Abstracts (first author)
Updating the Y-chromosomal phylogeny based on SNPs in available WGS data
The sex-determining Y-chromosome is an interesting marker for many human evolutionary and population genetic studies, as it accurately tracks patrilineal descent. For these studies a high-resolution state-of-the-art Y-chromosomal phylogeny is essential to characterize Y-chromosomes. Due to the rapid progress in next generation sequencing technologies, an explosion of human whole genome sequencing (WGS) data has become available. WGS data is useful to verify, optimize and extend the current phylogeny for haploid markers such as single nucleotide polymorphisms in the Y-chromosome (Y-SNPs). We present two new open access software packages which analyse WGS data for Y-chromosomal phylogenetic applications. First, the AMY-tree software determines the haplogroup for a sample based on the Y-SNPs derived from WGS experiments and it also indicates ambiguities such as recurrent SNPs within the used tree. Because of these features AMY-tree is able to include all reported Y-SNPs within one phylogenetic framework. Second, the PENNY software detects new informative Y-SNPs from WGS data by in silico analysis to increase the resolution of the Y-chromosomal tree. The AMY-tree and PENNY software and all their capabilities were tested in detail on more than 750 male full genomes with different geographical origins. An analysis of these data provides a much more detailed tree than the last 'officially' published tree of the Y Chromosome Consortium (YCC) in 2008. On the other hand, further sequencing will still be required since currently full genomes of only a limited set of Y-chromosomal (sub-)haplogroups are available. Overall, these advances of the Y-chromosomal tree will provide many applications for research on recent human evolution.