TY  - JOUR
A1  - Wei, Wei
A1  - Ayub, Qasim
A1  - Chen, Yuan
A1  - McCarthy, Shane
A1  - Hou, Yiping
A1  - Carbone, Ignazio
A1  - Xue, Yali
A1  - Tyler-Smith, Chris
T1  - A calibrated human Y-chromosomal phylogeny based on resequencing
Y1  - 2013/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 388 
EP  - 395 
DO  - 10.1101/gr.143198.112 
VL  - 23 
IS  - 2 
UR  - http://genome.cshlp.org/content/23/2/388.abstract 
N2  - 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. 
ER  -