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AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications

Anneleen Van Geystelen12, Ronny Decorte13 and Maarten HD Larmuseau134*

Author Affiliations

1 UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium

2 Department of Biology, KU Leuven, Laboratory of Entomology, Leuven, Belgium

3 Department of Imaging & Pathology, KU Leuven, Forensic Medicine, Kapucijnenvoer 33, Leuven, B–3000, Belgium

4 Department of Biology, KU Leuven, Laboratory of Biodiversity and Evolutionary Genomics, Leuven, Belgium

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BMC Genomics 2013, 14:101  doi:10.1186/1471-2164-14-101

Published: 13 February 2013



Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.


We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.


Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.

Haploid marker; Phylogeny; Next-generation sequencing; SNP calling; Y-SNP mutations; Y chromosome haplogroups