51
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Wang M, Wang Z, He G, Liu J, Wang S, Qian X, Lang M, Li J, Xie M, Li C, Hou Y. Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system. Forensic Sci Int Genet 2019; 38:70-76. [DOI: 10.1016/j.fsigen.2018.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 09/18/2018] [Accepted: 10/09/2018] [Indexed: 02/03/2023]
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Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa. Forensic Sci Int Genet 2019; 38:185-194. [DOI: 10.1016/j.fsigen.2018.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
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Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, Lacerda DR, Solli A, Norstedt J, Reed K, Dawtry K, González-Andrade F, Paz-Y-Miño C, Revollo S, Cuellar C, Jota MS, Santos JE, Ayub Q, Kivisild T, Sandoval JR, Fujita R, Xue Y, Roewer L, Santos FR, Tyler-Smith C. Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders. Curr Biol 2018; 29:149-157.e3. [PMID: 30581024 DOI: 10.1016/j.cub.2018.11.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/03/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
Abstract
The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.
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Affiliation(s)
- Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil; The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Anders Bergström
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Maria Geppert
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matt Bawn
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martin de Porres, 15009 Lima, Peru; The Earlham Institute, NR4 7UG Norwich, UK
| | - Dominique Ohasi
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - Wentao Shi
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, 300070 Tianjin, China
| | - Daniela R Lacerda
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - Arne Solli
- Q Nordic Independent Researchers; Department of Archaeology, History, Cultural Studies and Religion (AHKR), University of Bergen, Norway
| | | | | | | | - Fabricio González-Andrade
- Translational Medicine Unit, Central University of Ecuador, Faculty of Medical Sciences, Iquique N14-121 y Sodiro-Itchimbía, Sector El Dorado, 170403 Quito, Ecuador
| | - Cesar Paz-Y-Miño
- Universidad de las Americas, Av. de los Granados E12-41, 170513 Quito, Ecuador
| | - Susana Revollo
- Universidad Mayor de San Andrés, Av. Villazón 1995, 2008 La Paz, Bolivia
| | - Cinthia Cuellar
- Universidad Mayor de San Andrés, Av. Villazón 1995, 2008 La Paz, Bolivia
| | - Marilza S Jota
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - José E Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil
| | - Qasim Ayub
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK; Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, CB2 1QH Cambridge, UK; Estonian Biocentre, 51010 Tartu, Estonia
| | - José R Sandoval
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martin de Porres, 15009 Lima, Peru
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martin de Porres, 15009 Lima, Peru
| | - Yali Xue
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Fabrício R Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-010 Belo Horizonte, Brazil.
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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Oliveira S, Hübner A, Fehn AM, Aço T, Lages F, Pakendorf B, Stoneking M, Rocha J. The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola. Eur J Hum Genet 2018; 27:475-483. [PMID: 30467412 DOI: 10.1038/s41431-018-0304-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 11/09/2022] Open
Abstract
Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi, and Bantu languages. Although present-day Bantu speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been thought to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the male-specific region of the Y chromosome (MSY) from 170 individuals with previously reported mitochondrial DNA (mtDNA) genomes, to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun), and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu MSY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for MSY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.
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Affiliation(s)
- Sandra Oliveira
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Anne-Maria Fehn
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.,Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 00745, Jena, Germany.,Institute for African Studies, Goethe University, 60323, Frankfurt, Germany
| | - Teresa Aço
- Centro de Estudos do Deserto (CEDO), Namibe, Angola
| | - Fernanda Lages
- ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS & Univ Lyon, 69007, Lyon, France
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Jorge Rocha
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
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55
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Genetic diversities and phylogenetic analyses of three Chinese main ethnic groups in southwest China: A Y-Chromosomal STR study. Sci Rep 2018; 8:15339. [PMID: 30337624 PMCID: PMC6193932 DOI: 10.1038/s41598-018-33751-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 10/05/2018] [Indexed: 01/25/2023] Open
Abstract
Short tandem repeats (STRs) located on the Y chromosome with the properties of male-specific inheritance and haploidy are widely used in forensics to analyze paternal genealogies and match male trace donors to evidence. Besides, Y-chromosomal haplotypes play an important role in providing breathtaking insights into population genetic history. However, the genetic diversity and forensic characteristics of Y-STRs in Guizhou main ethnic groups (Hans, Miaos and Bouyeis) remain uncharacterized. Here, we obtained Y-chromosomal 23-marker haplotypes in three Guizhou populations and submitted the first batch of Y-STR haplotype data to the YHRD. The HD in the aforementioned three populations are 0.99990, 0.99983, and 0.99979, respectively, and DC values are 0.9902, 0.9908, and 0.97959, respectively. Subsequently, genetic differentiation between our newly studied populations and reference groups along ethnic/administrative divisions, as well as national/continental boundaries were investigated via AMOVA, MDS, and phylogenetic relationship reconstruction. Significant genetic differentiations from our subjects and other groups are identified in ethnically, linguistically and geographically diverse populations, including most prominently Tibetans and Uyghurs among 30 mainland Chinese populations, Taiwanese groups and others among 58 Asian populations, as well as African groups and others among 89 worldwide populations. Qiannan Bouyei has a close genetic relationship with Guangxi Zhuang, and Zunyi Han and Qiandongnan Miao have close genetic affinity with Hunan Han and Guizhou Shui, respectively. Collectively, this new-generation Y-STR amplification system can be used as a supplementary tool in forensic identification and male parentage testing and even pedigree search.
