title: Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome.
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.
authors.affiliation: Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
authors.forename: Mannis
authors.initials: M
authors.lastname: van Oven
authors.forename: Anneleen
authors.initials: A
authors.lastname: Van Geystelen
authors.forename: Manfred
authors.initials: M
authors.lastname: Kayser
authors.forename: Ronny
authors.initials: R
authors.lastname: Decorte
authors.forename: Maarten H D
authors.initials: MH
authors.lastname: Larmuseau
mesh_terms: D041322:Chromosomes, Human, Y / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008958:Models, Molecular; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
keywords: Y chromosome; Y-SNP; genealogy; haplogroup; human evolution; patrilineal ancestry; phylogeny