Estimating the age of single nucleotide polymorphic sites in humans. 2021

Branko Borštnik, and Danilo Pumpernik
National Institute of Chemistry, Ljubljana, Slovenia. branko.borstnik@ki.si.

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.

UI MeSH Term Description Entries
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D019143 Evolution, Molecular The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations. Molecular Evolution,Genetic Evolution,Evolution, Genetic
D020641 Polymorphism, Single Nucleotide A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. SNPs,Single Nucleotide Polymorphism,Nucleotide Polymorphism, Single,Nucleotide Polymorphisms, Single,Polymorphisms, Single Nucleotide,Single Nucleotide Polymorphisms

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