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56
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Poriswanish N, Neumann R, Wetton JH, Wagstaff J, Larmuseau MHD, Jobling MA, May CA. Recombination hotspots in an extended human pseudoautosomal domain predicted from double-strand break maps and characterized by sperm-based crossover analysis. PLoS Genet 2018; 14:e1007680. [PMID: 30296256 PMCID: PMC6193736 DOI: 10.1371/journal.pgen.1007680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/18/2018] [Accepted: 09/05/2018] [Indexed: 01/11/2023] Open
Abstract
The human X and Y chromosomes are heteromorphic but share a region of homology at the tips of their short arms, pseudoautosomal region 1 (PAR1), that supports obligate crossover in male meiosis. Although the boundary between pseudoautosomal and sex-specific DNA has traditionally been regarded as conserved among primates, it was recently discovered that the boundary position varies among human males, due to a translocation of ~110 kb from the X to the Y chromosome that creates an extended PAR1 (ePAR). This event has occurred at least twice in human evolution. So far, only limited evidence has been presented to suggest this extension is recombinationally active. Here, we sought direct proof by examining thousands of gametes from each of two ePAR-carrying men, for two subregions chosen on the basis of previously published male X-chromosomal meiotic double-strand break (DSB) maps. Crossover activity comparable to that seen at autosomal hotspots was observed between the X and the ePAR borne on the Y chromosome both at a distal and a proximal site within the 110-kb extension. Other hallmarks of classic recombination hotspots included evidence of transmission distortion and GC-biased gene conversion. We observed good correspondence between the male DSB clusters and historical recombination activity of this region in the X chromosomes of females, as ascertained from linkage disequilibrium analysis; this suggests that this region is similarly primed for crossover in both male and female germlines, although sex-specific differences may also exist. Extensive resequencing and inference of ePAR haplotypes, placed in the framework of the Y phylogeny as ascertained by both Y microsatellites and single nucleotide polymorphisms, allowed us to estimate a minimum rate of crossover over the entire ePAR region of 6-fold greater than genome average, comparable with pedigree estimates of PAR1 activity generally. We conclude ePAR very likely contributes to the critical crossover function of PAR1. 95% of our genome is contained in 22 pairs of chromosomes shared by all humans. However, women and men differ in their sex chromosomes: while women have two X chromosomes, men have an X and a smaller, sex-determining Y chromosome. To ensure correct partition of X and Y into sperm, genetic exchange (crossover) must occur between these very different chromosomes in a short, shared region. The location of the boundary of this region was thought to have been conserved since before the divergence from old world monkeys at least 27 million years ago, but recently it has been shown that some human males carry an extended version on their Y chromosomes, thanks to the transposition of a piece of DNA from the X chromosome. Here, we asked if genetic exchange occurs in this newly extended region. To do this, we used previously published information that signposted the positions within the X chromosome segment which exhibit the hallmarks of crossover initiation. We then sought direct evidence of crossover in the sperm of men carrying the extension. This work showed that the signposts were accurate, pointing to frequent crossover in this novel shared sex-chromosomal domain.
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Affiliation(s)
- Nitikorn Poriswanish
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Forensic Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jon H. Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - John Wagstaff
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Maarten H. D. Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, Department of Imaging and Pathology, KU Leuven, Belgium
| | - Mark A. Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Celia A. May
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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58
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Amorim CEG, Vai S, Posth C, Modi A, Koncz I, Hakenbeck S, La Rocca MC, Mende B, Bobo D, Pohl W, Baricco LP, Bedini E, Francalacci P, Giostra C, Vida T, Winger D, von Freeden U, Ghirotto S, Lari M, Barbujani G, Krause J, Caramelli D, Geary PJ, Veeramah KR. Understanding 6th-century barbarian social organization and migration through paleogenomics. Nat Commun 2018; 9:3547. [PMID: 30206220 PMCID: PMC6134036 DOI: 10.1038/s41467-018-06024-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/09/2018] [Indexed: 11/12/2022] Open
Abstract
Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy. The Longobards invaded and conquered much of Italy after the fall of the Western Roman Empire. Here, the authors sequence and analyze ancient genomic DNA from 63 samples from two cemeteries associated with the Longobards and identify kinship networks and two distinct genetic and cultural groups in each.
