View Full Version : F-series SNPs from 1000 Genomes Project

Jean M
10-26-2013, 08:47 PM
Chuan-Chao Wang, Hui Li, Discovery of Phylogenetic Relevant Y-chromosome Variants in 1000 Genomes Project Data, arXiv:1310.6590v1


Current Y chromosome research is limited in the poor resolution of Y chromosome phylogenetic tree. Entirely sequenced Y chromosomes in numerous human individuals have only recently become available by the advent of next-generation sequencing technology. The 1000 Genomes Project has sequenced Y chromosomes from more than 1000 males. Here, we analyzed 1000 Genomes Project Y chromosome data of 1269 individuals and discovered about 25,000 phylogenetic relevant SNPs. Those new markers are useful in the phylogeny of Y chromosome and will lead to an increased phylogenetic resolution for many Y chromosome studies.

They have given the newly discovered SNPs F-numbers (F for Fudan University.)


During the last ten years, a robust genealogical tree of human Y chromosomes based on about three thousand stable SNPs has been built, permitting inference of human population demographic history. However, current Y chromosome research is still limited in the poor resolution for some specific Y chromosome branches, such as haplogroup C-M130, D-M174, N-M231, O-M175, H-M69, and L-M11. Despite the huge population of those haplogroups, there have been fewer markers defined in those haplogroups than in haplogroups R and E. For instance, three Y-SNP markers, 002611, M134 and M117, represent about 260 million people in East Asia, but downstream markers are far from enough to reveal informative genetic substructures of those populations.

Jean M
10-27-2013, 02:09 AM
They have set up a website with a new Y tree: http://comonca.org.cn/Y_tree/