New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Abstract

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Figure 1.

An abbreviated form of the Y chromosome parsimony tree shown in the accompanying poster enclosed in this issue. Mutation names are indicated on the branches. The subtrees corresponding to major clades A–T are collapsed in this figure and are shown in Supplemental Figures 1–13, 15–18, and in the accompanying poster enclosed in this issue, wherein the maximum parsimony tree of 311 Y chromosome haplogroups is shown. Haplogroup names are given at the tips of the tree, and major clades are labeled with large capital letters and shaded in color (the entire cladogram is designated “haplogroup Y”). Mutation names are given along the branches; the length of each branch is not proportional to the number of mutations or the age of the mutation. The order of phylogenetically equivalent markers shown on each branch is arbitrary.