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Affiliation(s)
| | - Stefania Vai
- Dipartimento di Biologia Università degli Studi di Firenze, 50122, Firenze, Italy
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany.,Institute for Archaeological Sciences Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany
| | - Alessandra Modi
- Dipartimento di Biologia Università degli Studi di Firenze, 50122, Firenze, Italy
| | - István Koncz
- Institute of Archaeological Sciences, Eötvös Loránd University, Múzeum körút 4/B, Budapest, 1088, Hungary
| | - Susanne Hakenbeck
- Department of Archaeology, University of Cambridge, Cambridge, CB2 3DZ, UK
| | | | - Balazs Mende
- Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Walter Pohl
- Institut für Mittelalterforschung, Österreichische Akadamie der Wissenschaften, 1020, Vienna, Austria
| | - Luisella Pejrani Baricco
- Dipartimento di Storia, Archeologia e Storia dell'Arte, Università cattolica del Sacro Cuore, 20123, Milano, Italy
| | - Elena Bedini
- Dipartimento di Storia, Archeologia e Storia dell'Arte, Università cattolica del Sacro Cuore, 20123, Milano, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Via T. Fiorelli, 1, 09126, Cagliari, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell'Arte, Università cattolica del Sacro Cuore, 20123, Milano, Italy
| | - Tivadar Vida
- Institute of Archaeological Sciences, Eötvös Loránd University, Múzeum körút 4/B, Budapest, 1088, Hungary.,Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Daniel Winger
- Heinrich Schliemann-Institut für Altertumswissenschaften Universität Rostock, 18055, Rostock, Germany
| | - Uta von Freeden
- Römisch-Germanische Kommission des Deutschen Archäologischen Instituts, 60325, Frankfurt am Main, Germany
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotenologie, Università degli Studi di Ferrara, 44121, Ferrara, Italy
| | - Martina Lari
- Dipartimento di Biologia Università degli Studi di Firenze, 50122, Firenze, Italy
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotenologie, Università degli Studi di Ferrara, 44121, Ferrara, Italy
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745, Jena, Germany. .,Institute for Archaeological Sciences Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.
| | - David Caramelli
- Dipartimento di Biologia Università degli Studi di Firenze, 50122, Firenze, Italy.
| | | | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA.
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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60
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Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences. Eur J Hum Genet 2018; 26:1687-1696. [PMID: 29991739 DOI: 10.1038/s41431-018-0211-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/25/2018] [Accepted: 06/12/2018] [Indexed: 11/08/2022] Open
Abstract
The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3-14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.
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61
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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Wang LX, Lu Y, Zhang C, Wei LH, Yan S, Huang YZ, Wang CC, Mallick S, Wen SQ, Jin L, Xu SH, Li H. Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations. Mol Genet Genomics 2018; 293:1293-1300. [DOI: 10.1007/s00438-018-1461-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/11/2018] [Indexed: 11/30/2022]
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63
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Kayser M, Ralf A. Small number of slowly-mutating (SM) Y-STRs not suitable for forensic and evolutionary applications. Forensic Sci Int Genet 2018; 36:e13. [PMID: 29885981 DOI: 10.1016/j.fsigen.2018.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 05/24/2018] [Accepted: 06/02/2018] [Indexed: 10/14/2022]
Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.
| | - Arwin Ralf
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
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A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Sci Rep 2018; 8:7465. [PMID: 29748665 PMCID: PMC5945646 DOI: 10.1038/s41598-018-25912-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022] Open
Abstract
In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.
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65
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Claerhout S, Vandenbosch M, Nivelle K, Gruyters L, Peeters A, Larmuseau MH, Decorte R. Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences. Forensic Sci Int Genet 2018; 34:1-10. [DOI: 10.1016/j.fsigen.2018.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
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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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67
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D’Atanasio E, Trombetta B, Bonito M, Finocchio A, Di Vito G, Seghizzi M, Romano R, Russo G, Paganotti GM, Watson E, Coppa A, Anagnostou P, Dugoujon JM, Moral P, Sellitto D, Novelletto A, Cruciani F. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biol 2018; 19:20. [PMID: 29433568 PMCID: PMC5809971 DOI: 10.1186/s13059-018-1393-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. CONCLUSIONS Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.
