Abstract
We have identified variants present in high-coverage complete sequences of 36 diverse human Y chromosomes from Africa, Europe, South Asia, East Asia and the Americas representing eight major haplogroups. After restricting our analysis to 8.97 Mb of unique male-specific Y sequence, we identified 6,662 high-confidence variants including SNPs, MNPs and indels. We constructed phylogenetic trees using these variants, or subsets of them, and recapitulated the known structure of the tree. Assuming a male mutation rate of 1x10-9 per bp per year, the time depth of the tree (haplogroups A3-R) was about 101-115 thousand years, and the lineages found outside Africa dated to 57-74 thousand years, both as expected. In addition, we dated a striking Paleolithic male lineage expansion to 41-52 thousand years ago and the node representing the major European Y lineage, R1b, to 4-13 thousand years ago, supporting a Neolithic origin for these modern European Y chromosomes. In all, we provide a nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree.