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland, United Kingdom
| | - Saskia C A de Jager
- Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom; Division of Medicine, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Hester M den Ruijter
- Experimental Cardiology Laboratory, University Medical Center Utrecht, Utrecht, The Netherlands.
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137
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Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R, Al-Zahery N, Raveane A, Wen SQ, Yan S, Wang X, Zalloua P, Marafi A, Koshel S, Semino O, Tyler-Smith C, Balanovska E. Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration. BMC Evol Biol 2017; 17:18. [PMID: 28251872 PMCID: PMC5333174 DOI: 10.1186/s12862-016-0870-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history. Results We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi. Conclusions This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0870-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oleg Balanovsky
- Vavilov Institute of General Genetics, Moscow, Russia. .,Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Valery Zaporozhchenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Nadia Al-Zahery
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xianpin Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | | | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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138
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Ansari-Pour N, Moñino Y, Duque C, Gallego N, Bedoya G, Thomas MG, Bradman N. Palenque de San Basilio in Colombia: genetic data support an oral history of a paternal ancestry in Congo. Proc Biol Sci 2016; 283:20152980. [PMID: 27030413 DOI: 10.1098/rspb.2015.2980] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/29/2016] [Indexed: 11/12/2022] Open
Abstract
The Palenque, a black community in rural Colombia, have an oral history of fugitive African slaves founding a free village near Cartagena in the seventeenth century. Recently, linguists have identified some 200 words in regular use that originate in a Kikongo language, with Yombe, mainly spoken in the Congo region, being the most likely source. The non-recombining portion of the Y chromosome (NRY) and mitochondrial DNA were analysed to establish whether there was greater similarity between present-day members of the Palenque and Yombe than between the Palenque and 42 other African groups (for all individuals,n= 2799) from which forced slaves might have been taken. NRY data are consistent with the linguistic evidence that Yombe is the most likely group from which the original male settlers of Palenque came. Mitochondrial DNA data suggested substantial maternal sub-Saharan African ancestry and a strong founder effect but did not associate Palenque with any particular African group. In addition, based on cultural data including inhabitants' claims of linguistic differences, it has been hypothesized that the two districts of the village (Abajo and Arriba) have different origins, with Arriba founded by men originating in Congo and Abajo by those born in Colombia. Although significant genetic structuring distinguished the two from each other, no supporting evidence for this hypothesis was found.
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Affiliation(s)
- Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran
| | | | | | - Natalia Gallego
- School of Health Sciences, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Gabriel Bedoya
- Universidad de Antioquia UdeA, Calle 70 No 52-21 Medellín, Colombia
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Neil Bradman
- Henry Stewart Group, 29/30 Little Russell Street, London, UK
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139
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Y-chromosomal haplogroup distribution in the Tuzla Canton of Bosnia and Herzegovina: A concordance study using four different in silico assignment algorithms based on Y-STR data. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2016; 67:471-483. [DOI: 10.1016/j.jchb.2016.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/19/2016] [Indexed: 11/19/2022]
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140
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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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141
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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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142
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Piniewska D, Sanak M, Wojtas M, Polanska N. The genetic evidence for human origin of Jivaroan shrunken heads in collections from the Polish museums. Int J Legal Med 2016; 131:643-650. [PMID: 27640190 PMCID: PMC5388730 DOI: 10.1007/s00414-016-1448-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/29/2016] [Indexed: 11/20/2022]
Abstract
Advances in forensic identification using molecular genetics are helpful in resolving some historical mysteries. The aim of this study was to confirm the authenticity of shrunken-head artifacts exhibited by two Polish museums. Shrunken heads, known as tsantsas, were headhunting trophies of South American Indians (Jivaroan). A special preparation preserved their hair and facial appearance. However, it was quite common to offer counterfeit shrunken heads of sloths or monkeys to collectors of curiosities. We sampled small skin specimens of four shrunken-head skin from the museum collection from Warsaw and Krakow, Poland. Following genomic DNA isolation, highly polymorphic short tandem repeats were genotyped using a commercial chemistry and DNA sequencing analyzer. Haplogroups of human Y chromosome were identified. We obtained an informative genetic profile of genomic short tandem repeats from all the samples of shrunken heads. Moreover, amplification of amelogenin loci allowed for sex determination. All four studied shrunken heads were of human origin. In two ones, a shared Y-chromosome haplogroup Q characteristic for Indigenous Americans was detected. Another artifact was counterfeited because Y-chromosome haplogroup I2 was found, characteristic for the Southeastern European origin. Commercial genetic methods of identification can be applied successfully in studies on the origin and authenticity of some unusual collection items.