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Affiliation(s)
- Eugenia D’Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Finocchio
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Genny Di Vito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Mara Seghizzi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Rita Romano
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3–Paul-Sabatier, Toulouse, France
| | - Pedro Moral
- Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | | | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
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Khubrani YM, Wetton JH, Jobling MA. Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs. Forensic Sci Int Genet 2017; 33:98-105. [PMID: 29220824 DOI: 10.1016/j.fsigen.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 10/18/2022]
Abstract
Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for Saudi Arabia generally, and caution is needed when considering expatriate groups as representative of country of origin. Our study shows the importance of geographical and social structuring that may affect the utility of forensic databases and the interpretation of Y-STR profiles.
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Affiliation(s)
- Yahya M Khubrani
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK; Forensic Genetics Laboratory, General Administration of Criminal Evidence, Public Security, Ministry of Interior, Saudi Arabia
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
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Balanovska EV, Agdzhoyan AT, Skhalyakho RA, Balaganskaya OA, Freydin GS, Chernevskii KG, Chernevskii DK, Stepanov GD, Kagazezheva ZA, Zaporozhchenko VV, Markina NV, Palipana D, Koshel SM, Kozlov SA, Balanovsky OP. Gene pool of the Novgorod population: Between the north and the south. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417110023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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70
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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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71
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Defining Y-SNP variation among the Flemish population (Western Europe) by full genome sequencing. Forensic Sci Int Genet 2017; 31:e12-e16. [PMID: 29089250 DOI: 10.1016/j.fsigen.2017.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/10/2017] [Accepted: 10/24/2017] [Indexed: 12/27/2022]
Abstract
Y-chromosomal single nucleotide polymorphisms (Y-SNPs) represent a powerful tool in forensic research and casework, especially for inferring paternal ancestry of unknown perpetrators and unidentified bodies. However, the wealth of recently discovered Y-SNPs, the 'jungle' of different evolutionary lineage trees and nomenclatures, and the lack of population-wide data of many phylogenetically mapped Y-SNPs, limits the use of Y-SNPs in routine forensic approaches. Recently, a concise reference phylogeny of the human Y chromosome, the 'Minimal Reference Y-tree', was introduced aiming to provide a stable phylogeny with optimal global discrimination capacity by including the most resolving Y-SNPs. Here, we obtained a representative sample of 270 whole-genome sequences (WGS) to grasp the Y-SNP variation within the autochthonous Flemish population (Belgium, Western Europe) according to this reference Y-tree. The high quality of the Y-SNP calling was guaranteed for the WGS sample as well as its representativeness for the Flemish population based on the comparison of the main haplogroup frequencies with those from earlier studies on Flanders and the Netherlands. The 270 Flemish Y chromosomes were assigned to 98 different sub-haplogroups of the Minimal Reference Y-tree, showing its high potential of discrimination and confirming the spectrum of evolutionary lineages within Western Europe in general and within Flanders in particular. The full database with all Y-SNP calls of the Flemish sample is public available for future updates including forensic and population genetic studies. New initiatives to categorise Y-SNP variation in other populations according to the reference phylogeny of the Y chromosome are highly encouraged for forensic applications. Recommendations to realise such future population sample sets are discussed based on this study.
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72
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Yardumian A, Shengelia R, Chitanava D, Laliashvili S, Bitadze L, Laliashvili I, Villanea F, Sanders A, Azzam A, Groner V, Edleson K, Vilar MG, Schurr TG. Genetic diversity in Svaneti and its implications for the human settlement of the Highland Caucasus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:837-852. [PMID: 29076141 DOI: 10.1002/ajpa.23324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/19/2017] [Accepted: 09/10/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVES In this study, we characterized genetic diversity in the Svans from northwestern Georgia to better understand the phylogeography of their genetic lineages, determine whether genetic diversity in the highland South Caucasus has been shaped by language or geography, and assess whether Svan genetic diversity was structured by regional residence patterns. MATERIALS AND METHODS We analyzed mtDNA and Y-chromosome variation in 184 individuals from 13 village districts and townlets located throughout the region. For all individuals, we analyzed mtDNA diversity through control region sequencing, and, for males, we analyzed Y-chromosome diversity through SNP and STR genotyping. The resulting data were compared with those for populations from the Caucasus and Middle East. RESULTS We observed significant mtDNA heterogeneity in Svans, with haplogroups U1-U7, H, K, and W6 being common there. By contrast, ∼78% of Svan males belonged to haplogroup G2a, with the remainder falling into four other haplogroups (J2a1, I2, N, and R1a). While showing a distinct genetic profile, Svans also clustered with Caucasus populations speaking languages from different families, suggesting a deep common ancestry for all of them. The mtDNA data were not structured by geography or linguistic affiliation, whereas the NRY data were influenced only by geography. DISCUSSION These patterns of genetic variation confirm a complex set of geographic sources and settlement phases for the Caucasus highlands. Such patterns may also reflect social and cultural practices in the region. The high frequency and antiquity of Y-chromosome haplogroup G2a in this region further points to its emergence there.
