New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
Tatiana M. Karafet,Fernando L. Mendez,Monica B. Meilerman,Peter A. Underhill,Stephen L. Zegura,Michael F. Hammer +5 more
Reads0
Chats0
TLDR
Major changes in the topology of the parsimony tree are described and names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002 are provided.Abstract:
Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.read more
Citations
More filters
Journal ArticleDOI
Updated Comprehensive Phylogenetic Tree of Global Human Mitochondrial DNA Variation
Mannis van Oven,Manfred Kayser +1 more
TL;DR: This complete mtDNA tree includes previously published as well as newly identified haplogroups, is easily navigable, will be continuously and regularly updated in the future, and is online available at http://www.phylotree.org.
Journal ArticleDOI
Massive migration from the steppe was a source for Indo-European languages in Europe
Wolfgang Haak,Iosif Lazaridis,Nick Patterson,Nadin Rohland,Swapan Mallick,Bastien Llamas,Guido Brandt,Susanne Nordenfelt,Eadaoin Harney,Kristin Stewardson,Qiaomei Fu,Alissa Mittnik,Eszter Bánffy,Christos Economou,Michael Francken,Susanne Friederich,Rafael Garrido Pena,Fredrik Hallgren,Valery Khartanovich,Aleksandr Khokhlov,Michael Kunst,Pavel Kuznetsov,Harald Meller,Oleg Mochalov,Vayacheslav Moiseyev,Nicole Nicklisch,Sandra Pichler,Roberto Risch,Manuel Ángel Rojo Guerra,Christina Roth,Anna Szécsényi-Nagy,Joachim Wahl,Matthias Meyer,Johannes Krause,Dorcas Brown,David W. Anthony,Alan Cooper,Kurt W. Alt,David Reich +38 more
TL;DR: In this paper, the authors generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms.
Journal ArticleDOI
Ancient human genomes suggest three ancestral populations for present-day Europeans
Iosif Lazaridis,Iosif Lazaridis,Nick Patterson,Alissa Mittnik,Gabriel Renaud,Swapan Mallick,Swapan Mallick,Karola Kirsanow,Peter H. Sudmant,Joshua G. Schraiber,Joshua G. Schraiber,Sergi Castellano,Mark Lipson,Bonnie Berger,Bonnie Berger,Christos Economou,Ruth Bollongino,Qiaomei Fu,Kirsten I. Bos,Susanne Nordenfelt,Susanne Nordenfelt,Heng Li,Heng Li,Cesare de Filippo,Kay Prüfer,Susanna Sawyer,Cosimo Posth,Wolfgang Haak,Fredrik Hallgren,Elin Fornander,Nadin Rohland,Nadin Rohland,Dominique Delsate,Michael Francken,Jean-Michel Guinet,Joachim Wahl,George Ayodo,Hamza A. Babiker,Hamza A. Babiker,Graciela Bailliet,Elena Balanovska,Oleg Balanovsky,Ramiro Barrantes,Gabriel Bedoya,Haim Ben-Ami,Judit Bene,Fouad Berrada,Claudio M. Bravi,Francesca Brisighelli,George B.J. Busby,Francesco Calì,Mikhail Churnosov,David E. C. Cole,Daniel Corach,Larissa Damba,George van Driem,Stanislav Dryomov,Jean-Michel Dugoujon,Sardana A. Fedorova,Irene Gallego Romero,Marina Gubina,Michael F. Hammer,Brenna M. Henn,Tor Hervig,Ugur Hodoglugil,Aashish R. Jha,Sena Karachanak-Yankova,Rita Khusainova,Elza Khusnutdinova,Rick A. Kittles,Toomas Kivisild,William Klitz,Vaidutis Kučinskas,Alena Kushniarevich,Leila Laredj,Sergey Litvinov,Theologos Loukidis,Theologos Loukidis,Robert W. Mahley,Béla Melegh,Ene Metspalu,Julio Molina,Joanna L. Mountain,Klemetti Näkkäläjärvi,Desislava Nesheva,Thomas B. Nyambo,Ludmila P. Osipova,Jüri Parik,Fedor Platonov,Olga L. Posukh,Valentino Romano,Francisco Rothhammer,Francisco Rothhammer,Igor Rudan,Ruslan Ruizbakiev,Hovhannes Sahakyan,Hovhannes Sahakyan,Antti Sajantila,Antonio Salas,Elena B. Starikovskaya,Ayele Tarekegn,Draga Toncheva,Shahlo Turdikulova,Ingrida Uktveryte,Olga Utevska,René Vasquez,Mercedes Villena,Mikhail Voevoda,Cheryl A. Winkler,Levon Yepiskoposyan,Pierre Zalloua,Pierre Zalloua,Tatijana Zemunik,Alan Cooper,Cristian Capelli,Mark G. Thomas,Andres Ruiz-Linares,Sarah A. Tishkoff,Lalji Singh,Kumarasamy Thangaraj,Richard Villems,Richard Villems,Richard Villems,David Comas,Rem I. Sukernik,Mait Metspalu,Matthias Meyer,Evan E. Eichler,Joachim Burger,Montgomery Slatkin,Svante Pääbo,Janet Kelso,David Reich,David Reich,David Reich,Johannes Krause,Johannes Krause +136 more
TL;DR: It is shown that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians; and early European farmers, who were mainly of Near Eastern origin but also harboured west Europeanhunter-gatherer related ancestry.