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Affiliation(s)
- Danuta Piniewska
- Present address: Department of Forensic Medicine, Jagiellonian University Medical College, Grzegorzecka Str. 16, 31-531, Krakow, Poland.
| | - Marek Sanak
- Department of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Marta Wojtas
- Present address: Department of Forensic Medicine, Jagiellonian University Medical College, Grzegorzecka Str. 16, 31-531, Krakow, Poland
| | - Nina Polanska
- Present address: Department of Forensic Medicine, Jagiellonian University Medical College, Grzegorzecka Str. 16, 31-531, Krakow, Poland
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143
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Lu C, Wen Y, Hu W, Lu F, Qin Y, Wang Y, Li S, Yang S, Lin Y, Wang C, Jin L, Shen H, Sha J, Wang X, Hu Z, Xia Y. Y chromosome haplogroups based genome-wide association study pinpoints revelation for interactions on non-obstructive azoospermia. Sci Rep 2016; 6:33363. [PMID: 27628680 PMCID: PMC5024297 DOI: 10.1038/srep33363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/25/2016] [Indexed: 01/02/2023] Open
Abstract
The Y chromosome has high genetic variability with low rates of parallel and back mutations, which make up the most informative haplotyping system. To examine whether Y chromosome haplogroups (Y-hgs) could modify the effects of autosomal variants on non-obstructive azoospermia (NOA), based on our previous genome-wide association study (GWAS), we conducted a genetic interaction analysis in GWAS subjects. Logistic regression analysis demonstrated a protective effect of Y-hg O3e* on NOA. Then, we explored the potential interaction between Y-hg O3e* and autosomal variants. Our results demonstrated that there was a suggestively significant interaction between Y-hg O3e* and rs11135484 on NOA (Pinter = 9.89 × 10−5). Bioinformatic analysis revealed that genes annotated by significant single nucleotide polymorphisms (SNPs) were mainly enriched in immunological pathways. This is the first study of interactions between Y-hgs and autosomal variants on a genome-wide scale, which addresses the missing heritability in spermatogenic impairment and sheds new light on the pathogenesis of male infertility.