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Affiliation(s)
- Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Pennsylvania 19009.,Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ramaz Shengelia
- Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 01747, Georgia
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Fernando Villanea
- Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Akiva Sanders
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Andrew Azzam
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Victoria Groner
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kristi Edleson
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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73
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Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, Margaryan A, Vasilyev SV, Veselovskaya EV, Borutskaya SB, Deviese T, Comeskey D, Higham T, Manica A, Foley R, Meltzer DJ, Nielsen R, Excoffier L, Mirazon Lahr M, Orlando L, Willerslev E. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 2017; 358:659-662. [DOI: 10.1126/science.aao1807] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023]
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74
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Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions. Sci Rep 2017; 7:12086. [PMID: 28935946 PMCID: PMC5608872 DOI: 10.1038/s41598-017-11307-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/22/2017] [Indexed: 11/17/2022] Open
Abstract
Interpretations of genetic data concerning the prehistory of Europe have long been a subject of great debate, but increasing amounts of ancient and modern DNA data are now providing new and more informative evidence. Y-chromosome resequencing studies in Europe have highlighted the prevalence of recent expansions of male lineages, and focused interest on the Bronze Age as a period of cultural and demographic change. These findings contrast with phylogeographic studies based on mitochondrial DNA (mtDNA), which have been interpreted as supporting expansions from glacial refugia. Here we have undertaken a population-based resequencing of complete mitochondrial genomes in Europe and the Middle East, in 340 samples from 17 populations for which Y-chromosome sequence data are also available. Demographic reconstructions show no signal of Bronze Age expansion, but evidence of Paleolithic expansions in all populations except the Saami, and with an absence of detectable geographical pattern. In agreement with previous inference from modern and ancient DNA data, the unbiased comparison between the mtDNA and Y-chromosome population datasets emphasizes the sex-biased nature of recent demographic transitions in Europe.
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75
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Qian X, Hou J, Wang Z, Ye Y, Lang M, Gao T, Liu J, Hou Y. Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches. Sci Rep 2017; 7:11324. [PMID: 28900279 PMCID: PMC5595879 DOI: 10.1038/s41598-017-11955-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/01/2017] [Indexed: 11/17/2022] Open
Abstract
There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term ‘NGS+’ for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.
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Affiliation(s)
- Xiaoqin Qian
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jiayi Hou
- Clinical and Translational Research Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yi Ye
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Min Lang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Tianzhen Gao
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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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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77
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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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78
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The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana. Sci Rep 2017; 7:3085. [PMID: 28596519 PMCID: PMC5465200 DOI: 10.1038/s41598-017-03176-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
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79
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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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80
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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81
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Kivisild T. The study of human Y chromosome variation through ancient DNA. Hum Genet 2017; 136:529-546. [PMID: 28260210 PMCID: PMC5418327 DOI: 10.1007/s00439-017-1773-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/24/2017] [Indexed: 12/15/2022]
Abstract
High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.
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Affiliation(s)
- Toomas Kivisild
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, CB2 1QH, UK.
- Estonian Biocentre, 51010, Tartu, Estonia.
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82
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Toward a consensus on SNP and STR mutation rates on the human Y-chromosome. Hum Genet 2017; 136:575-590. [PMID: 28455625 DOI: 10.1007/s00439-017-1805-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
The mutation rate on the Y-chromosome matters for estimating the time-to-the-most-recent-common-ancestor (TMRCA, i.e. haplogroup age) in population genetics, as well as for forensic, medical, and genealogical studies. Large-scale sequencing efforts have produced several independent estimates of Y-SNP mutation rates. Genealogical, or pedigree, rates tend to be slightly faster than evolutionary rates obtained from ancient DNA or calibrations using dated (pre)historical events. It is, therefore, suggested to report TMRCAs using an envelope defined by the average aDNA-based rate and the average pedigree-based rate. The current estimate of the "envelope rate" is 0.75-0.89 substitutions per billion base pairs per year. The available Y-SNP mutation rates can be applied to high-coverage data from the entire X-degenerate region, but other datasets may demand recalibrated rates. While a consensus on Y-SNP rates is approaching, the debate on Y-STR rates has continued for two decades, because multiple genealogical rates were consistent with each other but three times faster than the single evolutionary estimate. Applying Y-SNP and Y-STR rates to the same haplogroups recently helped to clarify the issue. Genealogical and evolutionary STR rates typically provide lower and upper bounds of the "true" (SNP-based) age. The genealogical rate often-but not always-works well for haplogroups less than 7000 years old. The evolutionary rate, although calibrated using recent events, inflates ages of young haplogroups and deflates the age of the entire Y-chromosomal tree, but often provides reasonable estimates for intermediate ages (old haplogroups). Future rate estimates and accumulating case studies should further clarify the Y-SNP rates.
