title: Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.
abstract: The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last 'official' published tree many publications reported additional Y-chromosomal lineages and other phylogenetic topologies. Therefore, it is difficult for forensic scientists to interpret those reports and use an up-to-date tree and corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data is useful to verify and optimise the current phylogenetic tree for haploid markers. The AMY-tree software is the first open access program which analyses WGS data for Y-chromosomal phylogenetic applications. Here, all published information is collected in a phylogenetic tree and the correctness of this tree is checked based on the first large analysis of 747 WGS samples with AMY-tree. The obtained result is one phylogenetic tree with all peer-reviewed reported Y-SNPs without the observed recurrent and ambiguous mutations. Nevertheless, the results showed that currently only the genomes of a limited set of Y-chromosomal (sub-)haplogroups is available and that many newly reported Y-SNPs based on WGS projects are false positives, even with high sequencing coverage methods. This study demonstrates the usefulness of AMY-tree in the process of checking the quality of the present Y-chromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods.
authors.affiliation: UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Biology, Laboratory of Socioecology and Social Evolution, Leuven, Belgium.
authors.forename: A
authors.initials: A
authors.lastname: Van Geystelen
authors.affiliation: UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Imaging & Pathology, Forensic Medicine, Leuven, Belgium.
authors.forename: R
authors.initials: R
authors.lastname: Decorte
authors.affiliation: UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Imaging & Pathology, Forensic Medicine, Leuven, Belgium; KU Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Leuven, Belgium. Electronic address: maarten.larmuseau@bio.kuleuven.be.
authors.forename: M H D
authors.initials: MHD
authors.lastname: Larmuseau
mesh_terms: D041322:Chromosomes, Human, Y; D053803:Forensic Genetics; D006239:Haplotypes; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
keywords: Bio-informatics; Haploid markers; Phylogenetic tree; Whole-genome SNP calling; Y-SNPs; Y-chromosome