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Affiliation(s)
- Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Yang Wen
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Weiyue Hu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Feng Lu
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yufeng Qin
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Ying Wang
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Shuping Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Lin
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Department of Epidemiology and Biostatistics and Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
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144
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Molecular Genealogy of a Mongol Queen's Family and Her Possible Kinship with Genghis Khan. PLoS One 2016; 11:e0161622. [PMID: 27627454 PMCID: PMC5023095 DOI: 10.1371/journal.pone.0161622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/12/2016] [Indexed: 11/28/2022] Open
Abstract
Members of the Mongol imperial family (designated the Golden family) are buried in a secret necropolis; therefore, none of their burial grounds have been found. In 2004, we first discovered 5 graves belonging to the Golden family in Tavan Tolgoi, Eastern Mongolia. To define the genealogy of the 5 bodies and the kinship among them, SNP and/or STR profiles of mitochondria, autosomes, and Y chromosomes were analyzed. Four of the 5 bodies were determined to carry the mitochondrial DNA haplogroup D4, while the fifth carried haplogroup CZ, indicating that this individual had no kinship with the others. Meanwhile, Y-SNP and Y-STR profiles indicate that the males examined belonged to the R1b-M343 haplogroup. Thus, their East Asian D4 or CZ matrilineal and West Eurasian R1b-M343 patrilineal origins reveal genealogical admixture between Caucasoid and Mongoloid ethnic groups, despite a Mongoloid physical appearance. In addition, Y chromosomal and autosomal STR profiles revealed that the four D4-carrying bodies bore the relationship of either mother and three sons or four full siblings with almost the same probability. Moreover, the geographical distribution of R1b-M343-carrying modern-day individuals demonstrates that descendants of Tavan Tolgoi bodies today live mainly in Western Eurasia, with a high frequency in the territories of the past Mongol khanates. Here, we propose that Genghis Khan and his family carried Y-haplogroup R1b-M343, which is prevalent in West Eurasia, rather than the Y-haplogroup C3c-M48, which is prevalent in Asia and which is widely accepted to be present in the family members of Genghis Khan. Additionally, Tavan Tolgoi bodies may have been the product of marriages between the lineage of Genghis Khan’s Borjigin clan and the lineage of either the Ongud or Hongirad clans, indicating that these individuals were members of Genghis Khan’s immediate family or his close relatives.
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145
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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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146
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Coronary Artery Disease: Why We should Consider the Y Chromosome. Heart Lung Circ 2016; 25:791-801. [DOI: 10.1016/j.hlc.2015.12.100] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/17/2015] [Accepted: 12/20/2015] [Indexed: 12/16/2022]
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147
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Gurkan C, Sevay H, Demirdov DK, Hossoz S, Ceker D, Teralı K, Erol AS. Turkish Cypriot paternal lineages bear an autochthonous character and closest resemblance to those from neighbouring Near Eastern populations. Ann Hum Biol 2016; 44:164-174. [DOI: 10.1080/03014460.2016.1207805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Cemal Gurkan
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Huseyin Sevay
- Department of Information Systems Engineering, Near East University, Nicosia (North Cyprus), Turkey
| | - Damla Kanliada Demirdov
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Sinem Hossoz
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Deren Ceker
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Kerem Teralı
- Turkish Cypriot DNA Laboratory, Committee on Missing Persons in Cyprus Turkish Cypriot Member Office, Nicosia (North Cyprus), Turkey
| | - Ayla Sevim Erol
- Department of Anthropology, Ankara University, Ankara, Turkey
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148
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Caputo M, Amador MA, Santos S, Corach D. Potential forensic use of a 33 X-InDel panel in the Argentinean population. Int J Legal Med 2016; 131:107-112. [DOI: 10.1007/s00414-016-1399-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/03/2016] [Indexed: 01/16/2023]
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149
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Azmi AM. Identification of tandem repeats over large-alphabet inputs. Inf Sci (N Y) 2016. [DOI: 10.1016/j.ins.2016.01.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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150
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Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GRS, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, Bustamante CD, Tyler-Smith C. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet 2016; 48:593-9. [PMID: 27111036 PMCID: PMC4884158 DOI: 10.1038/ng.3559] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 04/01/2016] [Indexed: 12/21/2022]
Abstract
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
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Affiliation(s)
- G David Poznik
- Program in Biomedical Informatics, Stanford University, Stanford, California, USA
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fernando L Mendez
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Thomas F Willems
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- New York Genome Center, New York, New York, USA
| | - Andrea Massaia
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Qasim Ayub
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shane A McCarthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Yuan Chen
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ruby Banerjee
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Maria Cerezo
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Haojing Shao
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Melissa Gymrek
- New York Genome Center, New York, New York, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ankit Malhotra
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Sandra Louzada
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rob Desalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Graham R S Ritchie
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | - Erik Garrison
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anthony Marcketta
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David Mittelman
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | | | - Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Xiangqun Zheng-Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Gonçalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Lachlan Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Adam Auton
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yaniv Erlich
- New York Genome Center, New York, New York, USA
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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