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83
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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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84
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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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85
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Lipson M, Reich D. A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa. Mol Biol Evol 2017; 34:889-902. [PMID: 28074030 PMCID: PMC5400393 DOI: 10.1093/molbev/msw293] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogenetic tree with gene flow events for a wide diversity of non-Africans remains a difficult problem. Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. While our results still represent a simplified picture, they provide a useful summary of deep Eurasian population history that can serve as a null model for future studies and a baseline for further discoveries.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA
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86
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Batini C, Jobling MA. Detecting past male-mediated expansions using the Y chromosome. Hum Genet 2017; 136:547-557. [PMID: 28349239 DOI: 10.1007/s00439-017-1781-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/15/2017] [Indexed: 12/29/2022]
Abstract
Males and females display biological differences that lead to a higher variance of offspring number in males, and this is frequently exacerbated in human societies by mating practices, and possibly by past socio-cultural circumstances. This implies that the genetic record might contain the imprint of past male-mediated expansions, which can be investigated by analysing the male-specific region of the Y chromosome (MSY). Here, we review studies that have used MSY data to infer such expansions. Sets of short-tandem repeats define haplotypes of very low average frequencies, but in a few cases, high-frequency haplotypes are observed, forming the core of descent clusters. Estimates of the ages of such clusters, together with geographical information, have been used to propose powerful historical founders, including Genghis Khan, although without direct supporting evidence. Resequencing of multi-megabase segments of MSY has allowed the construction of detailed phylogenies in which branch lengths are proportional to time, leading to the identification of lineage expansions in the last few millennia as well as the more distant past. Comparisons with maternally-inherited mitochondrial DNA sequence data allow the male specificity of some of these expansions to be demonstrated. These include expansions in Europe in the last ~5000 years that may be associated with a cultural shift during the Bronze Age, as well as expansions elsewhere in the world for which explanations from archaeological evidence are not yet clear.
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Affiliation(s)
- Chiara Batini
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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87
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Kayser M. Forensic use of Y-chromosome DNA: a general overview. Hum Genet 2017; 136:621-635. [PMID: 28315050 PMCID: PMC5418305 DOI: 10.1007/s00439-017-1776-9] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022]
Abstract
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
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88
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Y chromosome palindromes and gene conversion. Hum Genet 2017; 136:605-619. [PMID: 28303348 DOI: 10.1007/s00439-017-1777-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/07/2017] [Indexed: 02/02/2023]
Abstract
The presence of large and near-identical inverted repeat sequences (called palindromes) is a common feature of the constitutively haploid sex chromosomes of different species. Despite the fact palindromes originated in a non-recombining context, they have evolved a strong recombinational activity in the form of abundant arm-to-arm gene conversion. Their independent appearance in different species suggests they can have a profound biological significance that has yet to be fully clarified. It has been theorized that natural selection may have favored palindromic organization of male-specific genes and that the establishment of intra-palindrome gene conversion has strong adaptive significance. Arm-to-arm gene conversion allows the efficient removal of deleterious mutations, increases the fixation rate of beneficial mutations and has played an important role in modulating the equilibrium between gene loss and acquisition during Y chromosome evolution. Additionally, a palindromic organization of duplicates could favor the formation of unusual chromatin structures and could optimize the use of gene conversion as a mechanism to maintain the structural integrity of male-specific genes. In this review, we describe the structural features of palindromes on mammalian sex chromosomes and summarize different hypotheses regarding palindrome evolution and the functional benefits of arm-to-arm gene conversion on the unique haploid portion of the nuclear genome.
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89
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Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia. Hum Genet 2017; 136:437-450. [DOI: 10.1007/s00439-017-1770-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/20/2017] [Indexed: 12/22/2022]
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90
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Abstract
The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes.
