title: The phylogenetic and geographic structure of Y-chromosome haplogroup R1a.
abstract: R1a-M420 is one of the most widely spread Y-chromosome haplogroups; however, its substructure within Europe and Asia has remained poorly characterized. Using a panel of 16 244 male subjects from 126 populations sampled across Eurasia, we identified 2923 R1a-M420 Y-chromosomes and analyzed them to a highly granular phylogeographic resolution. Whole Y-chromosome sequence analysis of eight R1a and five R1b individuals suggests a divergence time of ∼25,000 (95% CI: 21,300-29,000) years ago and a coalescence time within R1a-M417 of ∼5800 (95% CI: 4800-6800) years. The spatial frequency distributions of R1a sub-haplogroups conclusively indicate two major groups, one found primarily in Europe and the other confined to Central and South Asia. Beyond the major European versus Asian dichotomy, we describe several younger sub-haplogroups. Based on spatial distributions and diversity patterns within the R1a-M420 clade, particularly rare basal branches detected primarily within Iran and eastern Turkey, we conclude that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Underhill
authors.affiliation: Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, CA, USA.
authors.forename: G David
authors.initials: GD
authors.lastname: Poznik
authors.affiliation: Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
authors.forename: Siiri
authors.initials: S
authors.lastname: Rootsi
authors.affiliation: Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
authors.forename: Mari
authors.initials: M
authors.lastname: Järve
authors.affiliation: Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Alice A
authors.initials: AA
authors.lastname: Lin
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Jianbin
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Passarelli
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, CA, USA.
authors.forename: Jad
authors.initials: J
authors.lastname: Kanbar
authors.affiliation: Ancestry DNA, Provo, UT, USA.
authors.forename: Natalie M
authors.initials: NM
authors.lastname: Myres
authors.affiliation: Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Roy J
authors.initials: RJ
authors.lastname: King
authors.affiliation: UMR 7268 ADES, Aix-Marseille Université/EFS/CNRS, Marseille, France.
authors.forename: Julie
authors.initials: J
authors.lastname: Di Cristofaro
authors.affiliation: 1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.
authors.forename: Hovhannes
authors.initials: H
authors.lastname: Sahakyan
authors.affiliation: 1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel.
authors.forename: Doron M
authors.initials: DM
authors.lastname: Behar
authors.affiliation: Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
authors.forename: Alena
authors.initials: A
authors.lastname: Kushniarevich
authors.affiliation: 1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Institute for Anthropological Research, Zagreb, Croatia.
authors.forename: Jelena
authors.initials: J
authors.lastname: Sarac
authors.affiliation: 1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Institute for Anthropological Research, Zagreb, Croatia.
authors.forename: Tena
authors.initials: T
authors.lastname: Saric
authors.affiliation: 1] Institute for Anthropological Research, Zagreb, Croatia [2] Croatian Academy of Sciences and Arts, Zagreb, Croatia.
authors.forename: Pavao
authors.initials: P
authors.lastname: Rudan
authors.affiliation: Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
authors.forename: Ajai Kumar
authors.initials: AK
authors.lastname: Pathak
authors.affiliation: Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia.
authors.forename: Gyaneshwer
authors.initials: G
authors.lastname: Chaubey
authors.affiliation: Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università di Pavia, Pavia, Italy.
authors.forename: Viola
authors.initials: V
authors.lastname: Grugni
authors.affiliation: 1] Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università di Pavia, Pavia, Italy [2] Centro Interdipartimentale 'Studi di Genere', Università di Pavia, Pavia, Italy.
authors.forename: Ornella
authors.initials: O
authors.lastname: Semino
authors.affiliation: Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.
authors.forename: Levon
authors.initials: L
authors.lastname: Yepiskoposyan
authors.affiliation: Department of Medical Genetic, Shiraz University of Medical Sciences, Shiraz, Iran.
authors.forename: Ardeshir
authors.initials: A
authors.lastname: Bahmanimehr
authors.affiliation: Department of Immunology, Allergy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
authors.forename: Shirin
authors.initials: S
authors.lastname: Farjadian
authors.affiliation: Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia.
authors.forename: Oleg
authors.initials: O
authors.lastname: Balanovsky
authors.affiliation: 1] Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia [2] Department of Biology, Bashkir State University, Ufa, Russia.
authors.forename: Elza K
authors.initials: EK
authors.lastname: Khusnutdinova
authors.affiliation: Department of Human and Molecular Genetics, College of Medicine, Florida International University, Miami, FL, USA.
authors.forename: Rene J
authors.initials: RJ
authors.lastname: Herrera
authors.affiliation: UMR 7268 ADES, Aix-Marseille Université/EFS/CNRS, Marseille, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Chiaroni
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.affiliation: 1] Department of Bioengineering, Stanford University, Stanford, CA, USA [2] Department of Applied Physics, Stanford University, Stanford, CA, USA [3] Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
authors.affiliation: 1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Division of Biological Anthropology, University of Cambridge, Cambridge, UK.
authors.forename: Toomas
authors.initials: T
authors.lastname: Kivisild
authors.affiliation: 1] Estonian Biocentre and the Department of Evolutionary Biology, University of Tartu, Tartu, Estonia [2] Estonian Academy of Sciences, Tallinn, Estonia.
authors.forename: Richard
authors.initials: R
authors.lastname: Villems
mesh_terms: D000483:Alleles; D001208:Asia; D041322:Chromosomes, Human, Y; D005006:Ethnicity / Q000235:genetics; D005060:Europe; D019143:Evolution, Molecular; D005787:Gene Frequency; D008040:Genetic Linkage; D006239:Haplotypes; D006801:Humans; D008297:Male; D018895:Microsatellite Repeats; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D062206:Spatial Analysis