02 November 2012
By Wei Wei
My interest in studying variation on the Y chromosome led me to Chris Tyler-Smith’s group at the Wellcome Trust Sanger Institute which has studied variation on this chromosome in many human populations. The Y chromosome is passed on from father to son and offers a unique male perspective on human origins and migrations.
The aim of my study was to use Y chromosomal sequences generated by the current next-generation sequencing technology to obtain reliable age estimates for the major lineages of the Y chromosome, which are referred to as Y haplogroups. We used publically available high-coverage Y chromosome data generated by Complete Genomics. Using 35 Y chromosomal sequences obtained from 11 different populations representing four continents we identified 6,662 variants in the ~9 Mb single-copy, male-specific region of the Y chromosome, offering a tenfold increase in the number of high quality phylogenetically informative Y variants. Most of these variants were novel, thus representing a valuable resource for future studies on population genetics.
In order to refine the Y chromosomal phylogenetic, or genetic family tree we sequenced at high coverage a sample from the most basal human lineage (Y haplogroup A) as the Complete Genomics samples did not include any from this lineage. The tree reconstructed from these variants allowed us to estimate the times for the whole tree and some individual nodes of particular interest. I used three different methods to estimate times and all gave broadly similar results. The entire tree was about 101,000-115,000 years old, and the lineages found outside Africa 57,000-75,000 years old, both consistent with estimates for the origins of modern humans in Africa and their migration out of Africa. The major European Y lineage, represented by haplogroup R1b, dated between 4,000-13,000 years ago, supporting a Neolithic origin for these modern European Y chromosomes.
A novel finding was a striking Paleolithic male lineage expansion estimated to have occurred 41,000-52,000 years ago. We think this previously unknown population boom may have occurred as humans adapted to their new environment after they migrated out-of-Africa.
This study provides a nearly tenfold increase in the number of Y markers, and places them on a calibrated phylogenetic tree. Genotyping several of these novel markers in combination with the pre-existing ones in worldwide populations will provide a fine scale refinement of Y phologeny and lead to valuable insights into population origins, expansions and migration patterns from the male perspective. Many variants may also be useful in forensic genetics where they may eventually replace Y-STRs, short repeats on the Y chromosome, as markers of choice for male identification.
Wei W, Ayub Q, Chen Y, McCarthy S, et al. (2012). ‘A calibrated human Y-chromosomal phylogeny based on resequencing’
Genome Reserach October 4, 2012, doi: 10.1101/gr.143198.112