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91
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Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. Forensic Sci Int Genet 2017; 27:142-148. [DOI: 10.1016/j.fsigen.2016.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 12/22/2016] [Accepted: 12/29/2016] [Indexed: 11/20/2022]
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92
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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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93
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Maisano Delser P, Neumann R, Ballereau S, Hallast P, Batini C, Zadik D, Jobling MA. Signatures of human European Palaeolithic expansion shown by resequencing of non-recombining X-chromosome segments. Eur J Hum Genet 2017; 25:485-492. [PMID: 28120839 PMCID: PMC5386427 DOI: 10.1038/ejhg.2016.207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/07/2016] [Accepted: 12/14/2016] [Indexed: 11/09/2022] Open
Abstract
Human genetic diversity in Europe has been extensively studied using uniparentally inherited sequences (mitochondrial DNA (mtDNA) and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap single-nucleotide polymorphism data to identify genome-wide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as phylogeographically informative haplotypes on autosomes and X chromosome (PHAXs). Three such sequences on the X chromosome spanning a total of ~49 kb were resequenced in 240 males from Europe, the Middle East and Africa at an average coverage of 181 ×. These PHAXs were confirmed to be essentially non-recombining across European samples. All three loci show highly homogeneous patterns across Europe and are highly differentiated from the African sample. Star-like structures of European-specific haplotypes in median-joining networks indicate past population expansions. Bayesian skyline plots and time-to-most-recent-common-ancestor estimates suggest expansions pre-dating the Neolithic transition, a finding that is more compatible with data on mtDNA than the Y chromosome, and with the female bias of X-chromosomal inheritance. This study demonstrates the potential of the use of X-chromosomal haplotype blocks, and the utility of the accurate ascertainment of rare variants for inferring human demographic history.
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Affiliation(s)
| | - Rita Neumann
- Department of Genetics, University of Leicester, Leicester, UK
| | | | - Pille Hallast
- Department of Genetics, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, UK
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester, UK
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK
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94
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Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H, Spratt BG, Aanensen DM. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom 2016; 2:e000093. [PMID: 28348833 PMCID: PMC5320705 DOI: 10.1099/mgen.0.000093] [Citation(s) in RCA: 344] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 10/19/2016] [Indexed: 11/18/2022] Open
Abstract
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.
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Affiliation(s)
- Silvia Argimón
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Khalil Abudahab
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Richard J E Goater
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Artemij Fedosejev
- 2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Jyothish Bhai
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Corinna Glasner
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Edward J Feil
- 3The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | | | - Corin A Yeats
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - Hajo Grundmann
- 5Department of Infection Prevention and Hospital Hygiene, University Medical Centre Freiburg, Freiburg, Germany
| | - Brian G Spratt
- 2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
| | - David M Aanensen
- 1The Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,2Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK
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95
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Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families. Am J Hum Genet 2016; 99:163-73. [PMID: 27392075 DOI: 10.1016/j.ajhg.2016.05.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/22/2016] [Indexed: 11/21/2022] Open
Abstract
The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3'6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.
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96
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Šarac J, Šarić T, Havaš Auguštin D, Novokmet N, Vekarić N, Mustać M, Grahovac B, Kapović M, Nevajda B, Glasnović A, Missoni S, Rootsi S, Rudan P. Genetic heritage of Croatians in the Southeastern European gene pool-Y chromosome analysis of the Croatian continental and Island population. Am J Hum Biol 2016; 28:837-845. [PMID: 27279290 DOI: 10.1002/ajhb.22876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 03/22/2016] [Accepted: 05/10/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES The research objective of this study is to enlarge and deepen the Y chromosome research on the Croatian population and enable additional insights into the population diversity and historic events that shaped the current genetic landscape of Croatia and Southeastern Europe (SEE). MATERIALS AND METHODS A high-resolution phylogenetic and phylogeographic analysis of 66 biallelic (SNPs) and 17 microsatellite (STRs) markers of the Y chromosome was performed using 720 Croatian samples. The obtained results were placed in a wider European context by comparison with ∼4450 samples from a number of other European populations. RESULTS A high diversity of haplogroups was observed in the overall Croatian sample, and all typical European Y chromosome haplogroups with corresponding clinal patterns were observed. Three distinct genetic signals were identifiable in the Croatian paternal gene pool - I2a1b-M423, R1a1a1b1a*-M558, and E1b1b1a1b1a-V13 haplogroups. DISCUSSION The analyses of the dominant and autochthonous I2a1b-M423 lineage (>30%) suggest that SEE had a significant role in the Upper Paleolithic, the R1a1a1b1a*-M558 lineage (19%) represents a signal from present day Slavic populations of Central Europe in the Croatian population, and the phylogeography of the E1b1b1a1b1a-V13 clade (around 9%) implies cultural diffusion of agriculture into Europe via the Balkan Peninsula. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:837-845, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Jelena Šarac
