Seeing the Wood for the Trees: A Minimal Reference Phylogeny for the Human Y Chromosome

Authors

  • Mannis van Oven,

    Corresponding author
    1. Department of Forensic Molecular Biology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
    • Correspondence to: Mannis van Oven, Department of Forensic Molecular Biology, Erasmus MC – University Medical Center Rotterdam, PO Box #2040, Rotterdam 3000 CA, The Netherlands. E-mail: m.vanoven@erasmusmc.nl

      Correspondence to: Maarten HD Larmuseau, Katholieke Universiteit Leuven, Forensic Medicine, Kapucijnenvoer 33, Leuven B-3000, Belgium. E-mail: maarten.larmuseau@bio.kuleuven.be

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  • Anneleen Van Geystelen,

    1. Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
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  • Manfred Kayser,

    1. Department of Forensic Molecular Biology, Erasmus MC – University Medical Center Rotterdam, Rotterdam, The Netherlands
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  • Ronny Decorte,

    1. Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
    2. Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
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  • Maarten HD Larmuseau

    Corresponding author
    1. Laboratory of Forensic Genetics and Molecular Archaeology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
    2. Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
    3. Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium
    • Correspondence to: Mannis van Oven, Department of Forensic Molecular Biology, Erasmus MC – University Medical Center Rotterdam, PO Box #2040, Rotterdam 3000 CA, The Netherlands. E-mail: m.vanoven@erasmusmc.nl

      Correspondence to: Maarten HD Larmuseau, Katholieke Universiteit Leuven, Forensic Medicine, Kapucijnenvoer 33, Leuven B-3000, Belgium. E-mail: maarten.larmuseau@bio.kuleuven.be

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  • Communicated by Peter J. Oefner

  • Contract grant sponsors: Netherlands Genomic Initiative (NGI)/Netherlands Organization for Scientific Research (NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN); Research Foundation-Flanders (FWO-Vlaanderen); KU Leuven BOF - Centre of Excellence Financing on 'Eco- and socio-evolutionary dynamics' (Project number PF/2010/07).

ABSTRACT

During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the “complete” Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at http://www.phylotree.org/Y.

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