title: Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites.
abstract: Previous Y-chromosome studies have demonstrated that Ashkenazi Levites, members of a paternally inherited Jewish priestly caste, display a distinctive founder event within R1a, the most prevalent Y-chromosome haplogroup in Eastern Europe. Here we report the analysis of 16 whole R1 sequences and show that a set of 19 unique nucleotide substitutions defines the Ashkenazi R1a lineage. While our survey of one of these, M582, in 2,834 R1a samples reveals its absence in 922 Eastern Europeans, we show it is present in all sampled R1a Ashkenazi Levites, as well as in 33.8% of other R1a Ashkenazi Jewish males and 5.9% of 303 R1a Near Eastern males, where it shows considerably higher diversity. Moreover, the M582 lineage also occurs at low frequencies in non-Ashkenazi Jewish populations. In contrast to the previously suggested Eastern European origin for Ashkenazi Levites, the current data are indicative of a geographic source of the Levite founder lineage in the Near East and its likely presence among pre-Diaspora Hebrews.
authors.affiliation: 1] Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [2].
authors.forename: Siiri
authors.initials: S
authors.lastname: Rootsi
authors.affiliation: 1] Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [2] Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel [3].
authors.forename: Doron M
authors.initials: DM
authors.lastname: Behar
authors.affiliation: Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Mari
authors.initials: M
authors.lastname: Järve
authors.affiliation: Department of Psychiatry, Stanford University, Stanford, California 94305, USA.
authors.forename: Alice A
authors.initials: AA
authors.lastname: Lin
authors.affiliation: Ancestry.com DNA, Provo, Utah 84604, USA.
authors.forename: Natalie M
authors.initials: NM
authors.lastname: Myres
authors.affiliation: Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Passarelli
authors.affiliation: Program in Biomedical Informatics and Department of Statistics, Stanford University, Stanford, California 94305, USA.
authors.forename: G David
authors.initials: GD
authors.lastname: Poznik
authors.affiliation: Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel.
authors.forename: Shay
authors.initials: S
authors.lastname: Tzur
authors.affiliation: 1] Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [2] Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Yerevan 0014, Armenia.
authors.forename: Hovhannes
authors.initials: H
authors.lastname: Sahakyan
authors.affiliation: Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Ajai Kumar
authors.initials: AK
authors.lastname: Pathak
authors.affiliation: Department of Statistics and Operations Research, School of Mathematical Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.
authors.forename: Saharon
authors.initials: S
authors.lastname: Rosset
authors.affiliation: Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Mait
authors.initials: M
authors.lastname: Metspalu
authors.affiliation: Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università di Pavia, Pavia 27100, Italy.
authors.forename: Viola
authors.initials: V
authors.lastname: Grugni
authors.affiliation: 1] Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani', Università di Pavia, Pavia 27100, Italy [2] Centro Interdipartimentale 'Studi di Genere', Università di Pavia, Pavia 27100, Italy.
authors.forename: Ornella
authors.initials: O
authors.lastname: Semino
authors.affiliation: Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia.
authors.forename: Ene
authors.initials: E
authors.lastname: Metspalu
authors.affiliation: Department of Genetics, Stanford University, Stanford, California 94305, USA.
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.affiliation: 1] Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa 31096, Israel [2] Ruth and Bruce Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 31096, Israel.
authors.forename: Karl
authors.initials: K
authors.lastname: Skorecki
authors.affiliation: 1] Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [2].
authors.forename: Richard
authors.initials: R
authors.lastname: Villems
authors.affiliation: Division of Biological Anthropology, University of Cambridge, CB2 3QG Cambridge, UK.
authors.forename: Toomas
authors.initials: T
authors.lastname: Kivisild
authors.affiliation: Department of Genetics, Stanford University, Stanford, California 94305, USA.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Underhill
mesh_terms: D041322:Chromosomes, Human, Y; D005061:Europe, Eastern; D005787:Gene Frequency; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D007585:Jews / Q000235:genetics*; D008297:Male; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA