A Low-pass sequencing approach to phylogenetic analysis: reconstructing Sardinian and European demographic history with a panel of 1200 Y-chromosome samples

Aim:The origins of contemporary populations can be clarified by studying the genetic variation within the male-specific portion of the Y chromosome (MSY). The phylogenesis over this region has been subject of several studies in the past years. In the present study we took advantage of the large scale whole genome sequencing studies we have been carrying on to build a phylogenetic map of Y chromosome with an unprecedented resolution, over which we calculated the putative age for coalescence for our samples.Methods:The study involves 1,204 male samples from Sardinia. A complete variant call on the samples is performed and a statistical approach at a first stage and a second stage hierarchical approach are applied to respectively discard / correct errors and select informative variants. A phylogenetic tree is built and TMRCA calculations are performed.Results:The following haplogroups have been unambiguously detected (A, E, F, G, I, J, K, P, R) over the 1,204 samples and 11,763 informative markers have been discovered, among which 6,751 have not previously been observed. We calibrated the tree with archaeological data and used it to calculate a putative age for coalescence of (190±10)·10^3 years ago.Conclusion:This study shows that Sardinian population carries most of European variability, doubles the number of previously known human phylogenetically informative markers for Y chromosome and provides an estimate for coalescence which is closer to previous mitochondrial DNA estimates than in previous studies on the MSY.