A calibrated human Y-chromosomal phylogeny based on resequencing

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 the unique male-specific Y sequence, we identified 6662 high-confidence variants, including single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (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 1 × 10(-9) per base pair per year, the time depth of the tree (haplogroups A3-R) was ~101,000-115,000 yr, and the lineages found outside Africa dated to 57,000-74,000 yr, both as expected. In addition, we dated a striking Paleolithic male lineage expansion to 41,000-52,000 yr ago and the node representing the major European Y lineage, R1b, to 4000-13,000 yr 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.

Figure 1.

Regions of the Y chromosome analyzed and distributions of variants discovered. (A) Y chromosome. (B) Location of the centromere. (C) Scale (bp) used in sections D through L. (D) Y chromosome unique regions. (Yellow bar) Segment of the reference sequence derived from haplogroup G (14,328,588–15,370,586); (blue bar) Haplogroup R1b regions. (E) Landmark sequence-tagged sites (STSs) used to define unique regions. (F) Bases in the chimpanzee reference sequence that can be aligned with the human reference (gray), or gaps in the alignment (orange). (G) Published variants lying within the unique regions. (H) Published variants variable within the 36 individuals. (I) Region sequenced at high coverage in the haplogroup A individual. (J) Depth of coverage of the region in track I. (K) All variable sites discovered in this study.

Figure 2.

Rooted maximum parsimony phylogenetic tree of 36 Y chromosomes. Sample codes and haplogroups are shown on the right, along with a number to distinguish different individuals who share the same haplogroup or pedigree. The length of the branch is proportional to the number of mutations, which is given along each branch.