- Institute for Anthropological Research, 10000, Zagreb, Croatia
| | - Tena Šarić
- Institute for Anthropological Research, 10000, Zagreb, Croatia
| | | | | | - Nenad Vekarić
- Institute for Historical Sciences, Croatian Academy of Sciences and Arts, 20000, Dubrovnik, Croatia
| | - Mate Mustać
- Occupational Health Clinic, 23000, Zadar, Croatia
| | - Blaženka Grahovac
- Department of Pathology and Pathological Anatomy, School of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | - Miljenko Kapović
- Department of Biology and Medical Genetics, School of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | | | | | - Saša Missoni
- Institute for Anthropological Research, 10000, Zagreb, Croatia.,"Josip Juraj Strossmayer" University of Osijek, School of Medicine, Osijek, Croatia
| | - Siiri Rootsi
- Estonian Biocentre and Institute for Molecular and Cell Biology, Department of Evolutionary Biology, , University of Tartu, 51010, Tartu, Estonia
| | - Pavao Rudan
- Institute for Anthropological Research, 10000, Zagreb, Croatia.,Anthropological Center of the Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
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97
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98
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Sex bias in paediatric autoimmune disease – Not just about sex hormones? J Autoimmun 2016; 69:12-23. [DOI: 10.1016/j.jaut.2016.02.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/25/2016] [Accepted: 02/29/2016] [Indexed: 02/06/2023]
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99
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Barbieri C, Hübner A, Macholdt E, Ni S, Lippold S, Schröder R, Mpoloka SW, Purps J, Roewer L, Stoneking M, Pakendorf B. Refining the Y chromosome phylogeny with southern African sequences. Hum Genet 2016; 135:541-553. [PMID: 27043341 PMCID: PMC4835522 DOI: 10.1007/s00439-016-1651-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/18/2016] [Indexed: 12/04/2022]
Abstract
The recent availability of large-scale sequence data for the human Y chromosome has revolutionized analyses of and insights gained from this non-recombining, paternally inherited chromosome. However, the studies to date focus on Eurasian variation, and hence the diversity of early-diverging branches found in Africa has not been adequately documented. Here, we analyze over 900 kb of Y chromosome sequence obtained from 547 individuals from southern African Khoisan- and Bantu-speaking populations, identifying 232 new sequences from basal haplogroups A and B. We identify new clades in the phylogeny, an older age for the root, and substantially older ages for some individual haplogroups. Furthermore, while haplogroup B2a is traditionally associated with the spread of Bantu speakers, we find that it probably also existed in Khoisan groups before the arrival of Bantu speakers. Finally, there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species.
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Affiliation(s)
- Chiara Barbieri
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Shengyu Ni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Sebastian Lippold
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | | | - Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, 10559, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Brigitte Pakendorf
- Dynamique du Langage, UMR5596, CNRS & Université Lyon 2, 69363, Lyon Cedex 07, France.
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100
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New native South American Y chromosome lineages. J Hum Genet 2016; 61:593-603. [PMID: 27030145 DOI: 10.1038/jhg.2016.26] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/23/2016] [Accepted: 02/22/2016] [Indexed: 11/09/2022]
Abstract
Many single-nucleotide polymorphisms (SNPs) in the non-recombining region of the human Y chromosome have been described in the last decade. High-coverage sequencing has helped to characterize new SNPs, which has in turn increased the level of detail in paternal phylogenies. However, these paternal lineages still provide insufficient information on population history and demography, especially for Native Americans. The present study aimed to identify informative paternal sublineages derived from the main founder lineage of the Americas-haplogroup Q-L54-in a sample of 1841 native South Americans. For this purpose, we used a Y-chromosomal genotyping multiplex platform and conventional genotyping methods to validate 34 new SNPs that were identified in the present study by sequencing, together with many Y-SNPs previously described in the literature. We updated the haplogroup Q phylogeny and identified two new Q-M3 and three new Q-L54*(xM3) sublineages defined by five informative SNPs, designated SA04, SA05, SA02, SA03 and SA29. Within the Q-M3, sublineage Q-SA04 was mostly found in individuals from ethnic groups belonging to the Tukanoan linguistic family in the northwest Amazon, whereas sublineage Q-SA05 was found in Peruvian and Bolivian Amazon ethnic groups. Within Q-L54*, the derived sublineages Q-SA03 and Q-SA02 were exclusively found among Coyaima individuals (Cariban linguistic family) from Colombia, while Q-SA29 was found only in Maxacali individuals (Jean linguistic family) from southeast Brazil. Furthermore, we validated the usefulness of several published SNPs among indigenous South Americans. This new Y chromosome haplogroup Q phylogeny offers an informative paternal genealogy to investigate the pre-Columbian history of South America.Journal of Human Genetics advance online publication, 31 March 2016; doi:10.1038/jhg.2016.26.
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