Journal ArticleDOI
Ancient human genome sequence of an extinct Palaeo-Eskimo
Morten Rasmussen,Yingrui Li,Stinus Lindgreen,Jakob Skou Pedersen,Anders Albrechtsen,Ida Moltke,Mait Metspalu,Ene Metspalu,Toomas Kivisild,Toomas Kivisild,Ramneek Gupta,Marcelo Bertalan,Kasper Nielsen,M. Thomas P. Gilbert,Yong Wang,Maanasa Raghavan,Maanasa Raghavan,Paula F. Campos,Hanne Munkholm Kamp,Andrew Wilson,Andrew Gledhill,Silvana R. Tridico,Silvana R. Tridico,Michael Bunce,Eline D. Lorenzen,Jonas Binladen,Xiaosen Guo,Jing Zhao,Xiuqing Zhang,Hao Zhang,Zhuo Li,Minfeng Chen,Ludovic Orlando,Karsten Kristiansen,Mads Bak,Niels Tommerup,Christian Bendixen,Tracey Pierre,Bjarne Grønnow,Morten Meldgaard,Claus Andreasen,S. A. Fedorova,S. A. Fedorova,Ludmila P. Osipova,Thomas Higham,Christopher Bronk Ramsey,Thomas Hansen,Finn Cilius Nielsen,Michael H. Crawford,Søren Brunak,Søren Brunak,Thomas Sicheritz-Pontén,Richard Villems,Rasmus Nielsen,Rasmus Nielsen,Anders Krogh,Jun Wang,Eske Willerslev +57 more
TL;DR: This genome sequence of an ancient human obtained from ∼4,000-year-old permafrost-preserved hair provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
Journal ArticleDOI
Genomic evidence for the Pleistocene and recent population history of Native Americans
Maanasa Raghavan,Matthias Steinrücken,Matthias Steinrücken,Kelley Harris,Stephan Schiffels,Simon Rasmussen,Michael DeGiorgio,Anders Albrechtsen,Cristina Valdiosera,Cristina Valdiosera,María C. Ávila-Arcos,María C. Ávila-Arcos,Anna-Sapfo Malaspinas,Anders Eriksson,Anders Eriksson,Ida Moltke,Mait Metspalu,Mait Metspalu,Julian R. Homburger,Jeffrey D. Wall,Omar E. Cornejo,J. Víctor Moreno-Mayar,Thorfinn Sand Korneliussen,Tracey Pierre,Morten Rasmussen,Morten Rasmussen,Paula F. Campos,Paula F. Campos,Peter de Barros Damgaard,Morten E. Allentoft,John Lindo,Ene Metspalu,Ene Metspalu,Ricardo Rodríguez-Varela,Josefina Mansilla,Celeste Henrickson,Andaine Seguin-Orlando,Helena Malmström,Thomas W. Stafford,Thomas W. Stafford,Suyash Shringarpure,Andrés Moreno-Estrada,Monika Karmin,Monika Karmin,Kristiina Tambets,Anders Bergström,Yali Xue,Vera Warmuth,Andrew D. Friend,Joy S. Singarayer,Paul J. Valdes,Francois Balloux,Ilán Leboreiro,Jose Luis Vera,Héctor Rangel-Villalobos,Davide Pettener,Donata Luiselli,Loren G. Davis,Evelyne Heyer,Christoph P. E. Zollikofer,Marcia S. Ponce de León,Colin Smith,Vaughan Grimes,Vaughan Grimes,Kelly-Anne Pike,Michael Deal,Benjamin T. Fuller,Bernardo Arriaza,Vivien G. Standen,Maria F. Luz,Francois Ricaut,Niede Guidon,Ludmila P. Osipova,Ludmila P. Osipova,Mikhail Voevoda,Mikhail Voevoda,Olga L. Posukh,Olga L. Posukh,Oleg Balanovsky,Maria Lavryashina,Yuri Bogunov,Elza Khusnutdinova,Elza Khusnutdinova,Marina Gubina,Elena Balanovska,Sardana A. Fedorova,Sergey Litvinov,Sergey Litvinov,Boris Malyarchuk,Miroslava Derenko,M. J. Mosher,David Archer,Jerome S. Cybulski,Jerome S. Cybulski,Barbara Petzelt,Joycelynn Mitchell,Rosita Worl,Paul Norman,Peter Parham,Brian M. Kemp,Toomas Kivisild,Toomas Kivisild,Chris Tyler-Smith,Manjinder S. Sandhu,Manjinder S. Sandhu,Michael H. Crawford,Richard Villems,Richard Villems,David Glenn Smith,Michael R. Waters,Ted Goebel,John R. Johnson,Ripan S. Malhi,Mattias Jakobsson,David J. Meltzer,David J. Meltzer,Andrea Manica,Richard Durbin,Carlos Bustamante,Yun S. Song,Rasmus Nielsen,Eske Willerslev +121 more
