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, 88 (6), 814-818

A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa


A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa

Fulvio Cruciani et al. Am J Hum Genet.


To shed light on the structure of the basal backbone of the human Y chromosome phylogeny, we sequenced about 200 kb of the male-specific region of the human Y chromosome (MSY) from each of seven Y chromosomes belonging to clades A1, A2, A3, and BT. We detected 146 biallelic variant sites through this analysis. We used these variants to construct a patrilineal tree, without taking into account any previously reported information regarding the phylogenetic relationships among the seven Y chromosomes here analyzed. There are several key changes at the basal nodes as compared with the most recent reference Y chromosome tree. A different position of the root was determined, with important implications for the origin of human Y chromosome diversity. An estimate of 142 KY was obtained for the coalescence time of the revised MSY tree, which is earlier than that obtained in previous studies and easier to reconcile with plausible scenarios of modern human origin. The number of deep branchings leading to African-specific clades has doubled, further strengthening the MSY-based evidence for a modern human origin in the African continent. An analysis of 2204 African DNA samples showed that the deepest clades of the revised MSY phylogeny are currently found in central and northwest Africa, opening new perspectives on early human presence in the continent.


Figure 1
Figure 1
Revised Human Y Chromosome Phylogeny The tree is based on the 146 mutations detected in the present study. Mutations are shown along the branches (indels in italics). Branch lengths are proportional to the rho estimates of the time to the MRCA (TMRCA; estimates to the left). The nodes are shown in yellow. The sequenced chromosomes are indicated at the bottom (see also Table S1). Haplogroup nomenclature follows Karafet et al. However, the revised tree required the introduction of new names for higher-order haplogroups (A1a-T and A2-T; see main text).
Figure 2
Figure 2
Comparison of Human Y Chromosome Phylogenies Backbones of the MSY phylogeny as reported in the present study (to the left) and by Karafet et al. (to the right). Only mutations that identify “conflicting” clades between phylogenies are shown (in red).

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