Estimating the age of single nucleotide polymorphic sites in humans

Determining the ages of polymorphic sites in human genomes needs to be carried out in a careful balance between the degree of complexity of the approach and the desired accuracy.

We provide evidence that a simpler approach where age determination is based upon the degree to which the alternative allele is spread among the population can be competitive with more complex methods.

The information contained in the vcf files of Phase 1 of the 1000 Genomes Project combined with the genomic sequences of seven non-human primate species was analyzed. The analyses were supplemented by a computer simulation of the mutational changes in 10,000 model chromosomes with a length of 10,000 nucleotides over a period of 16 million years. The list of the birth dates of the derived alleles of homozygous and heterozygous components of the derived alleles served as a yardstick to estimate the ages of human alternative alleles.

The age of the derived alleles born in Africa before the "Out of Africa" event and not brought to other continents are estimated to be 0.17 Ma, the derived alleles present simultaneously on all continents are estimated to be 1.3 Ma old and the age of alleles arising in Europe or Asia is 0.06 Ma.

Our approach functions with polymorphisms that respect the "more frequent means older" principle. However, this shortcoming only leads to disagreement with the Atlas of Variant Age in about 20% of cases.