TL;DR: The results suggest that there has been gene flow between some Native Americans from both North and South America and groups related to East Asians and Australo-Melanesians, the latter possibly through an East Asian route that might have included ancestors of modern Aleutian Islanders.
References
More filters
Journal ArticleDOI
Whole-Genome Patterns of Common DNA Variation in Three Human Populations
David A. Hinds,David A. Hinds,Laura L. Stuve,Laura L. Stuve,Geoffrey B. Nilsen,Geoffrey B. Nilsen,Eran Halperin,Eran Halperin,Eleazar Eskin,Eleazar Eskin,Dennis G. Ballinger,Dennis G. Ballinger,Kelly A. Frazer,Kelly A. Frazer,David R. Cox,David R. Cox +15 more
TL;DR: This work has characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry and indicates that these SNPs capture most common genetic variation as a result of linkage disequilibrium.
Journal ArticleDOI
A Human Genome Diversity Cell Line Panel
Howard M. Cann,Claudia de Toma,Lucien Cazes,Marie Fernande Legrand,Valérie Morel,Laurence Piouffre,J. G. Bodmer,Walter F. Bodmer,Batsheva Bonne-Tamir,Anne Cambon-Thomsen,Zhu Chen,Jiayou Chu,Carlo Carcassi,Licinio Contu,Ruofu Du,Laurent Excoffier,G. B. Ferrara,Jonathan S. Friedlaender,Helena Groot,David Gurwitz,Trefor Jenkins,Rene J. Herrera,Xiaoyi Huang,Judith R. Kidd,Kenneth K. Kidd,André Langaney,Alice A. Lin,S. Qasim Mehdi,Peter Parham,Alberto Piazza,Maria Pia Pistillo,Yaping Qian,Qunfang Shu,Jiujin Xu,Shi-Yao Zhu,James L. Weber,Henry T. Greely,Marcus W. Feldman,Gilles Thomas,Jean Dausset,Luigi Luca Cavalli-Sforza +40 more
TL;DR: A resource of 1064 cultured lymphoblastoid cell lines from individuals in different world populations and corresponding milligram quantities of DNA is deposited at the Foundation Jean Dausset (CEPH) in Paris.
Journal ArticleDOI
Y chromosome sequence variation and the history of human populations
Peter A. Underhill,Peidong Shen,A. A. Lin,Li Jin,Giuseppe Passarino,Wei-Hsien Yang,Kauffman E,Batsheva Bonne-Tamir,Jaume Bertranpetit,Paolo Francalacci,Muntaser E. Ibrahim,Trefor Jenkins,Kidd,S.Q. Mehdi,Mark Seielstad,R. S. Wells,Alberto Piazza,Ronald W. Davis,Marcus W. Feldman,Luigi Luca Cavalli-Sforza,Peter J. Oefner +20 more
TL;DR: Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of the authors' species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history.
Journal ArticleDOI
The human Y chromosome: an evolutionary marker comes of age
TL;DR: The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution.
Journal ArticleDOI
A nomenclature system for the tree of human Y-chromosomal binary haplogroups
TL;DR: A simple set of rules was developed to unambiguously label the different clades nested within a single most parsimonious phylogeny, which supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered.